I: pbuilder: network access will be disabled during build I: Current time: Tue Jan 6 16:48:16 +14 2026 I: pbuilder-time-stamp: 1767667696 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [pyranges_0.0.111+ds-8.dsc] I: copying [./pyranges_0.0.111+ds.orig.tar.xz] I: copying [./pyranges_0.0.111+ds-8.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Sep 21 11:53:08 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./pyranges_0.0.111+ds-8.dsc: no acceptable signature found dpkg-source: info: extracting pyranges in pyranges-0.0.111+ds dpkg-source: info: unpacking pyranges_0.0.111+ds.orig.tar.xz dpkg-source: info: unpacking pyranges_0.0.111+ds-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_dtype.patch dpkg-source: info: applying reorder.patch dpkg-source: info: applying numpy_1.24.patch dpkg-source: info: applying healthcheck-all.patch dpkg-source: info: applying no_install_depends_cython.patch dpkg-source: info: applying pandas2.0.patch dpkg-source: info: applying fix-test_unary.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1718224/tmp/hooks/D01_modify_environment starting debug: Running on ionos5-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jan 6 02:48 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/1718224/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1718224/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.32(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=1afed17a5cd84e20bd65aa71389e6384 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=1718224 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.onRzAPlw/pbuilderrc_avXA --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.onRzAPlw/b2 --logfile b2/build.log pyranges_0.0.111+ds-8.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1718224/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, python3-setuptools, python3-all, python3-ncls, python3-pyrle, python3-pytest, python3-pytest-xdist, python3-sorted-nearest, python3-hypothesis, bedtools, samtools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19962 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-ncls; however: Package python3-ncls is not installed. pbuilder-satisfydepends-dummy depends on python3-pyrle; however: Package python3-pyrle is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest-xdist; however: Package python3-pytest-xdist is not installed. pbuilder-satisfydepends-dummy depends on python3-sorted-nearest; however: Package python3-sorted-nearest is not installed. pbuilder-satisfydepends-dummy depends on python3-hypothesis; however: Package python3-hypothesis is not installed. pbuilder-satisfydepends-dummy depends on bedtools; however: Package bedtools is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bedtools{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcom-err2{a} libcurl3t64-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgssapi-krb5-2{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnsl2{a} libpipeline1{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-all{a} python3-attr{a} python3-autocommand{a} python3-dateutil{a} python3-execnet{a} python3-hypothesis{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-minimal{a} python3-more-itertools{a} python3-natsort{a} python3-ncls{a} python3-numpy{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pkg-resources{a} python3-pluggy{a} python3-pyrle{a} python3-pytest{a} python3-pytest-xdist{a} python3-setuptools{a} python3-sorted-nearest{a} python3-sortedcontainers{a} python3-tabulate{a} python3-typeguard{a} python3-typing-extensions{a} python3-tz{a} python3-zipp{a} python3.12{a} python3.12-minimal{a} readline-common{a} samtools{a} sensible-utils{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix python3-bottleneck python3-bs4 python3-click python3-html5lib python3-jinja2 python3-lxml python3-matplotlib python3-numexpr python3-odf python3-openpyxl python3-pygments python3-scipy python3-tables wget 0 packages upgraded, 103 newly installed, 0 to remove and 0 not upgraded. Need to get 52.9 MB of archives. After unpacking 261 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.7-3 [815 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.7-3 [2162 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.12.6-1 [26.7 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024b-3 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.1-1+b1 [23.2 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 12 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.7-3 [1966 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.7-3 [671 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B] Get: 22 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.12.6-1 [27.8 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 bedtools amd64 2.31.1+dfsg-2 [678 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-8 [517 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 45 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 59 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 74.1.2-2 [213 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 74.1.2-2 [736 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 dh-python all 6.20241024 [109 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-4 [152 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.6.0-2 [64.8 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.9.1-1 [119 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.9.1-1 [18.5 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.11.0-1 [359 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.20+ds-2 [455 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-4 [2450 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libncurses6 amd64 6.5-2+b1 [105 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 python3-all amd64 3.12.6-1 [1040 B] Get: 84 http://deb.debian.org/debian trixie/main amd64 python3-attr all 23.2.0-2 [65.5 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 python3-dateutil all 2.9.0-3 [79.3 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 python3-execnet all 2.1.1-1 [40.2 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 python3-sortedcontainers all 2.4.0-2 [31.9 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 python3-hypothesis all 6.121.0-1 [325 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 90 http://deb.debian.org/debian trixie/main amd64 python3-natsort all 8.0.2-2 [39.0 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:1.26.4+ds-12 [4738 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 python3-ncls amd64 0.0.63-hotfix+ds-1+b6 [479 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 python3-tz all 2024.1-2 [30.9 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 python3-pandas-lib amd64 2.2.3+dfsg-5+b1 [7307 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 python3-pandas all 2.2.3+dfsg-5 [3096 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 python3-tabulate all 0.9.0-1 [45.9 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 python3-pyrle amd64 0.0.33-4.1+b2 [372 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 python3-pytest all 8.3.3-1 [249 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 python3-pytest-xdist all 3.6.1-1 [44.4 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 python3-sorted-nearest amd64 0.0.39+dfsg-2+b2 [604 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 samtools amd64 1.20-3 [653 kB] Fetched 52.9 MB in 4s (13.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19962 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.7-3_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.7-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.7-3_amd64.deb ... Unpacking python3.12-minimal (3.12.7-3) ... Setting up libpython3.12-minimal:amd64 (3.12.7-3) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.7-3) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20282 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_amd64.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-3_all.deb ... Unpacking tzdata (2024b-3) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../05-libcom-err2_1.47.1-1+b1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.1-1+b1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../14-libreadline8t64_8.2-5_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.7-3_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.7-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.7-3_amd64.deb ... Unpacking python3.12 (3.12.7-3) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21344 files and directories currently installed.) Preparing to unpack .../00-python3_3.12.6-1_amd64.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package sensible-utils. 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Preparing to unpack .../71-python3-packaging_24.2-1_all.deb ... Unpacking python3-packaging (24.2-1) ... Selecting previously unselected package python3-tz. Preparing to unpack .../72-python3-tz_2024.1-2_all.deb ... Unpacking python3-tz (2024.1-2) ... Selecting previously unselected package python3-pandas-lib:amd64. Preparing to unpack .../73-python3-pandas-lib_2.2.3+dfsg-5+b1_amd64.deb ... Unpacking python3-pandas-lib:amd64 (2.2.3+dfsg-5+b1) ... Selecting previously unselected package python3-pandas. Preparing to unpack .../74-python3-pandas_2.2.3+dfsg-5_all.deb ... Unpacking python3-pandas (2.2.3+dfsg-5) ... Selecting previously unselected package python3-pluggy. Preparing to unpack .../75-python3-pluggy_1.5.0-1_all.deb ... Unpacking python3-pluggy (1.5.0-1) ... Selecting previously unselected package python3-tabulate. Preparing to unpack .../76-python3-tabulate_0.9.0-1_all.deb ... Unpacking python3-tabulate (0.9.0-1) ... Selecting previously unselected package python3-pyrle. 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Setting up bsdextrautils (2.40.2-11) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:amd64 (1.1.0-2+b6) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libnghttp2-14:amd64 (1.64.0-1) ... Setting up libdeflate0:amd64 (1.22-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:amd64 (1.47.1-1+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Jan 6 02:48:43 UTC 2026. Universal Time is now: Tue Jan 6 02:48:43 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libblas3:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libncurses6:amd64 (6.5-2+b1) ... Setting up autopoint (0.22.5-2) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Setting up libgfortran5:amd64 (14.2.0-8) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:amd64 (1.6.0-2) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up netbase (6.4) ... Setting up libngtcp2-16:amd64 (1.9.1-1) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up readline-common (8.2-5) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up bedtools (2.31.1+dfsg-2) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.9.1-1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up liblapack3:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-8) ... Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:amd64 (8.11.0-1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libnsl2:amd64 (1.3.0-3+b3) ... Setting up libhts3t64:amd64 (1.20+ds-2) ... Setting up libpython3.12-stdlib:amd64 (3.12.7-3) ... Setting up python3.12 (3.12.7-3) ... Setting up debhelper (13.20) ... Setting up samtools (1.20-3) ... Setting up libpython3-stdlib:amd64 (3.12.6-1) ... Setting up python3 (3.12.6-1) ... Setting up python3-sortedcontainers (2.4.0-2) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-tz (2024.1-2) ... Setting up python3-natsort (8.0.2-2) ... Setting up python3-packaging (24.2-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-dateutil (2.9.0-3) ... Setting up python3-execnet (2.1.1-1) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-attr (23.2.0-2) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-pytest (8.3.3-1) ... Setting up python3-hypothesis (6.121.0-1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up python3-tabulate (0.9.0-1) ... Setting up python3-all (3.12.6-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-pkg-resources (74.1.2-2) ... Setting up python3-setuptools (74.1.2-2) ... Setting up python3-pytest-xdist (3.6.1-1) ... Setting up python3-numpy (1:1.26.4+ds-12) ... Setting up python3-ncls (0.0.63-hotfix+ds-1+b6) ... Setting up dh-python (6.20241024) ... Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-5+b1) ... Setting up python3-sorted-nearest (0.0.39+dfsg-2+b2) ... Setting up python3-pandas (2.2.3+dfsg-5) ... Setting up python3-pyrle (0.0.33-4.1+b2) ... Processing triggers for libc-bin (2.40-3) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/1718224/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/1718224/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/pyranges-0.0.111+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../pyranges_0.0.111+ds-8_source.changes dpkg-buildpackage: info: source package pyranges dpkg-buildpackage: info: source version 0.0.111+ds-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from pyranges-0.0.111+ds/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.12 setup.py clean 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.12 setup.py config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py build debian/rules execute_after_dh_auto_build make[1]: Entering directory '/build/reproducible-path/pyranges-0.0.111+ds' echo 'Generating corresponding files ...' Generating corresponding files ... cat debian/missing-sources/test_sorted.sam| samtools view -Sb - > tests/test_data/test_sorted.bam cat debian/missing-sources/control.sam| samtools view -Sb - > pyranges/example_data/control.bam samtools index tests/test_data/test_sorted.bam tests/test_data/test_sorted.bam.bai samtools index pyranges/example_data/control.bam pyranges/example_data/control.bam.bai make[1]: Leaving directory '/build/reproducible-path/pyranges-0.0.111+ds' dh_auto_test -O--buildsystem=pybuild I: pybuild pybuild:308: mkdir -pv /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges && cp -av /build/reproducible-path/pyranges-0.0.111+ds/tests/*.bed /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests && cp -av /build/reproducible-path/pyranges-0.0.111+ds/tests/test_data /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests && cp -av /build/reproducible-path/pyranges-0.0.111+ds/tests/data /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests && cp -av /build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges '/build/reproducible-path/pyranges-0.0.111+ds/tests/chip_10.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/chip_10.bed' '/build/reproducible-path/pyranges-0.0.111+ds/tests/f1.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/f1.bed' '/build/reproducible-path/pyranges-0.0.111+ds/tests/f2.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/f2.bed' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_data' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/test_sorted.bam' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_data/test_sorted.bam' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/ensembl.gtf' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_data/ensembl.gtf' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/gencode.gff3' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_data/gencode.gff3' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/ucsc_df_to_parse.txt' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_data/ucsc_df_to_parse.txt' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/test_sorted.bam.bai' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_data/test_sorted.bam.bai' '/build/reproducible-path/pyranges-0.0.111+ds/tests/data' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/data' '/build/reproducible-path/pyranges-0.0.111+ds/tests/data/test_data.py' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/data/test_data.py' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/exons.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/exons.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/ensembl.gtf' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/ensembl.gtf' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/ucsc_human.bed.gz' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/ucsc_human.bed.gz' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/chipseq_background.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/chipseq_background.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/f2.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/f2.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/bw.bw' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/bw.bw' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/f1.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/f1.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/cpg.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/cpg.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/lamina.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/lamina.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/gencode_human.gtf.gz' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/gencode_human.gtf.gz' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/chipseq.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/chipseq.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/aorta.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/aorta.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/ensembl_human.gtf.gz' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/ensembl_human.gtf.gz' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/chromsizes.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/chromsizes.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/aorta2.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/aorta2.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/control.bam' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/control.bam' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/control.bam.bai' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/example_data/control.bam.bai' I: pybuild base:311: cd /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build; python3.12 -m pytest -v -n 42 ============================= test session starts ============================== platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3.12 cachedir: .pytest_cache hypothesis profile 'default' -> database=DirectoryBasedExampleDatabase(PosixPath('/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/.hypothesis/examples')) rootdir: /build/reproducible-path/pyranges-0.0.111+ds plugins: typeguard-4.4.1, hypothesis-6.121.0, xdist-3.6.1 created: 42/42 workers 42 workers [531 items] scheduling tests via LoadScheduling tests/data/test_data.py::test_all_data tests/test_binary.py::test_overlap[same] tests/test_binary.py::test_intersect[same] tests/test_binary.py::test_set_union[False] tests/test_binary.py::test_subtraction[opposite] tests/test_binary.py::test_coverage[same] tests/test_binary.py::test_nearest[None-True-same] tests/test_binary.py::test_nearest[downstream-True-same] tests/test_binary.py::test_join[opposite] tests/test_binary.py::test_k_nearest[upstream-True-same-last] tests/test_binary.py::test_k_nearest[upstream-False-same-last] tests/test_binary.py::test_nearest[upstream-False-same] tests/test_change_chromosome_custom.py::test_change_chromosomes tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain19-method_chain19] tests/test_binary.py::test_k_nearest[downstream-False-same-last] tests/test_binary.py::test_nearest[None-False-same] tests/test_concat.py::test_concat_unstranded_stranded tests/test_binary.py::test_k_nearest[None-False-same-last] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain1-method_chain1] tests/test_binary.py::test_k_nearest[None-True-same-last] tests/test_binary.py::test_k_nearest[downstream-True-same-last] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain28-method_chain28] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain4-method_chain4] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain25-method_chain25] tests/test_binary.py::test_nearest[downstream-False-same] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain13-method_chain13] tests/test_binary.py::test_jaccard[same] tests/test_binary.py::test_nearest[upstream-True-same] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain22-method_chain22] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain16-method_chain16] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain10-method_chain10] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain31-method_chain31] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain7-method_chain7] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain37-method_chain37] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain43-method_chain43] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain40-method_chain40] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain55-method_chain55] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain34-method_chain34] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain49-method_chain49] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain52-method_chain52] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain46-method_chain46] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain58-method_chain58] [gw20] [ 0%] PASSED tests/test_change_chromosome_custom.py::test_change_chromosomes tests/test_concat.py::test_concat_stranded_unstranded [gw22] [ 0%] PASSED tests/test_concat.py::test_concat_unstranded_stranded tests/test_count_overlaps.py::test_strand_vs_strand_same [gw20] [ 0%] PASSED tests/test_concat.py::test_concat_stranded_unstranded tests/test_concat.py::test_concat_unstranded_unstranded [gw20] [ 0%] PASSED tests/test_concat.py::test_concat_unstranded_unstranded tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain61-method_chain61] [gw22] [ 0%] PASSED tests/test_count_overlaps.py::test_strand_vs_strand_same tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain0-method_chain0] [gw0] [ 1%] PASSED tests/data/test_data.py::test_all_data tests/test_binary.py::test_set_intersect[False] [gw27] [ 1%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain16-method_chain16] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain17-method_chain17] [gw32] [ 1%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain34-method_chain34] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain35-method_chain35] [gw30] [ 1%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain25-method_chain25] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain26-method_chain26] [gw37] [ 1%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain46-method_chain46] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain47-method_chain47] [gw33] [ 2%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain31-method_chain31] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain32-method_chain32] [gw35] [ 2%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain43-method_chain43] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain44-method_chain44] [gw41] [ 2%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain58-method_chain58] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain59-method_chain59] [gw25] [ 2%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain10-method_chain10] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain11-method_chain11] [gw29] [ 2%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain22-method_chain22] [gw31] [ 3%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain28-method_chain28] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain23-method_chain23] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain29-method_chain29] [gw28] [ 3%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain19-method_chain19] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain20-method_chain20] [gw26] [ 3%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain13-method_chain13] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain14-method_chain14] [gw40] [ 3%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain55-method_chain55] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain56-method_chain56] [gw23] [ 3%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain4-method_chain4] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain5-method_chain5] [gw38] [ 3%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain52-method_chain52] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain53-method_chain53] [gw34] [ 4%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain37-method_chain37] [gw20] [ 4%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain61-method_chain61] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain38-method_chain38] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain62-method_chain62] [gw21] [ 4%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain1-method_chain1] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain2-method_chain2] [gw24] [ 4%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain7-method_chain7] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain8-method_chain8] [gw39] [ 4%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain49-method_chain49] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain50-method_chain50] [gw27] [ 5%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain17-method_chain17] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain18-method_chain18] [gw36] [ 5%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain40-method_chain40] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain41-method_chain41] [gw22] [ 5%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain0-method_chain0] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain64-method_chain64] [gw33] [ 5%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain32-method_chain32] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain33-method_chain33] [gw35] [ 5%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain44-method_chain44] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain45-method_chain45] [gw37] [ 6%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain47-method_chain47] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain48-method_chain48] [gw28] [ 6%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain20-method_chain20] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain21-method_chain21] [gw30] [ 6%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain26-method_chain26] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain27-method_chain27] [gw31] [ 6%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain29-method_chain29] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain30-method_chain30] [gw41] [ 6%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain59-method_chain59] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain60-method_chain60] [gw29] [ 6%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain23-method_chain23] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain24-method_chain24] [gw26] [ 7%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain14-method_chain14] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain15-method_chain15] [gw25] [ 7%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain11-method_chain11] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain12-method_chain12] [gw24] [ 7%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain8-method_chain8] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain9-method_chain9] [gw38] [ 7%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain53-method_chain53] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain54-method_chain54] [gw20] [ 7%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain62-method_chain62] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain63-method_chain63] [gw32] [ 8%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain35-method_chain35] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain36-method_chain36] [gw40] [ 8%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain56-method_chain56] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain57-method_chain57] [gw27] [ 8%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain18-method_chain18] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain67-method_chain67] [gw21] [ 8%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain2-method_chain2] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain3-method_chain3] [gw34] [ 8%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain38-method_chain38] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain39-method_chain39] [gw35] [ 9%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain45-method_chain45] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain73-method_chain73] [gw22] [ 9%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain64-method_chain64] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain65-method_chain65] [gw39] [ 9%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain50-method_chain50] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain51-method_chain51] [gw33] [ 9%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain33-method_chain33] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain70-method_chain70] [gw37] [ 9%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain48-method_chain48] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain76-method_chain76] [gw23] [ 9%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain5-method_chain5] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain6-method_chain6] [gw36] [ 10%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain41-method_chain41] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain42-method_chain42] [gw31] [ 10%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain30-method_chain30] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain85-method_chain85] [gw30] [ 10%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain27-method_chain27] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain82-method_chain82] [gw28] [ 10%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain21-method_chain21] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain79-method_chain79] [gw29] [ 10%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain24-method_chain24] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain91-method_chain91] [gw26] [ 11%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain15-method_chain15] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain94-method_chain94] [gw41] [ 11%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain60-method_chain60] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain88-method_chain88] [gw27] [ 11%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain67-method_chain67] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain68-method_chain68] [gw25] [ 11%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain12-method_chain12] [gw24] [ 11%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain9-method_chain9] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain97-method_chain97] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain100-method_chain100] [gw20] [ 12%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain63-method_chain63] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain106-method_chain106] [gw40] [ 12%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain57-method_chain57] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain112-method_chain112] [gw22] [ 12%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain65-method_chain65] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain66-method_chain66] [gw35] [ 12%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain73-method_chain73] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain74-method_chain74] [gw37] [ 12%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain76-method_chain76] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain77-method_chain77] [gw21] [ 12%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain3-method_chain3] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain115-method_chain115] [gw32] [ 13%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain36-method_chain36] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain109-method_chain109] [gw34] [ 13%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain39-method_chain39] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain118-method_chain118] [gw33] [ 13%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain70-method_chain70] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain71-method_chain71] [gw28] [ 13%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain79-method_chain79] [gw36] [ 13%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain42-method_chain42] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain80-method_chain80] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain127-method_chain127] [gw39] [ 14%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain51-method_chain51] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain121-method_chain121] [gw26] [ 14%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain94-method_chain94] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain95-method_chain95] [gw30] [ 14%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain82-method_chain82] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain83-method_chain83] [gw23] [ 14%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain6-method_chain6] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain124-method_chain124] [gw38] [ 14%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain54-method_chain54] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain103-method_chain103] [gw29] [ 15%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain91-method_chain91] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain92-method_chain92] [gw27] [ 15%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain68-method_chain68] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain69-method_chain69] [gw25] [ 15%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain97-method_chain97] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain98-method_chain98] [gw31] [ 15%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain85-method_chain85] [gw41] [ 15%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain88-method_chain88] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain86-method_chain86] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain89-method_chain89] [gw24] [ 16%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain100-method_chain100] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain101-method_chain101] [gw22] [ 16%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain66-method_chain66] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain130-method_chain130] [gw20] [ 16%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain106-method_chain106] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain107-method_chain107] [gw35] [ 16%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain74-method_chain74] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain75-method_chain75] [gw40] [ 16%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain112-method_chain112] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain113-method_chain113] [gw21] [ 16%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain115-method_chain115] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain116-method_chain116] [gw34] [ 17%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain118-method_chain118] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain119-method_chain119] [gw37] [ 17%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain77-method_chain77] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain78-method_chain78] [gw28] [ 17%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain80-method_chain80] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain81-method_chain81] [gw33] [ 17%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain71-method_chain71] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain72-method_chain72] [gw26] [ 17%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain95-method_chain95] [gw32] [ 18%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain109-method_chain109] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain110-method_chain110] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain96-method_chain96] [gw36] [ 18%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain127-method_chain127] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain128-method_chain128] [gw30] [ 18%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain83-method_chain83] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain84-method_chain84] [gw39] [ 18%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain121-method_chain121] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain122-method_chain122] [gw27] [ 18%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain69-method_chain69] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain133-method_chain133] [gw29] [ 19%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain92-method_chain92] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain93-method_chain93] [gw22] [ 19%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain130-method_chain130] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain131-method_chain131] [gw23] [ 19%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain124-method_chain124] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain125-method_chain125] [gw31] [ 19%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain86-method_chain86] [gw20] [ 19%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain107-method_chain107] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain87-method_chain87] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain108-method_chain108] [gw21] [ 19%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain116-method_chain116] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain117-method_chain117] [gw40] [ 20%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain113-method_chain113] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain114-method_chain114] [gw38] [ 20%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain103-method_chain103] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain104-method_chain104] [gw36] [ 20%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain128-method_chain128] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain129-method_chain129] [gw28] [ 20%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain81-method_chain81] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain139-method_chain139] [gw33] [ 20%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain72-method_chain72] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain141-method_chain141] [gw37] [ 21%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain78-method_chain78] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain137-method_chain137] [gw24] [ 21%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain101-method_chain101] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain102-method_chain102] [gw35] [ 21%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain75-method_chain75] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain135-method_chain135] [gw25] [ 21%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain98-method_chain98] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain99-method_chain99] [gw39] [ 21%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain122-method_chain122] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain123-method_chain123] [gw26] [ 22%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain96-method_chain96] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain143-method_chain143] [gw29] [ 22%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain93-method_chain93] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain147-method_chain147] [gw34] [ 22%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain119-method_chain119] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain120-method_chain120] [gw32] [ 22%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain110-method_chain110] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain111-method_chain111] [gw41] [ 22%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain89-method_chain89] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain90-method_chain90] [gw23] [ 22%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain125-method_chain125] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain126-method_chain126] [gw22] [ 23%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain131-method_chain131] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain132-method_chain132] [gw30] [ 23%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain84-method_chain84] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain145-method_chain145] [gw40] [ 23%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain114-method_chain114] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain155-method_chain155] [gw21] [ 23%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain117-method_chain117] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain153-method_chain153] [gw33] [ 23%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain141-method_chain141] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain142-method_chain142] [gw36] [ 24%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain129-method_chain129] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain157-method_chain157] [gw20] [ 24%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain108-method_chain108] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain151-method_chain151] [gw38] [ 24%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain104-method_chain104] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain105-method_chain105] [gw39] [ 24%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain123-method_chain123] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain163-method_chain163] [gw27] [ 24%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain133-method_chain133] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain134-method_chain134] [gw31] [ 25%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain87-method_chain87] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain149-method_chain149] [gw26] [ 25%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain143-method_chain143] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain144-method_chain144] [gw35] [ 25%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain135-method_chain135] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain136-method_chain136] [gw28] [ 25%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain139-method_chain139] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain140-method_chain140] [gw32] [ 25%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain111-method_chain111] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain167-method_chain167] [gw24] [ 25%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain102-method_chain102] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain159-method_chain159] [gw22] [ 26%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain132-method_chain132] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain173-method_chain173] [gw34] [ 26%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain120-method_chain120] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain165-method_chain165] [gw37] [ 26%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain137-method_chain137] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain138-method_chain138] [gw25] [ 26%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain99-method_chain99] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain161-method_chain161] [gw23] [ 26%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain126-method_chain126] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain171-method_chain171] [gw33] [ 27%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain142-method_chain142] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain175-method_chain175] [gw30] [ 27%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain145-method_chain145] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain146-method_chain146] [gw40] [ 27%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain155-method_chain155] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain156-method_chain156] [gw41] [ 27%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain90-method_chain90] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain169-method_chain169] [gw39] [ 27%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain163-method_chain163] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain164-method_chain164] [gw36] [ 28%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain157-method_chain157] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain158-method_chain158] [gw29] [ 28%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain147-method_chain147] [gw26] [ 28%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain144-method_chain144] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain181-method_chain181] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain148-method_chain148] [gw32] [ 28%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain167-method_chain167] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain168-method_chain168] [gw28] [ 28%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain140-method_chain140] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain185-method_chain185] [gw38] [ 29%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain105-method_chain105] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain177-method_chain177] [gw34] [ 29%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain165-method_chain165] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain166-method_chain166] [gw21] [ 29%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain153-method_chain153] [gw31] [ 29%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain149-method_chain149] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain150-method_chain150] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain154-method_chain154] [gw24] [ 29%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain159-method_chain159] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain160-method_chain160] [gw22] [ 29%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain173-method_chain173] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain174-method_chain174] [gw25] [ 30%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain161-method_chain161] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain162-method_chain162] [gw20] [ 30%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain151-method_chain151] [gw35] [ 30%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain136-method_chain136] [gw27] [ 30%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain134-method_chain134] [gw13] [ 30%] PASSED tests/test_binary.py::test_join[opposite] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain183-method_chain183] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain179-method_chain179] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain152-method_chain152] tests/test_binary.py::test_reldist [gw23] [ 31%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain171-method_chain171] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain172-method_chain172] [gw30] [ 31%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain146-method_chain146] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain189-method_chain189] [gw39] [ 31%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain164-method_chain164] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain193-method_chain193] [gw41] [ 31%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain169-method_chain169] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain170-method_chain170] [gw33] [ 31%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain175-method_chain175] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain176-method_chain176] [gw40] [ 32%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain156-method_chain156] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain191-method_chain191] [gw26] [ 32%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain181-method_chain181] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain182-method_chain182] [gw2] [ 32%] PASSED tests/test_binary.py::test_overlap[same] tests/test_binary.py::test_overlap[opposite] [gw36] [ 32%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain158-method_chain158] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain195-method_chain195] [gw3] [ 32%] PASSED tests/test_binary.py::test_intersect[same] tests/test_binary.py::test_intersect[opposite] [gw37] [ 32%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain138-method_chain138] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain187-method_chain187] [gw38] [ 33%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain177-method_chain177] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain178-method_chain178] [gw34] [ 33%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain166-method_chain166] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain201-method_chain201] [gw27] [ 33%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain179-method_chain179] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain180-method_chain180] [gw32] [ 33%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain168-method_chain168] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain199-method_chain199] [gw23] [ 33%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain172-method_chain172] [gw22] [ 34%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain174-method_chain174] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain215-method_chain215] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain209-method_chain209] [gw24] [ 34%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain160-method_chain160] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain207-method_chain207] [gw25] [ 34%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain162-method_chain162] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain211-method_chain211] [gw39] [ 34%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain193-method_chain193] [gw21] [ 34%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain154-method_chain154] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain194-method_chain194] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain203-method_chain203] [gw29] [ 35%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain148-method_chain148] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain197-method_chain197] [gw28] [ 35%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain185-method_chain185] [gw40] [ 35%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain191-method_chain191] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain186-method_chain186] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain192-method_chain192] [gw41] [ 35%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain170-method_chain170] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain216-method_chain216] [gw11] [ 35%] PASSED tests/test_binary.py::test_nearest[downstream-False-same] tests/test_binary.py::test_nearest[downstream-False-opposite] [gw33] [ 35%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain176-method_chain176] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain217-method_chain217] [gw30] [ 36%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain189-method_chain189] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain190-method_chain190] [gw9] [ 36%] PASSED tests/test_binary.py::test_nearest[upstream-False-same] [gw36] [ 36%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain195-method_chain195] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain196-method_chain196] tests/test_binary.py::test_nearest[upstream-False-opposite] [gw12] [ 36%] PASSED tests/test_binary.py::test_jaccard[same] tests/test_binary.py::test_join[False] [gw31] [ 36%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain150-method_chain150] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain205-method_chain205] [gw38] [ 37%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain178-method_chain178] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain219-method_chain219] [gw35] [ 37%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain183-method_chain183] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain184-method_chain184] [gw20] [ 37%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain152-method_chain152] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain213-method_chain213] [gw27] [ 37%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain180-method_chain180] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain220-method_chain220] [gw26] [ 37%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain182-method_chain182] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain218-method_chain218] [gw7] [ 38%] PASSED tests/test_binary.py::test_nearest[None-False-same] tests/test_binary.py::test_nearest[None-False-opposite] [gw25] [ 38%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain211-method_chain211] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain212-method_chain212] [gw23] [ 38%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain215-method_chain215] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain221-method_chain221] [gw40] [ 38%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain192-method_chain192] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain224-method_chain224] [gw41] [ 38%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain216-method_chain216] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain225-method_chain225] [gw22] [ 38%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain209-method_chain209] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain210-method_chain210] [gw24] [ 39%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain207-method_chain207] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain208-method_chain208] [gw39] [ 39%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain194-method_chain194] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain222-method_chain222] [gw21] [ 39%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain203-method_chain203] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain204-method_chain204] [gw30] [ 39%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain190-method_chain190] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain227-method_chain227] [gw28] [ 39%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain186-method_chain186] [gw33] [ 40%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain217-method_chain217] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain223-method_chain223] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain226-method_chain226] [gw32] [ 40%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain199-method_chain199] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain200-method_chain200] [gw37] [ 40%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain187-method_chain187] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain188-method_chain188] [gw8] [ 40%] PASSED tests/test_binary.py::test_nearest[upstream-True-same] [gw38] [ 40%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain219-method_chain219] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain229-method_chain229] tests/test_binary.py::test_nearest[upstream-True-opposite] [gw20] [ 41%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain213-method_chain213] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain214-method_chain214] [gw31] [ 41%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain205-method_chain205] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain206-method_chain206] [gw27] [ 41%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain220-method_chain220] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain231-method_chain231] [gw0] [ 41%] PASSED tests/test_binary.py::test_set_intersect[False] tests/test_binary.py::test_set_intersect[same] [gw25] [ 41%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain212-method_chain212] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain233-method_chain233] [gw6] [ 41%] PASSED tests/test_binary.py::test_nearest[None-True-same] tests/test_binary.py::test_nearest[None-True-opposite] [gw29] [ 42%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain197-method_chain197] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain198-method_chain198] [gw23] [ 42%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain221-method_chain221] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain234-method_chain234] [gw34] [ 42%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain201-method_chain201] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain202-method_chain202] [gw41] [ 42%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain225-method_chain225] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain236-method_chain236] [gw26] [ 42%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain218-method_chain218] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain232-method_chain232] [gw22] [ 43%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain210-method_chain210] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain237-method_chain237] [gw10] [ 43%] PASSED tests/test_binary.py::test_nearest[downstream-True-same] [gw35] [ 43%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain184-method_chain184] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain230-method_chain230] tests/test_binary.py::test_nearest[downstream-True-opposite] [gw36] [ 43%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain196-method_chain196] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain228-method_chain228] [gw40] [ 43%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain224-method_chain224] [gw30] [ 44%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain227-method_chain227] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain235-method_chain235] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain241-method_chain241] [gw24] [ 44%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain208-method_chain208] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain238-method_chain238] [gw33] [ 44%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain226-method_chain226] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain243-method_chain243] [gw21] [ 44%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain204-method_chain204] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain240-method_chain240] [gw28] [ 44%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain223-method_chain223] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain242-method_chain242] [gw14] [ 45%] PASSED tests/test_binary.py::test_k_nearest[downstream-False-same-last] [gw20] [ 45%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain214-method_chain214] tests/test_binary.py::test_k_nearest[downstream-False-False-last] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain247-method_chain247] [gw39] [ 45%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain222-method_chain222] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain239-method_chain239] [gw38] [ 45%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain229-method_chain229] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain246-method_chain246] [gw31] [ 45%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain206-method_chain206] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain248-method_chain248] [gw32] [ 45%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain200-method_chain200] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain244-method_chain244] [gw37] [ 46%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain188-method_chain188] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain245-method_chain245] [gw35] [ 46%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain230-method_chain230] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain258-method_chain258] [gw16] [ 46%] PASSED tests/test_binary.py::test_k_nearest[upstream-False-same-last] [gw36] [ 46%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain228-method_chain228] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain259-method_chain259] tests/test_binary.py::test_k_nearest[upstream-False-False-last] [gw30] [ 46%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain241-method_chain241] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain261-method_chain261] [gw21] [ 47%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain240-method_chain240] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain264-method_chain264] [gw33] [ 47%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain243-method_chain243] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain263-method_chain263] [gw28] [ 47%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain242-method_chain242] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain265-method_chain265] [gw26] [ 47%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain232-method_chain232] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain256-method_chain256] [gw27] [ 47%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain231-method_chain231] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain249-method_chain249] [gw25] [ 48%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain233-method_chain233] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain251-method_chain251] [gw29] [ 48%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain198-method_chain198] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain252-method_chain252] [gw39] [ 48%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain239-method_chain239] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain267-method_chain267] [gw22] [ 48%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain237-method_chain237] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain257-method_chain257] [gw34] [ 48%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain202-method_chain202] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain254-method_chain254] [gw23] [ 48%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain234-method_chain234] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain253-method_chain253] [gw24] [ 49%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain238-method_chain238] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain262-method_chain262] [gw40] [ 49%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain235-method_chain235] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain260-method_chain260] [gw32] [ 49%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain244-method_chain244] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain270-method_chain270] [gw38] [ 49%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain246-method_chain246] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain268-method_chain268] [gw1] [ 49%] PASSED tests/test_binary.py::test_set_union[False] [gw41] [ 50%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain236-method_chain236] tests/test_binary.py::test_set_union[same] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain255-method_chain255] [gw18] [ 50%] PASSED tests/test_binary.py::test_k_nearest[None-False-same-last] tests/test_binary.py::test_k_nearest[None-False-False-last] [gw30] [ 50%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain261-method_chain261] [gw20] [ 50%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain247-method_chain247] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain274-method_chain274] [gw31] [ 50%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain248-method_chain248] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain266-method_chain266] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain269-method_chain269] [gw35] [ 51%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain258-method_chain258] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain272-method_chain272] [gw28] [ 51%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain265-method_chain265] [gw33] [ 51%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain263-method_chain263] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain277-method_chain277] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain276-method_chain276] [gw21] [ 51%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain264-method_chain264] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain275-method_chain275] [gw26] [ 51%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain256-method_chain256] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain278-method_chain278] [gw36] [ 51%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain259-method_chain259] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain273-method_chain273] [gw24] [ 52%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain262-method_chain262] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain286-method_chain286] [gw39] [ 52%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain267-method_chain267] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain282-method_chain282] [gw40] [ 52%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain260-method_chain260] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain287-method_chain287] [gw25] [ 52%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain251-method_chain251] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain280-method_chain280] [gw34] [ 52%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain254-method_chain254] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain284-method_chain284] [gw22] [ 53%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain257-method_chain257] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain283-method_chain283] [gw38] [ 53%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain268-method_chain268] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain289-method_chain289] [gw32] [ 53%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain270-method_chain270] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain288-method_chain288] [gw23] [ 53%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain253-method_chain253] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain285-method_chain285] [gw27] [ 53%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain249-method_chain249] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain279-method_chain279] [gw37] [ 54%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain245-method_chain245] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain271-method_chain271] [gw29] [ 54%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain252-method_chain252] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain281-method_chain281] [gw41] [ 54%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain255-method_chain255] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain290-method_chain290] [gw35] [ 54%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain272-method_chain272] [gw33] [ 54%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain276-method_chain276] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain294-method_chain294] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain296-method_chain296] [gw30] [ 54%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain274-method_chain274] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain291-method_chain291] [gw28] [ 55%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain277-method_chain277] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain295-method_chain295] [gw21] [ 55%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain275-method_chain275] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain297-method_chain297] [gw31] [ 55%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain269-method_chain269] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain293-method_chain293] [gw20] [ 55%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain266-method_chain266] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain292-method_chain292] [gw26] [ 55%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain278-method_chain278] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain298-method_chain298] [gw38] [ 56%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain289-method_chain289] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain306-method_chain306] [gw32] [ 56%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain288-method_chain288] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain307-method_chain307] [gw36] [ 56%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain273-method_chain273] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain299-method_chain299] [gw27] [ 56%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain279-method_chain279] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain309-method_chain309] [gw24] [ 56%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain286-method_chain286] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain300-method_chain300] [gw4] [ 57%] PASSED tests/test_binary.py::test_coverage[same] tests/test_binary.py::test_coverage[opposite] [gw40] [ 57%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain287-method_chain287] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain302-method_chain302] [gw41] [ 57%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain290-method_chain290] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain312-method_chain312] [gw34] [ 57%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain284-method_chain284] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain304-method_chain304] [gw39] [ 57%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain282-method_chain282] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain301-method_chain301] [gw30] [ 58%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain291-method_chain291] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain315-method_chain315] [gw22] [ 58%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain283-method_chain283] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain305-method_chain305] [gw17] [ 58%] PASSED tests/test_binary.py::test_k_nearest[upstream-True-same-last] tests/test_binary.py::test_k_nearest[upstream-True-False-last] [gw31] [ 58%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain293-method_chain293] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain318-method_chain318] [gw25] [ 58%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain280-method_chain280] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain303-method_chain303] [gw37] [ 58%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain271-method_chain271] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain310-method_chain310] [gw20] [ 59%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain292-method_chain292] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain319-method_chain319] [gw29] [ 59%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain281-method_chain281] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain311-method_chain311] [gw33] [ 59%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain296-method_chain296] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain314-method_chain314] [gw28] [ 59%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain295-method_chain295] [gw5] [ 59%] PASSED tests/test_binary.py::test_subtraction[opposite] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain316-method_chain316] tests/test_binary.py::test_subtraction[False] [gw23] [ 60%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain285-method_chain285] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain308-method_chain308] [gw21] [ 60%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain297-method_chain297] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain317-method_chain317] [gw27] [ 60%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain309-method_chain309] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain324-method_chain324] [gw32] [ 60%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain307-method_chain307] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain322-method_chain322] [gw26] [ 60%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain298-method_chain298] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain320-method_chain320] [gw38] [ 61%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain306-method_chain306] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain321-method_chain321] [gw41] [ 61%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain312-method_chain312] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain327-method_chain327] [gw35] [ 61%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain294-method_chain294] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain313-method_chain313] [gw34] [ 61%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain304-method_chain304] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain328-method_chain328] [gw24] [ 61%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain300-method_chain300] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain325-method_chain325] [gw13] [ 61%] PASSED tests/test_binary.py::test_reldist tests/test_binary.py::test_k_nearest[downstream-False-opposite-last] [gw15] [ 62%] PASSED tests/test_binary.py::test_k_nearest[downstream-True-same-last] [gw22] [ 62%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain305-method_chain305] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain331-method_chain331] tests/test_binary.py::test_k_nearest[downstream-True-False-last] [gw37] [ 62%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain310-method_chain310] [gw40] [ 62%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain302-method_chain302] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain334-method_chain334] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain326-method_chain326] [gw36] [ 62%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain299-method_chain299] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain323-method_chain323] [gw29] [ 63%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain311-method_chain311] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain336-method_chain336] [gw39] [ 63%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain301-method_chain301] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain329-method_chain329] [gw25] [ 63%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain303-method_chain303] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain333-method_chain333] [gw20] [ 63%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain319-method_chain319] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain335-method_chain335] [gw31] [ 63%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain318-method_chain318] [gw33] [ 64%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain314-method_chain314] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain337-method_chain337] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain332-method_chain332] [gw30] [ 64%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain315-method_chain315] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain330-method_chain330] [gw21] [ 64%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain317-method_chain317] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain340-method_chain340] [gw27] [ 64%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain324-method_chain324] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain341-method_chain341] [gw28] [ 64%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain316-method_chain316] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain338-method_chain338] [gw38] [ 64%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain321-method_chain321] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain344-method_chain344] [gw23] [ 65%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain308-method_chain308] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain339-method_chain339] [gw32] [ 65%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain322-method_chain322] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain342-method_chain342] [gw41] [ 65%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain327-method_chain327] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain345-method_chain345] [gw2] [ 65%] PASSED tests/test_binary.py::test_overlap[opposite] [gw26] [ 65%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain320-method_chain320] tests/test_binary.py::test_intersect[False] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain343-method_chain343] [gw35] [ 66%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain313-method_chain313] [gw3] [ 66%] PASSED tests/test_binary.py::test_intersect[opposite] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain346-method_chain346] [gw34] [ 66%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain328-method_chain328] [gw24] [ 66%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain325-method_chain325] tests/test_binary.py::test_coverage[False] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain347-method_chain347] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain348-method_chain348] [gw40] [ 66%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain326-method_chain326] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain352-method_chain352] [gw36] [ 67%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain323-method_chain323] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain353-method_chain353] [gw21] [ 67%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain340-method_chain340] [gw22] [ 67%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain331-method_chain331] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain361-method_chain361] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain350-method_chain350] [gw33] [ 67%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain337-method_chain337] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain358-method_chain358] [gw28] [ 67%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain338-method_chain338] [gw25] [ 67%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain333-method_chain333] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain363-method_chain363] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain356-method_chain356] [gw20] [ 68%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain335-method_chain335] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain357-method_chain357] [gw32] [ 68%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain342-method_chain342] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain366-method_chain366] [gw29] [ 68%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain336-method_chain336] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain354-method_chain354] [gw23] [ 68%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain339-method_chain339] [gw27] [ 68%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain341-method_chain341] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain362-method_chain362] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain365-method_chain365] [gw31] [ 69%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain332-method_chain332] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain359-method_chain359] [gw38] [ 69%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain344-method_chain344] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain364-method_chain364] [gw41] [ 69%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain345-method_chain345] [gw37] [ 69%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain334-method_chain334] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain367-method_chain367] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain351-method_chain351] [gw30] [ 69%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain330-method_chain330] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain360-method_chain360] [gw39] [ 70%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain329-method_chain329] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain355-method_chain355] [gw34] [ 70%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain347-method_chain347] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain372-method_chain372] [gw21] [ 70%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain361-method_chain361] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain376-method_chain376] [gw40] [ 70%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain352-method_chain352] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain374-method_chain374] [gw35] [ 70%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain346-method_chain346] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain370-method_chain370] [gw36] [ 70%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain353-method_chain353] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain375-method_chain375] [gw33] [ 71%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain358-method_chain358] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain378-method_chain378] [gw32] [ 71%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain366-method_chain366] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain382-method_chain382] [gw25] [ 71%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain356-method_chain356] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain380-method_chain380] [gw28] [ 71%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain363-method_chain363] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain379-method_chain379] [gw22] [ 71%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain350-method_chain350] [gw31] [ 72%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain359-method_chain359] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain386-method_chain386] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain377-method_chain377] [gw26] [ 72%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain343-method_chain343] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain369-method_chain369] [gw27] [ 72%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain362-method_chain362] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain384-method_chain384] [gw29] [ 72%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain354-method_chain354] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain383-method_chain383] [gw23] [ 72%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain365-method_chain365] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain385-method_chain385] [gw24] [ 73%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain348-method_chain348] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain373-method_chain373] [gw20] [ 73%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain357-method_chain357] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain381-method_chain381] [gw30] [ 73%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain360-method_chain360] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain390-method_chain390] [gw9] [ 73%] PASSED tests/test_binary.py::test_nearest[upstream-False-opposite] [gw38] [ 73%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain364-method_chain364] tests/test_binary.py::test_nearest[downstream-True-False] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain387-method_chain387] [gw41] [ 74%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain367-method_chain367] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain388-method_chain388] [gw37] [ 74%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain351-method_chain351] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain389-method_chain389] [gw34] [ 74%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain372-method_chain372] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain392-method_chain392] [gw40] [ 74%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain374-method_chain374] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain394-method_chain394] [gw11] [ 74%] PASSED tests/test_binary.py::test_nearest[downstream-False-opposite] [gw35] [ 74%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain370-method_chain370] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain395-method_chain395] [gw21] [ 75%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain376-method_chain376] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain393-method_chain393] tests/test_binary.py::test_jaccard[False] [gw36] [ 75%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain375-method_chain375] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain396-method_chain396] [gw39] [ 75%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain355-method_chain355] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain391-method_chain391] [gw22] [ 75%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain377-method_chain377] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain402-method_chain402] [gw24] [ 75%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain373-method_chain373] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain407-method_chain407] [gw31] [ 76%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain386-method_chain386] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain401-method_chain401] [gw23] [ 76%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain385-method_chain385] [gw25] [ 76%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain380-method_chain380] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain406-method_chain406] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain399-method_chain399] [gw28] [ 76%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain379-method_chain379] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain400-method_chain400] [gw26] [ 76%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain369-method_chain369] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain403-method_chain403] [gw30] [ 77%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain390-method_chain390] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain409-method_chain409] [gw32] [ 77%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain382-method_chain382] [gw38] [ 77%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain387-method_chain387] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain411-method_chain411] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain398-method_chain398] [gw12] [ 77%] PASSED tests/test_binary.py::test_join[False] [gw33] [ 77%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain378-method_chain378] [gw37] [ 77%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain389-method_chain389] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain397-method_chain397] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain413-method_chain413] [gw27] [ 78%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain384-method_chain384] tests/test_binary.py::test_join[same] [gw41] [ 78%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain388-method_chain388] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain404-method_chain404] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain412-method_chain412] [gw20] [ 78%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain381-method_chain381] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain408-method_chain408] [gw39] [ 78%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain391-method_chain391] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain420-method_chain420] [gw7] [ 78%] PASSED tests/test_binary.py::test_nearest[None-False-opposite] tests/test_binary.py::test_nearest[upstream-True-False] [gw40] [ 79%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain394-method_chain394] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain415-method_chain415] [gw22] [ 79%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain402-method_chain402] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain421-method_chain421] [gw29] [ 79%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain383-method_chain383] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain405-method_chain405] [gw36] [ 79%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain396-method_chain396] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain419-method_chain419] [gw35] [ 79%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain395-method_chain395] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain416-method_chain416] [gw24] [ 80%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain407-method_chain407] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain422-method_chain422] [gw31] [ 80%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain401-method_chain401] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain423-method_chain423] [gw30] [ 80%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain409-method_chain409] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain428-method_chain428] [gw23] [ 80%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain406-method_chain406] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain424-method_chain424] [gw21] [ 80%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain393-method_chain393] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain417-method_chain417] [gw38] [ 80%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain411-method_chain411] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain429-method_chain429] [gw41] [ 81%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain412-method_chain412] [gw25] [ 81%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain399-method_chain399] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain435-method_chain435] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain425-method_chain425] [gw26] [ 81%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain403-method_chain403] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain427-method_chain427] [gw28] [ 81%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain400-method_chain400] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain426-method_chain426] [gw34] [ 81%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain392-method_chain392] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain414-method_chain414] [gw20] [ 82%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain408-method_chain408] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain436-method_chain436] [gw8] [ 82%] PASSED tests/test_binary.py::test_nearest[upstream-True-opposite] tests/test_binary.py::test_nearest[upstream-False-False] [gw37] [ 82%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain413-method_chain413] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain432-method_chain432] [gw32] [ 82%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain398-method_chain398] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain430-method_chain430] [gw27] [ 82%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain404-method_chain404] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain434-method_chain434] [gw10] [ 83%] PASSED tests/test_binary.py::test_nearest[downstream-True-opposite] tests/test_binary.py::test_nearest[downstream-False-False] [gw39] [ 83%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain420-method_chain420] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain437-method_chain437] [gw40] [ 83%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain415-method_chain415] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain439-method_chain439] [gw22] [ 83%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain421-method_chain421] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain440-method_chain440] [gw36] [ 83%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain419-method_chain419] tests/test_getset_attr.py::test_getsetattr [gw36] [ 83%] PASSED tests/test_getset_attr.py::test_getsetattr tests/windows/test_windows.py::test_windows [gw36] [ 84%] PASSED tests/windows/test_windows.py::test_windows tests/windows/test_windows.py::test_windows2 [gw36] [ 84%] PASSED tests/windows/test_windows.py::test_windows2 [gw35] [ 84%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain416-method_chain416] tests/test_getset_attr.py::test_getsetattr_fails [gw35] [ 84%] PASSED tests/test_getset_attr.py::test_getsetattr_fails [gw29] [ 84%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain405-method_chain405] tests/test_genomicfeatures.py::test_introns_single [gw24] [ 85%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain422-method_chain422] [gw23] [ 85%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain424-method_chain424] tests/test_getset_attr.py::test_getsetattr_with_str [gw24] [ 85%] PASSED tests/test_getset_attr.py::test_getsetattr_with_str tests/test_io.py::test_read_bed [gw23] [ 85%] PASSED tests/test_io.py::test_read_bed [gw31] [ 85%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain423-method_chain423] tests/test_io.py::test_read_gtf [gw31] [ 86%] PASSED tests/test_io.py::test_read_gtf [gw6] [ 86%] PASSED tests/test_binary.py::test_nearest[None-True-opposite] tests/test_binary.py::test_nearest[None-False-False] [gw21] [ 86%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain417-method_chain417] tests/test_pickle.py::test_pickle [gw21] [ 86%] PASSED tests/test_pickle.py::test_pickle [gw20] [ 86%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain436-method_chain436] tests/test_unary.py::test_cluster_by[True] [gw28] [ 87%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain426-method_chain426] tests/test_unary.py::test_cluster[True] [gw34] [ 87%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain414-method_chain414] tests/test_unary.py::test_cluster[False] [gw38] [ 87%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain429-method_chain429] tests/test_stranded.py::test_stranded [gw33] [ 87%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain397-method_chain397] [gw41] [ 87%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain435-method_chain435] [gw38] [ 87%] PASSED tests/test_stranded.py::test_stranded tests/test_stranded.py::test_unstrand tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain431-method_chain431] [gw25] [ 88%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain425-method_chain425] [gw41] [ 88%] PASSED tests/test_stranded.py::test_unstrand tests/test_unary.py::test_merge[True] [gw30] [ 88%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain428-method_chain428] tests/test_io.py::test_read_gff3 [gw30] [ 88%] PASSED tests/test_io.py::test_read_gff3 [gw39] [ 88%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain437-method_chain437] tests/test_unary.py::test_init[False] [gw22] [ 89%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain440-method_chain440] tests/test_unary.py::test_summary [gw40] [ 89%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain439-method_chain439] tests/test_unary.py::test_getitem [gw27] [ 89%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain434-method_chain434] tests/test_unary.py::test_windows [gw29] [ 89%] PASSED tests/test_genomicfeatures.py::test_introns_single [gw32] [ 89%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain430-method_chain430] tests/test_unary.py::test_merge_by[False] [gw37] [ 90%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain432-method_chain432] tests/test_unary.py::test_merge_by[True] [gw0] [ 90%] PASSED tests/test_binary.py::test_set_intersect[same] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain250-method_chain250] [gw26] [ 90%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain427-method_chain427] tests/test_unary.py::test_merge[False] [gw33] [ 90%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain431-method_chain431] [gw19] [ 90%] FAILED tests/test_binary.py::test_k_nearest[None-True-same-last] tests/test_binary.py::test_k_nearest[None-True-False-last] [gw14] [ 90%] PASSED tests/test_binary.py::test_k_nearest[downstream-False-False-last] tests/test_binary.py::test_k_nearest[downstream-True-opposite-last] [gw39] [ 91%] PASSED tests/test_unary.py::test_init[False] [gw1] [ 91%] PASSED tests/test_binary.py::test_set_union[same] tests/test_binary.py::test_overlap[False] [gw16] [ 91%] PASSED tests/test_binary.py::test_k_nearest[upstream-False-False-last] [gw2] [ 91%] PASSED tests/test_binary.py::test_intersect[False] tests/test_binary.py::test_k_nearest[upstream-True-opposite-last] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain368-method_chain368] [gw0] [ 91%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain250-method_chain250] [gw2] [ 92%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain368-method_chain368] [gw40] [ 92%] PASSED tests/test_unary.py::test_getitem [gw18] [ 92%] PASSED tests/test_binary.py::test_k_nearest[None-False-False-last] tests/test_binary.py::test_k_nearest[None-True-opposite-last] [gw13] [ 92%] PASSED tests/test_binary.py::test_k_nearest[downstream-False-opposite-last] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain349-method_chain349] [gw5] [ 92%] PASSED tests/test_binary.py::test_subtraction[False] tests/test_binary.py::test_nearest[None-True-False] [gw4] [ 93%] PASSED tests/test_binary.py::test_coverage[opposite] tests/test_binary.py::test_subtraction[same] [gw13] [ 93%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain349-method_chain349] [gw12] [ 93%] PASSED tests/test_binary.py::test_join[same] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain433-method_chain433] [gw22] [ 93%] PASSED tests/test_unary.py::test_summary [gw11] [ 93%] PASSED tests/test_binary.py::test_jaccard[False] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain418-method_chain418] [gw3] [ 93%] PASSED tests/test_binary.py::test_coverage[False] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain371-method_chain371] [gw12] [ 94%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain433-method_chain433] [gw9] [ 94%] PASSED tests/test_binary.py::test_nearest[downstream-True-False] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain410-method_chain410] [gw17] [ 94%] PASSED tests/test_binary.py::test_k_nearest[upstream-True-False-last] tests/test_binary.py::test_k_nearest[None-False-opposite-last] [gw25] [ 94%] PASSED tests/test_unary.py::test_merge[True] [gw8] [ 94%] PASSED tests/test_binary.py::test_nearest[upstream-False-False] [gw11] [ 95%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain418-method_chain418] tests/test_unary.py::test_cluster_by[False] [gw3] [ 95%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain371-method_chain371] [gw9] [ 95%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain410-method_chain410] [gw10] [ 95%] PASSED tests/test_binary.py::test_nearest[downstream-False-False] tests/test_unary.py::test_init[True] [gw26] [ 95%] PASSED tests/test_unary.py::test_merge[False] [gw7] [ 96%] PASSED tests/test_binary.py::test_nearest[upstream-True-False] tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain438-method_chain438] [gw6] [ 96%] PASSED tests/test_binary.py::test_nearest[None-False-False] [gw7] [ 96%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain438-method_chain438] [gw15] [ 96%] PASSED tests/test_binary.py::test_k_nearest[downstream-True-False-last] tests/test_binary.py::test_k_nearest[upstream-False-opposite-last] [gw1] [ 96%] PASSED tests/test_binary.py::test_overlap[False] [gw27] [ 96%] PASSED tests/test_unary.py::test_windows [gw32] [ 97%] PASSED tests/test_unary.py::test_merge_by[False] [gw10] [ 97%] PASSED tests/test_unary.py::test_init[True] [gw37] [ 97%] PASSED tests/test_unary.py::test_merge_by[True] [gw28] [ 97%] PASSED tests/test_unary.py::test_cluster[True] [gw34] [ 97%] PASSED tests/test_unary.py::test_cluster[False] [gw14] [ 98%] PASSED tests/test_binary.py::test_k_nearest[downstream-True-opposite-last] [gw20] [ 98%] PASSED tests/test_unary.py::test_cluster_by[True] [gw16] [ 98%] PASSED tests/test_binary.py::test_k_nearest[upstream-True-opposite-last] [gw5] [ 98%] PASSED tests/test_binary.py::test_nearest[None-True-False] [gw18] [ 98%] PASSED tests/test_binary.py::test_k_nearest[None-True-opposite-last] [gw4] [ 99%] PASSED tests/test_binary.py::test_subtraction[same] [gw17] [ 99%] PASSED tests/test_binary.py::test_k_nearest[None-False-opposite-last] [gw15] [ 99%] PASSED tests/test_binary.py::test_k_nearest[upstream-False-opposite-last] [gw19] [ 99%] PASSED tests/test_binary.py::test_k_nearest[None-True-False-last] tests/test_binary.py::test_k_nearest_1_vs_nearest [gw8] [ 99%] PASSED tests/test_unary.py::test_cluster_by[False] [gw19] [100%] PASSED tests/test_binary.py::test_k_nearest_1_vs_nearest =================================== FAILURES =================================== _____________________ test_k_nearest[None-True-same-last] ______________________ [gw19] linux -- Python 3.12.7 /usr/bin/python3.12 nearest_how = None, overlap = True, strandedness = 'same', ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:559: in test_k_nearest compare_results_nearest(bedtools_df, result) tests/test_binary.py:107: in compare_results_nearest assert_df_equal(result_df, bedtools_df) tests/helpers.py:58: in assert_df_equal print("index equal", df1.index == df2.index) /usr/lib/python3/dist-packages/pandas/core/ops/common.py:76: in new_method return method(self, other) /usr/lib/python3/dist-packages/pandas/core/arraylike.py:40: in __eq__ return self._cmp_method(other, operator.eq) /usr/lib/python3/dist-packages/pandas/core/indexes/range.py:1070: in _cmp_method return super()._cmp_method(other, op) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = RangeIndex(start=0, stop=4, step=1) other = RangeIndex(start=0, stop=3, step=1), op = def _cmp_method(self, other, op): """ Wrapper used to dispatch comparison operations. """ if self.is_(other): # fastpath if op in {operator.eq, operator.le, operator.ge}: arr = np.ones(len(self), dtype=bool) if self._can_hold_na and not isinstance(self, ABCMultiIndex): # TODO: should set MultiIndex._can_hold_na = False? arr[self.isna()] = False return arr elif op is operator.ne: arr = np.zeros(len(self), dtype=bool) if self._can_hold_na and not isinstance(self, ABCMultiIndex): arr[self.isna()] = True return arr if isinstance(other, (np.ndarray, Index, ABCSeries, ExtensionArray)) and len( self ) != len(other): > raise ValueError("Lengths must match to compare") E ValueError: Lengths must match to compare E Falsifying example: test_k_nearest( E nearest_how=None, E overlap=True, E strandedness='same', E ties='last', E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E | chr1 | 3 | 4 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E Explanation: E These lines were always and only run by failing examples: E /usr/lib/python3/dist-packages/pandas/core/indexes/base.py:7182 E /usr/lib/python3/dist-packages/pandas/core/indexes/base.py:7184 E /usr/lib/python3/dist-packages/pandas/core/indexes/range.py:1070 E E You can reproduce this example by temporarily adding @reproduce_failure('6.121.0', b'AXicY2RgCOx0YmRg8Es9wQAEjIxgkgEJQIQgYiwgLpjFhKIEAKbCAqo=') as a decorator on your test case /usr/lib/python3/dist-packages/pandas/core/indexes/base.py:7185: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpta5nblur/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpta5nblur/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjg90vzgt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjg90vzgt/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr83vk8t2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr83vk8t2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0ei5oe0j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0ei5oe0j/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2330779 2337746 + 6180969 1 chr1 2634451 2636149 + 5882566 2 chr11 8697054 8699791 + 6165157 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2634451 | 2636149 | a | 0 | ... | | chr1 | 2330779 | 2337746 | a | 0 | ... | | chr11 | 8697054 | 8699791 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 2330779 2337746 + 6180969 0 chr1 2634451 2636149 + 5882566 2 chr11 8697054 8699791 + 6165157 df2 Chromosome Start End Strand Distance 0 chr1 2330779 2337746 + 6180969 1 chr1 2634451 2636149 + 5882566 2 chr11 8697054 8699791 + 6165157 Actual Chromosome Start End Strand Distance 0 chr1 2330779 2337746 + 6180969 1 chr1 2634451 2636149 + 5882566 2 chr11 8697054 8699791 + 6165157 Expected Chromosome Start End Strand Distance 0 chr1 2330779 2337746 + 6180969 1 chr1 2634451 2636149 + 5882566 2 chr11 8697054 8699791 + 6165157 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkzl_4ivr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkzl_4ivr/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnlhy_ni5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnlhy_ni5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwawdafzl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwawdafzl/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpryl0_cvp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpryl0_cvp/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 2 chr1 4766581 4770435 + 3721286 4 chr1 4766581 4771425 + 3720296 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4766581 | 4770435 | a | 0 | ... | | chr1 | 4766581 | 4771425 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4766581 4770435 + 3721286 1 chr1 4766581 4771425 + 3720296 df2 Chromosome Start End Strand Distance 2 chr1 4766581 4770435 + 3721286 4 chr1 4766581 4771425 + 3720296 Actual Chromosome Start End Strand Distance 0 chr1 4766581 4770435 + 3721286 1 chr1 4766581 4771425 + 3720296 Expected Chromosome Start End Strand Distance 0 chr1 4766581 4770435 + 3721286 1 chr1 4766581 4771425 + 3720296 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuv2q4jhs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuv2q4jhs/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4fllp2oo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4fllp2oo/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0iu_y1f_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0iu_y1f_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmplgcf147x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplgcf147x/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsq07_7bf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsq07_7bf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9_88lyll/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9_88lyll/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpghd02x5k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpghd02x5k/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3yniy_cc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3yniy_cc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaom26oxx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaom26oxx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3vw_12w1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3vw_12w1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpea89m_x1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpea89m_x1/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 9582058 9582059 + 9582057 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9582058 | 9582059 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 9582058 9582059 + 9582057 df2 Chromosome Start End Strand Distance 0 chr1 9582058 9582059 + 9582057 Actual Chromosome Start End Strand Distance 0 chr1 9582058 9582059 + 9582057 Expected Chromosome Start End Strand Distance 0 chr1 9582058 9582059 + 9582057 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmptxq_0_2u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptxq_0_2u/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 9582058 9582059 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9582058 | 9582059 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 9582058 9582059 + 0 df2 Chromosome Start End Strand Distance 0 chr1 9582058 9582059 + 0 Actual Chromosome Start End Strand Distance 0 chr1 9582058 9582059 + 0 Expected Chromosome Start End Strand Distance 0 chr1 9582058 9582059 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpviw47654/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpviw47654/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0_ry2nke/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0_ry2nke/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkxogu7_g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkxogu7_g/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1232879 1235924 - 2170228 1 chr1 1232879 1235924 - 8764077 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1232879 | 1235924 | a | 0 | ... | | chr1 | 1232879 | 1235924 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1232879 1235924 - 2170228 1 chr1 1232879 1235924 - 8764077 df2 Chromosome Start End Strand Distance 0 chr1 1232879 1235924 - 2170228 1 chr1 1232879 1235924 - 8764077 Actual Chromosome Start End Strand Distance 0 chr1 1232879 1235924 - 2170228 1 chr1 1232879 1235924 - 8764077 Expected Chromosome Start End Strand Distance 0 chr1 1232879 1235924 - 2170228 1 chr1 1232879 1235924 - 8764077 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyrvf1r85/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyrvf1r85/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1232879 1235924 - 1232878 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1232879 | 1235924 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1232879 1235924 - 1232878 df2 Chromosome Start End Strand Distance 0 chr1 1232879 1235924 - 1232878 Actual Chromosome Start End Strand Distance 0 chr1 1232879 1235924 - 1232878 Expected Chromosome Start End Strand Distance 0 chr1 1232879 1235924 - 1232878 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmprh_6ue6y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprh_6ue6y/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1232879 1232880 - 1232878 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1232879 | 1232880 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1232879 1232880 - 1232878 df2 Chromosome Start End Strand Distance 0 chr1 1232879 1232880 - 1232878 Actual Chromosome Start End Strand Distance 0 chr1 1232879 1232880 - 1232878 Expected Chromosome Start End Strand Distance 0 chr1 1232879 1232880 - 1232878 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm7qin_gq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm7qin_gq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu356ojfd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu356ojfd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa70d1oeg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa70d1oeg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcxaphy0f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcxaphy0f/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmper4e22qo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmper4e22qo/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2awf0h1u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2awf0h1u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5_w0q0l5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5_w0q0l5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7fpuhg6i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7fpuhg6i/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmprjn47rei/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprjn47rei/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbnphlz25/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbnphlz25/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgc8y91q7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgc8y91q7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl5nrkvuj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl5nrkvuj/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5euns0v2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5euns0v2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5t21pjeh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5t21pjeh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcazf99zz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcazf99zz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp05i2rfr9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp05i2rfr9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr7 5003832 5010957 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr7 | 5003832 | 5010957 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr7 5003832 5010957 - 0 df2 Chromosome Start End Strand Distance 0 chr7 5003832 5010957 - 0 Actual Chromosome Start End Strand Distance 0 chr7 5003832 5010957 - 0 Expected Chromosome Start End Strand Distance 0 chr7 5003832 5010957 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7cwt7y4e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7cwt7y4e/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqcjhqafj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqcjhqafj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt7xfy94r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt7xfy94r/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe7enxp67/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe7enxp67/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj28tw6hm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj28tw6hm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmppyok5mmq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppyok5mmq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmposg6o62e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmposg6o62e/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpomeyfaqy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpomeyfaqy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg_dutnv_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg_dutnv_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpridhtneg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpridhtneg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr16 1 3458 - 0 1 chrX 504559 510854 + 0 2 chrX 504559 510854 + 1188797 3 chrX 1699650 1707554 + 0 4 chrX 1699650 1707554 + 1188797 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr16 | 1 | 3458 | a | 0 | ... | | chrX | 1699650 | 1707554 | a | 0 | ... | | chrX | 1699650 | 1707554 | a | 0 | ... | | chrX | 504559 | 510854 | a | 0 | ... | | chrX | 504559 | 510854 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr16 1 3458 - 0 3 chrX 504559 510854 + 0 4 chrX 504559 510854 + 1188797 1 chrX 1699650 1707554 + 0 2 chrX 1699650 1707554 + 1188797 df2 Chromosome Start End Strand Distance 0 chr16 1 3458 - 0 1 chrX 504559 510854 + 0 2 chrX 504559 510854 + 1188797 3 chrX 1699650 1707554 + 0 4 chrX 1699650 1707554 + 1188797 Actual Chromosome Start End Strand Distance 0 chr16 1 3458 - 0 1 chrX 504559 510854 + 0 2 chrX 504559 510854 + 1188797 3 chrX 1699650 1707554 + 0 4 chrX 1699650 1707554 + 1188797 Expected Chromosome Start End Strand Distance 0 chr16 1 3458 - 0 1 chrX 504559 510854 + 0 2 chrX 504559 510854 + 1188797 3 chrX 1699650 1707554 + 0 4 chrX 1699650 1707554 + 1188797 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx26kxjkl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx26kxjkl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzzssty4k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzzssty4k/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 22 1993 - 21 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 22 | 1993 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 22 1993 - 21 df2 Chromosome Start End Strand Distance 0 chr1 22 1993 - 21 Actual Chromosome Start End Strand Distance 0 chr1 22 1993 - 21 Expected Chromosome Start End Strand Distance 0 chr1 22 1993 - 21 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq386hl48/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq386hl48/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 264977 267931 + 256716 1 chr1 264977 267931 + 1518481 2 chr1 264977 269855 + 256716 3 chr1 264977 269855 + 1516557 4 chr1 264977 271615 - 273943 5 chr1 264977 271615 - 594811 6 chr1 264977 271893 - 273665 7 chr1 264977 271893 - 594533 8 chr18 264977 271123 - 6213667 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 264977 | 267931 | a | 0 | ... | | chr1 | 264977 | 267931 | a | 0 | ... | | chr1 | 264977 | 269855 | a | 0 | ... | | chr1 | 264977 | 269855 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 264977 | 271893 | a | 0 | ... | | chr1 | 264977 | 271893 | a | 0 | ... | | chr1 | 264977 | 271615 | a | 0 | ... | | chr1 | 264977 | 271615 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 264977 267931 + 256716 1 chr1 264977 267931 + 1518481 2 chr1 264977 269855 + 256716 3 chr1 264977 269855 + 1516557 8 chr18 264977 271123 - 6213667 6 chr1 264977 271615 - 273943 7 chr1 264977 271615 - 594811 4 chr1 264977 271893 - 273665 5 chr1 264977 271893 - 594533 df2 Chromosome Start End Strand Distance 0 chr1 264977 267931 + 256716 1 chr1 264977 267931 + 1518481 2 chr1 264977 269855 + 256716 3 chr1 264977 269855 + 1516557 8 chr18 264977 271123 - 6213667 4 chr1 264977 271615 - 273943 5 chr1 264977 271615 - 594811 6 chr1 264977 271893 - 273665 7 chr1 264977 271893 - 594533 Actual Chromosome Start End Strand Distance 0 chr1 264977 267931 + 256716 1 chr1 264977 267931 + 1518481 2 chr1 264977 269855 + 256716 3 chr1 264977 269855 + 1516557 4 chr1 264977 271615 - 273943 5 chr1 264977 271615 - 594811 6 chr1 264977 271893 - 273665 7 chr1 264977 271893 - 594533 8 chr18 264977 271123 - 6213667 Expected Chromosome Start End Strand Distance 0 chr1 264977 267931 + 256716 1 chr1 264977 267931 + 1518481 2 chr1 264977 269855 + 256716 3 chr1 264977 269855 + 1516557 4 chr1 264977 271615 - 273943 5 chr1 264977 271615 - 594811 6 chr1 264977 271893 - 273665 7 chr1 264977 271893 - 594533 8 chr18 264977 271123 - 6213667 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=9, step=1) index equal [ True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd20avl19/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd20avl19/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 2 chr1 264977 271615 - 264975 3 chr1 264977 271615 - 273943 4 chr1 264977 271893 - 264975 5 chr1 264977 271893 - 273665 6 chr18 264977 271123 - 6213667 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 264977 | 271893 | a | 0 | ... | | chr1 | 264977 | 271893 | a | 0 | ... | | chr1 | 264977 | 271615 | a | 0 | ... | | chr1 | 264977 | 271615 | a | 0 | ... | | chr18 | 264977 | 271123 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr18 264977 271123 - 6213667 2 chr1 264977 271615 - 264975 3 chr1 264977 271615 - 273943 0 chr1 264977 271893 - 264975 1 chr1 264977 271893 - 273665 df2 Chromosome Start End Strand Distance 6 chr18 264977 271123 - 6213667 2 chr1 264977 271615 - 264975 3 chr1 264977 271615 - 273943 4 chr1 264977 271893 - 264975 5 chr1 264977 271893 - 273665 Actual Chromosome Start End Strand Distance 0 chr1 264977 271615 - 264975 1 chr1 264977 271615 - 273943 2 chr1 264977 271893 - 264975 3 chr1 264977 271893 - 273665 4 chr18 264977 271123 - 6213667 Expected Chromosome Start End Strand Distance 0 chr1 264977 271615 - 264975 1 chr1 264977 271615 - 273943 2 chr1 264977 271893 - 264975 3 chr1 264977 271893 - 273665 4 chr18 264977 271123 - 6213667 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpryo6ukj5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpryo6ukj5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 2 chr1 264977 271615 - 264975 3 chr1 264977 271615 - 273943 4 chr1 264977 271893 - 264975 5 chr1 264977 271893 - 273665 6 chr18 264977 271123 - 6213667 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 264977 | 271893 | a | 0 | ... | | chr1 | 264977 | 271893 | a | 0 | ... | | chr1 | 264977 | 271615 | a | 0 | ... | | chr1 | 264977 | 271615 | a | 0 | ... | | chr18 | 264977 | 271123 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr18 264977 271123 - 6213667 2 chr1 264977 271615 - 264975 3 chr1 264977 271615 - 273943 0 chr1 264977 271893 - 264975 1 chr1 264977 271893 - 273665 df2 Chromosome Start End Strand Distance 6 chr18 264977 271123 - 6213667 2 chr1 264977 271615 - 264975 3 chr1 264977 271615 - 273943 4 chr1 264977 271893 - 264975 5 chr1 264977 271893 - 273665 Actual Chromosome Start End Strand Distance 0 chr1 264977 271615 - 264975 1 chr1 264977 271615 - 273943 2 chr1 264977 271893 - 264975 3 chr1 264977 271893 - 273665 4 chr18 264977 271123 - 6213667 Expected Chromosome Start End Strand Distance 0 chr1 264977 271615 - 264975 1 chr1 264977 271615 - 273943 2 chr1 264977 271893 - 264975 3 chr1 264977 271893 - 273665 4 chr18 264977 271123 - 6213667 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp807g1z22/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp807g1z22/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 0 1 chr1 2 3 - 545555 2 chr1 545557 545558 - 0 3 chr1 545557 545558 - 320868 4 chr1 866425 866426 - 0 5 chr1 866425 866426 - 320868 6 chr1 1786411 1786412 - 0 7 chr1 1786411 1786412 - 919986 8 chr1 5646286 5655247 - 0 9 chr1 5646286 5655247 - 279981 10 chr1 5935227 5935228 - 0 11 chr1 5935227 5935228 - 279981 12 chr10 5132592 5132598 + 0 13 chr18 6484789 6484790 - 0 14 chr2 7723615 7723616 - 0 15 chr8 1 2 - 0 16 chrY 6876498 6876499 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5935227 | 5935228 | a | 0 | ... | | chr1 | 5935227 | 5935228 | a | 0 | ... | | chr1 | 1786411 | 1786412 | a | 0 | ... | | chr1 | 1786411 | 1786412 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr8 | 1 | 2 | a | 0 | ... | | chr10 | 5132592 | 5132598 | a | 0 | ... | | chr18 | 6484789 | 6484790 | a | 0 | ... | | chrY | 6876498 | 6876499 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 17 rows and 12 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 13 chr8 1 2 - 0 8 chr1 2 3 - 0 9 chr1 2 3 - 545555 4 chr1 545557 545558 - 0 5 chr1 545557 545558 - 320868 10 chr1 866425 866426 - 0 11 chr1 866425 866426 - 320868 2 chr1 1786411 1786412 - 0 3 chr1 1786411 1786412 - 919986 14 chr10 5132592 5132598 + 0 6 chr1 5646286 5655247 - 0 7 chr1 5646286 5655247 - 279981 0 chr1 5935227 5935228 - 0 1 chr1 5935227 5935228 - 279981 15 chr18 6484789 6484790 - 0 16 chrY 6876498 6876499 - 0 12 chr2 7723615 7723616 - 0 df2 Chromosome Start End Strand Distance 15 chr8 1 2 - 0 0 chr1 2 3 - 0 1 chr1 2 3 - 545555 2 chr1 545557 545558 - 0 3 chr1 545557 545558 - 320868 4 chr1 866425 866426 - 0 5 chr1 866425 866426 - 320868 6 chr1 1786411 1786412 - 0 7 chr1 1786411 1786412 - 919986 12 chr10 5132592 5132598 + 0 8 chr1 5646286 5655247 - 0 9 chr1 5646286 5655247 - 279981 10 chr1 5935227 5935228 - 0 11 chr1 5935227 5935228 - 279981 13 chr18 6484789 6484790 - 0 16 chrY 6876498 6876499 - 0 14 chr2 7723615 7723616 - 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 0 1 chr1 2 3 - 545555 2 chr1 545557 545558 - 0 3 chr1 545557 545558 - 320868 4 chr1 866425 866426 - 0 5 chr1 866425 866426 - 320868 6 chr1 1786411 1786412 - 0 7 chr1 1786411 1786412 - 919986 8 chr1 5646286 5655247 - 0 9 chr1 5646286 5655247 - 279981 10 chr1 5935227 5935228 - 0 11 chr1 5935227 5935228 - 279981 12 chr10 5132592 5132598 + 0 13 chr18 6484789 6484790 - 0 14 chr2 7723615 7723616 - 0 15 chr8 1 2 - 0 16 chrY 6876498 6876499 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 0 1 chr1 2 3 - 545555 2 chr1 545557 545558 - 0 3 chr1 545557 545558 - 320868 4 chr1 866425 866426 - 0 5 chr1 866425 866426 - 320868 6 chr1 1786411 1786412 - 0 7 chr1 1786411 1786412 - 919986 8 chr1 5646286 5655247 - 0 9 chr1 5646286 5655247 - 279981 10 chr1 5935227 5935228 - 0 11 chr1 5935227 5935228 - 279981 12 chr10 5132592 5132598 + 0 13 chr18 6484789 6484790 - 0 14 chr2 7723615 7723616 - 0 15 chr8 1 2 - 0 16 chrY 6876498 6876499 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=17, step=1) Expected index RangeIndex(start=0, stop=17, step=1) index equal [ True True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbt1hmy38/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbt1hmy38/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 0 1 chr1 2 3 - 545555 2 chr1 545557 545558 - 0 3 chr1 545557 545558 - 320868 4 chr1 866425 866426 - 0 5 chr1 866425 866426 - 320868 6 chr1 1786411 1786412 - 0 7 chr1 1786411 1786412 - 919986 8 chr1 5646286 5646287 - 0 9 chr1 5646286 5646287 - 288941 10 chr1 5935227 5935228 - 0 11 chr1 5935227 5935228 - 279981 12 chr10 5132592 5132593 + 0 13 chr18 6484789 6484790 - 0 14 chr2 7723615 7723616 - 0 15 chr8 1 2 - 0 16 chrY 6876498 6876499 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5935227 | 5935228 | a | 0 | ... | | chr1 | 5935227 | 5935228 | a | 0 | ... | | chr1 | 1786411 | 1786412 | a | 0 | ... | | chr1 | 1786411 | 1786412 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr8 | 1 | 2 | a | 0 | ... | | chr10 | 5132592 | 5132593 | a | 0 | ... | | chr18 | 6484789 | 6484790 | a | 0 | ... | | chrY | 6876498 | 6876499 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 17 rows and 12 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 13 chr8 1 2 - 0 8 chr1 2 3 - 0 9 chr1 2 3 - 545555 4 chr1 545557 545558 - 0 5 chr1 545557 545558 - 320868 10 chr1 866425 866426 - 0 11 chr1 866425 866426 - 320868 2 chr1 1786411 1786412 - 0 3 chr1 1786411 1786412 - 919986 14 chr10 5132592 5132593 + 0 6 chr1 5646286 5646287 - 0 7 chr1 5646286 5646287 - 288941 0 chr1 5935227 5935228 - 0 1 chr1 5935227 5935228 - 279981 15 chr18 6484789 6484790 - 0 16 chrY 6876498 6876499 - 0 12 chr2 7723615 7723616 - 0 df2 Chromosome Start End Strand Distance 15 chr8 1 2 - 0 0 chr1 2 3 - 0 1 chr1 2 3 - 545555 2 chr1 545557 545558 - 0 3 chr1 545557 545558 - 320868 4 chr1 866425 866426 - 0 5 chr1 866425 866426 - 320868 6 chr1 1786411 1786412 - 0 7 chr1 1786411 1786412 - 919986 12 chr10 5132592 5132593 + 0 8 chr1 5646286 5646287 - 0 9 chr1 5646286 5646287 - 288941 10 chr1 5935227 5935228 - 0 11 chr1 5935227 5935228 - 279981 13 chr18 6484789 6484790 - 0 16 chrY 6876498 6876499 - 0 14 chr2 7723615 7723616 - 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 0 1 chr1 2 3 - 545555 2 chr1 545557 545558 - 0 3 chr1 545557 545558 - 320868 4 chr1 866425 866426 - 0 5 chr1 866425 866426 - 320868 6 chr1 1786411 1786412 - 0 7 chr1 1786411 1786412 - 919986 8 chr1 5646286 5646287 - 0 9 chr1 5646286 5646287 - 288941 10 chr1 5935227 5935228 - 0 11 chr1 5935227 5935228 - 279981 12 chr10 5132592 5132593 + 0 13 chr18 6484789 6484790 - 0 14 chr2 7723615 7723616 - 0 15 chr8 1 2 - 0 16 chrY 6876498 6876499 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 0 1 chr1 2 3 - 545555 2 chr1 545557 545558 - 0 3 chr1 545557 545558 - 320868 4 chr1 866425 866426 - 0 5 chr1 866425 866426 - 320868 6 chr1 1786411 1786412 - 0 7 chr1 1786411 1786412 - 919986 8 chr1 5646286 5646287 - 0 9 chr1 5646286 5646287 - 288941 10 chr1 5935227 5935228 - 0 11 chr1 5935227 5935228 - 279981 12 chr10 5132592 5132593 + 0 13 chr18 6484789 6484790 - 0 14 chr2 7723615 7723616 - 0 15 chr8 1 2 - 0 16 chrY 6876498 6876499 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=17, step=1) Expected index RangeIndex(start=0, stop=17, step=1) index equal [ True True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3royg147/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3royg147/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 0 1 chr1 2 3 - 545555 2 chr1 545557 545558 - 0 3 chr1 545557 545558 - 320868 4 chr1 866425 866426 - 0 5 chr1 866425 866426 - 320868 6 chr1 1786411 1786412 - 0 7 chr1 1786411 1786412 - 919986 8 chr1 5646286 5646287 - 0 9 chr1 5646286 5646287 - 288941 10 chr1 5935227 5935228 - 0 11 chr1 5935227 5935228 - 288941 12 chr10 5132592 5132593 + 0 13 chr18 6484789 6484790 - 0 14 chr2 7723615 7723616 - 0 15 chr8 1 2 - 0 16 chrY 6876498 6876499 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5935227 | 5935228 | a | 0 | ... | | chr1 | 5935227 | 5935228 | a | 0 | ... | | chr1 | 1786411 | 1786412 | a | 0 | ... | | chr1 | 1786411 | 1786412 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr8 | 1 | 2 | a | 0 | ... | | chr10 | 5132592 | 5132593 | a | 0 | ... | | chr18 | 6484789 | 6484790 | a | 0 | ... | | chrY | 6876498 | 6876499 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 17 rows and 12 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 13 chr8 1 2 - 0 8 chr1 2 3 - 0 9 chr1 2 3 - 545555 4 chr1 545557 545558 - 0 5 chr1 545557 545558 - 320868 10 chr1 866425 866426 - 0 11 chr1 866425 866426 - 320868 2 chr1 1786411 1786412 - 0 3 chr1 1786411 1786412 - 919986 14 chr10 5132592 5132593 + 0 6 chr1 5646286 5646287 - 0 7 chr1 5646286 5646287 - 288941 0 chr1 5935227 5935228 - 0 1 chr1 5935227 5935228 - 288941 15 chr18 6484789 6484790 - 0 16 chrY 6876498 6876499 - 0 12 chr2 7723615 7723616 - 0 df2 Chromosome Start End Strand Distance 15 chr8 1 2 - 0 0 chr1 2 3 - 0 1 chr1 2 3 - 545555 2 chr1 545557 545558 - 0 3 chr1 545557 545558 - 320868 4 chr1 866425 866426 - 0 5 chr1 866425 866426 - 320868 6 chr1 1786411 1786412 - 0 7 chr1 1786411 1786412 - 919986 12 chr10 5132592 5132593 + 0 8 chr1 5646286 5646287 - 0 9 chr1 5646286 5646287 - 288941 10 chr1 5935227 5935228 - 0 11 chr1 5935227 5935228 - 288941 13 chr18 6484789 6484790 - 0 16 chrY 6876498 6876499 - 0 14 chr2 7723615 7723616 - 0 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 0 1 chr1 2 3 - 545555 2 chr1 545557 545558 - 0 3 chr1 545557 545558 - 320868 4 chr1 866425 866426 - 0 5 chr1 866425 866426 - 320868 6 chr1 1786411 1786412 - 0 7 chr1 1786411 1786412 - 919986 8 chr1 5646286 5646287 - 0 9 chr1 5646286 5646287 - 288941 10 chr1 5935227 5935228 - 0 11 chr1 5935227 5935228 - 288941 12 chr10 5132592 5132593 + 0 13 chr18 6484789 6484790 - 0 14 chr2 7723615 7723616 - 0 15 chr8 1 2 - 0 16 chrY 6876498 6876499 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 0 1 chr1 2 3 - 545555 2 chr1 545557 545558 - 0 3 chr1 545557 545558 - 320868 4 chr1 866425 866426 - 0 5 chr1 866425 866426 - 320868 6 chr1 1786411 1786412 - 0 7 chr1 1786411 1786412 - 919986 8 chr1 5646286 5646287 - 0 9 chr1 5646286 5646287 - 288941 10 chr1 5935227 5935228 - 0 11 chr1 5935227 5935228 - 288941 12 chr10 5132592 5132593 + 0 13 chr18 6484789 6484790 - 0 14 chr2 7723615 7723616 - 0 15 chr8 1 2 - 0 16 chrY 6876498 6876499 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=17, step=1) Expected index RangeIndex(start=0, stop=17, step=1) index equal [ True True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp69pi2le9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp69pi2le9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 545557 545558 - 545556 2 chr1 866425 866426 - 866424 3 chr1 1786411 1786412 - 1786410 4 chr1 5646286 5646287 - 5646285 5 chr1 5935227 5935228 - 5935226 6 chr10 5132592 5132593 + 5132591 9 chr8 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5935227 | 5935228 | a | 0 | ... | | chr1 | 1786411 | 1786412 | a | 0 | ... | | chr1 | 545557 | 545558 | a | 0 | ... | | chr1 | 5646286 | 5646287 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 866425 | 866426 | a | 0 | ... | | chr8 | 1 | 2 | a | 0 | ... | | chr10 | 5132592 | 5132593 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr8 1 2 - 0 4 chr1 2 3 - 1 2 chr1 545557 545558 - 545556 5 chr1 866425 866426 - 866424 1 chr1 1786411 1786412 - 1786410 7 chr10 5132592 5132593 + 5132591 3 chr1 5646286 5646287 - 5646285 0 chr1 5935227 5935228 - 5935226 df2 Chromosome Start End Strand Distance 9 chr8 1 2 - 0 0 chr1 2 3 - 1 1 chr1 545557 545558 - 545556 2 chr1 866425 866426 - 866424 3 chr1 1786411 1786412 - 1786410 6 chr10 5132592 5132593 + 5132591 4 chr1 5646286 5646287 - 5646285 5 chr1 5935227 5935228 - 5935226 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 545557 545558 - 545556 2 chr1 866425 866426 - 866424 3 chr1 1786411 1786412 - 1786410 4 chr1 5646286 5646287 - 5646285 5 chr1 5935227 5935228 - 5935226 6 chr10 5132592 5132593 + 5132591 7 chr8 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 545557 545558 - 545556 2 chr1 866425 866426 - 866424 3 chr1 1786411 1786412 - 1786410 4 chr1 5646286 5646287 - 5646285 5 chr1 5935227 5935228 - 5935226 6 chr10 5132592 5132593 + 5132591 7 chr8 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2vna4sh2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2vna4sh2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5n65j3qy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5n65j3qy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0urfr8pj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0urfr8pj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmphx727aql/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphx727aql/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr15 7868774 7873918 - 7868771 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr15 | 7868774 | 7873918 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr15 7868774 7873918 - 7868771 df2 Chromosome Start End Strand Distance 0 chr15 7868774 7873918 - 7868771 Actual Chromosome Start End Strand Distance 0 chr15 7868774 7873918 - 7868771 Expected Chromosome Start End Strand Distance 0 chr15 7868774 7873918 - 7868771 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmphkdqzy17/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphkdqzy17/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4xdatq8d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4xdatq8d/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr15 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr15 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr15 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr15 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr15 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr15 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmptrblxgmm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptrblxgmm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmprtsdaf4v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprtsdaf4v/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 944496 946061 - 283841 1 chr1 944496 946061 - 3862387 2 chr1 5324879 5332244 - 508907 3 chr1 5324879 5332244 - 4664224 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5324879 | 5332244 | a | 0 | ... | | chr1 | 5324879 | 5332244 | a | 0 | ... | | chr1 | 944496 | 946061 | a | 0 | ... | | chr1 | 944496 | 946061 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 944496 946061 - 283841 3 chr1 944496 946061 - 3862387 0 chr1 5324879 5332244 - 508907 1 chr1 5324879 5332244 - 4664224 df2 Chromosome Start End Strand Distance 0 chr1 944496 946061 - 283841 1 chr1 944496 946061 - 3862387 2 chr1 5324879 5332244 - 508907 3 chr1 5324879 5332244 - 4664224 Actual Chromosome Start End Strand Distance 0 chr1 944496 946061 - 283841 1 chr1 944496 946061 - 3862387 2 chr1 5324879 5332244 - 508907 3 chr1 5324879 5332244 - 4664224 Expected Chromosome Start End Strand Distance 0 chr1 944496 946061 - 283841 1 chr1 944496 946061 - 3862387 2 chr1 5324879 5332244 - 508907 3 chr1 5324879 5332244 - 4664224 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc_a5fgui/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc_a5fgui/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 944496 946061 - 283841 1 chr1 944496 946061 - 3862387 2 chr1 5324879 5332244 - 508907 3 chr1 5324879 5332244 - 4664224 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5324879 | 5332244 | a | 0 | ... | | chr1 | 5324879 | 5332244 | a | 0 | ... | | chr1 | 944496 | 946061 | a | 0 | ... | | chr1 | 944496 | 946061 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 944496 946061 - 283841 3 chr1 944496 946061 - 3862387 0 chr1 5324879 5332244 - 508907 1 chr1 5324879 5332244 - 4664224 df2 Chromosome Start End Strand Distance 0 chr1 944496 946061 - 283841 1 chr1 944496 946061 - 3862387 2 chr1 5324879 5332244 - 508907 3 chr1 5324879 5332244 - 4664224 Actual Chromosome Start End Strand Distance 0 chr1 944496 946061 - 283841 1 chr1 944496 946061 - 3862387 2 chr1 5324879 5332244 - 508907 3 chr1 5324879 5332244 - 4664224 Expected Chromosome Start End Strand Distance 0 chr1 944496 946061 - 283841 1 chr1 944496 946061 - 3862387 2 chr1 5324879 5332244 - 508907 3 chr1 5324879 5332244 - 4664224 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfa3on7h4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfa3on7h4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 944496 946061 - 283841 1 chr1 944496 946061 - 3862387 2 chr1 5324879 5332244 - 508907 3 chr1 5324879 5332244 - 4664224 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5324879 | 5332244 | a | 0 | ... | | chr1 | 5324879 | 5332244 | a | 0 | ... | | chr1 | 944496 | 946061 | a | 0 | ... | | chr1 | 944496 | 946061 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 944496 946061 - 283841 3 chr1 944496 946061 - 3862387 0 chr1 5324879 5332244 - 508907 1 chr1 5324879 5332244 - 4664224 df2 Chromosome Start End Strand Distance 0 chr1 944496 946061 - 283841 1 chr1 944496 946061 - 3862387 2 chr1 5324879 5332244 - 508907 3 chr1 5324879 5332244 - 4664224 Actual Chromosome Start End Strand Distance 0 chr1 944496 946061 - 283841 1 chr1 944496 946061 - 3862387 2 chr1 5324879 5332244 - 508907 3 chr1 5324879 5332244 - 4664224 Expected Chromosome Start End Strand Distance 0 chr1 944496 946061 - 283841 1 chr1 944496 946061 - 3862387 2 chr1 5324879 5332244 - 508907 3 chr1 5324879 5332244 - 4664224 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa8k9puxk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa8k9puxk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 944496 946061 - 944495 1 chr1 944496 946061 - 3862387 2 chr1 5324879 5332244 - 516432 3 chr1 5324879 5332244 - 5324878 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5324879 | 5332244 | a | 0 | ... | | chr1 | 5324879 | 5332244 | a | 0 | ... | | chr1 | 944496 | 946061 | a | 0 | ... | | chr1 | 944496 | 946061 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 944496 946061 - 944495 3 chr1 944496 946061 - 3862387 0 chr1 5324879 5332244 - 516432 1 chr1 5324879 5332244 - 5324878 df2 Chromosome Start End Strand Distance 0 chr1 944496 946061 - 944495 1 chr1 944496 946061 - 3862387 2 chr1 5324879 5332244 - 516432 3 chr1 5324879 5332244 - 5324878 Actual Chromosome Start End Strand Distance 0 chr1 944496 946061 - 944495 1 chr1 944496 946061 - 3862387 2 chr1 5324879 5332244 - 516432 3 chr1 5324879 5332244 - 5324878 Expected Chromosome Start End Strand Distance 0 chr1 944496 946061 - 944495 1 chr1 944496 946061 - 3862387 2 chr1 5324879 5332244 - 516432 3 chr1 5324879 5332244 - 5324878 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp232vbs72/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp232vbs72/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 944496 946061 - 944495 1 chr1 944496 946061 - 3862387 2 chr1 5324879 5332244 - 516432 3 chr1 5324879 5332244 - 5324878 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5324879 | 5332244 | a | 0 | ... | | chr1 | 5324879 | 5332244 | a | 0 | ... | | chr1 | 944496 | 946061 | a | 0 | ... | | chr1 | 944496 | 946061 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 944496 946061 - 944495 3 chr1 944496 946061 - 3862387 0 chr1 5324879 5332244 - 516432 1 chr1 5324879 5332244 - 5324878 df2 Chromosome Start End Strand Distance 0 chr1 944496 946061 - 944495 1 chr1 944496 946061 - 3862387 2 chr1 5324879 5332244 - 516432 3 chr1 5324879 5332244 - 5324878 Actual Chromosome Start End Strand Distance 0 chr1 944496 946061 - 944495 1 chr1 944496 946061 - 3862387 2 chr1 5324879 5332244 - 516432 3 chr1 5324879 5332244 - 5324878 Expected Chromosome Start End Strand Distance 0 chr1 944496 946061 - 944495 1 chr1 944496 946061 - 3862387 2 chr1 5324879 5332244 - 516432 3 chr1 5324879 5332244 - 5324878 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpssfi3j4v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpssfi3j4v/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 944496 946061 - 944495 1 chr1 944496 946061 - 3862387 2 chr1 5324879 5332244 - 516432 3 chr1 5324879 5332244 - 5324878 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5324879 | 5332244 | a | 0 | ... | | chr1 | 5324879 | 5332244 | a | 0 | ... | | chr1 | 944496 | 946061 | a | 0 | ... | | chr1 | 944496 | 946061 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 944496 946061 - 944495 3 chr1 944496 946061 - 3862387 0 chr1 5324879 5332244 - 516432 1 chr1 5324879 5332244 - 5324878 df2 Chromosome Start End Strand Distance 0 chr1 944496 946061 - 944495 1 chr1 944496 946061 - 3862387 2 chr1 5324879 5332244 - 516432 3 chr1 5324879 5332244 - 5324878 Actual Chromosome Start End Strand Distance 0 chr1 944496 946061 - 944495 1 chr1 944496 946061 - 3862387 2 chr1 5324879 5332244 - 516432 3 chr1 5324879 5332244 - 5324878 Expected Chromosome Start End Strand Distance 0 chr1 944496 946061 - 944495 1 chr1 944496 946061 - 3862387 2 chr1 5324879 5332244 - 516432 3 chr1 5324879 5332244 - 5324878 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6dzng6we/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6dzng6we/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 4808446 2 chr1 4808447 4808448 - 0 3 chr1 4808447 4808448 - 4808446 4 chr1 4808447 4808448 - 0 5 chr1 4808447 4808448 - 4808446 6 chr1 4808447 4808448 - 0 7 chr1 4808447 4808448 - 4808446 8 chr1 4808447 4808448 - 0 9 chr1 4808447 4808448 - 4808446 10 chr1 4808447 4808448 - 0 11 chr1 4808447 4808448 - 4808446 12 chr3 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 4808447 | 4808448 | a | 0 | ... | | chr1 | 4808447 | 4808448 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 4808447 | 4808448 | a | 0 | ... | | chr1 | 4808447 | 4808448 | a | 0 | ... | | chr1 | 4808447 | 4808448 | a | 0 | ... | | chr1 | 4808447 | 4808448 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 13 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 12 chr3 1 2 - 0 1 chr1 1 2 - 4808446 2 chr1 4808447 4808448 - 0 4 chr1 4808447 4808448 - 0 6 chr1 4808447 4808448 - 0 8 chr1 4808447 4808448 - 0 10 chr1 4808447 4808448 - 0 3 chr1 4808447 4808448 - 4808446 5 chr1 4808447 4808448 - 4808446 7 chr1 4808447 4808448 - 4808446 9 chr1 4808447 4808448 - 4808446 11 chr1 4808447 4808448 - 4808446 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 12 chr3 1 2 - 0 1 chr1 1 2 - 4808446 2 chr1 4808447 4808448 - 0 4 chr1 4808447 4808448 - 0 6 chr1 4808447 4808448 - 0 8 chr1 4808447 4808448 - 0 10 chr1 4808447 4808448 - 0 3 chr1 4808447 4808448 - 4808446 5 chr1 4808447 4808448 - 4808446 7 chr1 4808447 4808448 - 4808446 9 chr1 4808447 4808448 - 4808446 11 chr1 4808447 4808448 - 4808446 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 4808446 2 chr1 4808447 4808448 - 0 3 chr1 4808447 4808448 - 0 4 chr1 4808447 4808448 - 0 5 chr1 4808447 4808448 - 0 6 chr1 4808447 4808448 - 0 7 chr1 4808447 4808448 - 4808446 8 chr1 4808447 4808448 - 4808446 9 chr1 4808447 4808448 - 4808446 10 chr1 4808447 4808448 - 4808446 11 chr1 4808447 4808448 - 4808446 12 chr3 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 4808446 2 chr1 4808447 4808448 - 0 3 chr1 4808447 4808448 - 0 4 chr1 4808447 4808448 - 0 5 chr1 4808447 4808448 - 0 6 chr1 4808447 4808448 - 0 7 chr1 4808447 4808448 - 4808446 8 chr1 4808447 4808448 - 4808446 9 chr1 4808447 4808448 - 4808446 10 chr1 4808447 4808448 - 4808446 11 chr1 4808447 4808448 - 4808446 12 chr3 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=13, step=1) Expected index RangeIndex(start=0, stop=13, step=1) index equal [ True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvhqrkhlx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvhqrkhlx/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3960088 3962116 + 1324817 1 chr1 3960088 3962116 + 1933956 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3960088 | 3962116 | a | 0 | ... | | chr1 | 3960088 | 3962116 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3960088 3962116 + 1324817 1 chr1 3960088 3962116 + 1933956 df2 Chromosome Start End Strand Distance 0 chr1 3960088 3962116 + 1324817 1 chr1 3960088 3962116 + 1933956 Actual Chromosome Start End Strand Distance 0 chr1 3960088 3962116 + 1324817 1 chr1 3960088 3962116 + 1933956 Expected Chromosome Start End Strand Distance 0 chr1 3960088 3962116 + 1324817 1 chr1 3960088 3962116 + 1933956 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5hig1b92/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5hig1b92/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3960088 3962116 + 1324817 1 chr1 3960088 3962116 + 1933956 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3960088 | 3962116 | a | 0 | ... | | chr1 | 3960088 | 3962116 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3960088 3962116 + 1324817 1 chr1 3960088 3962116 + 1933956 df2 Chromosome Start End Strand Distance 0 chr1 3960088 3962116 + 1324817 1 chr1 3960088 3962116 + 1933956 Actual Chromosome Start End Strand Distance 0 chr1 3960088 3962116 + 1324817 1 chr1 3960088 3962116 + 1933956 Expected Chromosome Start End Strand Distance 0 chr1 3960088 3962116 + 1324817 1 chr1 3960088 3962116 + 1933956 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdcqj6p0a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdcqj6p0a/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3960088 3962116 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3960088 | 3962116 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3960088 3962116 + 0 df2 Chromosome Start End Strand Distance 0 chr1 3960088 3962116 + 0 Actual Chromosome Start End Strand Distance 0 chr1 3960088 3962116 + 0 Expected Chromosome Start End Strand Distance 0 chr1 3960088 3962116 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvuqn_i_i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvuqn_i_i/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3960088 3962116 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3960088 | 3962116 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3960088 3962116 + 0 df2 Chromosome Start End Strand Distance 0 chr1 3960088 3962116 + 0 Actual Chromosome Start End Strand Distance 0 chr1 3960088 3962116 + 0 Expected Chromosome Start End Strand Distance 0 chr1 3960088 3962116 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpybuwxahy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpybuwxahy/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3960088 3962116 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3960088 | 3962116 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3960088 3962116 + 0 df2 Chromosome Start End Strand Distance 0 chr1 3960088 3962116 + 0 Actual Chromosome Start End Strand Distance 0 chr1 3960088 3962116 + 0 Expected Chromosome Start End Strand Distance 0 chr1 3960088 3962116 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt2a6f9zp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt2a6f9zp/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3960088 3960089 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3960088 | 3960089 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3960088 3960089 + 0 df2 Chromosome Start End Strand Distance 0 chr1 3960088 3960089 + 0 Actual Chromosome Start End Strand Distance 0 chr1 3960088 3960089 + 0 Expected Chromosome Start End Strand Distance 0 chr1 3960088 3960089 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk3ay2eal/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk3ay2eal/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3960088 3960089 + 3954199 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3960088 | 3960089 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3960088 3960089 + 3954199 df2 Chromosome Start End Strand Distance 0 chr1 3960088 3960089 + 3954199 Actual Chromosome Start End Strand Distance 0 chr1 3960088 3960089 + 3954199 Expected Chromosome Start End Strand Distance 0 chr1 3960088 3960089 + 3954199 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmtfmhx03/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmtfmhx03/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1kkci_rd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1kkci_rd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2dmqz3r3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2dmqz3r3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr22 4312132 4318894 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr22 | 4312132 | 4318894 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr22 4312132 4318894 + 0 df2 Chromosome Start End Strand Distance 0 chr22 4312132 4318894 + 0 Actual Chromosome Start End Strand Distance 0 chr22 4312132 4318894 + 0 Expected Chromosome Start End Strand Distance 0 chr22 4312132 4318894 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzhpq6qfo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzhpq6qfo/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr22 4312132 4318894 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr22 | 4312132 | 4318894 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr22 4312132 4318894 + 0 df2 Chromosome Start End Strand Distance 0 chr22 4312132 4318894 + 0 Actual Chromosome Start End Strand Distance 0 chr22 4312132 4318894 + 0 Expected Chromosome Start End Strand Distance 0 chr22 4312132 4318894 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpybgpqdt8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpybgpqdt8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr22 4312132 4318894 + 4298609 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr22 | 4312132 | 4318894 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr22 4312132 4318894 + 4298609 df2 Chromosome Start End Strand Distance 0 chr22 4312132 4318894 + 4298609 Actual Chromosome Start End Strand Distance 0 chr22 4312132 4318894 + 4298609 Expected Chromosome Start End Strand Distance 0 chr22 4312132 4318894 + 4298609 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvdhpyxpz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvdhpyxpz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr22 4312132 4318894 + 4298609 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr22 | 4312132 | 4318894 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr22 4312132 4318894 + 4298609 df2 Chromosome Start End Strand Distance 0 chr22 4312132 4318894 + 4298609 Actual Chromosome Start End Strand Distance 0 chr22 4312132 4318894 + 4298609 Expected Chromosome Start End Strand Distance 0 chr22 4312132 4318894 + 4298609 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv1zl8hwc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv1zl8hwc/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr22 4312132 4318894 + 4305370 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr22 | 4312132 | 4318894 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr22 4312132 4318894 + 4305370 df2 Chromosome Start End Strand Distance 0 chr22 4312132 4318894 + 4305370 Actual Chromosome Start End Strand Distance 0 chr22 4312132 4318894 + 4305370 Expected Chromosome Start End Strand Distance 0 chr22 4312132 4318894 + 4305370 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmykfbl4o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmykfbl4o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmplefdbxzg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplefdbxzg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwcalw1u2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwcalw1u2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmppt1l9_z0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppt1l9_z0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjx0fq1jr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjx0fq1jr/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5506370 5507965 + 805503 1 chr1 7395586 7399890 - 341853 2 chr1 7395586 7399890 - 808849 3 chr1 8995620 9001106 - 1245908 4 chr1 8995620 9001106 - 2408883 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5506370 | 5507965 | a | 0 | ... | | chr1 | 7395586 | 7399890 | a | 0 | ... | | chr1 | 7395586 | 7399890 | a | 0 | ... | | chr1 | 8995620 | 9001106 | a | 0 | ... | | chr1 | 8995620 | 9001106 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 5506370 5507965 + 805503 1 chr1 7395586 7399890 - 341853 2 chr1 7395586 7399890 - 808849 3 chr1 8995620 9001106 - 1245908 4 chr1 8995620 9001106 - 2408883 df2 Chromosome Start End Strand Distance 0 chr1 5506370 5507965 + 805503 1 chr1 7395586 7399890 - 341853 2 chr1 7395586 7399890 - 808849 3 chr1 8995620 9001106 - 1245908 4 chr1 8995620 9001106 - 2408883 Actual Chromosome Start End Strand Distance 0 chr1 5506370 5507965 + 805503 1 chr1 7395586 7399890 - 341853 2 chr1 7395586 7399890 - 808849 3 chr1 8995620 9001106 - 1245908 4 chr1 8995620 9001106 - 2408883 Expected Chromosome Start End Strand Distance 0 chr1 5506370 5507965 + 805503 1 chr1 7395586 7399890 - 341853 2 chr1 7395586 7399890 - 808849 3 chr1 8995620 9001106 - 1245908 4 chr1 8995620 9001106 - 2408883 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu8htdpuf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu8htdpuf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5506370 5507965 + 805503 1 chr1 7395586 7399890 - 341853 2 chr1 7395586 7399890 - 808849 3 chr1 8995620 9001106 - 1245908 4 chr1 8995620 9001106 - 2408883 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5506370 | 5507965 | a | 0 | ... | | chr1 | 7395586 | 7399890 | a | 0 | ... | | chr1 | 7395586 | 7399890 | a | 0 | ... | | chr1 | 8995620 | 9001106 | a | 0 | ... | | chr1 | 8995620 | 9001106 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 5506370 5507965 + 805503 1 chr1 7395586 7399890 - 341853 2 chr1 7395586 7399890 - 808849 3 chr1 8995620 9001106 - 1245908 4 chr1 8995620 9001106 - 2408883 df2 Chromosome Start End Strand Distance 0 chr1 5506370 5507965 + 805503 1 chr1 7395586 7399890 - 341853 2 chr1 7395586 7399890 - 808849 3 chr1 8995620 9001106 - 1245908 4 chr1 8995620 9001106 - 2408883 Actual Chromosome Start End Strand Distance 0 chr1 5506370 5507965 + 805503 1 chr1 7395586 7399890 - 341853 2 chr1 7395586 7399890 - 808849 3 chr1 8995620 9001106 - 1245908 4 chr1 8995620 9001106 - 2408883 Expected Chromosome Start End Strand Distance 0 chr1 5506370 5507965 + 805503 1 chr1 7395586 7399890 - 341853 2 chr1 7395586 7399890 - 808849 3 chr1 8995620 9001106 - 1245908 4 chr1 8995620 9001106 - 2408883 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp08fsjo9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp08fsjo9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5506370 5507965 + 805503 1 chr1 5506370 5507965 + 900019 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5506370 | 5507965 | a | 0 | ... | | chr1 | 5506370 | 5507965 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 5506370 5507965 + 805503 1 chr1 5506370 5507965 + 900019 df2 Chromosome Start End Strand Distance 0 chr1 5506370 5507965 + 805503 1 chr1 5506370 5507965 + 900019 Actual Chromosome Start End Strand Distance 0 chr1 5506370 5507965 + 805503 1 chr1 5506370 5507965 + 900019 Expected Chromosome Start End Strand Distance 0 chr1 5506370 5507965 + 805503 1 chr1 5506370 5507965 + 900019 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkg4lssm2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkg4lssm2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5506370 5507965 + 805503 1 chr1 5506370 5507965 + 900019 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5506370 | 5507965 | a | 0 | ... | | chr1 | 5506370 | 5507965 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 5506370 5507965 + 805503 1 chr1 5506370 5507965 + 900019 df2 Chromosome Start End Strand Distance 0 chr1 5506370 5507965 + 805503 1 chr1 5506370 5507965 + 900019 Actual Chromosome Start End Strand Distance 0 chr1 5506370 5507965 + 805503 1 chr1 5506370 5507965 + 900019 Expected Chromosome Start End Strand Distance 0 chr1 5506370 5507965 + 805503 1 chr1 5506370 5507965 + 900019 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpptvedo1z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpptvedo1z/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5506370 5507965 + 805503 1 chr1 5506370 5507965 + 900019 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5506370 | 5507965 | a | 0 | ... | | chr1 | 5506370 | 5507965 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 5506370 5507965 + 805503 1 chr1 5506370 5507965 + 900019 df2 Chromosome Start End Strand Distance 0 chr1 5506370 5507965 + 805503 1 chr1 5506370 5507965 + 900019 Actual Chromosome Start End Strand Distance 0 chr1 5506370 5507965 + 805503 1 chr1 5506370 5507965 + 900019 Expected Chromosome Start End Strand Distance 0 chr1 5506370 5507965 + 805503 1 chr1 5506370 5507965 + 900019 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpawnv2k_j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpawnv2k_j/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5506370 5507965 + 805503 1 chr1 5506370 5507965 + 900019 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5506370 | 5507965 | a | 0 | ... | | chr1 | 5506370 | 5507965 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 5506370 5507965 + 805503 1 chr1 5506370 5507965 + 900019 df2 Chromosome Start End Strand Distance 0 chr1 5506370 5507965 + 805503 1 chr1 5506370 5507965 + 900019 Actual Chromosome Start End Strand Distance 0 chr1 5506370 5507965 + 805503 1 chr1 5506370 5507965 + 900019 Expected Chromosome Start End Strand Distance 0 chr1 5506370 5507965 + 805503 1 chr1 5506370 5507965 + 900019 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmptk39cgt_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptk39cgt_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpavsuq267/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpavsuq267/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 409367 417076 - 8624853 1 chr1 1801816 1808991 - 7232938 2 chr1 7039825 7043490 - 1998439 3 chr1 9360697 9361978 + 1122628 4 chr1 9360697 9361978 + 2286013 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9360697 | 9361978 | a | 0 | ... | | chr1 | 9360697 | 9361978 | a | 0 | ... | | chr1 | 1801816 | 1808991 | a | 0 | ... | | chr1 | 7039825 | 7043490 | a | 0 | ... | | chr1 | 409367 | 417076 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 409367 417076 - 8624853 2 chr1 1801816 1808991 - 7232938 3 chr1 7039825 7043490 - 1998439 0 chr1 9360697 9361978 + 1122628 1 chr1 9360697 9361978 + 2286013 df2 Chromosome Start End Strand Distance 0 chr1 409367 417076 - 8624853 1 chr1 1801816 1808991 - 7232938 2 chr1 7039825 7043490 - 1998439 3 chr1 9360697 9361978 + 1122628 4 chr1 9360697 9361978 + 2286013 Actual Chromosome Start End Strand Distance 0 chr1 409367 417076 - 8624853 1 chr1 1801816 1808991 - 7232938 2 chr1 7039825 7043490 - 1998439 3 chr1 9360697 9361978 + 1122628 4 chr1 9360697 9361978 + 2286013 Expected Chromosome Start End Strand Distance 0 chr1 409367 417076 - 8624853 1 chr1 1801816 1808991 - 7232938 2 chr1 7039825 7043490 - 1998439 3 chr1 9360697 9361978 + 1122628 4 chr1 9360697 9361978 + 2286013 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1nsybqmd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1nsybqmd/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 409367 417076 - 8624853 1 chr1 1801816 1808991 - 7232938 2 chr1 7039825 7043490 - 1998439 3 chr1 9360697 9361978 + 1122628 4 chr1 9360697 9361978 + 2286013 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9360697 | 9361978 | a | 0 | ... | | chr1 | 9360697 | 9361978 | a | 0 | ... | | chr1 | 1801816 | 1808991 | a | 0 | ... | | chr1 | 7039825 | 7043490 | a | 0 | ... | | chr1 | 409367 | 417076 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 409367 417076 - 8624853 2 chr1 1801816 1808991 - 7232938 3 chr1 7039825 7043490 - 1998439 0 chr1 9360697 9361978 + 1122628 1 chr1 9360697 9361978 + 2286013 df2 Chromosome Start End Strand Distance 0 chr1 409367 417076 - 8624853 1 chr1 1801816 1808991 - 7232938 2 chr1 7039825 7043490 - 1998439 3 chr1 9360697 9361978 + 1122628 4 chr1 9360697 9361978 + 2286013 Actual Chromosome Start End Strand Distance 0 chr1 409367 417076 - 8624853 1 chr1 1801816 1808991 - 7232938 2 chr1 7039825 7043490 - 1998439 3 chr1 9360697 9361978 + 1122628 4 chr1 9360697 9361978 + 2286013 Expected Chromosome Start End Strand Distance 0 chr1 409367 417076 - 8624853 1 chr1 1801816 1808991 - 7232938 2 chr1 7039825 7043490 - 1998439 3 chr1 9360697 9361978 + 1122628 4 chr1 9360697 9361978 + 2286013 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq52g3jri/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq52g3jri/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 1801816 1808991 - 1801815 8 chr1 9360697 9361978 - 9360696 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1801816 | 1808991 | a | 0 | ... | | chr1 | 9360697 | 9361978 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1801816 1808991 - 1801815 1 chr1 9360697 9361978 - 9360696 df2 Chromosome Start End Strand Distance 1 chr1 1801816 1808991 - 1801815 8 chr1 9360697 9361978 - 9360696 Actual Chromosome Start End Strand Distance 0 chr1 1801816 1808991 - 1801815 1 chr1 9360697 9361978 - 9360696 Expected Chromosome Start End Strand Distance 0 chr1 1801816 1808991 - 1801815 1 chr1 9360697 9361978 - 9360696 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmptn8mi6c9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptn8mi6c9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 409367 417076 + 0 1 chr1 409367 417076 + 6622750 2 chr1 1801816 1808991 - 0 3 chr1 1801816 1808991 - 7551707 4 chr1 7039825 7039826 + 0 5 chr1 7039825 7039826 + 6622750 6 chr1 7039825 7039826 + 0 7 chr1 7039825 7039826 + 6622750 8 chr1 7039825 7039826 + 0 9 chr1 7039825 7039826 + 6622750 10 chr1 7039825 7039826 + 0 11 chr1 7039825 7039826 + 6622750 12 chr1 7039825 7039826 + 0 13 chr1 7039825 7039826 + 6622750 14 chr1 7039825 7043490 + 0 15 chr1 7039825 7043490 + 6622750 16 chr1 9360697 9361978 - 0 17 chr1 9360697 9361978 - 7551707 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7039825 | 7043490 | a | 0 | ... | | chr1 | 7039825 | 7043490 | a | 0 | ... | | chr1 | 409367 | 417076 | a | 0 | ... | | chr1 | 409367 | 417076 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1801816 | 1808991 | a | 0 | ... | | chr1 | 1801816 | 1808991 | a | 0 | ... | | chr1 | 9360697 | 9361978 | a | 0 | ... | | chr1 | 9360697 | 9361978 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 18 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 409367 417076 + 0 3 chr1 409367 417076 + 6622750 14 chr1 1801816 1808991 - 0 15 chr1 1801816 1808991 - 7551707 4 chr1 7039825 7039826 + 0 6 chr1 7039825 7039826 + 0 8 chr1 7039825 7039826 + 0 10 chr1 7039825 7039826 + 0 12 chr1 7039825 7039826 + 0 5 chr1 7039825 7039826 + 6622750 7 chr1 7039825 7039826 + 6622750 9 chr1 7039825 7039826 + 6622750 11 chr1 7039825 7039826 + 6622750 13 chr1 7039825 7039826 + 6622750 0 chr1 7039825 7043490 + 0 1 chr1 7039825 7043490 + 6622750 16 chr1 9360697 9361978 - 0 17 chr1 9360697 9361978 - 7551707 df2 Chromosome Start End Strand Distance 0 chr1 409367 417076 + 0 1 chr1 409367 417076 + 6622750 2 chr1 1801816 1808991 - 0 3 chr1 1801816 1808991 - 7551707 4 chr1 7039825 7039826 + 0 6 chr1 7039825 7039826 + 0 8 chr1 7039825 7039826 + 0 10 chr1 7039825 7039826 + 0 12 chr1 7039825 7039826 + 0 5 chr1 7039825 7039826 + 6622750 7 chr1 7039825 7039826 + 6622750 9 chr1 7039825 7039826 + 6622750 11 chr1 7039825 7039826 + 6622750 13 chr1 7039825 7039826 + 6622750 14 chr1 7039825 7043490 + 0 15 chr1 7039825 7043490 + 6622750 16 chr1 9360697 9361978 - 0 17 chr1 9360697 9361978 - 7551707 Actual Chromosome Start End Strand Distance 0 chr1 409367 417076 + 0 1 chr1 409367 417076 + 6622750 2 chr1 1801816 1808991 - 0 3 chr1 1801816 1808991 - 7551707 4 chr1 7039825 7039826 + 0 5 chr1 7039825 7039826 + 0 6 chr1 7039825 7039826 + 0 7 chr1 7039825 7039826 + 0 8 chr1 7039825 7039826 + 0 9 chr1 7039825 7039826 + 6622750 10 chr1 7039825 7039826 + 6622750 11 chr1 7039825 7039826 + 6622750 12 chr1 7039825 7039826 + 6622750 13 chr1 7039825 7039826 + 6622750 14 chr1 7039825 7043490 + 0 15 chr1 7039825 7043490 + 6622750 16 chr1 9360697 9361978 - 0 17 chr1 9360697 9361978 - 7551707 Expected Chromosome Start End Strand Distance 0 chr1 409367 417076 + 0 1 chr1 409367 417076 + 6622750 2 chr1 1801816 1808991 - 0 3 chr1 1801816 1808991 - 7551707 4 chr1 7039825 7039826 + 0 5 chr1 7039825 7039826 + 0 6 chr1 7039825 7039826 + 0 7 chr1 7039825 7039826 + 0 8 chr1 7039825 7039826 + 0 9 chr1 7039825 7039826 + 6622750 10 chr1 7039825 7039826 + 6622750 11 chr1 7039825 7039826 + 6622750 12 chr1 7039825 7039826 + 6622750 13 chr1 7039825 7039826 + 6622750 14 chr1 7039825 7043490 + 0 15 chr1 7039825 7043490 + 6622750 16 chr1 9360697 9361978 - 0 17 chr1 9360697 9361978 - 7551707 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=18, step=1) Expected index RangeIndex(start=0, stop=18, step=1) index equal [ True True True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcp7b4azq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcp7b4azq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 409367 417076 + 0 1 chr1 409367 417076 + 6622750 2 chr1 1801816 1808991 - 0 3 chr1 1801816 1808991 - 7551707 4 chr1 7039825 7039826 + 0 5 chr1 7039825 7039826 + 6622750 6 chr1 7039825 7039826 + 0 7 chr1 7039825 7039826 + 6622750 8 chr1 7039825 7039826 + 0 9 chr1 7039825 7039826 + 6622750 10 chr1 7039825 7039826 + 0 11 chr1 7039825 7039826 + 6622750 12 chr1 7039825 7043490 + 0 13 chr1 7039825 7043490 + 6622750 14 chr1 9360697 9361978 - 0 15 chr1 9360697 9361978 - 7551707 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7039825 | 7043490 | a | 0 | ... | | chr1 | 7039825 | 7043490 | a | 0 | ... | | chr1 | 409367 | 417076 | a | 0 | ... | | chr1 | 409367 | 417076 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1801816 | 1808991 | a | 0 | ... | | chr1 | 1801816 | 1808991 | a | 0 | ... | | chr1 | 9360697 | 9361978 | a | 0 | ... | | chr1 | 9360697 | 9361978 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 16 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 409367 417076 + 0 3 chr1 409367 417076 + 6622750 12 chr1 1801816 1808991 - 0 13 chr1 1801816 1808991 - 7551707 4 chr1 7039825 7039826 + 0 6 chr1 7039825 7039826 + 0 8 chr1 7039825 7039826 + 0 10 chr1 7039825 7039826 + 0 5 chr1 7039825 7039826 + 6622750 7 chr1 7039825 7039826 + 6622750 9 chr1 7039825 7039826 + 6622750 11 chr1 7039825 7039826 + 6622750 0 chr1 7039825 7043490 + 0 1 chr1 7039825 7043490 + 6622750 14 chr1 9360697 9361978 - 0 15 chr1 9360697 9361978 - 7551707 df2 Chromosome Start End Strand Distance 0 chr1 409367 417076 + 0 1 chr1 409367 417076 + 6622750 2 chr1 1801816 1808991 - 0 3 chr1 1801816 1808991 - 7551707 4 chr1 7039825 7039826 + 0 6 chr1 7039825 7039826 + 0 8 chr1 7039825 7039826 + 0 10 chr1 7039825 7039826 + 0 5 chr1 7039825 7039826 + 6622750 7 chr1 7039825 7039826 + 6622750 9 chr1 7039825 7039826 + 6622750 11 chr1 7039825 7039826 + 6622750 12 chr1 7039825 7043490 + 0 13 chr1 7039825 7043490 + 6622750 14 chr1 9360697 9361978 - 0 15 chr1 9360697 9361978 - 7551707 Actual Chromosome Start End Strand Distance 0 chr1 409367 417076 + 0 1 chr1 409367 417076 + 6622750 2 chr1 1801816 1808991 - 0 3 chr1 1801816 1808991 - 7551707 4 chr1 7039825 7039826 + 0 5 chr1 7039825 7039826 + 0 6 chr1 7039825 7039826 + 0 7 chr1 7039825 7039826 + 0 8 chr1 7039825 7039826 + 6622750 9 chr1 7039825 7039826 + 6622750 10 chr1 7039825 7039826 + 6622750 11 chr1 7039825 7039826 + 6622750 12 chr1 7039825 7043490 + 0 13 chr1 7039825 7043490 + 6622750 14 chr1 9360697 9361978 - 0 15 chr1 9360697 9361978 - 7551707 Expected Chromosome Start End Strand Distance 0 chr1 409367 417076 + 0 1 chr1 409367 417076 + 6622750 2 chr1 1801816 1808991 - 0 3 chr1 1801816 1808991 - 7551707 4 chr1 7039825 7039826 + 0 5 chr1 7039825 7039826 + 0 6 chr1 7039825 7039826 + 0 7 chr1 7039825 7039826 + 0 8 chr1 7039825 7039826 + 6622750 9 chr1 7039825 7039826 + 6622750 10 chr1 7039825 7039826 + 6622750 11 chr1 7039825 7039826 + 6622750 12 chr1 7039825 7043490 + 0 13 chr1 7039825 7043490 + 6622750 14 chr1 9360697 9361978 - 0 15 chr1 9360697 9361978 - 7551707 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=16, step=1) Expected index RangeIndex(start=0, stop=16, step=1) index equal [ True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkxm5o2xe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkxm5o2xe/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfr1zuibr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfr1zuibr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc4uig7xg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc4uig7xg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy05xydht/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy05xydht/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 2 chr17 8523657 8528869 + 7088889 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr17 | 8523657 | 8528869 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr17 8523657 8528869 + 7088889 df2 Chromosome Start End Strand Distance 2 chr17 8523657 8528869 + 7088889 Actual Chromosome Start End Strand Distance 0 chr17 8523657 8528869 + 7088889 Expected Chromosome Start End Strand Distance 0 chr17 8523657 8528869 + 7088889 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyh_eu6ma/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyh_eu6ma/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo2vdww8x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo2vdww8x/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr2 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr2 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr2 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr2 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmppeq7idza/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppeq7idza/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmph5_9ehwo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph5_9ehwo/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgjzfhkhf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgjzfhkhf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3410768 3414834 - 1191401 1 chr1 3410768 3414834 - 2148245 2 chr1 6280952 6285018 - 3542373 3 chr1 6280952 6285018 - 4061585 4 chr1 8386802 8390868 + 1443512 5 chr1 8612309 8620629 - 1206762 6 chr1 8612309 8620629 - 6392942 8 chr13 2034147 2042790 + 3764275 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8386802 | 8390868 | a | 0 | ... | | chr1 | 8612309 | 8620629 | a | 0 | ... | | chr1 | 8612309 | 8620629 | a | 0 | ... | | chr1 | 3410768 | 3414834 | a | 0 | ... | | chr1 | 3410768 | 3414834 | a | 0 | ... | | chr1 | 6280952 | 6285018 | a | 0 | ... | | chr1 | 6280952 | 6285018 | a | 0 | ... | | chr13 | 2034147 | 2042790 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 7 chr13 2034147 2042790 + 3764275 3 chr1 3410768 3414834 - 1191401 4 chr1 3410768 3414834 - 2148245 5 chr1 6280952 6285018 - 3542373 6 chr1 6280952 6285018 - 4061585 0 chr1 8386802 8390868 + 1443512 1 chr1 8612309 8620629 - 1206762 2 chr1 8612309 8620629 - 6392942 df2 Chromosome Start End Strand Distance 8 chr13 2034147 2042790 + 3764275 0 chr1 3410768 3414834 - 1191401 1 chr1 3410768 3414834 - 2148245 2 chr1 6280952 6285018 - 3542373 3 chr1 6280952 6285018 - 4061585 4 chr1 8386802 8390868 + 1443512 5 chr1 8612309 8620629 - 1206762 6 chr1 8612309 8620629 - 6392942 Actual Chromosome Start End Strand Distance 0 chr1 3410768 3414834 - 1191401 1 chr1 3410768 3414834 - 2148245 2 chr1 6280952 6285018 - 3542373 3 chr1 6280952 6285018 - 4061585 4 chr1 8386802 8390868 + 1443512 5 chr1 8612309 8620629 - 1206762 6 chr1 8612309 8620629 - 6392942 7 chr13 2034147 2042790 + 3764275 Expected Chromosome Start End Strand Distance 0 chr1 3410768 3414834 - 1191401 1 chr1 3410768 3414834 - 2148245 2 chr1 6280952 6285018 - 3542373 3 chr1 6280952 6285018 - 4061585 4 chr1 8386802 8390868 + 1443512 5 chr1 8612309 8620629 - 1206762 6 chr1 8612309 8620629 - 6392942 7 chr13 2034147 2042790 + 3764275 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_hi63y38/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_hi63y38/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3410768 3414834 - 5197476 1 chr1 3410768 3414834 - 6585167 2 chr1 6280952 6285018 - 2327292 3 chr1 6280952 6285018 - 3714983 4 chr1 8386802 8390868 + 1609133 5 chr1 8612309 8620629 - 0 6 chr1 8612309 8620629 - 1379372 8 chr13 2034147 2042790 + 7854858 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8386802 | 8390868 | a | 0 | ... | | chr1 | 8612309 | 8620629 | a | 0 | ... | | chr1 | 8612309 | 8620629 | a | 0 | ... | | chr1 | 3410768 | 3414834 | a | 0 | ... | | chr1 | 3410768 | 3414834 | a | 0 | ... | | chr1 | 6280952 | 6285018 | a | 0 | ... | | chr1 | 6280952 | 6285018 | a | 0 | ... | | chr13 | 2034147 | 2042790 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 7 chr13 2034147 2042790 + 7854858 3 chr1 3410768 3414834 - 5197476 4 chr1 3410768 3414834 - 6585167 5 chr1 6280952 6285018 - 2327292 6 chr1 6280952 6285018 - 3714983 0 chr1 8386802 8390868 + 1609133 1 chr1 8612309 8620629 - 0 2 chr1 8612309 8620629 - 1379372 df2 Chromosome Start End Strand Distance 8 chr13 2034147 2042790 + 7854858 0 chr1 3410768 3414834 - 5197476 1 chr1 3410768 3414834 - 6585167 2 chr1 6280952 6285018 - 2327292 3 chr1 6280952 6285018 - 3714983 4 chr1 8386802 8390868 + 1609133 5 chr1 8612309 8620629 - 0 6 chr1 8612309 8620629 - 1379372 Actual Chromosome Start End Strand Distance 0 chr1 3410768 3414834 - 5197476 1 chr1 3410768 3414834 - 6585167 2 chr1 6280952 6285018 - 2327292 3 chr1 6280952 6285018 - 3714983 4 chr1 8386802 8390868 + 1609133 5 chr1 8612309 8620629 - 0 6 chr1 8612309 8620629 - 1379372 7 chr13 2034147 2042790 + 7854858 Expected Chromosome Start End Strand Distance 0 chr1 3410768 3414834 - 5197476 1 chr1 3410768 3414834 - 6585167 2 chr1 6280952 6285018 - 2327292 3 chr1 6280952 6285018 - 3714983 4 chr1 8386802 8390868 + 1609133 5 chr1 8612309 8620629 - 0 6 chr1 8612309 8620629 - 1379372 7 chr13 2034147 2042790 + 7854858 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo3zw_d1a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo3zw_d1a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmppa1vs25s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppa1vs25s/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3 - 7944 1 chr1 1 3 - 7944 2 chr1 11 13 - 7934 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 11 | 13 | a | 0 | ... | | chr1 | 1 | 3 | a | 0 | ... | | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1 3 - 7944 2 chr1 1 3 - 7944 0 chr1 11 13 - 7934 df2 Chromosome Start End Strand Distance 0 chr1 1 3 - 7944 1 chr1 1 3 - 7944 2 chr1 11 13 - 7934 Actual Chromosome Start End Strand Distance 0 chr1 1 3 - 7944 1 chr1 1 3 - 7944 2 chr1 11 13 - 7934 Expected Chromosome Start End Strand Distance 0 chr1 1 3 - 7944 1 chr1 1 3 - 7944 2 chr1 11 13 - 7934 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_v2wyokh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_v2wyokh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3 - 7944 1 chr1 1 3 - 7944 2 chr1 11 13 - 7934 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 11 | 13 | a | 0 | ... | | chr1 | 1 | 3 | a | 0 | ... | | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1 3 - 7944 2 chr1 1 3 - 7944 0 chr1 11 13 - 7934 df2 Chromosome Start End Strand Distance 0 chr1 1 3 - 7944 1 chr1 1 3 - 7944 2 chr1 11 13 - 7934 Actual Chromosome Start End Strand Distance 0 chr1 1 3 - 7944 1 chr1 1 3 - 7944 2 chr1 11 13 - 7934 Expected Chromosome Start End Strand Distance 0 chr1 1 3 - 7944 1 chr1 1 3 - 7944 2 chr1 11 13 - 7934 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj_7qwidv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj_7qwidv/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3 - 0 1 chr1 1 3 - 9 2 chr1 1 3 - 0 3 chr1 1 3 - 9 4 chr1 11 13 - 0 5 chr1 11 13 - 9 6 chr13 1 3 - 0 7 chr13 1 3 - 0 8 chr13 1 3 - 0 9 chr13 1 3 - 0 10 chr13 1 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 11 | 13 | a | 0 | ... | | chr1 | 11 | 13 | a | 0 | ... | | chr1 | 1 | 3 | a | 0 | ... | | chr1 | 1 | 3 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr13 | 1 | 3 | a | 0 | ... | | chr13 | 1 | 3 | a | 0 | ... | | chr13 | 1 | 3 | a | 0 | ... | | chr13 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 11 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1 3 - 0 4 chr1 1 3 - 0 6 chr13 1 3 - 0 7 chr13 1 3 - 0 8 chr13 1 3 - 0 9 chr13 1 3 - 0 10 chr13 1 3 - 0 3 chr1 1 3 - 9 5 chr1 1 3 - 9 0 chr1 11 13 - 0 1 chr1 11 13 - 9 df2 Chromosome Start End Strand Distance 0 chr1 1 3 - 0 2 chr1 1 3 - 0 6 chr13 1 3 - 0 7 chr13 1 3 - 0 8 chr13 1 3 - 0 9 chr13 1 3 - 0 10 chr13 1 3 - 0 1 chr1 1 3 - 9 3 chr1 1 3 - 9 4 chr1 11 13 - 0 5 chr1 11 13 - 9 Actual Chromosome Start End Strand Distance 0 chr1 1 3 - 0 1 chr1 1 3 - 0 2 chr1 1 3 - 9 3 chr1 1 3 - 9 4 chr1 11 13 - 0 5 chr1 11 13 - 9 6 chr13 1 3 - 0 7 chr13 1 3 - 0 8 chr13 1 3 - 0 9 chr13 1 3 - 0 10 chr13 1 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 3 - 0 1 chr1 1 3 - 0 2 chr1 1 3 - 9 3 chr1 1 3 - 9 4 chr1 11 13 - 0 5 chr1 11 13 - 9 6 chr13 1 3 - 0 7 chr13 1 3 - 0 8 chr13 1 3 - 0 9 chr13 1 3 - 0 10 chr13 1 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=11, step=1) Expected index RangeIndex(start=0, stop=11, step=1) index equal [ True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl_av8dm3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl_av8dm3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3q070e0c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3q070e0c/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 7006358 7013398 + 0 1 chr1 7006358 7013398 + 701268 2 chr1 7714665 7720720 + 0 3 chr1 7714665 7720720 + 701268 4 chr1 9155439 9159643 + 0 5 chr1 9155439 9159643 + 1434720 6 chr13 271561 274112 + 0 7 chr5 1497012 1507011 + 0 8 chr7 1723066 1727013 + 0 9 chr8 9535157 9543891 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7714665 | 7720720 | a | 0 | ... | | chr1 | 7714665 | 7720720 | a | 0 | ... | | chr1 | 9155439 | 9159643 | a | 0 | ... | | chr1 | 9155439 | 9159643 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr5 | 1497012 | 1507011 | a | 0 | ... | | chr7 | 1723066 | 1727013 | a | 0 | ... | | chr8 | 9535157 | 9543891 | a | 0 | ... | | chr13 | 271561 | 274112 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 9 chr13 271561 274112 + 0 6 chr5 1497012 1507011 + 0 7 chr7 1723066 1727013 + 0 4 chr1 7006358 7013398 + 0 5 chr1 7006358 7013398 + 701268 0 chr1 7714665 7720720 + 0 1 chr1 7714665 7720720 + 701268 2 chr1 9155439 9159643 + 0 3 chr1 9155439 9159643 + 1434720 8 chr8 9535157 9543891 - 0 df2 Chromosome Start End Strand Distance 6 chr13 271561 274112 + 0 7 chr5 1497012 1507011 + 0 8 chr7 1723066 1727013 + 0 0 chr1 7006358 7013398 + 0 1 chr1 7006358 7013398 + 701268 2 chr1 7714665 7720720 + 0 3 chr1 7714665 7720720 + 701268 4 chr1 9155439 9159643 + 0 5 chr1 9155439 9159643 + 1434720 9 chr8 9535157 9543891 - 0 Actual Chromosome Start End Strand Distance 0 chr1 7006358 7013398 + 0 1 chr1 7006358 7013398 + 701268 2 chr1 7714665 7720720 + 0 3 chr1 7714665 7720720 + 701268 4 chr1 9155439 9159643 + 0 5 chr1 9155439 9159643 + 1434720 6 chr13 271561 274112 + 0 7 chr5 1497012 1507011 + 0 8 chr7 1723066 1727013 + 0 9 chr8 9535157 9543891 - 0 Expected Chromosome Start End Strand Distance 0 chr1 7006358 7013398 + 0 1 chr1 7006358 7013398 + 701268 2 chr1 7714665 7720720 + 0 3 chr1 7714665 7720720 + 701268 4 chr1 9155439 9159643 + 0 5 chr1 9155439 9159643 + 1434720 6 chr13 271561 274112 + 0 7 chr5 1497012 1507011 + 0 8 chr7 1723066 1727013 + 0 9 chr8 9535157 9543891 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4cqfm_oq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4cqfm_oq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 7714665 7720720 + 0 1 chr1 7714665 7720720 + 701268 2 chr1 9155439 9159643 + 0 3 chr1 9155439 9159643 + 1434720 4 chr13 271561 274112 + 0 5 chr5 1497012 1507011 + 0 6 chr7 1723066 1727013 + 0 8 chr8 9535157 9543891 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7714665 | 7720720 | a | 0 | ... | | chr1 | 7714665 | 7720720 | a | 0 | ... | | chr1 | 9155439 | 9159643 | a | 0 | ... | | chr1 | 9155439 | 9159643 | a | 0 | ... | | chr5 | 1497012 | 1507011 | a | 0 | ... | | chr7 | 1723066 | 1727013 | a | 0 | ... | | chr8 | 9535157 | 9543891 | a | 0 | ... | | chr13 | 271561 | 274112 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 7 chr13 271561 274112 + 0 4 chr5 1497012 1507011 + 0 5 chr7 1723066 1727013 + 0 0 chr1 7714665 7720720 + 0 1 chr1 7714665 7720720 + 701268 2 chr1 9155439 9159643 + 0 3 chr1 9155439 9159643 + 1434720 6 chr8 9535157 9543891 - 0 df2 Chromosome Start End Strand Distance 4 chr13 271561 274112 + 0 5 chr5 1497012 1507011 + 0 6 chr7 1723066 1727013 + 0 0 chr1 7714665 7720720 + 0 1 chr1 7714665 7720720 + 701268 2 chr1 9155439 9159643 + 0 3 chr1 9155439 9159643 + 1434720 8 chr8 9535157 9543891 - 0 Actual Chromosome Start End Strand Distance 0 chr1 7714665 7720720 + 0 1 chr1 7714665 7720720 + 701268 2 chr1 9155439 9159643 + 0 3 chr1 9155439 9159643 + 1434720 4 chr13 271561 274112 + 0 5 chr5 1497012 1507011 + 0 6 chr7 1723066 1727013 + 0 7 chr8 9535157 9543891 - 0 Expected Chromosome Start End Strand Distance 0 chr1 7714665 7720720 + 0 1 chr1 7714665 7720720 + 701268 2 chr1 9155439 9159643 + 0 3 chr1 9155439 9159643 + 1434720 4 chr13 271561 274112 + 0 5 chr5 1497012 1507011 + 0 6 chr7 1723066 1727013 + 0 7 chr8 9535157 9543891 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgjjg752s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgjjg752s/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 7714665 7720720 + 0 1 chr1 7714665 7720720 + 701268 2 chr1 9155439 9159643 + 0 3 chr1 9155439 9159643 + 1434720 4 chr13 271561 274112 + 0 5 chr5 1497012 1507011 + 0 6 chr7 1723066 1727013 + 0 8 chr8 9535157 9543891 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7714665 | 7720720 | a | 0 | ... | | chr1 | 7714665 | 7720720 | a | 0 | ... | | chr1 | 9155439 | 9159643 | a | 0 | ... | | chr1 | 9155439 | 9159643 | a | 0 | ... | | chr5 | 1497012 | 1507011 | a | 0 | ... | | chr7 | 1723066 | 1727013 | a | 0 | ... | | chr8 | 9535157 | 9543891 | a | 0 | ... | | chr13 | 271561 | 274112 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 7 chr13 271561 274112 + 0 4 chr5 1497012 1507011 + 0 5 chr7 1723066 1727013 + 0 0 chr1 7714665 7720720 + 0 1 chr1 7714665 7720720 + 701268 2 chr1 9155439 9159643 + 0 3 chr1 9155439 9159643 + 1434720 6 chr8 9535157 9543891 - 0 df2 Chromosome Start End Strand Distance 4 chr13 271561 274112 + 0 5 chr5 1497012 1507011 + 0 6 chr7 1723066 1727013 + 0 0 chr1 7714665 7720720 + 0 1 chr1 7714665 7720720 + 701268 2 chr1 9155439 9159643 + 0 3 chr1 9155439 9159643 + 1434720 8 chr8 9535157 9543891 - 0 Actual Chromosome Start End Strand Distance 0 chr1 7714665 7720720 + 0 1 chr1 7714665 7720720 + 701268 2 chr1 9155439 9159643 + 0 3 chr1 9155439 9159643 + 1434720 4 chr13 271561 274112 + 0 5 chr5 1497012 1507011 + 0 6 chr7 1723066 1727013 + 0 7 chr8 9535157 9543891 - 0 Expected Chromosome Start End Strand Distance 0 chr1 7714665 7720720 + 0 1 chr1 7714665 7720720 + 701268 2 chr1 9155439 9159643 + 0 3 chr1 9155439 9159643 + 1434720 4 chr13 271561 274112 + 0 5 chr5 1497012 1507011 + 0 6 chr7 1723066 1727013 + 0 7 chr8 9535157 9543891 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5oxxvmip/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5oxxvmip/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 3 4 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 4 - 2 df2 Chromosome Start End Strand Distance 1 chr1 3 4 - 2 Actual Chromosome Start End Strand Distance 0 chr1 3 4 - 2 Expected Chromosome Start End Strand Distance 0 chr1 3 4 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpau9wg1p6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpau9wg1p6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpffpk1ixp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpffpk1ixp/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbz28vvgz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbz28vvgz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1945581 1954414 - 6544162 1 chr1 1945581 1954414 - 6620922 2 chr1 4869633 4871023 - 3627553 3 chr1 4869633 4871023 - 3704313 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4869633 | 4871023 | a | 0 | ... | | chr1 | 4869633 | 4871023 | a | 0 | ... | | chr1 | 1945581 | 1954414 | a | 0 | ... | | chr1 | 1945581 | 1954414 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1945581 1954414 - 6544162 3 chr1 1945581 1954414 - 6620922 0 chr1 4869633 4871023 - 3627553 1 chr1 4869633 4871023 - 3704313 df2 Chromosome Start End Strand Distance 0 chr1 1945581 1954414 - 6544162 1 chr1 1945581 1954414 - 6620922 2 chr1 4869633 4871023 - 3627553 3 chr1 4869633 4871023 - 3704313 Actual Chromosome Start End Strand Distance 0 chr1 1945581 1954414 - 6544162 1 chr1 1945581 1954414 - 6620922 2 chr1 4869633 4871023 - 3627553 3 chr1 4869633 4871023 - 3704313 Expected Chromosome Start End Strand Distance 0 chr1 1945581 1954414 - 6544162 1 chr1 1945581 1954414 - 6620922 2 chr1 4869633 4871023 - 3627553 3 chr1 4869633 4871023 - 3704313 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpruchopdn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpruchopdn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6mv9dm5a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6mv9dm5a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8u9cm6uw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8u9cm6uw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1uvdfsot/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1uvdfsot/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwmvwafax/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwmvwafax/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 4869633 4869634 - 4869632 3 chr1 4869633 4869634 - 4869632 4 chr1 4869633 4869634 - 4869632 5 chr1 4869633 4869634 - 4869632 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 4869633 | 4869634 | a | 0 | ... | | chr1 | 4869633 | 4869634 | a | 0 | ... | | chr1 | 4869633 | 4869634 | a | 0 | ... | | chr1 | 4869633 | 4869634 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 4869633 4869634 - 4869632 3 chr1 4869633 4869634 - 4869632 4 chr1 4869633 4869634 - 4869632 5 chr1 4869633 4869634 - 4869632 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 4869633 4869634 - 4869632 3 chr1 4869633 4869634 - 4869632 4 chr1 4869633 4869634 - 4869632 5 chr1 4869633 4869634 - 4869632 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 4869633 4869634 - 4869632 3 chr1 4869633 4869634 - 4869632 4 chr1 4869633 4869634 - 4869632 5 chr1 4869633 4869634 - 4869632 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 4869633 4869634 - 4869632 3 chr1 4869633 4869634 - 4869632 4 chr1 4869633 4869634 - 4869632 5 chr1 4869633 4869634 - 4869632 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpepnfh8xs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpepnfh8xs/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 4869632 2 chr1 1 2 - 0 3 chr1 1 2 - 4869632 4 chr1 4869633 4869634 - 0 5 chr1 4869633 4869634 - 4869632 6 chr1 4869633 4869634 - 0 7 chr1 4869633 4869634 - 4869632 8 chr1 4869633 4869634 - 0 9 chr1 4869633 4869634 - 4869632 10 chr1 4869633 4869634 - 0 11 chr1 4869633 4869634 - 4869632 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 4869633 | 4869634 | a | 0 | ... | | chr1 | 4869633 | 4869634 | a | 0 | ... | | chr1 | 4869633 | 4869634 | a | 0 | ... | | chr1 | 4869633 | 4869634 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 2 chr1 1 2 - 0 1 chr1 1 2 - 4869632 3 chr1 1 2 - 4869632 4 chr1 4869633 4869634 - 0 6 chr1 4869633 4869634 - 0 8 chr1 4869633 4869634 - 0 10 chr1 4869633 4869634 - 0 5 chr1 4869633 4869634 - 4869632 7 chr1 4869633 4869634 - 4869632 9 chr1 4869633 4869634 - 4869632 11 chr1 4869633 4869634 - 4869632 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 2 chr1 1 2 - 0 1 chr1 1 2 - 4869632 3 chr1 1 2 - 4869632 4 chr1 4869633 4869634 - 0 6 chr1 4869633 4869634 - 0 8 chr1 4869633 4869634 - 0 10 chr1 4869633 4869634 - 0 5 chr1 4869633 4869634 - 4869632 7 chr1 4869633 4869634 - 4869632 9 chr1 4869633 4869634 - 4869632 11 chr1 4869633 4869634 - 4869632 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 4869632 3 chr1 1 2 - 4869632 4 chr1 4869633 4869634 - 0 5 chr1 4869633 4869634 - 0 6 chr1 4869633 4869634 - 0 7 chr1 4869633 4869634 - 0 8 chr1 4869633 4869634 - 4869632 9 chr1 4869633 4869634 - 4869632 10 chr1 4869633 4869634 - 4869632 11 chr1 4869633 4869634 - 4869632 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 4869632 3 chr1 1 2 - 4869632 4 chr1 4869633 4869634 - 0 5 chr1 4869633 4869634 - 0 6 chr1 4869633 4869634 - 0 7 chr1 4869633 4869634 - 0 8 chr1 4869633 4869634 - 4869632 9 chr1 4869633 4869634 - 4869632 10 chr1 4869633 4869634 - 4869632 11 chr1 4869633 4869634 - 4869632 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpge7fzgzc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpge7fzgzc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvnvfa9tb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvnvfa9tb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqjaoh32a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqjaoh32a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp615xync9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp615xync9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4lkjioei/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4lkjioei/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp35s93e5i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp35s93e5i/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd6gzhmmg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd6gzhmmg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 294155 298413 - 2664182 1 chr1 294155 298413 - 6271735 2 chr1 3494985 3500245 - 527682 3 chr1 3494985 3500245 - 3069903 4 chr1 5263271 5263272 + 92668 5 chr1 5263271 5263272 + 298347 6 chr1 6332820 6335604 - 234544 7 chr1 6332820 6335604 - 1054057 8 chr1 8818348 8819934 - 1419311 9 chr1 8818348 8819934 - 2247117 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5263271 | 5263272 | a | 0 | ... | | chr1 | 5263271 | 5263272 | a | 0 | ... | | chr1 | 294155 | 298413 | a | 0 | ... | | chr1 | 294155 | 298413 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 8818348 | 8819934 | a | 0 | ... | | chr1 | 8818348 | 8819934 | a | 0 | ... | | chr1 | 3494985 | 3500245 | a | 0 | ... | | chr1 | 3494985 | 3500245 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 294155 298413 - 2664182 3 chr1 294155 298413 - 6271735 8 chr1 3494985 3500245 - 527682 9 chr1 3494985 3500245 - 3069903 0 chr1 5263271 5263272 + 92668 1 chr1 5263271 5263272 + 298347 4 chr1 6332820 6335604 - 234544 5 chr1 6332820 6335604 - 1054057 6 chr1 8818348 8819934 - 1419311 7 chr1 8818348 8819934 - 2247117 df2 Chromosome Start End Strand Distance 0 chr1 294155 298413 - 2664182 1 chr1 294155 298413 - 6271735 2 chr1 3494985 3500245 - 527682 3 chr1 3494985 3500245 - 3069903 4 chr1 5263271 5263272 + 92668 5 chr1 5263271 5263272 + 298347 6 chr1 6332820 6335604 - 234544 7 chr1 6332820 6335604 - 1054057 8 chr1 8818348 8819934 - 1419311 9 chr1 8818348 8819934 - 2247117 Actual Chromosome Start End Strand Distance 0 chr1 294155 298413 - 2664182 1 chr1 294155 298413 - 6271735 2 chr1 3494985 3500245 - 527682 3 chr1 3494985 3500245 - 3069903 4 chr1 5263271 5263272 + 92668 5 chr1 5263271 5263272 + 298347 6 chr1 6332820 6335604 - 234544 7 chr1 6332820 6335604 - 1054057 8 chr1 8818348 8819934 - 1419311 9 chr1 8818348 8819934 - 2247117 Expected Chromosome Start End Strand Distance 0 chr1 294155 298413 - 2664182 1 chr1 294155 298413 - 6271735 2 chr1 3494985 3500245 - 527682 3 chr1 3494985 3500245 - 3069903 4 chr1 5263271 5263272 + 92668 5 chr1 5263271 5263272 + 298347 6 chr1 6332820 6335604 - 234544 7 chr1 6332820 6335604 - 1054057 8 chr1 8818348 8819934 - 1419311 9 chr1 8818348 8819934 - 2247117 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc0j33oeh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc0j33oeh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 294155 298413 - 294154 1 chr1 3494985 3500245 - 3494984 3 chr1 6332820 6335604 - 6332819 4 chr1 8818348 8819934 - 8818347 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 294155 | 298413 | a | 0 | ... | | chr1 | 6332820 | 6335604 | a | 0 | ... | | chr1 | 8818348 | 8819934 | a | 0 | ... | | chr1 | 3494985 | 3500245 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 294155 298413 - 294154 3 chr1 3494985 3500245 - 3494984 1 chr1 6332820 6335604 - 6332819 2 chr1 8818348 8819934 - 8818347 df2 Chromosome Start End Strand Distance 0 chr1 294155 298413 - 294154 1 chr1 3494985 3500245 - 3494984 3 chr1 6332820 6335604 - 6332819 4 chr1 8818348 8819934 - 8818347 Actual Chromosome Start End Strand Distance 0 chr1 294155 298413 - 294154 1 chr1 3494985 3500245 - 3494984 2 chr1 6332820 6335604 - 6332819 3 chr1 8818348 8819934 - 8818347 Expected Chromosome Start End Strand Distance 0 chr1 294155 298413 - 294154 1 chr1 3494985 3500245 - 3494984 2 chr1 6332820 6335604 - 6332819 3 chr1 8818348 8819934 - 8818347 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9nstt21q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9nstt21q/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 294155 298413 - 294154 1 chr1 3494985 3500245 - 3494984 3 chr1 6332820 6335604 - 6332819 4 chr1 8818348 8819934 - 8818347 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 294155 | 298413 | a | 0 | ... | | chr1 | 6332820 | 6335604 | a | 0 | ... | | chr1 | 8818348 | 8819934 | a | 0 | ... | | chr1 | 3494985 | 3500245 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 294155 298413 - 294154 3 chr1 3494985 3500245 - 3494984 1 chr1 6332820 6335604 - 6332819 2 chr1 8818348 8819934 - 8818347 df2 Chromosome Start End Strand Distance 0 chr1 294155 298413 - 294154 1 chr1 3494985 3500245 - 3494984 3 chr1 6332820 6335604 - 6332819 4 chr1 8818348 8819934 - 8818347 Actual Chromosome Start End Strand Distance 0 chr1 294155 298413 - 294154 1 chr1 3494985 3500245 - 3494984 2 chr1 6332820 6335604 - 6332819 3 chr1 8818348 8819934 - 8818347 Expected Chromosome Start End Strand Distance 0 chr1 294155 298413 - 294154 1 chr1 3494985 3500245 - 3494984 2 chr1 6332820 6335604 - 6332819 3 chr1 8818348 8819934 - 8818347 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6or7u5fz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6or7u5fz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8mue5q33/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8mue5q33/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_vxjx087/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_vxjx087/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr2 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr2 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr2 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr2 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn7xjs97r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn7xjs97r/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyc_5y_4b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyc_5y_4b/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 703407 711828 - 701768 1 chr1 703407 711828 - 8637495 2 chr1 4519167 4526407 - 4517528 3 chr1 4519167 4526407 - 4822916 4 chr1 5638692 5646990 - 3702333 5 chr1 5638692 5646990 - 5637053 6 chr1 7814264 7814847 + 484659 7 chr1 7814264 7814847 + 3718474 8 chr1 8711076 8713443 + 409452 9 chr1 8711076 8713443 + 4615286 10 chr1 9875682 9884103 + 1574058 11 chr1 9875682 9884103 + 5779892 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9875682 | 9884103 | a | 0 | ... | | chr1 | 9875682 | 9884103 | a | 0 | ... | | chr1 | 7814264 | 7814847 | a | 0 | ... | | chr1 | 7814264 | 7814847 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 4519167 | 4526407 | a | 0 | ... | | chr1 | 4519167 | 4526407 | a | 0 | ... | | chr1 | 703407 | 711828 | a | 0 | ... | | chr1 | 703407 | 711828 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 10 chr1 703407 711828 - 701768 11 chr1 703407 711828 - 8637495 8 chr1 4519167 4526407 - 4517528 9 chr1 4519167 4526407 - 4822916 6 chr1 5638692 5646990 - 3702333 7 chr1 5638692 5646990 - 5637053 2 chr1 7814264 7814847 + 484659 3 chr1 7814264 7814847 + 3718474 4 chr1 8711076 8713443 + 409452 5 chr1 8711076 8713443 + 4615286 0 chr1 9875682 9884103 + 1574058 1 chr1 9875682 9884103 + 5779892 df2 Chromosome Start End Strand Distance 0 chr1 703407 711828 - 701768 1 chr1 703407 711828 - 8637495 2 chr1 4519167 4526407 - 4517528 3 chr1 4519167 4526407 - 4822916 4 chr1 5638692 5646990 - 3702333 5 chr1 5638692 5646990 - 5637053 6 chr1 7814264 7814847 + 484659 7 chr1 7814264 7814847 + 3718474 8 chr1 8711076 8713443 + 409452 9 chr1 8711076 8713443 + 4615286 10 chr1 9875682 9884103 + 1574058 11 chr1 9875682 9884103 + 5779892 Actual Chromosome Start End Strand Distance 0 chr1 703407 711828 - 701768 1 chr1 703407 711828 - 8637495 2 chr1 4519167 4526407 - 4517528 3 chr1 4519167 4526407 - 4822916 4 chr1 5638692 5646990 - 3702333 5 chr1 5638692 5646990 - 5637053 6 chr1 7814264 7814847 + 484659 7 chr1 7814264 7814847 + 3718474 8 chr1 8711076 8713443 + 409452 9 chr1 8711076 8713443 + 4615286 10 chr1 9875682 9884103 + 1574058 11 chr1 9875682 9884103 + 5779892 Expected Chromosome Start End Strand Distance 0 chr1 703407 711828 - 701768 1 chr1 703407 711828 - 8637495 2 chr1 4519167 4526407 - 4517528 3 chr1 4519167 4526407 - 4822916 4 chr1 5638692 5646990 - 3702333 5 chr1 5638692 5646990 - 5637053 6 chr1 7814264 7814847 + 484659 7 chr1 7814264 7814847 + 3718474 8 chr1 8711076 8713443 + 409452 9 chr1 8711076 8713443 + 4615286 10 chr1 9875682 9884103 + 1574058 11 chr1 9875682 9884103 + 5779892 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbr53xdc0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbr53xdc0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 703407 711828 - 0 1 chr1 703407 711828 - 3807340 2 chr1 4519167 4526407 - 0 3 chr1 4519167 4526407 - 1112286 4 chr1 5638692 5646990 - 0 5 chr1 5638692 5646990 - 1112286 6 chr1 7814264 7814847 + 0 7 chr1 7814264 7814847 + 896230 8 chr1 8711076 8713443 + 0 9 chr1 8711076 8713443 + 896230 10 chr1 9875682 9884103 + 0 11 chr1 9875682 9884103 + 1162240 12 chr17 8616368 8624901 + 0 13 chr2 2044578 2053527 - 0 14 chr20 4692559 4700980 - 0 15 chr3 6273392 6273394 - 0 16 chr4 2700866 2707377 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9875682 | 9884103 | a | 0 | ... | | chr1 | 9875682 | 9884103 | a | 0 | ... | | chr1 | 7814264 | 7814847 | a | 0 | ... | | chr1 | 7814264 | 7814847 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr3 | 6273392 | 6273394 | a | 0 | ... | | chr4 | 2700866 | 2707377 | a | 0 | ... | | chr17 | 8616368 | 8624901 | a | 0 | ... | | chr20 | 4692559 | 4700980 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 17 rows and 12 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 10 chr1 703407 711828 - 0 11 chr1 703407 711828 - 3807340 12 chr2 2044578 2053527 - 0 14 chr4 2700866 2707377 + 0 8 chr1 4519167 4526407 - 0 9 chr1 4519167 4526407 - 1112286 16 chr20 4692559 4700980 - 0 6 chr1 5638692 5646990 - 0 7 chr1 5638692 5646990 - 1112286 13 chr3 6273392 6273394 - 0 2 chr1 7814264 7814847 + 0 3 chr1 7814264 7814847 + 896230 15 chr17 8616368 8624901 + 0 4 chr1 8711076 8713443 + 0 5 chr1 8711076 8713443 + 896230 0 chr1 9875682 9884103 + 0 1 chr1 9875682 9884103 + 1162240 df2 Chromosome Start End Strand Distance 0 chr1 703407 711828 - 0 1 chr1 703407 711828 - 3807340 13 chr2 2044578 2053527 - 0 16 chr4 2700866 2707377 + 0 2 chr1 4519167 4526407 - 0 3 chr1 4519167 4526407 - 1112286 14 chr20 4692559 4700980 - 0 4 chr1 5638692 5646990 - 0 5 chr1 5638692 5646990 - 1112286 15 chr3 6273392 6273394 - 0 6 chr1 7814264 7814847 + 0 7 chr1 7814264 7814847 + 896230 12 chr17 8616368 8624901 + 0 8 chr1 8711076 8713443 + 0 9 chr1 8711076 8713443 + 896230 10 chr1 9875682 9884103 + 0 11 chr1 9875682 9884103 + 1162240 Actual Chromosome Start End Strand Distance 0 chr1 703407 711828 - 0 1 chr1 703407 711828 - 3807340 2 chr1 4519167 4526407 - 0 3 chr1 4519167 4526407 - 1112286 4 chr1 5638692 5646990 - 0 5 chr1 5638692 5646990 - 1112286 6 chr1 7814264 7814847 + 0 7 chr1 7814264 7814847 + 896230 8 chr1 8711076 8713443 + 0 9 chr1 8711076 8713443 + 896230 10 chr1 9875682 9884103 + 0 11 chr1 9875682 9884103 + 1162240 12 chr17 8616368 8624901 + 0 13 chr2 2044578 2053527 - 0 14 chr20 4692559 4700980 - 0 15 chr3 6273392 6273394 - 0 16 chr4 2700866 2707377 + 0 Expected Chromosome Start End Strand Distance 0 chr1 703407 711828 - 0 1 chr1 703407 711828 - 3807340 2 chr1 4519167 4526407 - 0 3 chr1 4519167 4526407 - 1112286 4 chr1 5638692 5646990 - 0 5 chr1 5638692 5646990 - 1112286 6 chr1 7814264 7814847 + 0 7 chr1 7814264 7814847 + 896230 8 chr1 8711076 8713443 + 0 9 chr1 8711076 8713443 + 896230 10 chr1 9875682 9884103 + 0 11 chr1 9875682 9884103 + 1162240 12 chr17 8616368 8624901 + 0 13 chr2 2044578 2053527 - 0 14 chr20 4692559 4700980 - 0 15 chr3 6273392 6273394 - 0 16 chr4 2700866 2707377 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=17, step=1) Expected index RangeIndex(start=0, stop=17, step=1) index equal [ True True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmplym8a1cc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplym8a1cc/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 703407 711828 - 703397 1 chr1 703407 711828 - 703406 2 chr1 4519167 4526407 - 4519157 3 chr1 4519167 4526407 - 4519166 4 chr1 5638692 5646990 - 5638682 5 chr1 5638692 5646990 - 5638691 6 chr1 7814264 7814847 + 7814254 7 chr1 7814264 7814847 + 7814263 8 chr1 8711076 8713443 + 8711066 9 chr1 8711076 8713443 + 8711075 10 chr1 9875682 9884103 + 9875672 11 chr1 9875682 9884103 + 9875681 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9875682 | 9884103 | a | 0 | ... | | chr1 | 9875682 | 9884103 | a | 0 | ... | | chr1 | 7814264 | 7814847 | a | 0 | ... | | chr1 | 7814264 | 7814847 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 4519167 | 4526407 | a | 0 | ... | | chr1 | 4519167 | 4526407 | a | 0 | ... | | chr1 | 703407 | 711828 | a | 0 | ... | | chr1 | 703407 | 711828 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 10 chr1 703407 711828 - 703397 11 chr1 703407 711828 - 703406 8 chr1 4519167 4526407 - 4519157 9 chr1 4519167 4526407 - 4519166 6 chr1 5638692 5646990 - 5638682 7 chr1 5638692 5646990 - 5638691 2 chr1 7814264 7814847 + 7814254 3 chr1 7814264 7814847 + 7814263 4 chr1 8711076 8713443 + 8711066 5 chr1 8711076 8713443 + 8711075 0 chr1 9875682 9884103 + 9875672 1 chr1 9875682 9884103 + 9875681 df2 Chromosome Start End Strand Distance 0 chr1 703407 711828 - 703397 1 chr1 703407 711828 - 703406 2 chr1 4519167 4526407 - 4519157 3 chr1 4519167 4526407 - 4519166 4 chr1 5638692 5646990 - 5638682 5 chr1 5638692 5646990 - 5638691 6 chr1 7814264 7814847 + 7814254 7 chr1 7814264 7814847 + 7814263 8 chr1 8711076 8713443 + 8711066 9 chr1 8711076 8713443 + 8711075 10 chr1 9875682 9884103 + 9875672 11 chr1 9875682 9884103 + 9875681 Actual Chromosome Start End Strand Distance 0 chr1 703407 711828 - 703397 1 chr1 703407 711828 - 703406 2 chr1 4519167 4526407 - 4519157 3 chr1 4519167 4526407 - 4519166 4 chr1 5638692 5646990 - 5638682 5 chr1 5638692 5646990 - 5638691 6 chr1 7814264 7814847 + 7814254 7 chr1 7814264 7814847 + 7814263 8 chr1 8711076 8713443 + 8711066 9 chr1 8711076 8713443 + 8711075 10 chr1 9875682 9884103 + 9875672 11 chr1 9875682 9884103 + 9875681 Expected Chromosome Start End Strand Distance 0 chr1 703407 711828 - 703397 1 chr1 703407 711828 - 703406 2 chr1 4519167 4526407 - 4519157 3 chr1 4519167 4526407 - 4519166 4 chr1 5638692 5646990 - 5638682 5 chr1 5638692 5646990 - 5638691 6 chr1 7814264 7814847 + 7814254 7 chr1 7814264 7814847 + 7814263 8 chr1 8711076 8713443 + 8711066 9 chr1 8711076 8713443 + 8711075 10 chr1 9875682 9884103 + 9875672 11 chr1 9875682 9884103 + 9875681 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6gjeftgj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6gjeftgj/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 703407 711828 - 698177 1 chr1 703407 711828 - 703406 2 chr1 4519167 4526407 - 4513937 3 chr1 4519167 4526407 - 4519166 4 chr1 5638692 5646990 - 5633462 5 chr1 5638692 5646990 - 5638691 6 chr1 7814264 7814847 + 7814254 7 chr1 7814264 7814847 + 7814263 8 chr1 8711076 8713443 + 8711066 9 chr1 8711076 8713443 + 8711075 10 chr1 9875682 9884103 + 9875672 11 chr1 9875682 9884103 + 9875681 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9875682 | 9884103 | a | 0 | ... | | chr1 | 9875682 | 9884103 | a | 0 | ... | | chr1 | 7814264 | 7814847 | a | 0 | ... | | chr1 | 7814264 | 7814847 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 4519167 | 4526407 | a | 0 | ... | | chr1 | 4519167 | 4526407 | a | 0 | ... | | chr1 | 703407 | 711828 | a | 0 | ... | | chr1 | 703407 | 711828 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 10 chr1 703407 711828 - 698177 11 chr1 703407 711828 - 703406 8 chr1 4519167 4526407 - 4513937 9 chr1 4519167 4526407 - 4519166 6 chr1 5638692 5646990 - 5633462 7 chr1 5638692 5646990 - 5638691 2 chr1 7814264 7814847 + 7814254 3 chr1 7814264 7814847 + 7814263 4 chr1 8711076 8713443 + 8711066 5 chr1 8711076 8713443 + 8711075 0 chr1 9875682 9884103 + 9875672 1 chr1 9875682 9884103 + 9875681 df2 Chromosome Start End Strand Distance 0 chr1 703407 711828 - 698177 1 chr1 703407 711828 - 703406 2 chr1 4519167 4526407 - 4513937 3 chr1 4519167 4526407 - 4519166 4 chr1 5638692 5646990 - 5633462 5 chr1 5638692 5646990 - 5638691 6 chr1 7814264 7814847 + 7814254 7 chr1 7814264 7814847 + 7814263 8 chr1 8711076 8713443 + 8711066 9 chr1 8711076 8713443 + 8711075 10 chr1 9875682 9884103 + 9875672 11 chr1 9875682 9884103 + 9875681 Actual Chromosome Start End Strand Distance 0 chr1 703407 711828 - 698177 1 chr1 703407 711828 - 703406 2 chr1 4519167 4526407 - 4513937 3 chr1 4519167 4526407 - 4519166 4 chr1 5638692 5646990 - 5633462 5 chr1 5638692 5646990 - 5638691 6 chr1 7814264 7814847 + 7814254 7 chr1 7814264 7814847 + 7814263 8 chr1 8711076 8713443 + 8711066 9 chr1 8711076 8713443 + 8711075 10 chr1 9875682 9884103 + 9875672 11 chr1 9875682 9884103 + 9875681 Expected Chromosome Start End Strand Distance 0 chr1 703407 711828 - 698177 1 chr1 703407 711828 - 703406 2 chr1 4519167 4526407 - 4513937 3 chr1 4519167 4526407 - 4519166 4 chr1 5638692 5646990 - 5633462 5 chr1 5638692 5646990 - 5638691 6 chr1 7814264 7814847 + 7814254 7 chr1 7814264 7814847 + 7814263 8 chr1 8711076 8713443 + 8711066 9 chr1 8711076 8713443 + 8711075 10 chr1 9875682 9884103 + 9875672 11 chr1 9875682 9884103 + 9875681 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp81h4rxuj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp81h4rxuj/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 703407 711828 - 698177 1 chr1 703407 711828 - 703406 2 chr1 4519167 4526407 - 4513937 3 chr1 4519167 4526407 - 4519166 4 chr1 5638692 5646990 - 5633462 5 chr1 5638692 5646990 - 5638691 6 chr1 7814264 7814847 + 7814254 7 chr1 7814264 7814847 + 7814263 8 chr1 8711076 8713443 + 8711066 9 chr1 8711076 8713443 + 8711075 10 chr1 9875682 9884103 + 9875672 11 chr1 9875682 9884103 + 9875681 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9875682 | 9884103 | a | 0 | ... | | chr1 | 9875682 | 9884103 | a | 0 | ... | | chr1 | 7814264 | 7814847 | a | 0 | ... | | chr1 | 7814264 | 7814847 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 4519167 | 4526407 | a | 0 | ... | | chr1 | 4519167 | 4526407 | a | 0 | ... | | chr1 | 703407 | 711828 | a | 0 | ... | | chr1 | 703407 | 711828 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 10 chr1 703407 711828 - 698177 11 chr1 703407 711828 - 703406 8 chr1 4519167 4526407 - 4513937 9 chr1 4519167 4526407 - 4519166 6 chr1 5638692 5646990 - 5633462 7 chr1 5638692 5646990 - 5638691 2 chr1 7814264 7814847 + 7814254 3 chr1 7814264 7814847 + 7814263 4 chr1 8711076 8713443 + 8711066 5 chr1 8711076 8713443 + 8711075 0 chr1 9875682 9884103 + 9875672 1 chr1 9875682 9884103 + 9875681 df2 Chromosome Start End Strand Distance 0 chr1 703407 711828 - 698177 1 chr1 703407 711828 - 703406 2 chr1 4519167 4526407 - 4513937 3 chr1 4519167 4526407 - 4519166 4 chr1 5638692 5646990 - 5633462 5 chr1 5638692 5646990 - 5638691 6 chr1 7814264 7814847 + 7814254 7 chr1 7814264 7814847 + 7814263 8 chr1 8711076 8713443 + 8711066 9 chr1 8711076 8713443 + 8711075 10 chr1 9875682 9884103 + 9875672 11 chr1 9875682 9884103 + 9875681 Actual Chromosome Start End Strand Distance 0 chr1 703407 711828 - 698177 1 chr1 703407 711828 - 703406 2 chr1 4519167 4526407 - 4513937 3 chr1 4519167 4526407 - 4519166 4 chr1 5638692 5646990 - 5633462 5 chr1 5638692 5646990 - 5638691 6 chr1 7814264 7814847 + 7814254 7 chr1 7814264 7814847 + 7814263 8 chr1 8711076 8713443 + 8711066 9 chr1 8711076 8713443 + 8711075 10 chr1 9875682 9884103 + 9875672 11 chr1 9875682 9884103 + 9875681 Expected Chromosome Start End Strand Distance 0 chr1 703407 711828 - 698177 1 chr1 703407 711828 - 703406 2 chr1 4519167 4526407 - 4513937 3 chr1 4519167 4526407 - 4519166 4 chr1 5638692 5646990 - 5633462 5 chr1 5638692 5646990 - 5638691 6 chr1 7814264 7814847 + 7814254 7 chr1 7814264 7814847 + 7814263 8 chr1 8711076 8713443 + 8711066 9 chr1 8711076 8713443 + 8711075 10 chr1 9875682 9884103 + 9875672 11 chr1 9875682 9884103 + 9875681 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmps3jejm3z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps3jejm3z/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 703407 711828 - 698177 1 chr1 703407 711828 - 703406 2 chr1 4519167 4526407 - 4513937 3 chr1 4519167 4526407 - 4519166 4 chr1 5638692 5646990 - 5633462 5 chr1 5638692 5646990 - 5638691 6 chr1 7814264 7814847 + 7814254 7 chr1 8711076 8713443 + 8711066 8 chr1 9875682 9884103 + 9875672 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9875682 | 9884103 | a | 0 | ... | | chr1 | 7814264 | 7814847 | a | 0 | ... | | chr1 | 8711076 | 8713443 | a | 0 | ... | | chr1 | 5638692 | 5646990 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 4519167 | 4526407 | a | 0 | ... | | chr1 | 4519167 | 4526407 | a | 0 | ... | | chr1 | 703407 | 711828 | a | 0 | ... | | chr1 | 703407 | 711828 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 7 chr1 703407 711828 - 698177 8 chr1 703407 711828 - 703406 5 chr1 4519167 4526407 - 4513937 6 chr1 4519167 4526407 - 4519166 3 chr1 5638692 5646990 - 5633462 4 chr1 5638692 5646990 - 5638691 1 chr1 7814264 7814847 + 7814254 2 chr1 8711076 8713443 + 8711066 0 chr1 9875682 9884103 + 9875672 df2 Chromosome Start End Strand Distance 0 chr1 703407 711828 - 698177 1 chr1 703407 711828 - 703406 2 chr1 4519167 4526407 - 4513937 3 chr1 4519167 4526407 - 4519166 4 chr1 5638692 5646990 - 5633462 5 chr1 5638692 5646990 - 5638691 6 chr1 7814264 7814847 + 7814254 7 chr1 8711076 8713443 + 8711066 8 chr1 9875682 9884103 + 9875672 Actual Chromosome Start End Strand Distance 0 chr1 703407 711828 - 698177 1 chr1 703407 711828 - 703406 2 chr1 4519167 4526407 - 4513937 3 chr1 4519167 4526407 - 4519166 4 chr1 5638692 5646990 - 5633462 5 chr1 5638692 5646990 - 5638691 6 chr1 7814264 7814847 + 7814254 7 chr1 8711076 8713443 + 8711066 8 chr1 9875682 9884103 + 9875672 Expected Chromosome Start End Strand Distance 0 chr1 703407 711828 - 698177 1 chr1 703407 711828 - 703406 2 chr1 4519167 4526407 - 4513937 3 chr1 4519167 4526407 - 4519166 4 chr1 5638692 5646990 - 5633462 5 chr1 5638692 5646990 - 5638691 6 chr1 7814264 7814847 + 7814254 7 chr1 8711076 8713443 + 8711066 8 chr1 9875682 9884103 + 9875672 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=9, step=1) index equal [ True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmps9k7ufcg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps9k7ufcg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1014203 1023503 - 7108920 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1014203 | 1023503 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1014203 1023503 - 7108920 df2 Chromosome Start End Strand Distance 0 chr1 1014203 1023503 - 7108920 Actual Chromosome Start End Strand Distance 0 chr1 1014203 1023503 - 7108920 Expected Chromosome Start End Strand Distance 0 chr1 1014203 1023503 - 7108920 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn04psvua/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn04psvua/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 1 9244 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 9244 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 9244 - 0 df2 Chromosome Start End Strand Distance 1 chr1 1 9244 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 9244 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 9244 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmplm2sx4wz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplm2sx4wz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 1 9244 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 9244 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 9244 - 0 df2 Chromosome Start End Strand Distance 1 chr1 1 9244 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 9244 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 9244 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf_t1ockt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf_t1ockt/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmptvabs6ce/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptvabs6ce/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4318915 4324210 + 8327 1 chr1 7343420 7344757 + 3001962 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7343420 | 7344757 | a | 0 | ... | | chr1 | 4318915 | 4324210 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 4318915 4324210 + 8327 0 chr1 7343420 7344757 + 3001962 df2 Chromosome Start End Strand Distance 0 chr1 4318915 4324210 + 8327 1 chr1 7343420 7344757 + 3001962 Actual Chromosome Start End Strand Distance 0 chr1 4318915 4324210 + 8327 1 chr1 7343420 7344757 + 3001962 Expected Chromosome Start End Strand Distance 0 chr1 4318915 4324210 + 8327 1 chr1 7343420 7344757 + 3001962 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9e7n8jpc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9e7n8jpc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg6sftp_e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg6sftp_e/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf10kfqqc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf10kfqqc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_y2s3s1e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_y2s3s1e/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7x6xpxbd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7x6xpxbd/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1775 1776 - 0 1 chr1 1775 1776 - 0 2 chr1 1775 1776 - 0 3 chr1 1775 1776 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1775 | 1776 | a | 0 | ... | | chr1 | 1775 | 1776 | a | 0 | ... | | chr1 | 1775 | 1776 | a | 0 | ... | | chr1 | 1775 | 1776 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1775 1776 - 0 1 chr1 1775 1776 - 0 2 chr1 1775 1776 - 0 3 chr1 1775 1776 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1775 1776 - 0 1 chr1 1775 1776 - 0 2 chr1 1775 1776 - 0 3 chr1 1775 1776 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1775 1776 - 0 1 chr1 1775 1776 - 0 2 chr1 1775 1776 - 0 3 chr1 1775 1776 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1775 1776 - 0 1 chr1 1775 1776 - 0 2 chr1 1775 1776 - 0 3 chr1 1775 1776 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmprwi3veys/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprwi3veys/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqe3uvcrh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqe3uvcrh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpub41fayh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpub41fayh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnnc16rxz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnnc16rxz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx3vxcdz9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx3vxcdz9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1gror9b0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1gror9b0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 8947133 8947134 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8947133 | 8947134 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 8947133 8947134 + 0 df2 Chromosome Start End Strand Distance 0 chr1 8947133 8947134 + 0 Actual Chromosome Start End Strand Distance 0 chr1 8947133 8947134 + 0 Expected Chromosome Start End Strand Distance 0 chr1 8947133 8947134 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmt6x0qpn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmt6x0qpn/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpetluf3ek/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpetluf3ek/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxcixkefq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxcixkefq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr15 6622283 6628725 - 1054419 1 chr15 6622283 6628725 - 1064797 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr15 | 6622283 | 6628725 | a | 0 | ... | | chr15 | 6622283 | 6628725 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr15 6622283 6628725 - 1054419 1 chr15 6622283 6628725 - 1064797 df2 Chromosome Start End Strand Distance 0 chr15 6622283 6628725 - 1054419 1 chr15 6622283 6628725 - 1064797 Actual Chromosome Start End Strand Distance 0 chr15 6622283 6628725 - 1054419 1 chr15 6622283 6628725 - 1064797 Expected Chromosome Start End Strand Distance 0 chr15 6622283 6628725 - 1054419 1 chr15 6622283 6628725 - 1064797 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp405cfxmb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp405cfxmb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr15 6622283 6628725 - 1054419 1 chr15 6622283 6628725 - 1064797 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr15 | 6622283 | 6628725 | a | 0 | ... | | chr15 | 6622283 | 6628725 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr15 6622283 6628725 - 1054419 1 chr15 6622283 6628725 - 1064797 df2 Chromosome Start End Strand Distance 0 chr15 6622283 6628725 - 1054419 1 chr15 6622283 6628725 - 1064797 Actual Chromosome Start End Strand Distance 0 chr15 6622283 6628725 - 1054419 1 chr15 6622283 6628725 - 1064797 Expected Chromosome Start End Strand Distance 0 chr15 6622283 6628725 - 1054419 1 chr15 6622283 6628725 - 1064797 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf3uernl8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf3uernl8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr15 760534 762262 - 0 1 chr15 760534 762262 - 3329746 2 chr15 1518019 1527979 + 0 3 chr15 1518019 1527979 + 709319 4 chr15 2237297 2246540 + 0 5 chr15 2237297 2246540 + 709319 6 chr15 4092007 4095142 - 0 7 chr15 4092007 4095142 - 1462345 8 chr15 4356956 4366327 + 0 9 chr15 4356956 4366327 + 1288121 10 chr15 5557486 5557487 - 0 11 chr15 5557486 5557487 - 8796 12 chr15 5566282 5567865 - 0 13 chr15 5566282 5567865 - 8796 14 chr15 5654447 5664404 + 0 15 chr15 5654447 5664404 + 1288121 16 chr15 7376940 7381576 + 0 17 chr15 7376940 7381576 + 1712537 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr15 | 4356956 | 4366327 | a | 0 | ... | | chr15 | 4356956 | 4366327 | a | 0 | ... | | chr15 | 7376940 | 7381576 | a | 0 | ... | | chr15 | 7376940 | 7381576 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr15 | 5566282 | 5567865 | a | 0 | ... | | chr15 | 5566282 | 5567865 | a | 0 | ... | | chr15 | 4092007 | 4095142 | a | 0 | ... | | chr15 | 4092007 | 4095142 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 18 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 10 chr15 760534 762262 - 0 11 chr15 760534 762262 - 3329746 4 chr15 1518019 1527979 + 0 5 chr15 1518019 1527979 + 709319 8 chr15 2237297 2246540 + 0 9 chr15 2237297 2246540 + 709319 16 chr15 4092007 4095142 - 0 17 chr15 4092007 4095142 - 1462345 0 chr15 4356956 4366327 + 0 1 chr15 4356956 4366327 + 1288121 12 chr15 5557486 5557487 - 0 13 chr15 5557486 5557487 - 8796 14 chr15 5566282 5567865 - 0 15 chr15 5566282 5567865 - 8796 6 chr15 5654447 5664404 + 0 7 chr15 5654447 5664404 + 1288121 2 chr15 7376940 7381576 + 0 3 chr15 7376940 7381576 + 1712537 df2 Chromosome Start End Strand Distance 0 chr15 760534 762262 - 0 1 chr15 760534 762262 - 3329746 2 chr15 1518019 1527979 + 0 3 chr15 1518019 1527979 + 709319 4 chr15 2237297 2246540 + 0 5 chr15 2237297 2246540 + 709319 6 chr15 4092007 4095142 - 0 7 chr15 4092007 4095142 - 1462345 8 chr15 4356956 4366327 + 0 9 chr15 4356956 4366327 + 1288121 10 chr15 5557486 5557487 - 0 11 chr15 5557486 5557487 - 8796 12 chr15 5566282 5567865 - 0 13 chr15 5566282 5567865 - 8796 14 chr15 5654447 5664404 + 0 15 chr15 5654447 5664404 + 1288121 16 chr15 7376940 7381576 + 0 17 chr15 7376940 7381576 + 1712537 Actual Chromosome Start End Strand Distance 0 chr15 760534 762262 - 0 1 chr15 760534 762262 - 3329746 2 chr15 1518019 1527979 + 0 3 chr15 1518019 1527979 + 709319 4 chr15 2237297 2246540 + 0 5 chr15 2237297 2246540 + 709319 6 chr15 4092007 4095142 - 0 7 chr15 4092007 4095142 - 1462345 8 chr15 4356956 4366327 + 0 9 chr15 4356956 4366327 + 1288121 10 chr15 5557486 5557487 - 0 11 chr15 5557486 5557487 - 8796 12 chr15 5566282 5567865 - 0 13 chr15 5566282 5567865 - 8796 14 chr15 5654447 5664404 + 0 15 chr15 5654447 5664404 + 1288121 16 chr15 7376940 7381576 + 0 17 chr15 7376940 7381576 + 1712537 Expected Chromosome Start End Strand Distance 0 chr15 760534 762262 - 0 1 chr15 760534 762262 - 3329746 2 chr15 1518019 1527979 + 0 3 chr15 1518019 1527979 + 709319 4 chr15 2237297 2246540 + 0 5 chr15 2237297 2246540 + 709319 6 chr15 4092007 4095142 - 0 7 chr15 4092007 4095142 - 1462345 8 chr15 4356956 4366327 + 0 9 chr15 4356956 4366327 + 1288121 10 chr15 5557486 5557487 - 0 11 chr15 5557486 5557487 - 8796 12 chr15 5566282 5567865 - 0 13 chr15 5566282 5567865 - 8796 14 chr15 5654447 5664404 + 0 15 chr15 5654447 5664404 + 1288121 16 chr15 7376940 7381576 + 0 17 chr15 7376940 7381576 + 1712537 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=18, step=1) Expected index RangeIndex(start=0, stop=18, step=1) index equal [ True True True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmphm0_tbgg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphm0_tbgg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr15 760534 762262 - 0 1 chr15 760534 762262 - 3329746 2 chr15 1518019 1527979 + 0 3 chr15 1518019 1527979 + 709319 4 chr15 2237297 2246540 + 0 5 chr15 2237297 2246540 + 713349 6 chr15 4092007 4095142 - 0 7 chr15 4092007 4095142 - 1462345 8 chr15 4356956 4366327 + 0 9 chr15 4356956 4366327 + 1288121 10 chr15 5557486 5557487 - 0 11 chr15 5557486 5557487 - 8796 12 chr15 5566282 5567865 - 0 13 chr15 5566282 5567865 - 3472 14 chr15 5654447 5664404 + 0 15 chr15 5654447 5664404 + 1296856 16 chr15 7376940 7381576 + 0 17 chr15 7376940 7381576 + 1716790 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr15 | 4356956 | 4366327 | a | 0 | ... | | chr15 | 4356956 | 4366327 | a | 0 | ... | | chr15 | 7376940 | 7381576 | a | 0 | ... | | chr15 | 7376940 | 7381576 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr15 | 5566282 | 5567865 | a | 0 | ... | | chr15 | 5566282 | 5567865 | a | 0 | ... | | chr15 | 4092007 | 4095142 | a | 0 | ... | | chr15 | 4092007 | 4095142 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 18 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 10 chr15 760534 762262 - 0 11 chr15 760534 762262 - 3329746 4 chr15 1518019 1527979 + 0 5 chr15 1518019 1527979 + 709319 8 chr15 2237297 2246540 + 0 9 chr15 2237297 2246540 + 713349 16 chr15 4092007 4095142 - 0 17 chr15 4092007 4095142 - 1462345 0 chr15 4356956 4366327 + 0 1 chr15 4356956 4366327 + 1288121 12 chr15 5557486 5557487 - 0 13 chr15 5557486 5557487 - 8796 14 chr15 5566282 5567865 - 0 15 chr15 5566282 5567865 - 3472 6 chr15 5654447 5664404 + 0 7 chr15 5654447 5664404 + 1296856 2 chr15 7376940 7381576 + 0 3 chr15 7376940 7381576 + 1716790 df2 Chromosome Start End Strand Distance 0 chr15 760534 762262 - 0 1 chr15 760534 762262 - 3329746 2 chr15 1518019 1527979 + 0 3 chr15 1518019 1527979 + 709319 4 chr15 2237297 2246540 + 0 5 chr15 2237297 2246540 + 713349 6 chr15 4092007 4095142 - 0 7 chr15 4092007 4095142 - 1462345 8 chr15 4356956 4366327 + 0 9 chr15 4356956 4366327 + 1288121 10 chr15 5557486 5557487 - 0 11 chr15 5557486 5557487 - 8796 12 chr15 5566282 5567865 - 0 13 chr15 5566282 5567865 - 3472 14 chr15 5654447 5664404 + 0 15 chr15 5654447 5664404 + 1296856 16 chr15 7376940 7381576 + 0 17 chr15 7376940 7381576 + 1716790 Actual Chromosome Start End Strand Distance 0 chr15 760534 762262 - 0 1 chr15 760534 762262 - 3329746 2 chr15 1518019 1527979 + 0 3 chr15 1518019 1527979 + 709319 4 chr15 2237297 2246540 + 0 5 chr15 2237297 2246540 + 713349 6 chr15 4092007 4095142 - 0 7 chr15 4092007 4095142 - 1462345 8 chr15 4356956 4366327 + 0 9 chr15 4356956 4366327 + 1288121 10 chr15 5557486 5557487 - 0 11 chr15 5557486 5557487 - 8796 12 chr15 5566282 5567865 - 0 13 chr15 5566282 5567865 - 3472 14 chr15 5654447 5664404 + 0 15 chr15 5654447 5664404 + 1296856 16 chr15 7376940 7381576 + 0 17 chr15 7376940 7381576 + 1716790 Expected Chromosome Start End Strand Distance 0 chr15 760534 762262 - 0 1 chr15 760534 762262 - 3329746 2 chr15 1518019 1527979 + 0 3 chr15 1518019 1527979 + 709319 4 chr15 2237297 2246540 + 0 5 chr15 2237297 2246540 + 713349 6 chr15 4092007 4095142 - 0 7 chr15 4092007 4095142 - 1462345 8 chr15 4356956 4366327 + 0 9 chr15 4356956 4366327 + 1288121 10 chr15 5557486 5557487 - 0 11 chr15 5557486 5557487 - 8796 12 chr15 5566282 5567865 - 0 13 chr15 5566282 5567865 - 3472 14 chr15 5654447 5664404 + 0 15 chr15 5654447 5664404 + 1296856 16 chr15 7376940 7381576 + 0 17 chr15 7376940 7381576 + 1716790 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=18, step=1) Expected index RangeIndex(start=0, stop=18, step=1) index equal [ True True True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7r4ykc_d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7r4ykc_d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1qxfjbm9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1qxfjbm9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7_0y8l4d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7_0y8l4d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8xg4cxm9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8xg4cxm9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpge63ouju/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpge63ouju/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 292979 292980 - 0 1 chr1 292979 292980 - 1196851 2 chr1 1489830 1489831 - 0 3 chr1 1489830 1489831 - 1196851 4 chr1 4275621 4275622 - 0 5 chr1 4275621 4275622 - 458245 6 chr1 4733866 4733867 - 0 7 chr1 4733866 4733867 - 240140 8 chr1 4974006 4974007 - 0 9 chr1 4974006 4974007 - 240140 10 chr1 5126236 5126237 + 0 11 chr16 107263 107264 + 0 12 chr18 62765 62766 - 0 13 chr20 1 2 - 0 14 chrY 9263826 9263827 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5126236 | 5126237 | a | 0 | ... | | chr1 | 292979 | 292980 | a | 0 | ... | | chr1 | 292979 | 292980 | a | 0 | ... | | chr1 | 1489830 | 1489831 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr16 | 107263 | 107264 | a | 0 | ... | | chr18 | 62765 | 62766 | a | 0 | ... | | chr20 | 1 | 2 | a | 0 | ... | | chrY | 9263826 | 9263827 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 15 rows and 12 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 13 chr20 1 2 - 0 12 chr18 62765 62766 - 0 11 chr16 107263 107264 + 0 1 chr1 292979 292980 - 0 2 chr1 292979 292980 - 1196851 3 chr1 1489830 1489831 - 0 4 chr1 1489830 1489831 - 1196851 7 chr1 4275621 4275622 - 0 8 chr1 4275621 4275622 - 458245 5 chr1 4733866 4733867 - 0 6 chr1 4733866 4733867 - 240140 9 chr1 4974006 4974007 - 0 10 chr1 4974006 4974007 - 240140 0 chr1 5126236 5126237 + 0 14 chrY 9263826 9263827 - 0 df2 Chromosome Start End Strand Distance 13 chr20 1 2 - 0 12 chr18 62765 62766 - 0 11 chr16 107263 107264 + 0 0 chr1 292979 292980 - 0 1 chr1 292979 292980 - 1196851 2 chr1 1489830 1489831 - 0 3 chr1 1489830 1489831 - 1196851 4 chr1 4275621 4275622 - 0 5 chr1 4275621 4275622 - 458245 6 chr1 4733866 4733867 - 0 7 chr1 4733866 4733867 - 240140 8 chr1 4974006 4974007 - 0 9 chr1 4974006 4974007 - 240140 10 chr1 5126236 5126237 + 0 14 chrY 9263826 9263827 - 0 Actual Chromosome Start End Strand Distance 0 chr1 292979 292980 - 0 1 chr1 292979 292980 - 1196851 2 chr1 1489830 1489831 - 0 3 chr1 1489830 1489831 - 1196851 4 chr1 4275621 4275622 - 0 5 chr1 4275621 4275622 - 458245 6 chr1 4733866 4733867 - 0 7 chr1 4733866 4733867 - 240140 8 chr1 4974006 4974007 - 0 9 chr1 4974006 4974007 - 240140 10 chr1 5126236 5126237 + 0 11 chr16 107263 107264 + 0 12 chr18 62765 62766 - 0 13 chr20 1 2 - 0 14 chrY 9263826 9263827 - 0 Expected Chromosome Start End Strand Distance 0 chr1 292979 292980 - 0 1 chr1 292979 292980 - 1196851 2 chr1 1489830 1489831 - 0 3 chr1 1489830 1489831 - 1196851 4 chr1 4275621 4275622 - 0 5 chr1 4275621 4275622 - 458245 6 chr1 4733866 4733867 - 0 7 chr1 4733866 4733867 - 240140 8 chr1 4974006 4974007 - 0 9 chr1 4974006 4974007 - 240140 10 chr1 5126236 5126237 + 0 11 chr16 107263 107264 + 0 12 chr18 62765 62766 - 0 13 chr20 1 2 - 0 14 chrY 9263826 9263827 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=15, step=1) Expected index RangeIndex(start=0, stop=15, step=1) index equal [ True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnvd423ks/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnvd423ks/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 292979 292980 - 0 1 chr1 292979 292980 - 1196851 2 chr1 1489830 1489831 - 0 3 chr1 1489830 1489831 - 1196851 4 chr1 4275621 4275622 - 0 5 chr1 4275621 4275622 - 458245 6 chr1 4733866 4733867 - 0 7 chr1 4733866 4733867 - 240140 8 chr1 4974006 4974007 - 0 9 chr1 4974006 4974007 - 152230 12 chr18 62765 62766 - 0 13 chr20 1 2 - 0 14 chrY 9263826 9263827 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 292979 | 292980 | a | 0 | ... | | chr1 | 292979 | 292980 | a | 0 | ... | | chr1 | 1489830 | 1489831 | a | 0 | ... | | chr1 | 1489830 | 1489831 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 4275621 | 4275622 | a | 0 | ... | | chr1 | 4275621 | 4275622 | a | 0 | ... | | chr1 | 4974006 | 4974007 | a | 0 | ... | | chr1 | 4974006 | 4974007 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 13 rows and 12 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 11 chr20 1 2 - 0 10 chr18 62765 62766 - 0 0 chr1 292979 292980 - 0 1 chr1 292979 292980 - 1196851 2 chr1 1489830 1489831 - 0 3 chr1 1489830 1489831 - 1196851 6 chr1 4275621 4275622 - 0 7 chr1 4275621 4275622 - 458245 4 chr1 4733866 4733867 - 0 5 chr1 4733866 4733867 - 240140 8 chr1 4974006 4974007 - 0 9 chr1 4974006 4974007 - 152230 12 chrY 9263826 9263827 - 0 df2 Chromosome Start End Strand Distance 13 chr20 1 2 - 0 12 chr18 62765 62766 - 0 0 chr1 292979 292980 - 0 1 chr1 292979 292980 - 1196851 2 chr1 1489830 1489831 - 0 3 chr1 1489830 1489831 - 1196851 4 chr1 4275621 4275622 - 0 5 chr1 4275621 4275622 - 458245 6 chr1 4733866 4733867 - 0 7 chr1 4733866 4733867 - 240140 8 chr1 4974006 4974007 - 0 9 chr1 4974006 4974007 - 152230 14 chrY 9263826 9263827 - 0 Actual Chromosome Start End Strand Distance 0 chr1 292979 292980 - 0 1 chr1 292979 292980 - 1196851 2 chr1 1489830 1489831 - 0 3 chr1 1489830 1489831 - 1196851 4 chr1 4275621 4275622 - 0 5 chr1 4275621 4275622 - 458245 6 chr1 4733866 4733867 - 0 7 chr1 4733866 4733867 - 240140 8 chr1 4974006 4974007 - 0 9 chr1 4974006 4974007 - 152230 10 chr18 62765 62766 - 0 11 chr20 1 2 - 0 12 chrY 9263826 9263827 - 0 Expected Chromosome Start End Strand Distance 0 chr1 292979 292980 - 0 1 chr1 292979 292980 - 1196851 2 chr1 1489830 1489831 - 0 3 chr1 1489830 1489831 - 1196851 4 chr1 4275621 4275622 - 0 5 chr1 4275621 4275622 - 458245 6 chr1 4733866 4733867 - 0 7 chr1 4733866 4733867 - 240140 8 chr1 4974006 4974007 - 0 9 chr1 4974006 4974007 - 152230 10 chr18 62765 62766 - 0 11 chr20 1 2 - 0 12 chrY 9263826 9263827 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=13, step=1) Expected index RangeIndex(start=0, stop=13, step=1) index equal [ True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5wft3q8b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5wft3q8b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnhx6488o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnhx6488o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpovdg97qm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpovdg97qm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr2 5126236 5126237 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 5126236 | 5126237 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 5126236 5126237 + 0 df2 Chromosome Start End Strand Distance 0 chr2 5126236 5126237 + 0 Actual Chromosome Start End Strand Distance 0 chr2 5126236 5126237 + 0 Expected Chromosome Start End Strand Distance 0 chr2 5126236 5126237 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmptycwb5ru/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptycwb5ru/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 7627 - 1485601 1 chr1 2 7627 - 3096343 2 chr1 9817571 9824274 + 4778032 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9817571 | 9824274 | a | 0 | ... | | chr1 | 2 | 7627 | a | 0 | ... | | chr1 | 2 | 7627 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 2 7627 - 1485601 2 chr1 2 7627 - 3096343 0 chr1 9817571 9824274 + 4778032 df2 Chromosome Start End Strand Distance 0 chr1 2 7627 - 1485601 1 chr1 2 7627 - 3096343 2 chr1 9817571 9824274 + 4778032 Actual Chromosome Start End Strand Distance 0 chr1 2 7627 - 1485601 1 chr1 2 7627 - 3096343 2 chr1 9817571 9824274 + 4778032 Expected Chromosome Start End Strand Distance 0 chr1 2 7627 - 1485601 1 chr1 2 7627 - 3096343 2 chr1 9817571 9824274 + 4778032 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjmu4lg_l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjmu4lg_l/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 7627 - 1485601 1 chr1 2 7627 - 3096343 2 chr1 9817571 9824274 + 4778032 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9817571 | 9824274 | a | 0 | ... | | chr1 | 2 | 7627 | a | 0 | ... | | chr1 | 2 | 7627 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 2 7627 - 1485601 2 chr1 2 7627 - 3096343 0 chr1 9817571 9824274 + 4778032 df2 Chromosome Start End Strand Distance 0 chr1 2 7627 - 1485601 1 chr1 2 7627 - 3096343 2 chr1 9817571 9824274 + 4778032 Actual Chromosome Start End Strand Distance 0 chr1 2 7627 - 1485601 1 chr1 2 7627 - 3096343 2 chr1 9817571 9824274 + 4778032 Expected Chromosome Start End Strand Distance 0 chr1 2 7627 - 1485601 1 chr1 2 7627 - 3096343 2 chr1 9817571 9824274 + 4778032 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3b4vqx5f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3b4vqx5f/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 7627 - 0 1 chr1 2 7627 - 1 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 7627 | a | 0 | ... | | chr1 | 2 | 7627 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 7627 - 0 1 chr1 2 7627 - 1 df2 Chromosome Start End Strand Distance 0 chr1 2 7627 - 0 1 chr1 2 7627 - 1 Actual Chromosome Start End Strand Distance 0 chr1 2 7627 - 0 1 chr1 2 7627 - 1 Expected Chromosome Start End Strand Distance 0 chr1 2 7627 - 0 1 chr1 2 7627 - 1 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi0t0l2rl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi0t0l2rl/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpac5iafk9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpac5iafk9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 2 3 - 1 2 chr1 9817571 9817572 - 9817568 3 chr1 9817571 9817572 - 9817570 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 2 3 - 1 2 chr1 9817571 9817572 - 9817568 3 chr1 9817571 9817572 - 9817570 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=3, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyqmojpfg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyqmojpfg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 2 3 - 1 2 chr1 9817571 9817572 - 9817568 3 chr1 9817571 9817572 - 9817570 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 2 3 - 1 2 chr1 9817571 9817572 - 9817568 3 chr1 9817571 9817572 - 9817570 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=3, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo7gkrsjh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo7gkrsjh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp35gijs3s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp35gijs3s/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 7127322 7128750 - 412323 1 chr1 7127322 7128750 - 1765596 2 chr1 7611802 7611803 - 896803 3 chr1 7611802 7611803 - 1282543 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7611802 | 7611803 | a | 0 | ... | | chr1 | 7611802 | 7611803 | a | 0 | ... | | chr1 | 7127322 | 7128750 | a | 0 | ... | | chr1 | 7127322 | 7128750 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 7127322 7128750 - 412323 3 chr1 7127322 7128750 - 1765596 0 chr1 7611802 7611803 - 896803 1 chr1 7611802 7611803 - 1282543 df2 Chromosome Start End Strand Distance 0 chr1 7127322 7128750 - 412323 1 chr1 7127322 7128750 - 1765596 2 chr1 7611802 7611803 - 896803 3 chr1 7611802 7611803 - 1282543 Actual Chromosome Start End Strand Distance 0 chr1 7127322 7128750 - 412323 1 chr1 7127322 7128750 - 1765596 2 chr1 7611802 7611803 - 896803 3 chr1 7611802 7611803 - 1282543 Expected Chromosome Start End Strand Distance 0 chr1 7127322 7128750 - 412323 1 chr1 7127322 7128750 - 1765596 2 chr1 7611802 7611803 - 896803 3 chr1 7611802 7611803 - 1282543 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp95ic57gz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp95ic57gz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd8gf0msq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd8gf0msq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfggbuqf8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfggbuqf8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnm2pa3b3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnm2pa3b3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4wpibfti/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4wpibfti/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2wye6gsq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2wye6gsq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3382990 3389695 - 308347 1 chr1 3382990 3389695 - 748817 2 chr1 3451451 3451821 + 813187 3 chr1 3451451 3451821 + 2004949 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3451451 | 3451821 | a | 0 | ... | | chr1 | 3451451 | 3451821 | a | 0 | ... | | chr1 | 3382990 | 3389695 | a | 0 | ... | | chr1 | 3382990 | 3389695 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 3382990 3389695 - 308347 3 chr1 3382990 3389695 - 748817 0 chr1 3451451 3451821 + 813187 1 chr1 3451451 3451821 + 2004949 df2 Chromosome Start End Strand Distance 0 chr1 3382990 3389695 - 308347 1 chr1 3382990 3389695 - 748817 2 chr1 3451451 3451821 + 813187 3 chr1 3451451 3451821 + 2004949 Actual Chromosome Start End Strand Distance 0 chr1 3382990 3389695 - 308347 1 chr1 3382990 3389695 - 748817 2 chr1 3451451 3451821 + 813187 3 chr1 3451451 3451821 + 2004949 Expected Chromosome Start End Strand Distance 0 chr1 3382990 3389695 - 308347 1 chr1 3382990 3389695 - 748817 2 chr1 3451451 3451821 + 813187 3 chr1 3451451 3451821 + 2004949 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp85uyvcxj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp85uyvcxj/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3382990 3389695 - 750553 1 chr1 3451451 3451821 + 246221 2 chr1 3451451 3451821 + 817278 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3451451 | 3451821 | a | 0 | ... | | chr1 | 3451451 | 3451821 | a | 0 | ... | | chr1 | 3382990 | 3389695 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 3382990 3389695 - 750553 0 chr1 3451451 3451821 + 246221 1 chr1 3451451 3451821 + 817278 df2 Chromosome Start End Strand Distance 0 chr1 3382990 3389695 - 750553 1 chr1 3451451 3451821 + 246221 2 chr1 3451451 3451821 + 817278 Actual Chromosome Start End Strand Distance 0 chr1 3382990 3389695 - 750553 1 chr1 3451451 3451821 + 246221 2 chr1 3451451 3451821 + 817278 Expected Chromosome Start End Strand Distance 0 chr1 3382990 3389695 - 750553 1 chr1 3451451 3451821 + 246221 2 chr1 3451451 3451821 + 817278 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzs7zyi7p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzs7zyi7p/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3382990 3382991 - 750553 1 chr1 3451451 3451452 + 246590 2 chr1 3451451 3451452 + 817278 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3451451 | 3451452 | a | 0 | ... | | chr1 | 3451451 | 3451452 | a | 0 | ... | | chr1 | 3382990 | 3382991 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 3382990 3382991 - 750553 0 chr1 3451451 3451452 + 246590 1 chr1 3451451 3451452 + 817278 df2 Chromosome Start End Strand Distance 0 chr1 3382990 3382991 - 750553 1 chr1 3451451 3451452 + 246590 2 chr1 3451451 3451452 + 817278 Actual Chromosome Start End Strand Distance 0 chr1 3382990 3382991 - 750553 1 chr1 3451451 3451452 + 246590 2 chr1 3451451 3451452 + 817278 Expected Chromosome Start End Strand Distance 0 chr1 3382990 3382991 - 750553 1 chr1 3451451 3451452 + 246590 2 chr1 3451451 3451452 + 817278 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpja0yvx9n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpja0yvx9n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbzbqobad/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbzbqobad/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3382990 3382991 - 0 1 chr13 1 2 - 0 2 chr15 1 2 - 0 3 chr3 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3382990 | 3382991 | a | 0 | ... | | chr3 | 1 | 2 | a | 0 | ... | | chr13 | 1 | 2 | a | 0 | ... | | chr15 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr3 1 2 - 0 2 chr13 1 2 - 0 3 chr15 1 2 - 0 0 chr1 3382990 3382991 - 0 df2 Chromosome Start End Strand Distance 1 chr13 1 2 - 0 2 chr15 1 2 - 0 3 chr3 1 2 - 0 0 chr1 3382990 3382991 - 0 Actual Chromosome Start End Strand Distance 0 chr1 3382990 3382991 - 0 1 chr13 1 2 - 0 2 chr15 1 2 - 0 3 chr3 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 3382990 3382991 - 0 1 chr13 1 2 - 0 2 chr15 1 2 - 0 3 chr3 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp41ltafri/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp41ltafri/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3382990 3382991 - 3382989 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3382990 | 3382991 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3382990 3382991 - 3382989 df2 Chromosome Start End Strand Distance 0 chr1 3382990 3382991 - 3382989 Actual Chromosome Start End Strand Distance 0 chr1 3382990 3382991 - 3382989 Expected Chromosome Start End Strand Distance 0 chr1 3382990 3382991 - 3382989 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmps4yqp5he/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps4yqp5he/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp24zpnvjd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp24zpnvjd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpopbhurna/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpopbhurna/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjk9oboor/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjk9oboor/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj5es1_6x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj5es1_6x/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcxdcls_r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcxdcls_r/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp47ng0kvw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp47ng0kvw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmph6dvzc_z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph6dvzc_z/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5206237 5211676 - 3826624 1 chr1 5206237 5211676 - 5197070 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5206237 | 5211676 | a | 0 | ... | | chr1 | 5206237 | 5211676 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 5206237 5211676 - 3826624 1 chr1 5206237 5211676 - 5197070 df2 Chromosome Start End Strand Distance 0 chr1 5206237 5211676 - 3826624 1 chr1 5206237 5211676 - 5197070 Actual Chromosome Start End Strand Distance 0 chr1 5206237 5211676 - 3826624 1 chr1 5206237 5211676 - 5197070 Expected Chromosome Start End Strand Distance 0 chr1 5206237 5211676 - 3826624 1 chr1 5206237 5211676 - 5197070 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjf3pr01y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjf3pr01y/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5206237 5211676 - 3826624 1 chr1 5206237 5211676 - 5197070 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5206237 | 5211676 | a | 0 | ... | | chr1 | 5206237 | 5211676 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 5206237 5211676 - 3826624 1 chr1 5206237 5211676 - 5197070 df2 Chromosome Start End Strand Distance 0 chr1 5206237 5211676 - 3826624 1 chr1 5206237 5211676 - 5197070 Actual Chromosome Start End Strand Distance 0 chr1 5206237 5211676 - 3826624 1 chr1 5206237 5211676 - 5197070 Expected Chromosome Start End Strand Distance 0 chr1 5206237 5211676 - 3826624 1 chr1 5206237 5211676 - 5197070 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5m7yakfc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5m7yakfc/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5206237 5211676 - 5197071 1 chr1 5206237 5211676 - 5201159 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5206237 | 5211676 | a | 0 | ... | | chr1 | 5206237 | 5211676 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 5206237 5211676 - 5197071 1 chr1 5206237 5211676 - 5201159 df2 Chromosome Start End Strand Distance 0 chr1 5206237 5211676 - 5197071 1 chr1 5206237 5211676 - 5201159 Actual Chromosome Start End Strand Distance 0 chr1 5206237 5211676 - 5197071 1 chr1 5206237 5211676 - 5201159 Expected Chromosome Start End Strand Distance 0 chr1 5206237 5211676 - 5197071 1 chr1 5206237 5211676 - 5201159 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoxhivthy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoxhivthy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvlakun3e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvlakun3e/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz0_flsan/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz0_flsan/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn873fpuo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn873fpuo/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmph7ej8mat/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph7ej8mat/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3147670 3149623 - 5869902 1 chr1 5500403 5504123 + 2169030 2 chr1 5500403 5504123 + 2257083 4 chr8 5225682 5230766 + 5112585 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5500403 | 5504123 | a | 0 | ... | | chr1 | 5500403 | 5504123 | a | 0 | ... | | chr1 | 3147670 | 3149623 | a | 0 | ... | | chr8 | 5225682 | 5230766 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 3147670 3149623 - 5869902 3 chr8 5225682 5230766 + 5112585 0 chr1 5500403 5504123 + 2169030 1 chr1 5500403 5504123 + 2257083 df2 Chromosome Start End Strand Distance 0 chr1 3147670 3149623 - 5869902 4 chr8 5225682 5230766 + 5112585 1 chr1 5500403 5504123 + 2169030 2 chr1 5500403 5504123 + 2257083 Actual Chromosome Start End Strand Distance 0 chr1 3147670 3149623 - 5869902 1 chr1 5500403 5504123 + 2169030 2 chr1 5500403 5504123 + 2257083 3 chr8 5225682 5230766 + 5112585 Expected Chromosome Start End Strand Distance 0 chr1 3147670 3149623 - 5869902 1 chr1 5500403 5504123 + 2169030 2 chr1 5500403 5504123 + 2257083 3 chr8 5225682 5230766 + 5112585 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmps6123rzd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps6123rzd/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3147670 3149623 - 3147669 1 chr1 5500403 5504123 + 5500402 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5500403 | 5504123 | a | 0 | ... | | chr1 | 3147670 | 3149623 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3147670 3149623 - 3147669 0 chr1 5500403 5504123 + 5500402 df2 Chromosome Start End Strand Distance 0 chr1 3147670 3149623 - 3147669 1 chr1 5500403 5504123 + 5500402 Actual Chromosome Start End Strand Distance 0 chr1 3147670 3149623 - 3147669 1 chr1 5500403 5504123 + 5500402 Expected Chromosome Start End Strand Distance 0 chr1 3147670 3149623 - 3147669 1 chr1 5500403 5504123 + 5500402 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfi2h59qm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfi2h59qm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr1 1 2 - 0 8 chr5 1 2 + 0 9 chrM 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr1 1 2 - 0 8 chr5 1 2 + 0 9 chrM 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr1 1 2 - 0 8 chr5 1 2 + 0 9 chrM 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr1 1 2 - 0 8 chr5 1 2 + 0 9 chrM 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr1 1 2 - 0 8 chr5 1 2 + 0 9 chrM 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp143499w5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp143499w5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr1 1 2 - 0 8 chr5 1 2 + 0 9 chrM 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr5 1 2 + 0 8 chrM 1 2 - 0 df2 Chromosome Start End Strand Distance 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr1 1 2 - 0 8 chr5 1 2 + 0 9 chrM 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr5 1 2 + 0 8 chrM 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr5 1 2 + 0 8 chrM 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=9, step=1) index equal [ True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmfp3kc0e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmfp3kc0e/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr1 1 2 - 0 8 chr5 1 2 + 0 9 chrM 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr5 1 2 + 0 8 chrM 1 2 - 0 df2 Chromosome Start End Strand Distance 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr1 1 2 - 0 8 chr5 1 2 + 0 9 chrM 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr5 1 2 + 0 8 chrM 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr5 1 2 + 0 8 chrM 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=9, step=1) index equal [ True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbhp0cyzp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbhp0cyzp/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcup3actc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcup3actc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg771gtpu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg771gtpu/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 7054129 7058124 - 3326443 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7054129 | 7058124 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 7054129 7058124 - 3326443 df2 Chromosome Start End Strand Distance 1 chr1 7054129 7058124 - 3326443 Actual Chromosome Start End Strand Distance 0 chr1 7054129 7058124 - 3326443 Expected Chromosome Start End Strand Distance 0 chr1 7054129 7058124 - 3326443 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcqqpdcq1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcqqpdcq1/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 7054129 7058124 - 3326443 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7054129 | 7058124 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 7054129 7058124 - 3326443 df2 Chromosome Start End Strand Distance 1 chr1 7054129 7058124 - 3326443 Actual Chromosome Start End Strand Distance 0 chr1 7054129 7058124 - 3326443 Expected Chromosome Start End Strand Distance 0 chr1 7054129 7058124 - 3326443 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpntynl6wa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpntynl6wa/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1835411 1836770 - 1882242 1 chr1 7054129 7058124 - 3326443 2 chr1 7672002 7676605 - 3944316 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7054129 | 7058124 | a | 0 | ... | | chr1 | 1835411 | 1836770 | a | 0 | ... | | chr1 | 7672002 | 7676605 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1835411 1836770 - 1882242 0 chr1 7054129 7058124 - 3326443 2 chr1 7672002 7676605 - 3944316 df2 Chromosome Start End Strand Distance 0 chr1 1835411 1836770 - 1882242 1 chr1 7054129 7058124 - 3326443 2 chr1 7672002 7676605 - 3944316 Actual Chromosome Start End Strand Distance 0 chr1 1835411 1836770 - 1882242 1 chr1 7054129 7058124 - 3326443 2 chr1 7672002 7676605 - 3944316 Expected Chromosome Start End Strand Distance 0 chr1 1835411 1836770 - 1882242 1 chr1 7054129 7058124 - 3326443 2 chr1 7672002 7676605 - 3944316 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmptlvem388/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptlvem388/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbezm3_x0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbezm3_x0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpghxss0sl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpghxss0sl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6bashcjt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6bashcjt/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmptc3id7le/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptc3id7le/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 10000000 10004461 + 9719948 1 chr1 10000000 10006452 + 9719948 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 10000000 | 10006452 | a | 0 | ... | | chr1 | 10000000 | 10004461 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 10000000 10004461 + 9719948 0 chr1 10000000 10006452 + 9719948 df2 Chromosome Start End Strand Distance 0 chr1 10000000 10004461 + 9719948 1 chr1 10000000 10006452 + 9719948 Actual Chromosome Start End Strand Distance 0 chr1 10000000 10004461 + 9719948 1 chr1 10000000 10006452 + 9719948 Expected Chromosome Start End Strand Distance 0 chr1 10000000 10004461 + 9719948 1 chr1 10000000 10006452 + 9719948 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqmj7w41m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqmj7w41m/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 10000000 10004461 + 9999997 1 chr1 10000000 10006452 + 9999997 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 10000000 | 10006452 | a | 0 | ... | | chr1 | 10000000 | 10004461 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 10000000 10004461 + 9999997 0 chr1 10000000 10006452 + 9999997 df2 Chromosome Start End Strand Distance 0 chr1 10000000 10004461 + 9999997 1 chr1 10000000 10006452 + 9999997 Actual Chromosome Start End Strand Distance 0 chr1 10000000 10004461 + 9999997 1 chr1 10000000 10006452 + 9999997 Expected Chromosome Start End Strand Distance 0 chr1 10000000 10004461 + 9999997 1 chr1 10000000 10006452 + 9999997 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr08ytg55/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr08ytg55/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 10000000 10004461 + 9999986 1 chr1 10000000 10006452 + 9999986 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 10000000 | 10006452 | a | 0 | ... | | chr1 | 10000000 | 10004461 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 10000000 10004461 + 9999986 0 chr1 10000000 10006452 + 9999986 df2 Chromosome Start End Strand Distance 0 chr1 10000000 10004461 + 9999986 1 chr1 10000000 10006452 + 9999986 Actual Chromosome Start End Strand Distance 0 chr1 10000000 10004461 + 9999986 1 chr1 10000000 10006452 + 9999986 Expected Chromosome Start End Strand Distance 0 chr1 10000000 10004461 + 9999986 1 chr1 10000000 10006452 + 9999986 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj7yoaj65/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj7yoaj65/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmptcvt6nao/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptcvt6nao/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp28vokuio/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp28vokuio/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 2 chr2 10000000 10000001 - 9999999 3 chr2 10000000 10000001 - 9999999 4 chr2 10000000 10000001 - 9999999 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 10000000 | 10000001 | a | 0 | ... | | chr2 | 10000000 | 10000001 | a | 0 | ... | | chr2 | 10000000 | 10000001 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 10000000 10000001 - 9999999 1 chr2 10000000 10000001 - 9999999 2 chr2 10000000 10000001 - 9999999 df2 Chromosome Start End Strand Distance 2 chr2 10000000 10000001 - 9999999 3 chr2 10000000 10000001 - 9999999 4 chr2 10000000 10000001 - 9999999 Actual Chromosome Start End Strand Distance 0 chr2 10000000 10000001 - 9999999 1 chr2 10000000 10000001 - 9999999 2 chr2 10000000 10000001 - 9999999 Expected Chromosome Start End Strand Distance 0 chr2 10000000 10000001 - 9999999 1 chr2 10000000 10000001 - 9999999 2 chr2 10000000 10000001 - 9999999 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7pk4i0io/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7pk4i0io/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4721652 4731485 - 220633 1 chr1 4721652 4731485 - 751690 2 chr1 5540792 5544662 - 52852 3 chr1 5540792 5544662 - 584844 4 chr1 9913174 9914097 - 880273 5 chr1 9913174 9914097 - 937078 6 chr1 9951606 9957069 - 918705 7 chr1 9951606 9957069 - 975510 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4721652 | 4731485 | a | 0 | ... | | chr1 | 4721652 | 4731485 | a | 0 | ... | | chr1 | 5540792 | 5544662 | a | 0 | ... | | chr1 | 5540792 | 5544662 | a | 0 | ... | | chr1 | 9913174 | 9914097 | a | 0 | ... | | chr1 | 9913174 | 9914097 | a | 0 | ... | | chr1 | 9951606 | 9957069 | a | 0 | ... | | chr1 | 9951606 | 9957069 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 4721652 4731485 - 220633 1 chr1 4721652 4731485 - 751690 2 chr1 5540792 5544662 - 52852 3 chr1 5540792 5544662 - 584844 4 chr1 9913174 9914097 - 880273 5 chr1 9913174 9914097 - 937078 6 chr1 9951606 9957069 - 918705 7 chr1 9951606 9957069 - 975510 df2 Chromosome Start End Strand Distance 0 chr1 4721652 4731485 - 220633 1 chr1 4721652 4731485 - 751690 2 chr1 5540792 5544662 - 52852 3 chr1 5540792 5544662 - 584844 4 chr1 9913174 9914097 - 880273 5 chr1 9913174 9914097 - 937078 6 chr1 9951606 9957069 - 918705 7 chr1 9951606 9957069 - 975510 Actual Chromosome Start End Strand Distance 0 chr1 4721652 4731485 - 220633 1 chr1 4721652 4731485 - 751690 2 chr1 5540792 5544662 - 52852 3 chr1 5540792 5544662 - 584844 4 chr1 9913174 9914097 - 880273 5 chr1 9913174 9914097 - 937078 6 chr1 9951606 9957069 - 918705 7 chr1 9951606 9957069 - 975510 Expected Chromosome Start End Strand Distance 0 chr1 4721652 4731485 - 220633 1 chr1 4721652 4731485 - 751690 2 chr1 5540792 5544662 - 52852 3 chr1 5540792 5544662 - 584844 4 chr1 9913174 9914097 - 880273 5 chr1 9913174 9914097 - 937078 6 chr1 9951606 9957069 - 918705 7 chr1 9951606 9957069 - 975510 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf17f8uyi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf17f8uyi/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3346815 3347942 - 492886 1 chr1 3346815 3347942 - 1604176 2 chr1 4721652 4731485 - 220633 3 chr1 4721652 4731485 - 751690 4 chr1 5540792 5544662 - 52852 5 chr1 5540792 5544662 - 584844 6 chr1 6465103 6473502 - 216725 7 chr1 6465103 6473502 - 977163 8 chr1 9913174 9914097 - 880273 9 chr1 9913174 9914097 - 937078 10 chr1 9951606 9957069 - 918705 11 chr1 9951606 9957069 - 975510 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6465103 | 6473502 | a | 0 | ... | | chr1 | 6465103 | 6473502 | a | 0 | ... | | chr1 | 3346815 | 3347942 | a | 0 | ... | | chr1 | 3346815 | 3347942 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 9913174 | 9914097 | a | 0 | ... | | chr1 | 9913174 | 9914097 | a | 0 | ... | | chr1 | 9951606 | 9957069 | a | 0 | ... | | chr1 | 9951606 | 9957069 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 3346815 3347942 - 492886 3 chr1 3346815 3347942 - 1604176 4 chr1 4721652 4731485 - 220633 5 chr1 4721652 4731485 - 751690 6 chr1 5540792 5544662 - 52852 7 chr1 5540792 5544662 - 584844 0 chr1 6465103 6473502 - 216725 1 chr1 6465103 6473502 - 977163 8 chr1 9913174 9914097 - 880273 9 chr1 9913174 9914097 - 937078 10 chr1 9951606 9957069 - 918705 11 chr1 9951606 9957069 - 975510 df2 Chromosome Start End Strand Distance 0 chr1 3346815 3347942 - 492886 1 chr1 3346815 3347942 - 1604176 2 chr1 4721652 4731485 - 220633 3 chr1 4721652 4731485 - 751690 4 chr1 5540792 5544662 - 52852 5 chr1 5540792 5544662 - 584844 6 chr1 6465103 6473502 - 216725 7 chr1 6465103 6473502 - 977163 8 chr1 9913174 9914097 - 880273 9 chr1 9913174 9914097 - 937078 10 chr1 9951606 9957069 - 918705 11 chr1 9951606 9957069 - 975510 Actual Chromosome Start End Strand Distance 0 chr1 3346815 3347942 - 492886 1 chr1 3346815 3347942 - 1604176 2 chr1 4721652 4731485 - 220633 3 chr1 4721652 4731485 - 751690 4 chr1 5540792 5544662 - 52852 5 chr1 5540792 5544662 - 584844 6 chr1 6465103 6473502 - 216725 7 chr1 6465103 6473502 - 977163 8 chr1 9913174 9914097 - 880273 9 chr1 9913174 9914097 - 937078 10 chr1 9951606 9957069 - 918705 11 chr1 9951606 9957069 - 975510 Expected Chromosome Start End Strand Distance 0 chr1 3346815 3347942 - 492886 1 chr1 3346815 3347942 - 1604176 2 chr1 4721652 4731485 - 220633 3 chr1 4721652 4731485 - 751690 4 chr1 5540792 5544662 - 52852 5 chr1 5540792 5544662 - 584844 6 chr1 6465103 6473502 - 216725 7 chr1 6465103 6473502 - 977163 8 chr1 9913174 9914097 - 880273 9 chr1 9913174 9914097 - 937078 10 chr1 9951606 9957069 - 918705 11 chr1 9951606 9957069 - 975510 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkczzb1fz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkczzb1fz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 69045 79045 + 0 1 chr1 2847731 2853930 - 0 2 chr1 2847731 2853930 - 2098188 3 chr1 4952117 4955949 - 0 4 chr1 4952117 4955949 - 527226 5 chr1 5483174 5487941 - 0 6 chr1 5483174 5487941 - 527226 7 chr1 6239262 6248379 - 0 8 chr1 6239262 6248379 - 751322 9 chr1 8976033 8976097 - 0 10 chr1 8976033 8976097 - 51646 11 chr1 9027742 9032902 - 0 12 chr1 9027742 9032902 - 51646 13 chr20 7940768 7949485 - 0 14 chr21 2453576 2456760 - 0 15 chr9 7642321 7650652 - 0 16 chrX 9999999 10000359 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 69045 | 79045 | a | 0 | ... | | chr1 | 2847731 | 2853930 | a | 0 | ... | | chr1 | 2847731 | 2853930 | a | 0 | ... | | chr1 | 4952117 | 4955949 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr9 | 7642321 | 7650652 | a | 0 | ... | | chr20 | 7940768 | 7949485 | a | 0 | ... | | chr21 | 2453576 | 2456760 | a | 0 | ... | | chrX | 9999999 | 10000359 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 17 rows and 12 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 69045 79045 + 0 15 chr21 2453576 2456760 - 0 1 chr1 2847731 2853930 - 0 2 chr1 2847731 2853930 - 2098188 3 chr1 4952117 4955949 - 0 4 chr1 4952117 4955949 - 527226 11 chr1 5483174 5487941 - 0 12 chr1 5483174 5487941 - 527226 7 chr1 6239262 6248379 - 0 8 chr1 6239262 6248379 - 751322 13 chr9 7642321 7650652 - 0 14 chr20 7940768 7949485 - 0 9 chr1 8976033 8976097 - 0 10 chr1 8976033 8976097 - 51646 5 chr1 9027742 9032902 - 0 6 chr1 9027742 9032902 - 51646 16 chrX 9999999 10000359 + 0 df2 Chromosome Start End Strand Distance 0 chr1 69045 79045 + 0 14 chr21 2453576 2456760 - 0 1 chr1 2847731 2853930 - 0 2 chr1 2847731 2853930 - 2098188 3 chr1 4952117 4955949 - 0 4 chr1 4952117 4955949 - 527226 5 chr1 5483174 5487941 - 0 6 chr1 5483174 5487941 - 527226 7 chr1 6239262 6248379 - 0 8 chr1 6239262 6248379 - 751322 15 chr9 7642321 7650652 - 0 13 chr20 7940768 7949485 - 0 9 chr1 8976033 8976097 - 0 10 chr1 8976033 8976097 - 51646 11 chr1 9027742 9032902 - 0 12 chr1 9027742 9032902 - 51646 16 chrX 9999999 10000359 + 0 Actual Chromosome Start End Strand Distance 0 chr1 69045 79045 + 0 1 chr1 2847731 2853930 - 0 2 chr1 2847731 2853930 - 2098188 3 chr1 4952117 4955949 - 0 4 chr1 4952117 4955949 - 527226 5 chr1 5483174 5487941 - 0 6 chr1 5483174 5487941 - 527226 7 chr1 6239262 6248379 - 0 8 chr1 6239262 6248379 - 751322 9 chr1 8976033 8976097 - 0 10 chr1 8976033 8976097 - 51646 11 chr1 9027742 9032902 - 0 12 chr1 9027742 9032902 - 51646 13 chr20 7940768 7949485 - 0 14 chr21 2453576 2456760 - 0 15 chr9 7642321 7650652 - 0 16 chrX 9999999 10000359 + 0 Expected Chromosome Start End Strand Distance 0 chr1 69045 79045 + 0 1 chr1 2847731 2853930 - 0 2 chr1 2847731 2853930 - 2098188 3 chr1 4952117 4955949 - 0 4 chr1 4952117 4955949 - 527226 5 chr1 5483174 5487941 - 0 6 chr1 5483174 5487941 - 527226 7 chr1 6239262 6248379 - 0 8 chr1 6239262 6248379 - 751322 9 chr1 8976033 8976097 - 0 10 chr1 8976033 8976097 - 51646 11 chr1 9027742 9032902 - 0 12 chr1 9027742 9032902 - 51646 13 chr20 7940768 7949485 - 0 14 chr21 2453576 2456760 - 0 15 chr9 7642321 7650652 - 0 16 chrX 9999999 10000359 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=17, step=1) Expected index RangeIndex(start=0, stop=17, step=1) index equal [ True True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwftsn9dd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwftsn9dd/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 69045 79045 + 49046 1 chr1 2847731 2853930 - 2829498 2 chr1 2847731 2853930 - 2835334 3 chr1 4952117 4955949 - 4933884 4 chr1 4952117 4955949 - 4939720 5 chr1 5483174 5487941 - 5464941 6 chr1 5483174 5487941 - 5470777 7 chr1 6239262 6248379 - 6221029 8 chr1 6239262 6248379 - 6226865 9 chr1 8976033 8976097 - 8957800 10 chr1 8976033 8976097 - 8963636 11 chr1 9027742 9032902 - 9009509 12 chr1 9027742 9032902 - 9015345 13 chr20 7940768 7949485 - 7923335 14 chr21 2453576 2456760 - 2447209 15 chr9 7642321 7650652 - 7625660 16 chrX 9999999 10000359 + 9999280 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 69045 | 79045 | a | 0 | ... | | chr1 | 2847731 | 2853930 | a | 0 | ... | | chr1 | 2847731 | 2853930 | a | 0 | ... | | chr1 | 4952117 | 4955949 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr9 | 7642321 | 7650652 | a | 0 | ... | | chr20 | 7940768 | 7949485 | a | 0 | ... | | chr21 | 2453576 | 2456760 | a | 0 | ... | | chrX | 9999999 | 10000359 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 17 rows and 12 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 69045 79045 + 49046 15 chr21 2453576 2456760 - 2447209 1 chr1 2847731 2853930 - 2829498 2 chr1 2847731 2853930 - 2835334 3 chr1 4952117 4955949 - 4933884 4 chr1 4952117 4955949 - 4939720 11 chr1 5483174 5487941 - 5464941 12 chr1 5483174 5487941 - 5470777 7 chr1 6239262 6248379 - 6221029 8 chr1 6239262 6248379 - 6226865 13 chr9 7642321 7650652 - 7625660 14 chr20 7940768 7949485 - 7923335 9 chr1 8976033 8976097 - 8957800 10 chr1 8976033 8976097 - 8963636 5 chr1 9027742 9032902 - 9009509 6 chr1 9027742 9032902 - 9015345 16 chrX 9999999 10000359 + 9999280 df2 Chromosome Start End Strand Distance 0 chr1 69045 79045 + 49046 14 chr21 2453576 2456760 - 2447209 1 chr1 2847731 2853930 - 2829498 2 chr1 2847731 2853930 - 2835334 3 chr1 4952117 4955949 - 4933884 4 chr1 4952117 4955949 - 4939720 5 chr1 5483174 5487941 - 5464941 6 chr1 5483174 5487941 - 5470777 7 chr1 6239262 6248379 - 6221029 8 chr1 6239262 6248379 - 6226865 15 chr9 7642321 7650652 - 7625660 13 chr20 7940768 7949485 - 7923335 9 chr1 8976033 8976097 - 8957800 10 chr1 8976033 8976097 - 8963636 11 chr1 9027742 9032902 - 9009509 12 chr1 9027742 9032902 - 9015345 16 chrX 9999999 10000359 + 9999280 Actual Chromosome Start End Strand Distance 0 chr1 69045 79045 + 49046 1 chr1 2847731 2853930 - 2829498 2 chr1 2847731 2853930 - 2835334 3 chr1 4952117 4955949 - 4933884 4 chr1 4952117 4955949 - 4939720 5 chr1 5483174 5487941 - 5464941 6 chr1 5483174 5487941 - 5470777 7 chr1 6239262 6248379 - 6221029 8 chr1 6239262 6248379 - 6226865 9 chr1 8976033 8976097 - 8957800 10 chr1 8976033 8976097 - 8963636 11 chr1 9027742 9032902 - 9009509 12 chr1 9027742 9032902 - 9015345 13 chr20 7940768 7949485 - 7923335 14 chr21 2453576 2456760 - 2447209 15 chr9 7642321 7650652 - 7625660 16 chrX 9999999 10000359 + 9999280 Expected Chromosome Start End Strand Distance 0 chr1 69045 79045 + 49046 1 chr1 2847731 2853930 - 2829498 2 chr1 2847731 2853930 - 2835334 3 chr1 4952117 4955949 - 4933884 4 chr1 4952117 4955949 - 4939720 5 chr1 5483174 5487941 - 5464941 6 chr1 5483174 5487941 - 5470777 7 chr1 6239262 6248379 - 6221029 8 chr1 6239262 6248379 - 6226865 9 chr1 8976033 8976097 - 8957800 10 chr1 8976033 8976097 - 8963636 11 chr1 9027742 9032902 - 9009509 12 chr1 9027742 9032902 - 9015345 13 chr20 7940768 7949485 - 7923335 14 chr21 2453576 2456760 - 2447209 15 chr9 7642321 7650652 - 7625660 16 chrX 9999999 10000359 + 9999280 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=17, step=1) Expected index RangeIndex(start=0, stop=17, step=1) index equal [ True True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaupqn0kn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaupqn0kn/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 69045 79045 + 62487 1 chr1 69045 79045 + 68685 2 chr1 2847731 2853930 - 2847366 3 chr1 2847731 2853930 - 2847371 4 chr1 4952117 4955949 - 4951752 5 chr1 4952117 4955949 - 4951757 6 chr1 5483174 5487941 - 5482809 7 chr1 5483174 5487941 - 5482814 8 chr1 6239262 6248379 - 6238897 9 chr1 6239262 6248379 - 6238902 10 chr1 8976033 8976097 - 8975668 11 chr1 8976033 8976097 - 8975673 12 chr1 9027742 9032902 - 9027377 13 chr1 9027742 9032902 - 9027382 14 chr20 7940768 7949485 - 7940408 16 chr9 7642321 7650652 - 7633631 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 69045 | 79045 | a | 0 | ... | | chr1 | 69045 | 79045 | a | 0 | ... | | chr1 | 2847731 | 2853930 | a | 0 | ... | | chr1 | 2847731 | 2853930 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 8976033 | 8976097 | a | 0 | ... | | chr1 | 8976033 | 8976097 | a | 0 | ... | | chr1 | 5483174 | 5487941 | a | 0 | ... | | chr1 | 5483174 | 5487941 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 16 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 69045 79045 + 62487 1 chr1 69045 79045 + 68685 2 chr1 2847731 2853930 - 2847366 3 chr1 2847731 2853930 - 2847371 4 chr1 4952117 4955949 - 4951752 5 chr1 4952117 4955949 - 4951757 12 chr1 5483174 5487941 - 5482809 13 chr1 5483174 5487941 - 5482814 8 chr1 6239262 6248379 - 6238897 9 chr1 6239262 6248379 - 6238902 14 chr9 7642321 7650652 - 7633631 15 chr20 7940768 7949485 - 7940408 10 chr1 8976033 8976097 - 8975668 11 chr1 8976033 8976097 - 8975673 6 chr1 9027742 9032902 - 9027377 7 chr1 9027742 9032902 - 9027382 df2 Chromosome Start End Strand Distance 0 chr1 69045 79045 + 62487 1 chr1 69045 79045 + 68685 2 chr1 2847731 2853930 - 2847366 3 chr1 2847731 2853930 - 2847371 4 chr1 4952117 4955949 - 4951752 5 chr1 4952117 4955949 - 4951757 6 chr1 5483174 5487941 - 5482809 7 chr1 5483174 5487941 - 5482814 8 chr1 6239262 6248379 - 6238897 9 chr1 6239262 6248379 - 6238902 16 chr9 7642321 7650652 - 7633631 14 chr20 7940768 7949485 - 7940408 10 chr1 8976033 8976097 - 8975668 11 chr1 8976033 8976097 - 8975673 12 chr1 9027742 9032902 - 9027377 13 chr1 9027742 9032902 - 9027382 Actual Chromosome Start End Strand Distance 0 chr1 69045 79045 + 62487 1 chr1 69045 79045 + 68685 2 chr1 2847731 2853930 - 2847366 3 chr1 2847731 2853930 - 2847371 4 chr1 4952117 4955949 - 4951752 5 chr1 4952117 4955949 - 4951757 6 chr1 5483174 5487941 - 5482809 7 chr1 5483174 5487941 - 5482814 8 chr1 6239262 6248379 - 6238897 9 chr1 6239262 6248379 - 6238902 10 chr1 8976033 8976097 - 8975668 11 chr1 8976033 8976097 - 8975673 12 chr1 9027742 9032902 - 9027377 13 chr1 9027742 9032902 - 9027382 14 chr20 7940768 7949485 - 7940408 15 chr9 7642321 7650652 - 7633631 Expected Chromosome Start End Strand Distance 0 chr1 69045 79045 + 62487 1 chr1 69045 79045 + 68685 2 chr1 2847731 2853930 - 2847366 3 chr1 2847731 2853930 - 2847371 4 chr1 4952117 4955949 - 4951752 5 chr1 4952117 4955949 - 4951757 6 chr1 5483174 5487941 - 5482809 7 chr1 5483174 5487941 - 5482814 8 chr1 6239262 6248379 - 6238897 9 chr1 6239262 6248379 - 6238902 10 chr1 8976033 8976097 - 8975668 11 chr1 8976033 8976097 - 8975673 12 chr1 9027742 9032902 - 9027377 13 chr1 9027742 9032902 - 9027382 14 chr20 7940768 7949485 - 7940408 15 chr9 7642321 7650652 - 7633631 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=16, step=1) Expected index RangeIndex(start=0, stop=16, step=1) index equal [ True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7vtqsw4z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7vtqsw4z/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 361 + 0 1 chr1 1 361 + 5839 2 chr1 1 361 + 0 3 chr1 1 361 + 5839 4 chr1 1 361 + 0 5 chr1 1 361 + 5839 6 chr1 1 361 - 0 7 chr1 1 361 - 0 8 chr1 6 366 - 0 9 chr1 6199 6559 + 0 10 chr1 6199 6559 + 5839 11 chr20 1 361 - 0 12 chr21 1 361 + 0 13 chr9 8331 8691 - 0 14 chrX 1 361 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6199 | 6559 | a | 0 | ... | | chr1 | 6199 | 6559 | a | 0 | ... | | chr1 | 1 | 361 | a | 0 | ... | | chr1 | 1 | 361 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr9 | 8331 | 8691 | a | 0 | ... | | chr20 | 1 | 361 | a | 0 | ... | | chr21 | 1 | 361 | a | 0 | ... | | chrX | 1 | 361 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 15 rows and 12 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1 361 + 0 4 chr1 1 361 + 0 6 chr1 1 361 + 0 9 chr1 1 361 - 0 10 chr1 1 361 - 0 12 chr20 1 361 - 0 13 chr21 1 361 + 0 14 chrX 1 361 - 0 3 chr1 1 361 + 5839 5 chr1 1 361 + 5839 7 chr1 1 361 + 5839 8 chr1 6 366 - 0 0 chr1 6199 6559 + 0 1 chr1 6199 6559 + 5839 11 chr9 8331 8691 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 361 + 0 2 chr1 1 361 + 0 4 chr1 1 361 + 0 6 chr1 1 361 - 0 7 chr1 1 361 - 0 11 chr20 1 361 - 0 12 chr21 1 361 + 0 14 chrX 1 361 - 0 1 chr1 1 361 + 5839 3 chr1 1 361 + 5839 5 chr1 1 361 + 5839 8 chr1 6 366 - 0 9 chr1 6199 6559 + 0 10 chr1 6199 6559 + 5839 13 chr9 8331 8691 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 361 + 0 1 chr1 1 361 + 0 2 chr1 1 361 + 0 3 chr1 1 361 + 5839 4 chr1 1 361 + 5839 5 chr1 1 361 + 5839 6 chr1 1 361 - 0 7 chr1 1 361 - 0 8 chr1 6 366 - 0 9 chr1 6199 6559 + 0 10 chr1 6199 6559 + 5839 11 chr20 1 361 - 0 12 chr21 1 361 + 0 13 chr9 8331 8691 - 0 14 chrX 1 361 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 361 + 0 1 chr1 1 361 + 0 2 chr1 1 361 + 0 3 chr1 1 361 + 5839 4 chr1 1 361 + 5839 5 chr1 1 361 + 5839 6 chr1 1 361 - 0 7 chr1 1 361 - 0 8 chr1 6 366 - 0 9 chr1 6199 6559 + 0 10 chr1 6199 6559 + 5839 11 chr20 1 361 - 0 12 chr21 1 361 + 0 13 chr9 8331 8691 - 0 14 chrX 1 361 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=15, step=1) Expected index RangeIndex(start=0, stop=15, step=1) index equal [ True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7uikw7xa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7uikw7xa/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 361 + 0 1 chr1 1 361 + 5839 2 chr1 1 361 + 0 3 chr1 1 361 + 5839 4 chr1 1 361 + 0 5 chr1 1 361 + 5839 6 chr1 1 361 - 0 7 chr1 1 361 - 0 8 chr1 6 366 + 0 9 chr1 6 366 + 5834 10 chr1 6199 6559 + 0 11 chr1 6199 6559 + 5839 12 chr20 1 361 - 0 13 chr21 1 361 + 0 14 chr9 8331 8691 - 0 15 chrX 1 361 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6 | 366 | a | 0 | ... | | chr1 | 6 | 366 | a | 0 | ... | | chr1 | 6199 | 6559 | a | 0 | ... | | chr1 | 6199 | 6559 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr9 | 8331 | 8691 | a | 0 | ... | | chr20 | 1 | 361 | a | 0 | ... | | chr21 | 1 | 361 | a | 0 | ... | | chrX | 1 | 361 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 16 rows and 12 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 1 361 + 0 6 chr1 1 361 + 0 8 chr1 1 361 + 0 10 chr1 1 361 - 0 11 chr1 1 361 - 0 13 chr20 1 361 - 0 14 chr21 1 361 + 0 15 chrX 1 361 - 0 5 chr1 1 361 + 5839 7 chr1 1 361 + 5839 9 chr1 1 361 + 5839 0 chr1 6 366 + 0 1 chr1 6 366 + 5834 2 chr1 6199 6559 + 0 3 chr1 6199 6559 + 5839 12 chr9 8331 8691 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 361 + 0 2 chr1 1 361 + 0 4 chr1 1 361 + 0 6 chr1 1 361 - 0 7 chr1 1 361 - 0 12 chr20 1 361 - 0 13 chr21 1 361 + 0 15 chrX 1 361 - 0 1 chr1 1 361 + 5839 3 chr1 1 361 + 5839 5 chr1 1 361 + 5839 8 chr1 6 366 + 0 9 chr1 6 366 + 5834 10 chr1 6199 6559 + 0 11 chr1 6199 6559 + 5839 14 chr9 8331 8691 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 361 + 0 1 chr1 1 361 + 0 2 chr1 1 361 + 0 3 chr1 1 361 + 5839 4 chr1 1 361 + 5839 5 chr1 1 361 + 5839 6 chr1 1 361 - 0 7 chr1 1 361 - 0 8 chr1 6 366 + 0 9 chr1 6 366 + 5834 10 chr1 6199 6559 + 0 11 chr1 6199 6559 + 5839 12 chr20 1 361 - 0 13 chr21 1 361 + 0 14 chr9 8331 8691 - 0 15 chrX 1 361 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 361 + 0 1 chr1 1 361 + 0 2 chr1 1 361 + 0 3 chr1 1 361 + 5839 4 chr1 1 361 + 5839 5 chr1 1 361 + 5839 6 chr1 1 361 - 0 7 chr1 1 361 - 0 8 chr1 6 366 + 0 9 chr1 6 366 + 5834 10 chr1 6199 6559 + 0 11 chr1 6199 6559 + 5839 12 chr20 1 361 - 0 13 chr21 1 361 + 0 14 chr9 8331 8691 - 0 15 chrX 1 361 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=16, step=1) Expected index RangeIndex(start=0, stop=16, step=1) index equal [ True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9pwngp_3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9pwngp_3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 2 chr1 5194220 5203517 + 1374968 3 chr1 5277154 5277794 + 1300691 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5194220 | 5203517 | a | 0 | ... | | chr1 | 5277154 | 5277794 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 5194220 5203517 + 1374968 1 chr1 5277154 5277794 + 1300691 df2 Chromosome Start End Strand Distance 2 chr1 5194220 5203517 + 1374968 3 chr1 5277154 5277794 + 1300691 Actual Chromosome Start End Strand Distance 0 chr1 5194220 5203517 + 1374968 1 chr1 5277154 5277794 + 1300691 Expected Chromosome Start End Strand Distance 0 chr1 5194220 5203517 + 1374968 1 chr1 5277154 5277794 + 1300691 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsq7toxm1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsq7toxm1/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 2 chr1 5194220 5203517 + 5187500 3 chr1 5277154 5277794 + 5270434 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5194220 | 5203517 | a | 0 | ... | | chr1 | 5277154 | 5277794 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 5194220 5203517 + 5187500 1 chr1 5277154 5277794 + 5270434 df2 Chromosome Start End Strand Distance 2 chr1 5194220 5203517 + 5187500 3 chr1 5277154 5277794 + 5270434 Actual Chromosome Start End Strand Distance 0 chr1 5194220 5203517 + 5187500 1 chr1 5277154 5277794 + 5270434 Expected Chromosome Start End Strand Distance 0 chr1 5194220 5203517 + 5187500 1 chr1 5277154 5277794 + 5270434 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn5e3hbza/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn5e3hbza/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3168 - 0 1 chr1 5194220 5194982 - 5184416 2 chr1 5194220 5203517 + 5187422 3 chr1 5194220 5203517 + 5187500 4 chr1 5277154 5277794 + 5270356 5 chr1 5277154 5277794 + 5270434 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5194220 | 5203517 | a | 0 | ... | | chr1 | 5194220 | 5203517 | a | 0 | ... | | chr1 | 5277154 | 5277794 | a | 0 | ... | | chr1 | 5277154 | 5277794 | a | 0 | ... | | chr1 | 5194220 | 5194982 | a | 0 | ... | | chr1 | 1 | 3168 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 5 chr1 1 3168 - 0 4 chr1 5194220 5194982 - 5184416 0 chr1 5194220 5203517 + 5187422 1 chr1 5194220 5203517 + 5187500 2 chr1 5277154 5277794 + 5270356 3 chr1 5277154 5277794 + 5270434 df2 Chromosome Start End Strand Distance 0 chr1 1 3168 - 0 1 chr1 5194220 5194982 - 5184416 2 chr1 5194220 5203517 + 5187422 3 chr1 5194220 5203517 + 5187500 4 chr1 5277154 5277794 + 5270356 5 chr1 5277154 5277794 + 5270434 Actual Chromosome Start End Strand Distance 0 chr1 1 3168 - 0 1 chr1 5194220 5194982 - 5184416 2 chr1 5194220 5203517 + 5187422 3 chr1 5194220 5203517 + 5187500 4 chr1 5277154 5277794 + 5270356 5 chr1 5277154 5277794 + 5270434 Expected Chromosome Start End Strand Distance 0 chr1 1 3168 - 0 1 chr1 5194220 5194982 - 5184416 2 chr1 5194220 5203517 + 5187422 3 chr1 5194220 5203517 + 5187500 4 chr1 5277154 5277794 + 5270356 5 chr1 5277154 5277794 + 5270434 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmppdtn8q75/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppdtn8q75/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3168 - 0 1 chr1 5194220 5194982 - 5184416 2 chr1 5277154 5277794 + 5270356 3 chr1 5277154 5277794 + 5270434 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5277154 | 5277794 | a | 0 | ... | | chr1 | 5277154 | 5277794 | a | 0 | ... | | chr1 | 5194220 | 5194982 | a | 0 | ... | | chr1 | 1 | 3168 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 1 3168 - 0 2 chr1 5194220 5194982 - 5184416 0 chr1 5277154 5277794 + 5270356 1 chr1 5277154 5277794 + 5270434 df2 Chromosome Start End Strand Distance 0 chr1 1 3168 - 0 1 chr1 5194220 5194982 - 5184416 2 chr1 5277154 5277794 + 5270356 3 chr1 5277154 5277794 + 5270434 Actual Chromosome Start End Strand Distance 0 chr1 1 3168 - 0 1 chr1 5194220 5194982 - 5184416 2 chr1 5277154 5277794 + 5270356 3 chr1 5277154 5277794 + 5270434 Expected Chromosome Start End Strand Distance 0 chr1 1 3168 - 0 1 chr1 5194220 5194982 - 5184416 2 chr1 5277154 5277794 + 5270356 3 chr1 5277154 5277794 + 5270434 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyseh8kze/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyseh8kze/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3168 - 0 1 chr1 5194220 5194982 - 5184416 2 chr1 5277154 5277794 + 5270356 3 chr1 5277154 5277794 + 5270434 4 chr1 9801347 9804732 + 9794549 5 chr1 9801347 9804732 + 9794627 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5277154 | 5277794 | a | 0 | ... | | chr1 | 5277154 | 5277794 | a | 0 | ... | | chr1 | 9801347 | 9804732 | a | 0 | ... | | chr1 | 9801347 | 9804732 | a | 0 | ... | | chr1 | 5194220 | 5194982 | a | 0 | ... | | chr1 | 1 | 3168 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 5 chr1 1 3168 - 0 4 chr1 5194220 5194982 - 5184416 0 chr1 5277154 5277794 + 5270356 1 chr1 5277154 5277794 + 5270434 2 chr1 9801347 9804732 + 9794549 3 chr1 9801347 9804732 + 9794627 df2 Chromosome Start End Strand Distance 0 chr1 1 3168 - 0 1 chr1 5194220 5194982 - 5184416 2 chr1 5277154 5277794 + 5270356 3 chr1 5277154 5277794 + 5270434 4 chr1 9801347 9804732 + 9794549 5 chr1 9801347 9804732 + 9794627 Actual Chromosome Start End Strand Distance 0 chr1 1 3168 - 0 1 chr1 5194220 5194982 - 5184416 2 chr1 5277154 5277794 + 5270356 3 chr1 5277154 5277794 + 5270434 4 chr1 9801347 9804732 + 9794549 5 chr1 9801347 9804732 + 9794627 Expected Chromosome Start End Strand Distance 0 chr1 1 3168 - 0 1 chr1 5194220 5194982 - 5184416 2 chr1 5277154 5277794 + 5270356 3 chr1 5277154 5277794 + 5270434 4 chr1 9801347 9804732 + 9794549 5 chr1 9801347 9804732 + 9794627 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp70fxugh6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp70fxugh6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 5194220 5203517 - 5184416 2 chr1 5277154 5277794 + 5270356 3 chr1 5277154 5277794 + 5270434 4 chr1 9801347 9804732 + 9794549 5 chr1 9801347 9804732 + 9794627 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5277154 | 5277794 | a | 0 | ... | | chr1 | 5277154 | 5277794 | a | 0 | ... | | chr1 | 9801347 | 9804732 | a | 0 | ... | | chr1 | 9801347 | 9804732 | a | 0 | ... | | chr1 | 5194220 | 5203517 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 5 chr1 1 2 - 0 4 chr1 5194220 5203517 - 5184416 0 chr1 5277154 5277794 + 5270356 1 chr1 5277154 5277794 + 5270434 2 chr1 9801347 9804732 + 9794549 3 chr1 9801347 9804732 + 9794627 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 5194220 5203517 - 5184416 2 chr1 5277154 5277794 + 5270356 3 chr1 5277154 5277794 + 5270434 4 chr1 9801347 9804732 + 9794549 5 chr1 9801347 9804732 + 9794627 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 5194220 5203517 - 5184416 2 chr1 5277154 5277794 + 5270356 3 chr1 5277154 5277794 + 5270434 4 chr1 9801347 9804732 + 9794549 5 chr1 9801347 9804732 + 9794627 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 5194220 5203517 - 5184416 2 chr1 5277154 5277794 + 5270356 3 chr1 5277154 5277794 + 5270434 4 chr1 9801347 9804732 + 9794549 5 chr1 9801347 9804732 + 9794627 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8qsm097i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8qsm097i/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 5194219 2 chr1 5194220 5203517 - 0 3 chr1 5194220 5203517 - 5194219 4 chr1 5277154 5277794 + 0 5 chr1 5277154 5277794 + 4523554 6 chr1 9801347 9804732 + 0 7 chr1 9801347 9804732 + 4523554 8 chr19 5194220 5194221 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5277154 | 5277794 | a | 0 | ... | | chr1 | 5277154 | 5277794 | a | 0 | ... | | chr1 | 9801347 | 9804732 | a | 0 | ... | | chr1 | 9801347 | 9804732 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 5194220 | 5203517 | a | 0 | ... | | chr1 | 5194220 | 5203517 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr1 1 2 - 0 7 chr1 1 2 - 5194219 8 chr19 5194220 5194221 + 0 4 chr1 5194220 5203517 - 0 5 chr1 5194220 5203517 - 5194219 0 chr1 5277154 5277794 + 0 1 chr1 5277154 5277794 + 4523554 2 chr1 9801347 9804732 + 0 3 chr1 9801347 9804732 + 4523554 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 5194219 8 chr19 5194220 5194221 + 0 2 chr1 5194220 5203517 - 0 3 chr1 5194220 5203517 - 5194219 4 chr1 5277154 5277794 + 0 5 chr1 5277154 5277794 + 4523554 6 chr1 9801347 9804732 + 0 7 chr1 9801347 9804732 + 4523554 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 5194219 2 chr1 5194220 5203517 - 0 3 chr1 5194220 5203517 - 5194219 4 chr1 5277154 5277794 + 0 5 chr1 5277154 5277794 + 4523554 6 chr1 9801347 9804732 + 0 7 chr1 9801347 9804732 + 4523554 8 chr19 5194220 5194221 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 5194219 2 chr1 5194220 5203517 - 0 3 chr1 5194220 5203517 - 5194219 4 chr1 5277154 5277794 + 0 5 chr1 5277154 5277794 + 4523554 6 chr1 9801347 9804732 + 0 7 chr1 9801347 9804732 + 4523554 8 chr19 5194220 5194221 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=9, step=1) index equal [ True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_fat4jyj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_fat4jyj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmppk6g0720/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppk6g0720/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq8j5a35k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq8j5a35k/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 3204 2 chr1 3205 3206 - 0 3 chr1 3205 3206 - 3204 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3205 | 3206 | a | 0 | ... | | chr1 | 3205 | 3206 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1 2 - 0 3 chr1 1 2 - 3204 0 chr1 3205 3206 - 0 1 chr1 3205 3206 - 3204 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 3204 2 chr1 3205 3206 - 0 3 chr1 3205 3206 - 3204 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 3204 2 chr1 3205 3206 - 0 3 chr1 3205 3206 - 3204 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 3204 2 chr1 3205 3206 - 0 3 chr1 3205 3206 - 3204 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy5d1bato/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy5d1bato/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 3205 3206 - 3204 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3205 | 3206 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1 2 - 0 0 chr1 3205 3206 - 3204 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 3205 3206 - 3204 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 3205 3206 - 3204 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 3205 3206 - 3204 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvkuz2cz9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvkuz2cz9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 3205 3206 - 3204 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3205 | 3206 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1 2 - 0 0 chr1 3205 3206 - 3204 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 3205 3206 - 3204 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 3205 3206 - 3204 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 3205 3206 - 3204 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoljuy7wv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoljuy7wv/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3206 - 0 1 chr1 3205 3206 - 3204 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3205 | 3206 | a | 0 | ... | | chr1 | 1 | 3206 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1 3206 - 0 0 chr1 3205 3206 - 3204 df2 Chromosome Start End Strand Distance 0 chr1 1 3206 - 0 1 chr1 3205 3206 - 3204 Actual Chromosome Start End Strand Distance 0 chr1 1 3206 - 0 1 chr1 3205 3206 - 3204 Expected Chromosome Start End Strand Distance 0 chr1 1 3206 - 0 1 chr1 3205 3206 - 3204 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb0ntdmst/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb0ntdmst/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3206 - 0 1 chr1 3205 3206 - 3204 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3205 | 3206 | a | 0 | ... | | chr1 | 1 | 3206 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1 3206 - 0 0 chr1 3205 3206 - 3204 df2 Chromosome Start End Strand Distance 0 chr1 1 3206 - 0 1 chr1 3205 3206 - 3204 Actual Chromosome Start End Strand Distance 0 chr1 1 3206 - 0 1 chr1 3205 3206 - 3204 Expected Chromosome Start End Strand Distance 0 chr1 1 3206 - 0 1 chr1 3205 3206 - 3204 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp50yjqkup/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp50yjqkup/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 574785 577296 + 439275 2 chr1 574785 578739 + 437832 3 chr1 574785 579102 + 437469 4 chr1 574785 581320 + 435251 6 chr1 574785 583741 + 432830 7 chr1 574785 584412 + 432159 9 chr1 7503242 7506301 + 6477988 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 574785 | 578739 | a | 0 | ... | | chr1 | 574785 | 577296 | a | 0 | ... | | chr1 | 574785 | 584412 | a | 0 | ... | | chr1 | 574785 | 581320 | a | 0 | ... | | chr1 | 7503242 | 7506301 | a | 0 | ... | | chr1 | 574785 | 583741 | a | 0 | ... | | chr1 | 574785 | 579102 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 574785 577296 + 439275 0 chr1 574785 578739 + 437832 6 chr1 574785 579102 + 437469 3 chr1 574785 581320 + 435251 5 chr1 574785 583741 + 432830 2 chr1 574785 584412 + 432159 4 chr1 7503242 7506301 + 6477988 df2 Chromosome Start End Strand Distance 1 chr1 574785 577296 + 439275 2 chr1 574785 578739 + 437832 3 chr1 574785 579102 + 437469 4 chr1 574785 581320 + 435251 6 chr1 574785 583741 + 432830 7 chr1 574785 584412 + 432159 9 chr1 7503242 7506301 + 6477988 Actual Chromosome Start End Strand Distance 0 chr1 574785 577296 + 439275 1 chr1 574785 578739 + 437832 2 chr1 574785 579102 + 437469 3 chr1 574785 581320 + 435251 4 chr1 574785 583741 + 432830 5 chr1 574785 584412 + 432159 6 chr1 7503242 7506301 + 6477988 Expected Chromosome Start End Strand Distance 0 chr1 574785 577296 + 439275 1 chr1 574785 578739 + 437832 2 chr1 574785 579102 + 437469 3 chr1 574785 581320 + 435251 4 chr1 574785 583741 + 432830 5 chr1 574785 584412 + 432159 6 chr1 7503242 7506301 + 6477988 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4f0zieni/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4f0zieni/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 574785 577296 + 439275 2 chr1 574785 578739 + 437832 3 chr1 574785 579102 + 437469 4 chr1 574785 581320 + 435251 6 chr1 574785 583741 + 432830 7 chr1 574785 584412 + 432159 9 chr1 7503242 7506301 + 6477988 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 574785 | 578739 | a | 0 | ... | | chr1 | 574785 | 577296 | a | 0 | ... | | chr1 | 574785 | 584412 | a | 0 | ... | | chr1 | 574785 | 581320 | a | 0 | ... | | chr1 | 7503242 | 7506301 | a | 0 | ... | | chr1 | 574785 | 583741 | a | 0 | ... | | chr1 | 574785 | 579102 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 574785 577296 + 439275 0 chr1 574785 578739 + 437832 6 chr1 574785 579102 + 437469 3 chr1 574785 581320 + 435251 5 chr1 574785 583741 + 432830 2 chr1 574785 584412 + 432159 4 chr1 7503242 7506301 + 6477988 df2 Chromosome Start End Strand Distance 1 chr1 574785 577296 + 439275 2 chr1 574785 578739 + 437832 3 chr1 574785 579102 + 437469 4 chr1 574785 581320 + 435251 6 chr1 574785 583741 + 432830 7 chr1 574785 584412 + 432159 9 chr1 7503242 7506301 + 6477988 Actual Chromosome Start End Strand Distance 0 chr1 574785 577296 + 439275 1 chr1 574785 578739 + 437832 2 chr1 574785 579102 + 437469 3 chr1 574785 581320 + 435251 4 chr1 574785 583741 + 432830 5 chr1 574785 584412 + 432159 6 chr1 7503242 7506301 + 6477988 Expected Chromosome Start End Strand Distance 0 chr1 574785 577296 + 439275 1 chr1 574785 578739 + 437832 2 chr1 574785 579102 + 437469 3 chr1 574785 581320 + 435251 4 chr1 574785 583741 + 432830 5 chr1 574785 584412 + 432159 6 chr1 7503242 7506301 + 6477988 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6hm_lqi6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6hm_lqi6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 574785 575784 - 0 1 chr1 574785 575784 - 970860 2 chr1 574785 577296 + 0 3 chr1 574785 577296 + 6925947 4 chr1 574785 578739 + 0 5 chr1 574785 578739 + 6924504 6 chr1 574785 579102 + 0 7 chr1 574785 579102 + 6924141 8 chr1 574785 581320 + 0 9 chr1 574785 581320 + 6921923 10 chr1 574785 582151 - 0 11 chr1 574785 582151 - 964493 12 chr1 574785 583741 + 0 13 chr1 574785 583741 + 6919502 14 chr1 574785 584412 + 0 15 chr1 574785 584412 + 6918831 16 chr1 1546643 1552246 - 0 17 chr1 1546643 1552246 - 964493 18 chr1 7503242 7506301 + 0 19 chr1 7503242 7506301 + 6918831 20 chr1 9341124 9347793 - 0 21 chr1 9341124 9347793 - 7788879 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 574785 | 578739 | a | 0 | ... | | chr1 | 574785 | 578739 | a | 0 | ... | | chr1 | 574785 | 577296 | a | 0 | ... | | chr1 | 574785 | 577296 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 574785 | 582151 | a | 0 | ... | | chr1 | 574785 | 582151 | a | 0 | ... | | chr1 | 574785 | 575784 | a | 0 | ... | | chr1 | 574785 | 575784 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 22 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 20 chr1 574785 575784 - 0 21 chr1 574785 575784 - 970860 2 chr1 574785 577296 + 0 3 chr1 574785 577296 + 6925947 0 chr1 574785 578739 + 0 1 chr1 574785 578739 + 6924504 12 chr1 574785 579102 + 0 13 chr1 574785 579102 + 6924141 6 chr1 574785 581320 + 0 7 chr1 574785 581320 + 6921923 18 chr1 574785 582151 - 0 19 chr1 574785 582151 - 964493 10 chr1 574785 583741 + 0 11 chr1 574785 583741 + 6919502 4 chr1 574785 584412 + 0 5 chr1 574785 584412 + 6918831 14 chr1 1546643 1552246 - 0 15 chr1 1546643 1552246 - 964493 8 chr1 7503242 7506301 + 0 9 chr1 7503242 7506301 + 6918831 16 chr1 9341124 9347793 - 0 17 chr1 9341124 9347793 - 7788879 df2 Chromosome Start End Strand Distance 0 chr1 574785 575784 - 0 1 chr1 574785 575784 - 970860 2 chr1 574785 577296 + 0 3 chr1 574785 577296 + 6925947 4 chr1 574785 578739 + 0 5 chr1 574785 578739 + 6924504 6 chr1 574785 579102 + 0 7 chr1 574785 579102 + 6924141 8 chr1 574785 581320 + 0 9 chr1 574785 581320 + 6921923 10 chr1 574785 582151 - 0 11 chr1 574785 582151 - 964493 12 chr1 574785 583741 + 0 13 chr1 574785 583741 + 6919502 14 chr1 574785 584412 + 0 15 chr1 574785 584412 + 6918831 16 chr1 1546643 1552246 - 0 17 chr1 1546643 1552246 - 964493 18 chr1 7503242 7506301 + 0 19 chr1 7503242 7506301 + 6918831 20 chr1 9341124 9347793 - 0 21 chr1 9341124 9347793 - 7788879 Actual Chromosome Start End Strand Distance 0 chr1 574785 575784 - 0 1 chr1 574785 575784 - 970860 2 chr1 574785 577296 + 0 3 chr1 574785 577296 + 6925947 4 chr1 574785 578739 + 0 5 chr1 574785 578739 + 6924504 6 chr1 574785 579102 + 0 7 chr1 574785 579102 + 6924141 8 chr1 574785 581320 + 0 9 chr1 574785 581320 + 6921923 10 chr1 574785 582151 - 0 11 chr1 574785 582151 - 964493 12 chr1 574785 583741 + 0 13 chr1 574785 583741 + 6919502 14 chr1 574785 584412 + 0 15 chr1 574785 584412 + 6918831 16 chr1 1546643 1552246 - 0 17 chr1 1546643 1552246 - 964493 18 chr1 7503242 7506301 + 0 19 chr1 7503242 7506301 + 6918831 20 chr1 9341124 9347793 - 0 21 chr1 9341124 9347793 - 7788879 Expected Chromosome Start End Strand Distance 0 chr1 574785 575784 - 0 1 chr1 574785 575784 - 970860 2 chr1 574785 577296 + 0 3 chr1 574785 577296 + 6925947 4 chr1 574785 578739 + 0 5 chr1 574785 578739 + 6924504 6 chr1 574785 579102 + 0 7 chr1 574785 579102 + 6924141 8 chr1 574785 581320 + 0 9 chr1 574785 581320 + 6921923 10 chr1 574785 582151 - 0 11 chr1 574785 582151 - 964493 12 chr1 574785 583741 + 0 13 chr1 574785 583741 + 6919502 14 chr1 574785 584412 + 0 15 chr1 574785 584412 + 6918831 16 chr1 1546643 1552246 - 0 17 chr1 1546643 1552246 - 964493 18 chr1 7503242 7506301 + 0 19 chr1 7503242 7506301 + 6918831 20 chr1 9341124 9347793 - 0 21 chr1 9341124 9347793 - 7788879 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=22, step=1) Expected index RangeIndex(start=0, stop=22, step=1) index equal [ True True True True True True True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsk2xmvh5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsk2xmvh5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 574785 575784 - 0 1 chr1 574785 575784 - 8765341 2 chr1 574785 577296 + 0 3 chr1 574785 577296 + 6925947 4 chr1 574785 578739 + 0 5 chr1 574785 578739 + 6924504 6 chr1 574785 579102 + 0 7 chr1 574785 579102 + 6924141 8 chr1 574785 581320 + 0 9 chr1 574785 581320 + 6921923 10 chr1 574785 582151 - 0 11 chr1 574785 582151 - 8758974 12 chr1 574785 583741 + 0 13 chr1 574785 583741 + 6919502 14 chr1 574785 584412 + 0 15 chr1 574785 584412 + 6918831 16 chr1 1546643 1552246 - 964493 17 chr1 1546643 1552246 - 970860 18 chr1 7503242 7506301 + 0 19 chr1 7503242 7506301 + 6918831 20 chr1 9341124 9347793 - 0 21 chr1 9341124 9347793 - 8758974 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 574785 | 578739 | a | 0 | ... | | chr1 | 574785 | 578739 | a | 0 | ... | | chr1 | 574785 | 577296 | a | 0 | ... | | chr1 | 574785 | 577296 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 574785 | 582151 | a | 0 | ... | | chr1 | 574785 | 582151 | a | 0 | ... | | chr1 | 574785 | 575784 | a | 0 | ... | | chr1 | 574785 | 575784 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 22 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 20 chr1 574785 575784 - 0 21 chr1 574785 575784 - 8765341 2 chr1 574785 577296 + 0 3 chr1 574785 577296 + 6925947 0 chr1 574785 578739 + 0 1 chr1 574785 578739 + 6924504 12 chr1 574785 579102 + 0 13 chr1 574785 579102 + 6924141 6 chr1 574785 581320 + 0 7 chr1 574785 581320 + 6921923 18 chr1 574785 582151 - 0 19 chr1 574785 582151 - 8758974 10 chr1 574785 583741 + 0 11 chr1 574785 583741 + 6919502 4 chr1 574785 584412 + 0 5 chr1 574785 584412 + 6918831 14 chr1 1546643 1552246 - 964493 15 chr1 1546643 1552246 - 970860 8 chr1 7503242 7506301 + 0 9 chr1 7503242 7506301 + 6918831 16 chr1 9341124 9347793 - 0 17 chr1 9341124 9347793 - 8758974 df2 Chromosome Start End Strand Distance 0 chr1 574785 575784 - 0 1 chr1 574785 575784 - 8765341 2 chr1 574785 577296 + 0 3 chr1 574785 577296 + 6925947 4 chr1 574785 578739 + 0 5 chr1 574785 578739 + 6924504 6 chr1 574785 579102 + 0 7 chr1 574785 579102 + 6924141 8 chr1 574785 581320 + 0 9 chr1 574785 581320 + 6921923 10 chr1 574785 582151 - 0 11 chr1 574785 582151 - 8758974 12 chr1 574785 583741 + 0 13 chr1 574785 583741 + 6919502 14 chr1 574785 584412 + 0 15 chr1 574785 584412 + 6918831 16 chr1 1546643 1552246 - 964493 17 chr1 1546643 1552246 - 970860 18 chr1 7503242 7506301 + 0 19 chr1 7503242 7506301 + 6918831 20 chr1 9341124 9347793 - 0 21 chr1 9341124 9347793 - 8758974 Actual Chromosome Start End Strand Distance 0 chr1 574785 575784 - 0 1 chr1 574785 575784 - 8765341 2 chr1 574785 577296 + 0 3 chr1 574785 577296 + 6925947 4 chr1 574785 578739 + 0 5 chr1 574785 578739 + 6924504 6 chr1 574785 579102 + 0 7 chr1 574785 579102 + 6924141 8 chr1 574785 581320 + 0 9 chr1 574785 581320 + 6921923 10 chr1 574785 582151 - 0 11 chr1 574785 582151 - 8758974 12 chr1 574785 583741 + 0 13 chr1 574785 583741 + 6919502 14 chr1 574785 584412 + 0 15 chr1 574785 584412 + 6918831 16 chr1 1546643 1552246 - 964493 17 chr1 1546643 1552246 - 970860 18 chr1 7503242 7506301 + 0 19 chr1 7503242 7506301 + 6918831 20 chr1 9341124 9347793 - 0 21 chr1 9341124 9347793 - 8758974 Expected Chromosome Start End Strand Distance 0 chr1 574785 575784 - 0 1 chr1 574785 575784 - 8765341 2 chr1 574785 577296 + 0 3 chr1 574785 577296 + 6925947 4 chr1 574785 578739 + 0 5 chr1 574785 578739 + 6924504 6 chr1 574785 579102 + 0 7 chr1 574785 579102 + 6924141 8 chr1 574785 581320 + 0 9 chr1 574785 581320 + 6921923 10 chr1 574785 582151 - 0 11 chr1 574785 582151 - 8758974 12 chr1 574785 583741 + 0 13 chr1 574785 583741 + 6919502 14 chr1 574785 584412 + 0 15 chr1 574785 584412 + 6918831 16 chr1 1546643 1552246 - 964493 17 chr1 1546643 1552246 - 970860 18 chr1 7503242 7506301 + 0 19 chr1 7503242 7506301 + 6918831 20 chr1 9341124 9347793 - 0 21 chr1 9341124 9347793 - 8758974 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=22, step=1) Expected index RangeIndex(start=0, stop=22, step=1) index equal [ True True True True True True True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa7espd6f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa7espd6f/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 2 chr1 574785 574786 - 574784 3 chr1 574785 574786 - 574784 4 chr1 574785 574786 - 574784 5 chr1 574785 577296 - 574784 6 chr1 574785 581320 - 574784 7 chr1 1546643 1547642 - 1546642 9 chr1 9341124 9347793 - 9341123 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1546643 | 1547642 | a | 0 | ... | | chr1 | 574785 | 577296 | a | 0 | ... | | chr1 | 574785 | 574786 | a | 0 | ... | | chr1 | 9341124 | 9347793 | a | 0 | ... | | chr1 | 574785 | 581320 | a | 0 | ... | | chr1 | 574785 | 574786 | a | 0 | ... | | chr1 | 574785 | 574786 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 574785 574786 - 574784 5 chr1 574785 574786 - 574784 6 chr1 574785 574786 - 574784 1 chr1 574785 577296 - 574784 4 chr1 574785 581320 - 574784 0 chr1 1546643 1547642 - 1546642 3 chr1 9341124 9347793 - 9341123 df2 Chromosome Start End Strand Distance 2 chr1 574785 574786 - 574784 3 chr1 574785 574786 - 574784 4 chr1 574785 574786 - 574784 5 chr1 574785 577296 - 574784 6 chr1 574785 581320 - 574784 7 chr1 1546643 1547642 - 1546642 9 chr1 9341124 9347793 - 9341123 Actual Chromosome Start End Strand Distance 0 chr1 574785 574786 - 574784 1 chr1 574785 574786 - 574784 2 chr1 574785 574786 - 574784 3 chr1 574785 577296 - 574784 4 chr1 574785 581320 - 574784 5 chr1 1546643 1547642 - 1546642 6 chr1 9341124 9347793 - 9341123 Expected Chromosome Start End Strand Distance 0 chr1 574785 574786 - 574784 1 chr1 574785 574786 - 574784 2 chr1 574785 574786 - 574784 3 chr1 574785 577296 - 574784 4 chr1 574785 581320 - 574784 5 chr1 1546643 1547642 - 1546642 6 chr1 9341124 9347793 - 9341123 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0in9jod6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0in9jod6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 2 chr1 574785 574786 - 574784 3 chr1 574785 574786 - 574784 4 chr1 574785 574786 - 574784 5 chr1 574785 577296 - 574784 6 chr1 574785 581320 - 574784 7 chr1 1546643 1547642 - 1546642 9 chr1 9341124 9347793 - 9341123 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1546643 | 1547642 | a | 0 | ... | | chr1 | 574785 | 577296 | a | 0 | ... | | chr1 | 574785 | 574786 | a | 0 | ... | | chr1 | 9341124 | 9347793 | a | 0 | ... | | chr1 | 574785 | 581320 | a | 0 | ... | | chr1 | 574785 | 574786 | a | 0 | ... | | chr1 | 574785 | 574786 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 574785 574786 - 574784 5 chr1 574785 574786 - 574784 6 chr1 574785 574786 - 574784 1 chr1 574785 577296 - 574784 4 chr1 574785 581320 - 574784 0 chr1 1546643 1547642 - 1546642 3 chr1 9341124 9347793 - 9341123 df2 Chromosome Start End Strand Distance 2 chr1 574785 574786 - 574784 3 chr1 574785 574786 - 574784 4 chr1 574785 574786 - 574784 5 chr1 574785 577296 - 574784 6 chr1 574785 581320 - 574784 7 chr1 1546643 1547642 - 1546642 9 chr1 9341124 9347793 - 9341123 Actual Chromosome Start End Strand Distance 0 chr1 574785 574786 - 574784 1 chr1 574785 574786 - 574784 2 chr1 574785 574786 - 574784 3 chr1 574785 577296 - 574784 4 chr1 574785 581320 - 574784 5 chr1 1546643 1547642 - 1546642 6 chr1 9341124 9347793 - 9341123 Expected Chromosome Start End Strand Distance 0 chr1 574785 574786 - 574784 1 chr1 574785 574786 - 574784 2 chr1 574785 574786 - 574784 3 chr1 574785 577296 - 574784 4 chr1 574785 581320 - 574784 5 chr1 1546643 1547642 - 1546642 6 chr1 9341124 9347793 - 9341123 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2dkfsruu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2dkfsruu/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 2 chr1 574785 574786 - 574784 3 chr1 574785 574786 - 574784 4 chr1 574785 577296 - 574784 5 chr1 574785 581320 - 574784 6 chr1 1546643 1547642 - 1546642 8 chr1 9341124 9347793 - 9341123 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1546643 | 1547642 | a | 0 | ... | | chr1 | 574785 | 577296 | a | 0 | ... | | chr1 | 574785 | 574786 | a | 0 | ... | | chr1 | 9341124 | 9347793 | a | 0 | ... | | chr1 | 574785 | 581320 | a | 0 | ... | | chr1 | 574785 | 574786 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 574785 574786 - 574784 5 chr1 574785 574786 - 574784 1 chr1 574785 577296 - 574784 4 chr1 574785 581320 - 574784 0 chr1 1546643 1547642 - 1546642 3 chr1 9341124 9347793 - 9341123 df2 Chromosome Start End Strand Distance 2 chr1 574785 574786 - 574784 3 chr1 574785 574786 - 574784 4 chr1 574785 577296 - 574784 5 chr1 574785 581320 - 574784 6 chr1 1546643 1547642 - 1546642 8 chr1 9341124 9347793 - 9341123 Actual Chromosome Start End Strand Distance 0 chr1 574785 574786 - 574784 1 chr1 574785 574786 - 574784 2 chr1 574785 577296 - 574784 3 chr1 574785 581320 - 574784 4 chr1 1546643 1547642 - 1546642 5 chr1 9341124 9347793 - 9341123 Expected Chromosome Start End Strand Distance 0 chr1 574785 574786 - 574784 1 chr1 574785 574786 - 574784 2 chr1 574785 577296 - 574784 3 chr1 574785 581320 - 574784 4 chr1 1546643 1547642 - 1546642 5 chr1 9341124 9347793 - 9341123 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmphh_naohl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphh_naohl/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1246294 1249041 + 1146300 1 chr1 1246294 1249041 + 3392863 2 chr1 3330763 3334891 + 1307013 3 chr1 3330763 3334891 + 3230769 4 chr1 6018155 6027305 - 263065 5 chr1 6326324 6326770 - 571234 6 chr1 6854221 6861911 - 1099131 7 chr1 7199036 7202808 - 1443946 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3330763 | 3334891 | a | 0 | ... | | chr1 | 3330763 | 3334891 | a | 0 | ... | | chr1 | 1246294 | 1249041 | a | 0 | ... | | chr1 | 1246294 | 1249041 | a | 0 | ... | | chr1 | 7199036 | 7202808 | a | 0 | ... | | chr1 | 6018155 | 6027305 | a | 0 | ... | | chr1 | 6326324 | 6326770 | a | 0 | ... | | chr1 | 6854221 | 6861911 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1246294 1249041 + 1146300 3 chr1 1246294 1249041 + 3392863 0 chr1 3330763 3334891 + 1307013 1 chr1 3330763 3334891 + 3230769 5 chr1 6018155 6027305 - 263065 6 chr1 6326324 6326770 - 571234 7 chr1 6854221 6861911 - 1099131 4 chr1 7199036 7202808 - 1443946 df2 Chromosome Start End Strand Distance 0 chr1 1246294 1249041 + 1146300 1 chr1 1246294 1249041 + 3392863 2 chr1 3330763 3334891 + 1307013 3 chr1 3330763 3334891 + 3230769 4 chr1 6018155 6027305 - 263065 5 chr1 6326324 6326770 - 571234 6 chr1 6854221 6861911 - 1099131 7 chr1 7199036 7202808 - 1443946 Actual Chromosome Start End Strand Distance 0 chr1 1246294 1249041 + 1146300 1 chr1 1246294 1249041 + 3392863 2 chr1 3330763 3334891 + 1307013 3 chr1 3330763 3334891 + 3230769 4 chr1 6018155 6027305 - 263065 5 chr1 6326324 6326770 - 571234 6 chr1 6854221 6861911 - 1099131 7 chr1 7199036 7202808 - 1443946 Expected Chromosome Start End Strand Distance 0 chr1 1246294 1249041 + 1146300 1 chr1 1246294 1249041 + 3392863 2 chr1 3330763 3334891 + 1307013 3 chr1 3330763 3334891 + 3230769 4 chr1 6018155 6027305 - 263065 5 chr1 6326324 6326770 - 571234 6 chr1 6854221 6861911 - 1099131 7 chr1 7199036 7202808 - 1443946 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp01zu9oix/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp01zu9oix/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1246294 1249041 + 1246293 1 chr1 3330763 3334891 + 3330762 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3330763 | 3334891 | a | 0 | ... | | chr1 | 1246294 | 1249041 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1246294 1249041 + 1246293 0 chr1 3330763 3334891 + 3330762 df2 Chromosome Start End Strand Distance 0 chr1 1246294 1249041 + 1246293 1 chr1 3330763 3334891 + 3330762 Actual Chromosome Start End Strand Distance 0 chr1 1246294 1249041 + 1246293 1 chr1 3330763 3334891 + 3330762 Expected Chromosome Start End Strand Distance 0 chr1 1246294 1249041 + 1246293 1 chr1 3330763 3334891 + 3330762 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx9zqyhlk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx9zqyhlk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1246294 1249041 + 1246293 1 chr1 3330763 3334891 + 3330762 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3330763 | 3334891 | a | 0 | ... | | chr1 | 1246294 | 1249041 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1246294 1249041 + 1246293 0 chr1 3330763 3334891 + 3330762 df2 Chromosome Start End Strand Distance 0 chr1 1246294 1249041 + 1246293 1 chr1 3330763 3334891 + 3330762 Actual Chromosome Start End Strand Distance 0 chr1 1246294 1249041 + 1246293 1 chr1 3330763 3334891 + 3330762 Expected Chromosome Start End Strand Distance 0 chr1 1246294 1249041 + 1246293 1 chr1 3330763 3334891 + 3330762 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxv_dn_3y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxv_dn_3y/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1246294 1249041 + 1246293 1 chr1 3330763 3334891 + 3330762 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3330763 | 3334891 | a | 0 | ... | | chr1 | 1246294 | 1249041 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1246294 1249041 + 1246293 0 chr1 3330763 3334891 + 3330762 df2 Chromosome Start End Strand Distance 0 chr1 1246294 1249041 + 1246293 1 chr1 3330763 3334891 + 3330762 Actual Chromosome Start End Strand Distance 0 chr1 1246294 1249041 + 1246293 1 chr1 3330763 3334891 + 3330762 Expected Chromosome Start End Strand Distance 0 chr1 1246294 1249041 + 1246293 1 chr1 3330763 3334891 + 3330762 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbqnjl6wv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbqnjl6wv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz7c1f4r2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz7c1f4r2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 6 2567 + 0 1 chr1 6 3079 + 0 2 chr1 6 4820 + 0 3 chr1 6 4875 + 0 4 chr1 6 7 + 0 5 chr1 6 7131 + 0 6 chr1 6 8335 + 0 7 chr14 6 3744 + 0 8 chr14 6 7 + 0 9 chr21 6 8967 + 0 10 chr9 6 2173 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6 | 2567 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7131 | a | 0 | ... | | chr1 | 6 | 4820 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr9 | 6 | 2173 | a | 0 | ... | | chr14 | 6 | 3744 | a | 0 | ... | | chr14 | 6 | 7 | a | 0 | ... | | chr21 | 6 | 8967 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 11 rows and 12 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 6 7 + 0 9 chr14 6 7 + 0 7 chr9 6 2173 + 0 0 chr1 6 2567 + 0 6 chr1 6 3079 + 0 8 chr14 6 3744 + 0 3 chr1 6 4820 + 0 5 chr1 6 4875 + 0 2 chr1 6 7131 + 0 4 chr1 6 8335 + 0 10 chr21 6 8967 + 0 df2 Chromosome Start End Strand Distance 4 chr1 6 7 + 0 8 chr14 6 7 + 0 10 chr9 6 2173 + 0 0 chr1 6 2567 + 0 1 chr1 6 3079 + 0 7 chr14 6 3744 + 0 2 chr1 6 4820 + 0 3 chr1 6 4875 + 0 5 chr1 6 7131 + 0 6 chr1 6 8335 + 0 9 chr21 6 8967 + 0 Actual Chromosome Start End Strand Distance 0 chr1 6 7 + 0 1 chr1 6 2567 + 0 2 chr1 6 3079 + 0 3 chr1 6 4820 + 0 4 chr1 6 4875 + 0 5 chr1 6 7131 + 0 6 chr1 6 8335 + 0 7 chr14 6 7 + 0 8 chr14 6 3744 + 0 9 chr21 6 8967 + 0 10 chr9 6 2173 + 0 Expected Chromosome Start End Strand Distance 0 chr1 6 7 + 0 1 chr1 6 2567 + 0 2 chr1 6 3079 + 0 3 chr1 6 4820 + 0 4 chr1 6 4875 + 0 5 chr1 6 7131 + 0 6 chr1 6 8335 + 0 7 chr14 6 7 + 0 8 chr14 6 3744 + 0 9 chr21 6 8967 + 0 10 chr9 6 2173 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=11, step=1) Expected index RangeIndex(start=0, stop=11, step=1) index equal [ True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3hgz1l47/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3hgz1l47/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 6 2567 + 0 1 chr1 6 3079 + 0 2 chr1 6 4820 + 0 3 chr1 6 7 + 0 4 chr1 6 7 + 0 5 chr1 6 7131 + 0 6 chr1 6 8335 + 0 7 chr14 6 3744 + 0 8 chr14 6 7 + 0 9 chr21 6 8967 + 0 10 chr9 6 2173 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6 | 2567 | a | 0 | ... | | chr1 | 6 | 7 | a | 0 | ... | | chr1 | 6 | 7131 | a | 0 | ... | | chr1 | 6 | 4820 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr9 | 6 | 2173 | a | 0 | ... | | chr14 | 6 | 3744 | a | 0 | ... | | chr14 | 6 | 7 | a | 0 | ... | | chr21 | 6 | 8967 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 11 rows and 12 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 6 7 + 0 5 chr1 6 7 + 0 9 chr14 6 7 + 0 7 chr9 6 2173 + 0 0 chr1 6 2567 + 0 6 chr1 6 3079 + 0 8 chr14 6 3744 + 0 3 chr1 6 4820 + 0 2 chr1 6 7131 + 0 4 chr1 6 8335 + 0 10 chr21 6 8967 + 0 df2 Chromosome Start End Strand Distance 3 chr1 6 7 + 0 4 chr1 6 7 + 0 8 chr14 6 7 + 0 10 chr9 6 2173 + 0 0 chr1 6 2567 + 0 1 chr1 6 3079 + 0 7 chr14 6 3744 + 0 2 chr1 6 4820 + 0 5 chr1 6 7131 + 0 6 chr1 6 8335 + 0 9 chr21 6 8967 + 0 Actual Chromosome Start End Strand Distance 0 chr1 6 7 + 0 1 chr1 6 7 + 0 2 chr1 6 2567 + 0 3 chr1 6 3079 + 0 4 chr1 6 4820 + 0 5 chr1 6 7131 + 0 6 chr1 6 8335 + 0 7 chr14 6 7 + 0 8 chr14 6 3744 + 0 9 chr21 6 8967 + 0 10 chr9 6 2173 + 0 Expected Chromosome Start End Strand Distance 0 chr1 6 7 + 0 1 chr1 6 7 + 0 2 chr1 6 2567 + 0 3 chr1 6 3079 + 0 4 chr1 6 4820 + 0 5 chr1 6 7131 + 0 6 chr1 6 8335 + 0 7 chr14 6 7 + 0 8 chr14 6 3744 + 0 9 chr21 6 8967 + 0 10 chr9 6 2173 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=11, step=1) Expected index RangeIndex(start=0, stop=11, step=1) index equal [ True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd5m51z4o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd5m51z4o/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3043179 3051325 - 530439 1 chr1 3043179 3051325 - 4610671 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3043179 | 3051325 | a | 0 | ... | | chr1 | 3043179 | 3051325 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3043179 3051325 - 530439 1 chr1 3043179 3051325 - 4610671 df2 Chromosome Start End Strand Distance 0 chr1 3043179 3051325 - 530439 1 chr1 3043179 3051325 - 4610671 Actual Chromosome Start End Strand Distance 0 chr1 3043179 3051325 - 530439 1 chr1 3043179 3051325 - 4610671 Expected Chromosome Start End Strand Distance 0 chr1 3043179 3051325 - 530439 1 chr1 3043179 3051325 - 4610671 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz13ptuk7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz13ptuk7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3043179 3051325 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3043179 | 3051325 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3043179 3051325 - 0 df2 Chromosome Start End Strand Distance 0 chr1 3043179 3051325 - 0 Actual Chromosome Start End Strand Distance 0 chr1 3043179 3051325 - 0 Expected Chromosome Start End Strand Distance 0 chr1 3043179 3051325 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmplcujn6pd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplcujn6pd/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 8146 16292 - 3026888 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8146 | 16292 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 8146 16292 - 3026888 df2 Chromosome Start End Strand Distance 0 chr1 8146 16292 - 3026888 Actual Chromosome Start End Strand Distance 0 chr1 8146 16292 - 3026888 Expected Chromosome Start End Strand Distance 0 chr1 8146 16292 - 3026888 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3f_oro1k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3f_oro1k/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 8146 16292 - 3026888 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8146 | 16292 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 8146 16292 - 3026888 df2 Chromosome Start End Strand Distance 0 chr1 8146 16292 - 3026888 Actual Chromosome Start End Strand Distance 0 chr1 8146 16292 - 3026888 Expected Chromosome Start End Strand Distance 0 chr1 8146 16292 - 3026888 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6wd6qmb3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6wd6qmb3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 8147 - 3035033 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 8147 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 8147 - 3035033 df2 Chromosome Start End Strand Distance 0 chr1 1 8147 - 3035033 Actual Chromosome Start End Strand Distance 0 chr1 1 8147 - 3035033 Expected Chromosome Start End Strand Distance 0 chr1 1 8147 - 3035033 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgub3agii/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgub3agii/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 8147 - 3035033 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 8147 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 8147 - 3035033 df2 Chromosome Start End Strand Distance 0 chr1 1 8147 - 3035033 Actual Chromosome Start End Strand Distance 0 chr1 1 8147 - 3035033 Expected Chromosome Start End Strand Distance 0 chr1 1 8147 - 3035033 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxsl991uv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxsl991uv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpukdxkgqa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpukdxkgqa/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5241015 5244544 - 0 1 chr15 890467 899241 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5241015 | 5244544 | a | 0 | ... | | chr15 | 890467 | 899241 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr15 890467 899241 - 0 0 chr1 5241015 5244544 - 0 df2 Chromosome Start End Strand Distance 1 chr15 890467 899241 - 0 0 chr1 5241015 5244544 - 0 Actual Chromosome Start End Strand Distance 0 chr1 5241015 5244544 - 0 1 chr15 890467 899241 - 0 Expected Chromosome Start End Strand Distance 0 chr1 5241015 5244544 - 0 1 chr15 890467 899241 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0b73iqsq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0b73iqsq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5241015 5244544 - 0 1 chr1 5241015 5244544 - 4341775 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5241015 | 5244544 | a | 0 | ... | | chr1 | 5241015 | 5244544 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 5241015 5244544 - 0 1 chr1 5241015 5244544 - 4341775 df2 Chromosome Start End Strand Distance 0 chr1 5241015 5244544 - 0 1 chr1 5241015 5244544 - 4341775 Actual Chromosome Start End Strand Distance 0 chr1 5241015 5244544 - 0 1 chr1 5241015 5244544 - 4341775 Expected Chromosome Start End Strand Distance 0 chr1 5241015 5244544 - 0 1 chr1 5241015 5244544 - 4341775 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmphha8ojpy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphha8ojpy/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5241015 5244544 - 0 1 chr15 890467 899241 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5241015 | 5244544 | a | 0 | ... | | chr15 | 890467 | 899241 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr15 890467 899241 - 0 0 chr1 5241015 5244544 - 0 df2 Chromosome Start End Strand Distance 1 chr15 890467 899241 - 0 0 chr1 5241015 5244544 - 0 Actual Chromosome Start End Strand Distance 0 chr1 5241015 5244544 - 0 1 chr15 890467 899241 - 0 Expected Chromosome Start End Strand Distance 0 chr1 5241015 5244544 - 0 1 chr15 890467 899241 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1yeyeo1k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1yeyeo1k/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr15 890467 899241 - 0 2 chr15 890467 899241 - 4341775 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr15 | 890467 | 899241 | a | 0 | ... | | chr15 | 890467 | 899241 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr15 890467 899241 - 0 1 chr15 890467 899241 - 4341775 df2 Chromosome Start End Strand Distance 1 chr15 890467 899241 - 0 2 chr15 890467 899241 - 4341775 Actual Chromosome Start End Strand Distance 0 chr15 890467 899241 - 0 1 chr15 890467 899241 - 4341775 Expected Chromosome Start End Strand Distance 0 chr15 890467 899241 - 0 1 chr15 890467 899241 - 4341775 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq5ecvq3u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq5ecvq3u/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr15 890467 899241 - 0 1 chr15 890467 899241 - 4341775 2 chr15 5241015 5244544 - 0 3 chr15 5241015 5244544 - 4341775 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr15 | 890467 | 899241 | a | 0 | ... | | chr15 | 890467 | 899241 | a | 0 | ... | | chr15 | 5241015 | 5244544 | a | 0 | ... | | chr15 | 5241015 | 5244544 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr15 890467 899241 - 0 1 chr15 890467 899241 - 4341775 2 chr15 5241015 5244544 - 0 3 chr15 5241015 5244544 - 4341775 df2 Chromosome Start End Strand Distance 0 chr15 890467 899241 - 0 1 chr15 890467 899241 - 4341775 2 chr15 5241015 5244544 - 0 3 chr15 5241015 5244544 - 4341775 Actual Chromosome Start End Strand Distance 0 chr15 890467 899241 - 0 1 chr15 890467 899241 - 4341775 2 chr15 5241015 5244544 - 0 3 chr15 5241015 5244544 - 4341775 Expected Chromosome Start End Strand Distance 0 chr15 890467 899241 - 0 1 chr15 890467 899241 - 4341775 2 chr15 5241015 5244544 - 0 3 chr15 5241015 5244544 - 4341775 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzxty6tee/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzxty6tee/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr15 890467 899241 - 0 1 chr15 890467 899241 - 4341775 2 chr15 5241015 5244544 - 0 3 chr15 5241015 5244544 - 4346351 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr15 | 890467 | 899241 | a | 0 | ... | | chr15 | 890467 | 899241 | a | 0 | ... | | chr15 | 5241015 | 5244544 | a | 0 | ... | | chr15 | 5241015 | 5244544 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr15 890467 899241 - 0 1 chr15 890467 899241 - 4341775 2 chr15 5241015 5244544 - 0 3 chr15 5241015 5244544 - 4346351 df2 Chromosome Start End Strand Distance 0 chr15 890467 899241 - 0 1 chr15 890467 899241 - 4341775 2 chr15 5241015 5244544 - 0 3 chr15 5241015 5244544 - 4346351 Actual Chromosome Start End Strand Distance 0 chr15 890467 899241 - 0 1 chr15 890467 899241 - 4341775 2 chr15 5241015 5244544 - 0 3 chr15 5241015 5244544 - 4346351 Expected Chromosome Start End Strand Distance 0 chr15 890467 899241 - 0 1 chr15 890467 899241 - 4341775 2 chr15 5241015 5244544 - 0 3 chr15 5241015 5244544 - 4346351 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcv62s3w9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcv62s3w9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 5579 - 4346295 1 chr1 1 5579 - 7466658 2 chr1 7531613 7538985 - 54385 3 chr1 7531613 7538985 - 2345635 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 5579 | a | 0 | ... | | chr1 | 1 | 5579 | a | 0 | ... | | chr1 | 7531613 | 7538985 | a | 0 | ... | | chr1 | 7531613 | 7538985 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 5579 - 4346295 1 chr1 1 5579 - 7466658 2 chr1 7531613 7538985 - 54385 3 chr1 7531613 7538985 - 2345635 df2 Chromosome Start End Strand Distance 0 chr1 1 5579 - 4346295 1 chr1 1 5579 - 7466658 2 chr1 7531613 7538985 - 54385 3 chr1 7531613 7538985 - 2345635 Actual Chromosome Start End Strand Distance 0 chr1 1 5579 - 4346295 1 chr1 1 5579 - 7466658 2 chr1 7531613 7538985 - 54385 3 chr1 7531613 7538985 - 2345635 Expected Chromosome Start End Strand Distance 0 chr1 1 5579 - 4346295 1 chr1 1 5579 - 7466658 2 chr1 7531613 7538985 - 54385 3 chr1 7531613 7538985 - 2345635 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm4_p4832/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm4_p4832/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 5579 - 0 1 chr1 1 5579 - 7526035 2 chr1 7531613 7538985 - 0 3 chr1 7531613 7538985 - 7526035 4 chrY 9561421 9567471 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 5579 | a | 0 | ... | | chr1 | 1 | 5579 | a | 0 | ... | | chr1 | 7531613 | 7538985 | a | 0 | ... | | chr1 | 7531613 | 7538985 | a | 0 | ... | | chrY | 9561421 | 9567471 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 5579 - 0 1 chr1 1 5579 - 7526035 2 chr1 7531613 7538985 - 0 3 chr1 7531613 7538985 - 7526035 4 chrY 9561421 9567471 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 5579 - 0 1 chr1 1 5579 - 7526035 2 chr1 7531613 7538985 - 0 3 chr1 7531613 7538985 - 7526035 4 chrY 9561421 9567471 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 5579 - 0 1 chr1 1 5579 - 7526035 2 chr1 7531613 7538985 - 0 3 chr1 7531613 7538985 - 7526035 4 chrY 9561421 9567471 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 5579 - 0 1 chr1 1 5579 - 7526035 2 chr1 7531613 7538985 - 0 3 chr1 7531613 7538985 - 7526035 4 chrY 9561421 9567471 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfb2j5k96/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfb2j5k96/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2sjbeya7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2sjbeya7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyke7352b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyke7352b/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 23 25 - 22 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 23 | 25 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1 2 - 0 0 chr1 23 25 - 22 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 23 25 - 22 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 23 25 - 22 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 23 25 - 22 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp19a7txvm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp19a7txvm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 3 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1 2 - 0 0 chr1 1 3 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 3 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 3 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 3 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpca8j84r3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpca8j84r3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp2s1k0sy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp2s1k0sy/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 896047 897970 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 896047 | 897970 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 896047 897970 - 0 df2 Chromosome Start End Strand Distance 0 chr1 896047 897970 - 0 Actual Chromosome Start End Strand Distance 0 chr1 896047 897970 - 0 Expected Chromosome Start End Strand Distance 0 chr1 896047 897970 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_oc15ofm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_oc15ofm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe7nkenxq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe7nkenxq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp26hp_k6s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp26hp_k6s/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxhiv0zbi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxhiv0zbi/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1923 1924 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1923 | 1924 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1923 1924 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1923 1924 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1923 1924 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1923 1924 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_mlbf7hq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_mlbf7hq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1923 1924 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1923 | 1924 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1923 1924 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1923 1924 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1923 1924 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1923 1924 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyp3gotdo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyp3gotdo/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 963245 966462 + 278566 1 chr1 1044002 1046201 - 8953800 2 chr1 3716919 3718301 - 6281700 3 chr1 3993578 3998706 - 6001295 8 chr8 2149098 2154600 - 211934 9 chr8 2149098 2154600 - 3639611 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 963245 | 966462 | a | 0 | ... | | chr1 | 3716919 | 3718301 | a | 0 | ... | | chr1 | 1044002 | 1046201 | a | 0 | ... | | chr1 | 3993578 | 3998706 | a | 0 | ... | | chr8 | 2149098 | 2154600 | a | 0 | ... | | chr8 | 2149098 | 2154600 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 963245 966462 + 278566 2 chr1 1044002 1046201 - 8953800 4 chr8 2149098 2154600 - 211934 5 chr8 2149098 2154600 - 3639611 1 chr1 3716919 3718301 - 6281700 3 chr1 3993578 3998706 - 6001295 df2 Chromosome Start End Strand Distance 0 chr1 963245 966462 + 278566 1 chr1 1044002 1046201 - 8953800 8 chr8 2149098 2154600 - 211934 9 chr8 2149098 2154600 - 3639611 2 chr1 3716919 3718301 - 6281700 3 chr1 3993578 3998706 - 6001295 Actual Chromosome Start End Strand Distance 0 chr1 963245 966462 + 278566 1 chr1 1044002 1046201 - 8953800 2 chr1 3716919 3718301 - 6281700 3 chr1 3993578 3998706 - 6001295 4 chr8 2149098 2154600 - 211934 5 chr8 2149098 2154600 - 3639611 Expected Chromosome Start End Strand Distance 0 chr1 963245 966462 + 278566 1 chr1 1044002 1046201 - 8953800 2 chr1 3716919 3718301 - 6281700 3 chr1 3993578 3998706 - 6001295 4 chr8 2149098 2154600 - 211934 5 chr8 2149098 2154600 - 3639611 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpioshmqtn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpioshmqtn/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 682523 684680 + 0 1 chr1 10000000 10002043 - 0 2 chr8 1935958 1937165 - 0 3 chr8 1935958 1937165 - 3857046 4 chr8 5794210 5800260 - 0 5 chr8 5794210 5800260 - 2482742 6 chr8 8283001 8290700 - 0 7 chr8 8283001 8290700 - 2482742 8 chr8 9030773 9040376 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 682523 | 684680 | a | 0 | ... | | chr1 | 10000000 | 10002043 | a | 0 | ... | | chr8 | 9030773 | 9040376 | a | 0 | ... | | chr8 | 5794210 | 5800260 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr8 | 8283001 | 8290700 | a | 0 | ... | | chr8 | 8283001 | 8290700 | a | 0 | ... | | chr8 | 1935958 | 1937165 | a | 0 | ... | | chr8 | 1935958 | 1937165 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 682523 684680 + 0 7 chr8 1935958 1937165 - 0 8 chr8 1935958 1937165 - 3857046 3 chr8 5794210 5800260 - 0 4 chr8 5794210 5800260 - 2482742 5 chr8 8283001 8290700 - 0 6 chr8 8283001 8290700 - 2482742 2 chr8 9030773 9040376 + 0 1 chr1 10000000 10002043 - 0 df2 Chromosome Start End Strand Distance 0 chr1 682523 684680 + 0 2 chr8 1935958 1937165 - 0 3 chr8 1935958 1937165 - 3857046 4 chr8 5794210 5800260 - 0 5 chr8 5794210 5800260 - 2482742 6 chr8 8283001 8290700 - 0 7 chr8 8283001 8290700 - 2482742 8 chr8 9030773 9040376 + 0 1 chr1 10000000 10002043 - 0 Actual Chromosome Start End Strand Distance 0 chr1 682523 684680 + 0 1 chr1 10000000 10002043 - 0 2 chr8 1935958 1937165 - 0 3 chr8 1935958 1937165 - 3857046 4 chr8 5794210 5800260 - 0 5 chr8 5794210 5800260 - 2482742 6 chr8 8283001 8290700 - 0 7 chr8 8283001 8290700 - 2482742 8 chr8 9030773 9040376 + 0 Expected Chromosome Start End Strand Distance 0 chr1 682523 684680 + 0 1 chr1 10000000 10002043 - 0 2 chr8 1935958 1937165 - 0 3 chr8 1935958 1937165 - 3857046 4 chr8 5794210 5800260 - 0 5 chr8 5794210 5800260 - 2482742 6 chr8 8283001 8290700 - 0 7 chr8 8283001 8290700 - 2482742 8 chr8 9030773 9040376 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=9, step=1) index equal [ True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsqam_apf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsqam_apf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 682523 684680 + 0 1 chr1 10000000 10002043 + 9315321 2 chr8 1935958 1937165 + 7093609 3 chr8 5794210 5800260 + 3230514 4 chr8 8283001 8290700 + 740074 5 chr8 9030773 9040376 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 10000000 | 10002043 | a | 0 | ... | | chr1 | 682523 | 684680 | a | 0 | ... | | chr8 | 5794210 | 5800260 | a | 0 | ... | | chr8 | 8283001 | 8290700 | a | 0 | ... | | chr8 | 9030773 | 9040376 | a | 0 | ... | | chr8 | 1935958 | 1937165 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 682523 684680 + 0 5 chr8 1935958 1937165 + 7093609 2 chr8 5794210 5800260 + 3230514 3 chr8 8283001 8290700 + 740074 4 chr8 9030773 9040376 + 0 0 chr1 10000000 10002043 + 9315321 df2 Chromosome Start End Strand Distance 0 chr1 682523 684680 + 0 2 chr8 1935958 1937165 + 7093609 3 chr8 5794210 5800260 + 3230514 4 chr8 8283001 8290700 + 740074 5 chr8 9030773 9040376 + 0 1 chr1 10000000 10002043 + 9315321 Actual Chromosome Start End Strand Distance 0 chr1 682523 684680 + 0 1 chr1 10000000 10002043 + 9315321 2 chr8 1935958 1937165 + 7093609 3 chr8 5794210 5800260 + 3230514 4 chr8 8283001 8290700 + 740074 5 chr8 9030773 9040376 + 0 Expected Chromosome Start End Strand Distance 0 chr1 682523 684680 + 0 1 chr1 10000000 10002043 + 9315321 2 chr8 1935958 1937165 + 7093609 3 chr8 5794210 5800260 + 3230514 4 chr8 8283001 8290700 + 740074 5 chr8 9030773 9040376 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkpynzi60/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkpynzi60/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 682523 684680 + 0 1 chr1 1935958 1937165 + 1251279 2 chr1 5794210 5800260 + 5109531 3 chr1 8283001 8290700 + 7598322 4 chr1 9030773 9040376 + 8346094 5 chr1 10000000 10002043 + 9315321 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5794210 | 5800260 | a | 0 | ... | | chr1 | 10000000 | 10002043 | a | 0 | ... | | chr1 | 8283001 | 8290700 | a | 0 | ... | | chr1 | 9030773 | 9040376 | a | 0 | ... | | chr1 | 682523 | 684680 | a | 0 | ... | | chr1 | 1935958 | 1937165 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 682523 684680 + 0 5 chr1 1935958 1937165 + 1251279 0 chr1 5794210 5800260 + 5109531 2 chr1 8283001 8290700 + 7598322 3 chr1 9030773 9040376 + 8346094 1 chr1 10000000 10002043 + 9315321 df2 Chromosome Start End Strand Distance 0 chr1 682523 684680 + 0 1 chr1 1935958 1937165 + 1251279 2 chr1 5794210 5800260 + 5109531 3 chr1 8283001 8290700 + 7598322 4 chr1 9030773 9040376 + 8346094 5 chr1 10000000 10002043 + 9315321 Actual Chromosome Start End Strand Distance 0 chr1 682523 684680 + 0 1 chr1 1935958 1937165 + 1251279 2 chr1 5794210 5800260 + 5109531 3 chr1 8283001 8290700 + 7598322 4 chr1 9030773 9040376 + 8346094 5 chr1 10000000 10002043 + 9315321 Expected Chromosome Start End Strand Distance 0 chr1 682523 684680 + 0 1 chr1 1935958 1937165 + 1251279 2 chr1 5794210 5800260 + 5109531 3 chr1 8283001 8290700 + 7598322 4 chr1 9030773 9040376 + 8346094 5 chr1 10000000 10002043 + 9315321 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7213hjjx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7213hjjx/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 682523 684680 + 678210 1 chr1 1935958 1937165 + 1931645 2 chr1 5794210 5800260 + 5789897 3 chr1 8283001 8290700 + 8278688 4 chr1 9030773 9040376 + 9026460 5 chr1 10000000 10002043 + 9995687 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5794210 | 5800260 | a | 0 | ... | | chr1 | 10000000 | 10002043 | a | 0 | ... | | chr1 | 8283001 | 8290700 | a | 0 | ... | | chr1 | 9030773 | 9040376 | a | 0 | ... | | chr1 | 682523 | 684680 | a | 0 | ... | | chr1 | 1935958 | 1937165 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 682523 684680 + 678210 5 chr1 1935958 1937165 + 1931645 0 chr1 5794210 5800260 + 5789897 2 chr1 8283001 8290700 + 8278688 3 chr1 9030773 9040376 + 9026460 1 chr1 10000000 10002043 + 9995687 df2 Chromosome Start End Strand Distance 0 chr1 682523 684680 + 678210 1 chr1 1935958 1937165 + 1931645 2 chr1 5794210 5800260 + 5789897 3 chr1 8283001 8290700 + 8278688 4 chr1 9030773 9040376 + 9026460 5 chr1 10000000 10002043 + 9995687 Actual Chromosome Start End Strand Distance 0 chr1 682523 684680 + 678210 1 chr1 1935958 1937165 + 1931645 2 chr1 5794210 5800260 + 5789897 3 chr1 8283001 8290700 + 8278688 4 chr1 9030773 9040376 + 9026460 5 chr1 10000000 10002043 + 9995687 Expected Chromosome Start End Strand Distance 0 chr1 682523 684680 + 678210 1 chr1 1935958 1937165 + 1931645 2 chr1 5794210 5800260 + 5789897 3 chr1 8283001 8290700 + 8278688 4 chr1 9030773 9040376 + 9026460 5 chr1 10000000 10002043 + 9995687 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmhb2jbyp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmhb2jbyp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf0yfiig5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf0yfiig5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2043 2044 - 0 1 chr1 2043 2044 - 114 2 chr1 2157 2158 - 0 3 chr1 2157 2158 - 114 4 chr8 1207 1208 - 0 5 chr8 1207 1208 - 4843 6 chr8 6050 6051 - 0 7 chr8 6050 6051 - 1649 8 chr8 7699 7700 - 0 9 chr8 7699 7700 - 1649 10 chr8 9603 9604 - 0 11 chr8 9603 9604 - 1904 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2043 | 2044 | a | 0 | ... | | chr1 | 2043 | 2044 | a | 0 | ... | | chr1 | 2157 | 2158 | a | 0 | ... | | chr1 | 2157 | 2158 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr8 | 9603 | 9604 | a | 0 | ... | | chr8 | 9603 | 9604 | a | 0 | ... | | chr8 | 1207 | 1208 | a | 0 | ... | | chr8 | 1207 | 1208 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 10 chr8 1207 1208 - 0 11 chr8 1207 1208 - 4843 0 chr1 2043 2044 - 0 1 chr1 2043 2044 - 114 2 chr1 2157 2158 - 0 3 chr1 2157 2158 - 114 4 chr8 6050 6051 - 0 5 chr8 6050 6051 - 1649 6 chr8 7699 7700 - 0 7 chr8 7699 7700 - 1649 8 chr8 9603 9604 - 0 9 chr8 9603 9604 - 1904 df2 Chromosome Start End Strand Distance 4 chr8 1207 1208 - 0 5 chr8 1207 1208 - 4843 0 chr1 2043 2044 - 0 1 chr1 2043 2044 - 114 2 chr1 2157 2158 - 0 3 chr1 2157 2158 - 114 6 chr8 6050 6051 - 0 7 chr8 6050 6051 - 1649 8 chr8 7699 7700 - 0 9 chr8 7699 7700 - 1649 10 chr8 9603 9604 - 0 11 chr8 9603 9604 - 1904 Actual Chromosome Start End Strand Distance 0 chr1 2043 2044 - 0 1 chr1 2043 2044 - 114 2 chr1 2157 2158 - 0 3 chr1 2157 2158 - 114 4 chr8 1207 1208 - 0 5 chr8 1207 1208 - 4843 6 chr8 6050 6051 - 0 7 chr8 6050 6051 - 1649 8 chr8 7699 7700 - 0 9 chr8 7699 7700 - 1649 10 chr8 9603 9604 - 0 11 chr8 9603 9604 - 1904 Expected Chromosome Start End Strand Distance 0 chr1 2043 2044 - 0 1 chr1 2043 2044 - 114 2 chr1 2157 2158 - 0 3 chr1 2157 2158 - 114 4 chr8 1207 1208 - 0 5 chr8 1207 1208 - 4843 6 chr8 6050 6051 - 0 7 chr8 6050 6051 - 1649 8 chr8 7699 7700 - 0 9 chr8 7699 7700 - 1649 10 chr8 9603 9604 - 0 11 chr8 9603 9604 - 1904 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpla3qvsej/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpla3qvsej/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2451171 2451172 - 421111 1 chr1 2451171 2451172 - 1015245 2 chr1 2451171 2453887 + 2445876 3 chr1 2451171 2453887 + 3003570 4 chr1 2451171 2455909 - 416374 5 chr1 2451171 2455909 - 1010508 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2451171 | 2453887 | a | 0 | ... | | chr1 | 2451171 | 2453887 | a | 0 | ... | | chr1 | 2451171 | 2451172 | a | 0 | ... | | chr1 | 2451171 | 2451172 | a | 0 | ... | | chr1 | 2451171 | 2455909 | a | 0 | ... | | chr1 | 2451171 | 2455909 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 2451171 2451172 - 421111 3 chr1 2451171 2451172 - 1015245 0 chr1 2451171 2453887 + 2445876 1 chr1 2451171 2453887 + 3003570 4 chr1 2451171 2455909 - 416374 5 chr1 2451171 2455909 - 1010508 df2 Chromosome Start End Strand Distance 0 chr1 2451171 2451172 - 421111 1 chr1 2451171 2451172 - 1015245 2 chr1 2451171 2453887 + 2445876 3 chr1 2451171 2453887 + 3003570 4 chr1 2451171 2455909 - 416374 5 chr1 2451171 2455909 - 1010508 Actual Chromosome Start End Strand Distance 0 chr1 2451171 2451172 - 421111 1 chr1 2451171 2451172 - 1015245 2 chr1 2451171 2453887 + 2445876 3 chr1 2451171 2453887 + 3003570 4 chr1 2451171 2455909 - 416374 5 chr1 2451171 2455909 - 1010508 Expected Chromosome Start End Strand Distance 0 chr1 2451171 2451172 - 421111 1 chr1 2451171 2451172 - 1015245 2 chr1 2451171 2453887 + 2445876 3 chr1 2451171 2453887 + 3003570 4 chr1 2451171 2455909 - 416374 5 chr1 2451171 2455909 - 1010508 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjfmtt01m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjfmtt01m/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2451171 2451172 - 421111 1 chr1 2451171 2451172 - 1015245 2 chr1 2451171 2453887 + 2445876 3 chr1 2451171 2453887 + 3003570 4 chr1 2451171 2455909 - 416374 5 chr1 2451171 2455909 - 1010508 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2451171 | 2453887 | a | 0 | ... | | chr1 | 2451171 | 2453887 | a | 0 | ... | | chr1 | 2451171 | 2451172 | a | 0 | ... | | chr1 | 2451171 | 2451172 | a | 0 | ... | | chr1 | 2451171 | 2455909 | a | 0 | ... | | chr1 | 2451171 | 2455909 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 2451171 2451172 - 421111 3 chr1 2451171 2451172 - 1015245 0 chr1 2451171 2453887 + 2445876 1 chr1 2451171 2453887 + 3003570 4 chr1 2451171 2455909 - 416374 5 chr1 2451171 2455909 - 1010508 df2 Chromosome Start End Strand Distance 0 chr1 2451171 2451172 - 421111 1 chr1 2451171 2451172 - 1015245 2 chr1 2451171 2453887 + 2445876 3 chr1 2451171 2453887 + 3003570 4 chr1 2451171 2455909 - 416374 5 chr1 2451171 2455909 - 1010508 Actual Chromosome Start End Strand Distance 0 chr1 2451171 2451172 - 421111 1 chr1 2451171 2451172 - 1015245 2 chr1 2451171 2453887 + 2445876 3 chr1 2451171 2453887 + 3003570 4 chr1 2451171 2455909 - 416374 5 chr1 2451171 2455909 - 1010508 Expected Chromosome Start End Strand Distance 0 chr1 2451171 2451172 - 421111 1 chr1 2451171 2451172 - 1015245 2 chr1 2451171 2453887 + 2445876 3 chr1 2451171 2453887 + 3003570 4 chr1 2451171 2455909 - 416374 5 chr1 2451171 2455909 - 1010508 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_pcg2bcn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_pcg2bcn/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2451171 2451172 - 421111 1 chr1 2451171 2451172 - 1015245 2 chr1 2451171 2453887 + 2445876 3 chr1 2451171 2453887 + 3003570 4 chr1 2451171 2455909 - 416374 5 chr1 2451171 2455909 - 1010508 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2451171 | 2453887 | a | 0 | ... | | chr1 | 2451171 | 2453887 | a | 0 | ... | | chr1 | 2451171 | 2451172 | a | 0 | ... | | chr1 | 2451171 | 2451172 | a | 0 | ... | | chr1 | 2451171 | 2455909 | a | 0 | ... | | chr1 | 2451171 | 2455909 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 2451171 2451172 - 421111 3 chr1 2451171 2451172 - 1015245 0 chr1 2451171 2453887 + 2445876 1 chr1 2451171 2453887 + 3003570 4 chr1 2451171 2455909 - 416374 5 chr1 2451171 2455909 - 1010508 df2 Chromosome Start End Strand Distance 0 chr1 2451171 2451172 - 421111 1 chr1 2451171 2451172 - 1015245 2 chr1 2451171 2453887 + 2445876 3 chr1 2451171 2453887 + 3003570 4 chr1 2451171 2455909 - 416374 5 chr1 2451171 2455909 - 1010508 Actual Chromosome Start End Strand Distance 0 chr1 2451171 2451172 - 421111 1 chr1 2451171 2451172 - 1015245 2 chr1 2451171 2453887 + 2445876 3 chr1 2451171 2453887 + 3003570 4 chr1 2451171 2455909 - 416374 5 chr1 2451171 2455909 - 1010508 Expected Chromosome Start End Strand Distance 0 chr1 2451171 2451172 - 421111 1 chr1 2451171 2451172 - 1015245 2 chr1 2451171 2453887 + 2445876 3 chr1 2451171 2453887 + 3003570 4 chr1 2451171 2455909 - 416374 5 chr1 2451171 2455909 - 1010508 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjyqujqxb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjyqujqxb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2451171 2451172 - 2451167 1 chr1 2451171 2451172 - 2451170 3 chr1 2451171 2455909 - 2451167 4 chr1 2451171 2455909 - 2451170 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2451171 | 2451172 | a | 0 | ... | | chr1 | 2451171 | 2451172 | a | 0 | ... | | chr1 | 2451171 | 2455909 | a | 0 | ... | | chr1 | 2451171 | 2455909 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2451171 2451172 - 2451167 1 chr1 2451171 2451172 - 2451170 2 chr1 2451171 2455909 - 2451167 3 chr1 2451171 2455909 - 2451170 df2 Chromosome Start End Strand Distance 0 chr1 2451171 2451172 - 2451167 1 chr1 2451171 2451172 - 2451170 3 chr1 2451171 2455909 - 2451167 4 chr1 2451171 2455909 - 2451170 Actual Chromosome Start End Strand Distance 0 chr1 2451171 2451172 - 2451167 1 chr1 2451171 2451172 - 2451170 2 chr1 2451171 2455909 - 2451167 3 chr1 2451171 2455909 - 2451170 Expected Chromosome Start End Strand Distance 0 chr1 2451171 2451172 - 2451167 1 chr1 2451171 2451172 - 2451170 2 chr1 2451171 2455909 - 2451167 3 chr1 2451171 2455909 - 2451170 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpysy86jn2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpysy86jn2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2451171 2451172 - 2451167 1 chr1 2451171 2451172 - 2451170 3 chr1 2451171 2455909 - 2451167 4 chr1 2451171 2455909 - 2451170 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2451171 | 2451172 | a | 0 | ... | | chr1 | 2451171 | 2451172 | a | 0 | ... | | chr1 | 2451171 | 2455909 | a | 0 | ... | | chr1 | 2451171 | 2455909 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2451171 2451172 - 2451167 1 chr1 2451171 2451172 - 2451170 2 chr1 2451171 2455909 - 2451167 3 chr1 2451171 2455909 - 2451170 df2 Chromosome Start End Strand Distance 0 chr1 2451171 2451172 - 2451167 1 chr1 2451171 2451172 - 2451170 3 chr1 2451171 2455909 - 2451167 4 chr1 2451171 2455909 - 2451170 Actual Chromosome Start End Strand Distance 0 chr1 2451171 2451172 - 2451167 1 chr1 2451171 2451172 - 2451170 2 chr1 2451171 2455909 - 2451167 3 chr1 2451171 2455909 - 2451170 Expected Chromosome Start End Strand Distance 0 chr1 2451171 2451172 - 2451167 1 chr1 2451171 2451172 - 2451170 2 chr1 2451171 2455909 - 2451167 3 chr1 2451171 2455909 - 2451170 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmya6ougx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmya6ougx/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2451171 2451172 - 2451167 1 chr1 2451171 2451172 - 2451170 3 chr1 2451171 2455909 - 2451167 4 chr1 2451171 2455909 - 2451170 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2451171 | 2451172 | a | 0 | ... | | chr1 | 2451171 | 2451172 | a | 0 | ... | | chr1 | 2451171 | 2455909 | a | 0 | ... | | chr1 | 2451171 | 2455909 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2451171 2451172 - 2451167 1 chr1 2451171 2451172 - 2451170 2 chr1 2451171 2455909 - 2451167 3 chr1 2451171 2455909 - 2451170 df2 Chromosome Start End Strand Distance 0 chr1 2451171 2451172 - 2451167 1 chr1 2451171 2451172 - 2451170 3 chr1 2451171 2455909 - 2451167 4 chr1 2451171 2455909 - 2451170 Actual Chromosome Start End Strand Distance 0 chr1 2451171 2451172 - 2451167 1 chr1 2451171 2451172 - 2451170 2 chr1 2451171 2455909 - 2451167 3 chr1 2451171 2455909 - 2451170 Expected Chromosome Start End Strand Distance 0 chr1 2451171 2451172 - 2451167 1 chr1 2451171 2451172 - 2451170 2 chr1 2451171 2455909 - 2451167 3 chr1 2451171 2455909 - 2451170 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_ci9x9id/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_ci9x9id/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 2451171 2453887 + 2451167 2 chr1 2451171 2453887 + 2451170 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2451171 | 2453887 | a | 0 | ... | | chr1 | 2451171 | 2453887 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2451171 2453887 + 2451167 1 chr1 2451171 2453887 + 2451170 df2 Chromosome Start End Strand Distance 1 chr1 2451171 2453887 + 2451167 2 chr1 2451171 2453887 + 2451170 Actual Chromosome Start End Strand Distance 0 chr1 2451171 2453887 + 2451167 1 chr1 2451171 2453887 + 2451170 Expected Chromosome Start End Strand Distance 0 chr1 2451171 2453887 + 2451167 1 chr1 2451171 2453887 + 2451170 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp95lxpzzb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp95lxpzzb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4182647 4186994 + 5813007 1 chr1 6221011 6224067 + 3775934 2 chr12 9266283 9273306 + 9210859 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6221011 | 6224067 | a | 0 | ... | | chr1 | 4182647 | 4186994 | a | 0 | ... | | chr12 | 9266283 | 9273306 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 4182647 4186994 + 5813007 0 chr1 6221011 6224067 + 3775934 2 chr12 9266283 9273306 + 9210859 df2 Chromosome Start End Strand Distance 0 chr1 4182647 4186994 + 5813007 1 chr1 6221011 6224067 + 3775934 2 chr12 9266283 9273306 + 9210859 Actual Chromosome Start End Strand Distance 0 chr1 4182647 4186994 + 5813007 1 chr1 6221011 6224067 + 3775934 2 chr12 9266283 9273306 + 9210859 Expected Chromosome Start End Strand Distance 0 chr1 4182647 4186994 + 5813007 1 chr1 6221011 6224067 + 3775934 2 chr12 9266283 9273306 + 9210859 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc4977ea6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc4977ea6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4182647 4186994 + 5813007 1 chr1 6221011 6224067 + 3775934 2 chr12 9266283 9273306 + 9210859 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6221011 | 6224067 | a | 0 | ... | | chr1 | 4182647 | 4186994 | a | 0 | ... | | chr12 | 9266283 | 9273306 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 4182647 4186994 + 5813007 0 chr1 6221011 6224067 + 3775934 2 chr12 9266283 9273306 + 9210859 df2 Chromosome Start End Strand Distance 0 chr1 4182647 4186994 + 5813007 1 chr1 6221011 6224067 + 3775934 2 chr12 9266283 9273306 + 9210859 Actual Chromosome Start End Strand Distance 0 chr1 4182647 4186994 + 5813007 1 chr1 6221011 6224067 + 3775934 2 chr12 9266283 9273306 + 9210859 Expected Chromosome Start End Strand Distance 0 chr1 4182647 4186994 + 5813007 1 chr1 6221011 6224067 + 3775934 2 chr12 9266283 9273306 + 9210859 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmplgmsnk5d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplgmsnk5d/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 5 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 5 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 5 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 5 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 5 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmppfn0si77/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppfn0si77/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 5 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 5 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 5 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 5 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 5 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmprtrk3hh_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprtrk3hh_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmprcty0_kb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprcty0_kb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmprc_gm_fx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprc_gm_fx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmfj12rh7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmfj12rh7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2844276 2852326 + 1364483 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2844276 | 2852326 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2844276 2852326 + 1364483 df2 Chromosome Start End Strand Distance 0 chr1 2844276 2852326 + 1364483 Actual Chromosome Start End Strand Distance 0 chr1 2844276 2852326 + 1364483 Expected Chromosome Start End Strand Distance 0 chr1 2844276 2852326 + 1364483 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9ebxdkkj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9ebxdkkj/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 858584 867728 - 0 1 chr1 858584 867728 - 3145103 2 chr1 4012830 4015504 - 0 3 chr1 4012830 4015504 - 3145103 4 chr1 4216808 4216884 + 0 5 chr1 7757708 7763765 - 0 6 chr1 7757708 7763765 - 3742205 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4216808 | 4216884 | a | 0 | ... | | chr1 | 4012830 | 4015504 | a | 0 | ... | | chr1 | 4012830 | 4015504 | a | 0 | ... | | chr1 | 7757708 | 7763765 | a | 0 | ... | | chr1 | 7757708 | 7763765 | a | 0 | ... | | chr1 | 858584 | 867728 | a | 0 | ... | | chr1 | 858584 | 867728 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 5 chr1 858584 867728 - 0 6 chr1 858584 867728 - 3145103 1 chr1 4012830 4015504 - 0 2 chr1 4012830 4015504 - 3145103 0 chr1 4216808 4216884 + 0 3 chr1 7757708 7763765 - 0 4 chr1 7757708 7763765 - 3742205 df2 Chromosome Start End Strand Distance 0 chr1 858584 867728 - 0 1 chr1 858584 867728 - 3145103 2 chr1 4012830 4015504 - 0 3 chr1 4012830 4015504 - 3145103 4 chr1 4216808 4216884 + 0 5 chr1 7757708 7763765 - 0 6 chr1 7757708 7763765 - 3742205 Actual Chromosome Start End Strand Distance 0 chr1 858584 867728 - 0 1 chr1 858584 867728 - 3145103 2 chr1 4012830 4015504 - 0 3 chr1 4012830 4015504 - 3145103 4 chr1 4216808 4216884 + 0 5 chr1 7757708 7763765 - 0 6 chr1 7757708 7763765 - 3742205 Expected Chromosome Start End Strand Distance 0 chr1 858584 867728 - 0 1 chr1 858584 867728 - 3145103 2 chr1 4012830 4015504 - 0 3 chr1 4012830 4015504 - 3145103 4 chr1 4216808 4216884 + 0 5 chr1 7757708 7763765 - 0 6 chr1 7757708 7763765 - 3742205 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp17fjty79/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp17fjty79/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 858584 867728 - 3145103 1 chr1 858584 867728 - 3349081 2 chr1 4012830 4015504 - 0 3 chr1 4012830 4015504 - 201305 4 chr1 4216808 4216884 + 3349081 5 chr1 4216808 4216884 + 3540825 6 chr1 7757708 7763765 - 3540825 7 chr1 7757708 7763765 - 3742205 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4216808 | 4216884 | a | 0 | ... | | chr1 | 4216808 | 4216884 | a | 0 | ... | | chr1 | 4012830 | 4015504 | a | 0 | ... | | chr1 | 4012830 | 4015504 | a | 0 | ... | | chr1 | 7757708 | 7763765 | a | 0 | ... | | chr1 | 7757708 | 7763765 | a | 0 | ... | | chr1 | 858584 | 867728 | a | 0 | ... | | chr1 | 858584 | 867728 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr1 858584 867728 - 3145103 7 chr1 858584 867728 - 3349081 2 chr1 4012830 4015504 - 0 3 chr1 4012830 4015504 - 201305 0 chr1 4216808 4216884 + 3349081 1 chr1 4216808 4216884 + 3540825 4 chr1 7757708 7763765 - 3540825 5 chr1 7757708 7763765 - 3742205 df2 Chromosome Start End Strand Distance 0 chr1 858584 867728 - 3145103 1 chr1 858584 867728 - 3349081 2 chr1 4012830 4015504 - 0 3 chr1 4012830 4015504 - 201305 4 chr1 4216808 4216884 + 3349081 5 chr1 4216808 4216884 + 3540825 6 chr1 7757708 7763765 - 3540825 7 chr1 7757708 7763765 - 3742205 Actual Chromosome Start End Strand Distance 0 chr1 858584 867728 - 3145103 1 chr1 858584 867728 - 3349081 2 chr1 4012830 4015504 - 0 3 chr1 4012830 4015504 - 201305 4 chr1 4216808 4216884 + 3349081 5 chr1 4216808 4216884 + 3540825 6 chr1 7757708 7763765 - 3540825 7 chr1 7757708 7763765 - 3742205 Expected Chromosome Start End Strand Distance 0 chr1 858584 867728 - 3145103 1 chr1 858584 867728 - 3349081 2 chr1 4012830 4015504 - 0 3 chr1 4012830 4015504 - 201305 4 chr1 4216808 4216884 + 3349081 5 chr1 4216808 4216884 + 3540825 6 chr1 7757708 7763765 - 3540825 7 chr1 7757708 7763765 - 3742205 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp18u43ryq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp18u43ryq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 858584 867728 - 858581 1 chr1 4012830 4015504 - 4012827 2 chr1 4216808 4216884 + 4216807 3 chr1 7757708 7763765 - 7757705 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4216808 | 4216884 | a | 0 | ... | | chr1 | 4012830 | 4015504 | a | 0 | ... | | chr1 | 7757708 | 7763765 | a | 0 | ... | | chr1 | 858584 | 867728 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 858584 867728 - 858581 1 chr1 4012830 4015504 - 4012827 0 chr1 4216808 4216884 + 4216807 2 chr1 7757708 7763765 - 7757705 df2 Chromosome Start End Strand Distance 0 chr1 858584 867728 - 858581 1 chr1 4012830 4015504 - 4012827 2 chr1 4216808 4216884 + 4216807 3 chr1 7757708 7763765 - 7757705 Actual Chromosome Start End Strand Distance 0 chr1 858584 867728 - 858581 1 chr1 4012830 4015504 - 4012827 2 chr1 4216808 4216884 + 4216807 3 chr1 7757708 7763765 - 7757705 Expected Chromosome Start End Strand Distance 0 chr1 858584 867728 - 858581 1 chr1 4012830 4015504 - 4012827 2 chr1 4216808 4216884 + 4216807 3 chr1 7757708 7763765 - 7757705 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd2t23yne/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd2t23yne/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 76 152 + 75 1 chr1 2674 5348 - 2671 2 chr1 6057 12114 - 6054 3 chr1 9144 18288 - 9141 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 76 | 152 | a | 0 | ... | | chr1 | 2674 | 5348 | a | 0 | ... | | chr1 | 6057 | 12114 | a | 0 | ... | | chr1 | 9144 | 18288 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 76 152 + 75 1 chr1 2674 5348 - 2671 2 chr1 6057 12114 - 6054 3 chr1 9144 18288 - 9141 df2 Chromosome Start End Strand Distance 0 chr1 76 152 + 75 1 chr1 2674 5348 - 2671 2 chr1 6057 12114 - 6054 3 chr1 9144 18288 - 9141 Actual Chromosome Start End Strand Distance 0 chr1 76 152 + 75 1 chr1 2674 5348 - 2671 2 chr1 6057 12114 - 6054 3 chr1 9144 18288 - 9141 Expected Chromosome Start End Strand Distance 0 chr1 76 152 + 75 1 chr1 2674 5348 - 2671 2 chr1 6057 12114 - 6054 3 chr1 9144 18288 - 9141 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpksim5ge4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpksim5ge4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 76 152 + 75 1 chr1 2674 5348 - 2673 2 chr1 6057 12114 - 6056 3 chr1 9144 18288 - 9143 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 76 | 152 | a | 0 | ... | | chr1 | 2674 | 5348 | a | 0 | ... | | chr1 | 6057 | 12114 | a | 0 | ... | | chr1 | 9144 | 18288 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 76 152 + 75 1 chr1 2674 5348 - 2673 2 chr1 6057 12114 - 6056 3 chr1 9144 18288 - 9143 df2 Chromosome Start End Strand Distance 0 chr1 76 152 + 75 1 chr1 2674 5348 - 2673 2 chr1 6057 12114 - 6056 3 chr1 9144 18288 - 9143 Actual Chromosome Start End Strand Distance 0 chr1 76 152 + 75 1 chr1 2674 5348 - 2673 2 chr1 6057 12114 - 6056 3 chr1 9144 18288 - 9143 Expected Chromosome Start End Strand Distance 0 chr1 76 152 + 75 1 chr1 2674 5348 - 2673 2 chr1 6057 12114 - 6056 3 chr1 9144 18288 - 9143 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw67pn83v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw67pn83v/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2675 - 0 1 chr1 1 6058 - 0 2 chr1 1 77 + 0 3 chr1 1 9145 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 77 | a | 0 | ... | | chr1 | 1 | 2675 | a | 0 | ... | | chr1 | 1 | 6058 | a | 0 | ... | | chr1 | 1 | 9145 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 77 + 0 1 chr1 1 2675 - 0 2 chr1 1 6058 - 0 3 chr1 1 9145 - 0 df2 Chromosome Start End Strand Distance 2 chr1 1 77 + 0 0 chr1 1 2675 - 0 1 chr1 1 6058 - 0 3 chr1 1 9145 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 77 + 0 1 chr1 1 2675 - 0 2 chr1 1 6058 - 0 3 chr1 1 9145 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 77 + 0 1 chr1 1 2675 - 0 2 chr1 1 6058 - 0 3 chr1 1 9145 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi8ailgv6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi8ailgv6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1079808 1080329 + 4340409 1 chr1 5560558 5565137 - 130347 2 chr1 5560558 5565137 - 135546 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1079808 | 1080329 | a | 0 | ... | | chr1 | 5560558 | 5565137 | a | 0 | ... | | chr1 | 5560558 | 5565137 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1079808 1080329 + 4340409 1 chr1 5560558 5565137 - 130347 2 chr1 5560558 5565137 - 135546 df2 Chromosome Start End Strand Distance 0 chr1 1079808 1080329 + 4340409 1 chr1 5560558 5565137 - 130347 2 chr1 5560558 5565137 - 135546 Actual Chromosome Start End Strand Distance 0 chr1 1079808 1080329 + 4340409 1 chr1 5560558 5565137 - 130347 2 chr1 5560558 5565137 - 135546 Expected Chromosome Start End Strand Distance 0 chr1 1079808 1080329 + 4340409 1 chr1 5560558 5565137 - 130347 2 chr1 5560558 5565137 - 135546 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn150_8xa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn150_8xa/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1guimvo6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1guimvo6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2749102 2749103 - 0 1 chr2 1 5338 - 0 2 chr2 1 5338 - 0 3 chr2 1 5338 - 0 4 chrY 1 5338 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2749102 | 2749103 | a | 0 | ... | | chr2 | 1 | 5338 | a | 0 | ... | | chr2 | 1 | 5338 | a | 0 | ... | | chr2 | 1 | 5338 | a | 0 | ... | | chrY | 1 | 5338 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr2 1 5338 - 0 2 chr2 1 5338 - 0 3 chr2 1 5338 - 0 4 chrY 1 5338 - 0 0 chr1 2749102 2749103 - 0 df2 Chromosome Start End Strand Distance 1 chr2 1 5338 - 0 2 chr2 1 5338 - 0 3 chr2 1 5338 - 0 4 chrY 1 5338 - 0 0 chr1 2749102 2749103 - 0 Actual Chromosome Start End Strand Distance 0 chr1 2749102 2749103 - 0 1 chr2 1 5338 - 0 2 chr2 1 5338 - 0 3 chr2 1 5338 - 0 4 chrY 1 5338 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2749102 2749103 - 0 1 chr2 1 5338 - 0 2 chr2 1 5338 - 0 3 chr2 1 5338 - 0 4 chrY 1 5338 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8uc6rfoq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8uc6rfoq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2749102 2749103 - 2749101 4 chrY 1 5338 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2749102 | 2749103 | a | 0 | ... | | chrY | 1 | 5338 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chrY 1 5338 - 0 0 chr1 2749102 2749103 - 2749101 df2 Chromosome Start End Strand Distance 4 chrY 1 5338 - 0 0 chr1 2749102 2749103 - 2749101 Actual Chromosome Start End Strand Distance 0 chr1 2749102 2749103 - 2749101 1 chrY 1 5338 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2749102 2749103 - 2749101 1 chrY 1 5338 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp00r2habb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp00r2habb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2749102 2749103 - 2749101 4 chrY 1 5338 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2749102 | 2749103 | a | 0 | ... | | chrY | 1 | 5338 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chrY 1 5338 - 0 0 chr1 2749102 2749103 - 2749101 df2 Chromosome Start End Strand Distance 4 chrY 1 5338 - 0 0 chr1 2749102 2749103 - 2749101 Actual Chromosome Start End Strand Distance 0 chr1 2749102 2749103 - 2749101 1 chrY 1 5338 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2749102 2749103 - 2749101 1 chrY 1 5338 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsq3mto2n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsq3mto2n/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2749102 2749103 - 2749101 4 chrY 1 5338 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2749102 | 2749103 | a | 0 | ... | | chrY | 1 | 5338 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chrY 1 5338 - 0 0 chr1 2749102 2749103 - 2749101 df2 Chromosome Start End Strand Distance 4 chrY 1 5338 - 0 0 chr1 2749102 2749103 - 2749101 Actual Chromosome Start End Strand Distance 0 chr1 2749102 2749103 - 2749101 1 chrY 1 5338 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2749102 2749103 - 2749101 1 chrY 1 5338 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb8jmwuu0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb8jmwuu0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2749102 2749103 - 2749101 4 chrY 1 5338 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2749102 | 2749103 | a | 0 | ... | | chrY | 1 | 5338 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chrY 1 5338 - 0 0 chr1 2749102 2749103 - 2749101 df2 Chromosome Start End Strand Distance 4 chrY 1 5338 - 0 0 chr1 2749102 2749103 - 2749101 Actual Chromosome Start End Strand Distance 0 chr1 2749102 2749103 - 2749101 1 chrY 1 5338 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2749102 2749103 - 2749101 1 chrY 1 5338 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf2rlfdto/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf2rlfdto/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 8 chr22 7984094 7986223 + 7641456 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr22 | 7984094 | 7986223 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr22 7984094 7986223 + 7641456 df2 Chromosome Start End Strand Distance 8 chr22 7984094 7986223 + 7641456 Actual Chromosome Start End Strand Distance 0 chr22 7984094 7986223 + 7641456 Expected Chromosome Start End Strand Distance 0 chr22 7984094 7986223 + 7641456 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmptmcv5nkr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptmcv5nkr/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 8 chr22 7984094 7986223 + 7641456 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr22 | 7984094 | 7986223 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr22 7984094 7986223 + 7641456 df2 Chromosome Start End Strand Distance 8 chr22 7984094 7986223 + 7641456 Actual Chromosome Start End Strand Distance 0 chr22 7984094 7986223 + 7641456 Expected Chromosome Start End Strand Distance 0 chr22 7984094 7986223 + 7641456 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyfyr2ht7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyfyr2ht7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1768591 1770720 + 0 1 chr1 1768591 1770720 + 2412879 2 chr1 4183598 4185727 + 0 3 chr1 4183598 4185727 + 249942 4 chr1 4435668 4437797 + 0 5 chr1 4435668 4437797 + 249942 6 chr1 7389316 7391445 + 0 7 chr1 7389316 7391445 + 1647630 8 chr1 9039074 9047999 + 0 9 chr1 9039074 9047999 + 1647630 10 chr17 3490501 3498209 - 0 11 chr2 2323090 2327667 + 0 12 chr2 2323090 2327667 + 6409916 13 chr2 8737582 8740811 + 0 14 chr2 8737582 8740811 + 6409916 15 chr22 7984094 7986223 + 0 16 chr6 4866858 4874359 + 0 17 chr7 5521075 5523204 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 4183598 | 4185727 | a | 0 | ... | | chr1 | 4183598 | 4185727 | a | 0 | ... | | chr1 | 7389316 | 7391445 | a | 0 | ... | | chr1 | 7389316 | 7391445 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr6 | 4866858 | 4874359 | a | 0 | ... | | chr7 | 5521075 | 5523204 | a | 0 | ... | | chr17 | 3490501 | 3498209 | a | 0 | ... | | chr22 | 7984094 | 7986223 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 18 rows and 12 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr1 1768591 1770720 + 0 7 chr1 1768591 1770720 + 2412879 10 chr2 2323090 2327667 + 0 11 chr2 2323090 2327667 + 6409916 16 chr17 3490501 3498209 - 0 0 chr1 4183598 4185727 + 0 1 chr1 4183598 4185727 + 249942 8 chr1 4435668 4437797 + 0 9 chr1 4435668 4437797 + 249942 14 chr6 4866858 4874359 + 0 15 chr7 5521075 5523204 + 0 2 chr1 7389316 7391445 + 0 3 chr1 7389316 7391445 + 1647630 17 chr22 7984094 7986223 + 0 12 chr2 8737582 8740811 + 0 13 chr2 8737582 8740811 + 6409916 4 chr1 9039074 9047999 + 0 5 chr1 9039074 9047999 + 1647630 df2 Chromosome Start End Strand Distance 0 chr1 1768591 1770720 + 0 1 chr1 1768591 1770720 + 2412879 11 chr2 2323090 2327667 + 0 12 chr2 2323090 2327667 + 6409916 10 chr17 3490501 3498209 - 0 2 chr1 4183598 4185727 + 0 3 chr1 4183598 4185727 + 249942 4 chr1 4435668 4437797 + 0 5 chr1 4435668 4437797 + 249942 16 chr6 4866858 4874359 + 0 17 chr7 5521075 5523204 + 0 6 chr1 7389316 7391445 + 0 7 chr1 7389316 7391445 + 1647630 15 chr22 7984094 7986223 + 0 13 chr2 8737582 8740811 + 0 14 chr2 8737582 8740811 + 6409916 8 chr1 9039074 9047999 + 0 9 chr1 9039074 9047999 + 1647630 Actual Chromosome Start End Strand Distance 0 chr1 1768591 1770720 + 0 1 chr1 1768591 1770720 + 2412879 2 chr1 4183598 4185727 + 0 3 chr1 4183598 4185727 + 249942 4 chr1 4435668 4437797 + 0 5 chr1 4435668 4437797 + 249942 6 chr1 7389316 7391445 + 0 7 chr1 7389316 7391445 + 1647630 8 chr1 9039074 9047999 + 0 9 chr1 9039074 9047999 + 1647630 10 chr17 3490501 3498209 - 0 11 chr2 2323090 2327667 + 0 12 chr2 2323090 2327667 + 6409916 13 chr2 8737582 8740811 + 0 14 chr2 8737582 8740811 + 6409916 15 chr22 7984094 7986223 + 0 16 chr6 4866858 4874359 + 0 17 chr7 5521075 5523204 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1768591 1770720 + 0 1 chr1 1768591 1770720 + 2412879 2 chr1 4183598 4185727 + 0 3 chr1 4183598 4185727 + 249942 4 chr1 4435668 4437797 + 0 5 chr1 4435668 4437797 + 249942 6 chr1 7389316 7391445 + 0 7 chr1 7389316 7391445 + 1647630 8 chr1 9039074 9047999 + 0 9 chr1 9039074 9047999 + 1647630 10 chr17 3490501 3498209 - 0 11 chr2 2323090 2327667 + 0 12 chr2 2323090 2327667 + 6409916 13 chr2 8737582 8740811 + 0 14 chr2 8737582 8740811 + 6409916 15 chr22 7984094 7986223 + 0 16 chr6 4866858 4874359 + 0 17 chr7 5521075 5523204 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=18, step=1) Expected index RangeIndex(start=0, stop=18, step=1) index equal [ True True True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyjughzng/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyjughzng/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 6 chr2 2323090 2327667 + 2323083 7 chr2 8737582 8740811 + 8737575 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 2323090 | 2327667 | a | 0 | ... | | chr2 | 8737582 | 8740811 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr2 2323090 2327667 + 2323083 1 chr2 8737582 8740811 + 8737575 df2 Chromosome Start End Strand Distance 6 chr2 2323090 2327667 + 2323083 7 chr2 8737582 8740811 + 8737575 Actual Chromosome Start End Strand Distance 0 chr2 2323090 2327667 + 2323083 1 chr2 8737582 8740811 + 8737575 Expected Chromosome Start End Strand Distance 0 chr2 2323090 2327667 + 2323083 1 chr2 8737582 8740811 + 8737575 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm10qo4kh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm10qo4kh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 2 chr1 1 7 - 0 3 chr1 1 7 - 0 4 chr1 1 7 - 0 5 chr1 1 7 - 0 6 chr1 1 7 - 0 7 chr1 1 9 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 9 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | | chr1 | 1 | 7 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1 7 - 0 2 chr1 1 7 - 0 3 chr1 1 7 - 0 4 chr1 1 7 - 0 5 chr1 1 7 - 0 0 chr1 1 9 - 0 df2 Chromosome Start End Strand Distance 2 chr1 1 7 - 0 3 chr1 1 7 - 0 4 chr1 1 7 - 0 5 chr1 1 7 - 0 6 chr1 1 7 - 0 7 chr1 1 9 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 7 - 0 1 chr1 1 7 - 0 2 chr1 1 7 - 0 3 chr1 1 7 - 0 4 chr1 1 7 - 0 5 chr1 1 9 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 7 - 0 1 chr1 1 7 - 0 2 chr1 1 7 - 0 3 chr1 1 7 - 0 4 chr1 1 7 - 0 5 chr1 1 9 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp17wutrqa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp17wutrqa/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr2 7 16 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr2 | 7 | 16 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr2 7 16 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr2 7 16 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr2 7 16 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr2 7 16 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpixg6hp4b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpixg6hp4b/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 909541 909664 + 53069 1 chr1 6778079 6782348 - 726603 2 chr1 6778079 6782348 - 1386547 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 909541 | 909664 | a | 0 | ... | | chr1 | 6778079 | 6782348 | a | 0 | ... | | chr1 | 6778079 | 6782348 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 909541 909664 + 53069 1 chr1 6778079 6782348 - 726603 2 chr1 6778079 6782348 - 1386547 df2 Chromosome Start End Strand Distance 0 chr1 909541 909664 + 53069 1 chr1 6778079 6782348 - 726603 2 chr1 6778079 6782348 - 1386547 Actual Chromosome Start End Strand Distance 0 chr1 909541 909664 + 53069 1 chr1 6778079 6782348 - 726603 2 chr1 6778079 6782348 - 1386547 Expected Chromosome Start End Strand Distance 0 chr1 909541 909664 + 53069 1 chr1 6778079 6782348 - 726603 2 chr1 6778079 6782348 - 1386547 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb0z754zr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb0z754zr/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 909541 909664 + 62909 1 chr1 6778079 6782348 - 726603 2 chr1 6778079 6782348 - 1386547 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 909541 | 909664 | a | 0 | ... | | chr1 | 6778079 | 6782348 | a | 0 | ... | | chr1 | 6778079 | 6782348 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 909541 909664 + 62909 1 chr1 6778079 6782348 - 726603 2 chr1 6778079 6782348 - 1386547 df2 Chromosome Start End Strand Distance 0 chr1 909541 909664 + 62909 1 chr1 6778079 6782348 - 726603 2 chr1 6778079 6782348 - 1386547 Actual Chromosome Start End Strand Distance 0 chr1 909541 909664 + 62909 1 chr1 6778079 6782348 - 726603 2 chr1 6778079 6782348 - 1386547 Expected Chromosome Start End Strand Distance 0 chr1 909541 909664 + 62909 1 chr1 6778079 6782348 - 726603 2 chr1 6778079 6782348 - 1386547 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx3aadfoq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx3aadfoq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 909541 909664 - 909540 1 chr1 6778079 6782348 - 6778078 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 909541 | 909664 | a | 0 | ... | | chr1 | 6778079 | 6782348 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 909541 909664 - 909540 1 chr1 6778079 6782348 - 6778078 df2 Chromosome Start End Strand Distance 0 chr1 909541 909664 - 909540 1 chr1 6778079 6782348 - 6778078 Actual Chromosome Start End Strand Distance 0 chr1 909541 909664 - 909540 1 chr1 6778079 6782348 - 6778078 Expected Chromosome Start End Strand Distance 0 chr1 909541 909664 - 909540 1 chr1 6778079 6782348 - 6778078 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz5wg5wie/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz5wg5wie/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 126 - 2 1 chr1 6778079 6782348 - 6778078 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 126 | a | 0 | ... | | chr1 | 6778079 | 6782348 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 126 - 2 1 chr1 6778079 6782348 - 6778078 df2 Chromosome Start End Strand Distance 0 chr1 3 126 - 2 1 chr1 6778079 6782348 - 6778078 Actual Chromosome Start End Strand Distance 0 chr1 3 126 - 2 1 chr1 6778079 6782348 - 6778078 Expected Chromosome Start End Strand Distance 0 chr1 3 126 - 2 1 chr1 6778079 6782348 - 6778078 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu2qambrn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu2qambrn/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3 126 - 2 1 chr1 6778079 6782348 - 6778078 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 126 | a | 0 | ... | | chr1 | 6778079 | 6782348 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3 126 - 2 1 chr1 6778079 6782348 - 6778078 df2 Chromosome Start End Strand Distance 0 chr1 3 126 - 2 1 chr1 6778079 6782348 - 6778078 Actual Chromosome Start End Strand Distance 0 chr1 3 126 - 2 1 chr1 6778079 6782348 - 6778078 Expected Chromosome Start End Strand Distance 0 chr1 3 126 - 2 1 chr1 6778079 6782348 - 6778078 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmcdo6xc0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmcdo6xc0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 2091035 2092639 - 5057291 3 chr1 2091035 2099931 - 5049999 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2091035 | 2099931 | a | 0 | ... | | chr1 | 2091035 | 2092639 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 2091035 2092639 - 5057291 0 chr1 2091035 2099931 - 5049999 df2 Chromosome Start End Strand Distance 1 chr1 2091035 2092639 - 5057291 3 chr1 2091035 2099931 - 5049999 Actual Chromosome Start End Strand Distance 0 chr1 2091035 2092639 - 5057291 1 chr1 2091035 2099931 - 5049999 Expected Chromosome Start End Strand Distance 0 chr1 2091035 2092639 - 5057291 1 chr1 2091035 2099931 - 5049999 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2b02fy7d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2b02fy7d/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 2091035 2092639 - 5057291 3 chr1 2091035 2099931 - 5049999 10 chr7 9794368 9803974 - 3586055 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2091035 | 2099931 | a | 0 | ... | | chr1 | 2091035 | 2092639 | a | 0 | ... | | chr7 | 9794368 | 9803974 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 2091035 2092639 - 5057291 0 chr1 2091035 2099931 - 5049999 2 chr7 9794368 9803974 - 3586055 df2 Chromosome Start End Strand Distance 1 chr1 2091035 2092639 - 5057291 3 chr1 2091035 2099931 - 5049999 10 chr7 9794368 9803974 - 3586055 Actual Chromosome Start End Strand Distance 0 chr1 2091035 2092639 - 5057291 1 chr1 2091035 2099931 - 5049999 2 chr7 9794368 9803974 - 3586055 Expected Chromosome Start End Strand Distance 0 chr1 2091035 2092639 - 5057291 1 chr1 2091035 2099931 - 5049999 2 chr7 9794368 9803974 - 3586055 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_g4cjtsn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_g4cjtsn/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 2 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 2 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd_grp9yv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd_grp9yv/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 2 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 2 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc2dab9ch/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc2dab9ch/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 3 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 3 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzke4fmwn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzke4fmwn/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 3 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 3 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyd5xh1j5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyd5xh1j5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3gm1jzyl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3gm1jzyl/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 482310 491073 - 3519862 1 chr1 482310 491073 - 7161815 2 chr1 3849832 3854051 - 156884 3 chr1 3849832 3854051 - 3798837 5 chr19 3271404 3276456 + 2912838 6 chr19 4298024 4303155 + 3939458 8 chr19 8495245 8499724 + 8136679 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 482310 | 491073 | a | 0 | ... | | chr1 | 482310 | 491073 | a | 0 | ... | | chr1 | 3849832 | 3854051 | a | 0 | ... | | chr1 | 3849832 | 3854051 | a | 0 | ... | | chr19 | 3271404 | 3276456 | a | 0 | ... | | chr19 | 4298024 | 4303155 | a | 0 | ... | | chr19 | 8495245 | 8499724 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 482310 491073 - 3519862 1 chr1 482310 491073 - 7161815 4 chr19 3271404 3276456 + 2912838 2 chr1 3849832 3854051 - 156884 3 chr1 3849832 3854051 - 3798837 5 chr19 4298024 4303155 + 3939458 6 chr19 8495245 8499724 + 8136679 df2 Chromosome Start End Strand Distance 0 chr1 482310 491073 - 3519862 1 chr1 482310 491073 - 7161815 5 chr19 3271404 3276456 + 2912838 2 chr1 3849832 3854051 - 156884 3 chr1 3849832 3854051 - 3798837 6 chr19 4298024 4303155 + 3939458 8 chr19 8495245 8499724 + 8136679 Actual Chromosome Start End Strand Distance 0 chr1 482310 491073 - 3519862 1 chr1 482310 491073 - 7161815 2 chr1 3849832 3854051 - 156884 3 chr1 3849832 3854051 - 3798837 4 chr19 3271404 3276456 + 2912838 5 chr19 4298024 4303155 + 3939458 6 chr19 8495245 8499724 + 8136679 Expected Chromosome Start End Strand Distance 0 chr1 482310 491073 - 3519862 1 chr1 482310 491073 - 7161815 2 chr1 3849832 3854051 - 156884 3 chr1 3849832 3854051 - 3798837 4 chr19 3271404 3276456 + 2912838 5 chr19 4298024 4303155 + 3939458 6 chr19 8495245 8499724 + 8136679 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwi0qqnt6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwi0qqnt6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy6bzt2kp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy6bzt2kp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9y5cx71d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9y5cx71d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmyumfv2m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmyumfv2m/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwr4vqa5m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwr4vqa5m/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpks7k43yx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpks7k43yx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu2ri4g11/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu2ri4g11/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4030951 4032693 - 1031784 1 chr1 6664428 6668133 - 3665261 2 chr1 6664428 6671333 - 3665261 3 chr1 6873933 6879593 - 3874766 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6664428 | 6668133 | a | 0 | ... | | chr1 | 4030951 | 4032693 | a | 0 | ... | | chr1 | 6873933 | 6879593 | a | 0 | ... | | chr1 | 6664428 | 6671333 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 4030951 4032693 - 1031784 0 chr1 6664428 6668133 - 3665261 3 chr1 6664428 6671333 - 3665261 2 chr1 6873933 6879593 - 3874766 df2 Chromosome Start End Strand Distance 0 chr1 4030951 4032693 - 1031784 1 chr1 6664428 6668133 - 3665261 2 chr1 6664428 6671333 - 3665261 3 chr1 6873933 6879593 - 3874766 Actual Chromosome Start End Strand Distance 0 chr1 4030951 4032693 - 1031784 1 chr1 6664428 6668133 - 3665261 2 chr1 6664428 6671333 - 3665261 3 chr1 6873933 6879593 - 3874766 Expected Chromosome Start End Strand Distance 0 chr1 4030951 4032693 - 1031784 1 chr1 6664428 6668133 - 3665261 2 chr1 6664428 6671333 - 3665261 3 chr1 6873933 6879593 - 3874766 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8fv_fri_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8fv_fri_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 4 chr1 7214955 7221860 + 4221330 5 chr1 9283190 9290095 + 6289565 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9283190 | 9290095 | a | 0 | ... | | chr1 | 7214955 | 7221860 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 7214955 7221860 + 4221330 0 chr1 9283190 9290095 + 6289565 df2 Chromosome Start End Strand Distance 4 chr1 7214955 7221860 + 4221330 5 chr1 9283190 9290095 + 6289565 Actual Chromosome Start End Strand Distance 0 chr1 7214955 7221860 + 4221330 1 chr1 9283190 9290095 + 6289565 Expected Chromosome Start End Strand Distance 0 chr1 7214955 7221860 + 4221330 1 chr1 9283190 9290095 + 6289565 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw0_u2uu5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw0_u2uu5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 4 767 + 3 6 chr2 1 2 + 0 7 chr2 5784769 5784770 + 5784768 8 chr2 6873933 6873934 + 6873932 9 chr2 9283190 9283191 + 9283189 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 4 | 767 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr2 | 9283190 | 9283191 | a | 0 | ... | | chr2 | 5784769 | 5784770 | a | 0 | ... | | chr2 | 6873933 | 6873934 | a | 0 | ... | | chr2 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 8 chr2 1 2 + 0 1 chr1 4 767 + 3 6 chr2 5784769 5784770 + 5784768 7 chr2 6873933 6873934 + 6873932 5 chr2 9283190 9283191 + 9283189 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 6 chr2 1 2 + 0 4 chr1 4 767 + 3 7 chr2 5784769 5784770 + 5784768 8 chr2 6873933 6873934 + 6873932 9 chr2 9283190 9283191 + 9283189 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 4 767 + 3 5 chr2 1 2 + 0 6 chr2 5784769 5784770 + 5784768 7 chr2 6873933 6873934 + 6873932 8 chr2 9283190 9283191 + 9283189 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 4 767 + 3 5 chr2 1 2 + 0 6 chr2 5784769 5784770 + 5784768 7 chr2 6873933 6873934 + 6873932 8 chr2 9283190 9283191 + 9283189 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=9, step=1) index equal [ True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpidsvqtml/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpidsvqtml/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 3074 - 0 7 chr1 1 3496 - 0 8 chr1 1 6214 - 0 9 chr1 1 7262 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 3496 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 3074 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 6 chr1 1 2 - 0 8 chr1 1 2 - 0 9 chr1 1 2 - 0 7 chr1 1 3074 - 0 1 chr1 1 3496 - 0 4 chr1 1 6214 - 0 5 chr1 1 7262 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 3074 - 0 7 chr1 1 3496 - 0 8 chr1 1 6214 - 0 9 chr1 1 7262 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 3074 - 0 7 chr1 1 3496 - 0 8 chr1 1 6214 - 0 9 chr1 1 7262 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 3074 - 0 7 chr1 1 3496 - 0 8 chr1 1 6214 - 0 9 chr1 1 7262 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw_91u1ug/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw_91u1ug/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr1 1 3074 - 0 8 chr1 1 3496 - 0 9 chr1 1 6214 - 0 10 chr1 1 7262 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 3496 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 3074 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 11 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 7 chr1 1 2 - 0 9 chr1 1 2 - 0 10 chr1 1 2 - 0 8 chr1 1 3074 - 0 2 chr1 1 3496 - 0 5 chr1 1 6214 - 0 6 chr1 1 7262 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr1 1 3074 - 0 8 chr1 1 3496 - 0 9 chr1 1 6214 - 0 10 chr1 1 7262 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr1 1 3074 - 0 8 chr1 1 3496 - 0 9 chr1 1 6214 - 0 10 chr1 1 7262 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr1 1 3074 - 0 8 chr1 1 3496 - 0 9 chr1 1 6214 - 0 10 chr1 1 7262 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=11, step=1) Expected index RangeIndex(start=0, stop=11, step=1) index equal [ True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsnz9ehy2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsnz9ehy2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg_8j8o71/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg_8j8o71/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 4910486 4916581 - 1041081 1 chr1 5830988 5837083 + 5664740 2 chr1 8181139 8187234 + 8014891 3 chr1 8230433 8230979 + 8064185 4 chr1 8988104 8990604 + 8821856 5 chr1 9374523 9377138 - 5505118 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8230433 | 8230979 | a | 0 | ... | | chr1 | 8988104 | 8990604 | a | 0 | ... | | chr1 | 5830988 | 5837083 | a | 0 | ... | | chr1 | 8181139 | 8187234 | a | 0 | ... | | chr1 | 9374523 | 9377138 | a | 0 | ... | | chr1 | 4910486 | 4916581 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 5 chr1 4910486 4916581 - 1041081 2 chr1 5830988 5837083 + 5664740 3 chr1 8181139 8187234 + 8014891 0 chr1 8230433 8230979 + 8064185 1 chr1 8988104 8990604 + 8821856 4 chr1 9374523 9377138 - 5505118 df2 Chromosome Start End Strand Distance 0 chr1 4910486 4916581 - 1041081 1 chr1 5830988 5837083 + 5664740 2 chr1 8181139 8187234 + 8014891 3 chr1 8230433 8230979 + 8064185 4 chr1 8988104 8990604 + 8821856 5 chr1 9374523 9377138 - 5505118 Actual Chromosome Start End Strand Distance 0 chr1 4910486 4916581 - 1041081 1 chr1 5830988 5837083 + 5664740 2 chr1 8181139 8187234 + 8014891 3 chr1 8230433 8230979 + 8064185 4 chr1 8988104 8990604 + 8821856 5 chr1 9374523 9377138 - 5505118 Expected Chromosome Start End Strand Distance 0 chr1 4910486 4916581 - 1041081 1 chr1 5830988 5837083 + 5664740 2 chr1 8181139 8187234 + 8014891 3 chr1 8230433 8230979 + 8064185 4 chr1 8988104 8990604 + 8821856 5 chr1 9374523 9377138 - 5505118 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5rioaoyy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5rioaoyy/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 158397 166249 + 0 1 chr1 3866378 3869406 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 158397 | 166249 | a | 0 | ... | | chr1 | 3866378 | 3869406 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 158397 166249 + 0 1 chr1 3866378 3869406 - 0 df2 Chromosome Start End Strand Distance 0 chr1 158397 166249 + 0 1 chr1 3866378 3869406 - 0 Actual Chromosome Start End Strand Distance 0 chr1 158397 166249 + 0 1 chr1 3866378 3869406 - 0 Expected Chromosome Start End Strand Distance 0 chr1 158397 166249 + 0 1 chr1 3866378 3869406 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp66ygp4q8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp66ygp4q8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 3866378 3869406 - 0 2 chr1 3866378 3869406 - 3700130 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3866378 | 3869406 | a | 0 | ... | | chr1 | 3866378 | 3869406 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3866378 3869406 - 0 1 chr1 3866378 3869406 - 3700130 df2 Chromosome Start End Strand Distance 1 chr1 3866378 3869406 - 0 2 chr1 3866378 3869406 - 3700130 Actual Chromosome Start End Strand Distance 0 chr1 3866378 3869406 - 0 1 chr1 3866378 3869406 - 3700130 Expected Chromosome Start End Strand Distance 0 chr1 3866378 3869406 - 0 1 chr1 3866378 3869406 - 3700130 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5rz9ttsn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5rz9ttsn/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 5214371 5223822 + 252878 1 chr1 5214371 5223822 + 2392646 2 chr1 6581746 6588849 - 5408 3 chr1 6581746 6588849 - 718515 4 chr1 7149646 7149648 + 2188153 5 chr1 7149646 7149648 + 4327921 6 chr1 8991849 9000352 + 4030356 7 chr1 8991849 9000352 + 6170124 8 chr1 9367184 9376986 - 2790846 9 chr1 9367184 9376986 - 3503953 10 chr1 9385523 9388732 + 4424030 11 chr1 9385523 9388732 + 6563798 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8991849 | 9000352 | a | 0 | ... | | chr1 | 8991849 | 9000352 | a | 0 | ... | | chr1 | 7149646 | 7149648 | a | 0 | ... | | chr1 | 7149646 | 7149648 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 6581746 | 6588849 | a | 0 | ... | | chr1 | 6581746 | 6588849 | a | 0 | ... | | chr1 | 9367184 | 9376986 | a | 0 | ... | | chr1 | 9367184 | 9376986 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 12 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 5214371 5223822 + 252878 5 chr1 5214371 5223822 + 2392646 8 chr1 6581746 6588849 - 5408 9 chr1 6581746 6588849 - 718515 2 chr1 7149646 7149648 + 2188153 3 chr1 7149646 7149648 + 4327921 0 chr1 8991849 9000352 + 4030356 1 chr1 8991849 9000352 + 6170124 10 chr1 9367184 9376986 - 2790846 11 chr1 9367184 9376986 - 3503953 6 chr1 9385523 9388732 + 4424030 7 chr1 9385523 9388732 + 6563798 df2 Chromosome Start End Strand Distance 0 chr1 5214371 5223822 + 252878 1 chr1 5214371 5223822 + 2392646 2 chr1 6581746 6588849 - 5408 3 chr1 6581746 6588849 - 718515 4 chr1 7149646 7149648 + 2188153 5 chr1 7149646 7149648 + 4327921 6 chr1 8991849 9000352 + 4030356 7 chr1 8991849 9000352 + 6170124 8 chr1 9367184 9376986 - 2790846 9 chr1 9367184 9376986 - 3503953 10 chr1 9385523 9388732 + 4424030 11 chr1 9385523 9388732 + 6563798 Actual Chromosome Start End Strand Distance 0 chr1 5214371 5223822 + 252878 1 chr1 5214371 5223822 + 2392646 2 chr1 6581746 6588849 - 5408 3 chr1 6581746 6588849 - 718515 4 chr1 7149646 7149648 + 2188153 5 chr1 7149646 7149648 + 4327921 6 chr1 8991849 9000352 + 4030356 7 chr1 8991849 9000352 + 6170124 8 chr1 9367184 9376986 - 2790846 9 chr1 9367184 9376986 - 3503953 10 chr1 9385523 9388732 + 4424030 11 chr1 9385523 9388732 + 6563798 Expected Chromosome Start End Strand Distance 0 chr1 5214371 5223822 + 252878 1 chr1 5214371 5223822 + 2392646 2 chr1 6581746 6588849 - 5408 3 chr1 6581746 6588849 - 718515 4 chr1 7149646 7149648 + 2188153 5 chr1 7149646 7149648 + 4327921 6 chr1 8991849 9000352 + 4030356 7 chr1 8991849 9000352 + 6170124 8 chr1 9367184 9376986 - 2790846 9 chr1 9367184 9376986 - 3503953 10 chr1 9385523 9388732 + 4424030 11 chr1 9385523 9388732 + 6563798 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=12, step=1) Expected index RangeIndex(start=0, stop=12, step=1) index equal [ True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9kiheren/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9kiheren/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3445rseb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3445rseb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpevzczdrj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpevzczdrj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmptnottwn7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptnottwn7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx6dkjhw9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx6dkjhw9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwim2b4v_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwim2b4v_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6xb6t5jg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6xb6t5jg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 149159 150036 - 6794729 1 chr1 1083624 1092889 - 5851876 2 chr1 1447905 1455463 + 5322233 3 chr1 1447905 1455463 + 8065811 4 chr1 3306323 3306324 + 3471372 5 chr1 3306323 3306324 + 6214950 6 chr1 3865112 3873752 - 3071013 7 chr1 4869654 4871133 + 1906563 8 chr1 4869654 4871133 + 4650141 9 chr1 9999999 10005019 + 475767 10 chr1 9999999 10005019 + 3218848 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3306323 | 3306324 | a | 0 | ... | | chr1 | 3306323 | 3306324 | a | 0 | ... | | chr1 | 1447905 | 1455463 | a | 0 | ... | | chr1 | 1447905 | 1455463 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 4869654 | 4871133 | a | 0 | ... | | chr1 | 3865112 | 3873752 | a | 0 | ... | | chr1 | 149159 | 150036 | a | 0 | ... | | chr1 | 1083624 | 1092889 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 11 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 9 chr1 149159 150036 - 6794729 10 chr1 1083624 1092889 - 5851876 2 chr1 1447905 1455463 + 5322233 3 chr1 1447905 1455463 + 8065811 0 chr1 3306323 3306324 + 3471372 1 chr1 3306323 3306324 + 6214950 8 chr1 3865112 3873752 - 3071013 6 chr1 4869654 4871133 + 1906563 7 chr1 4869654 4871133 + 4650141 4 chr1 9999999 10005019 + 475767 5 chr1 9999999 10005019 + 3218848 df2 Chromosome Start End Strand Distance 0 chr1 149159 150036 - 6794729 1 chr1 1083624 1092889 - 5851876 2 chr1 1447905 1455463 + 5322233 3 chr1 1447905 1455463 + 8065811 4 chr1 3306323 3306324 + 3471372 5 chr1 3306323 3306324 + 6214950 6 chr1 3865112 3873752 - 3071013 7 chr1 4869654 4871133 + 1906563 8 chr1 4869654 4871133 + 4650141 9 chr1 9999999 10005019 + 475767 10 chr1 9999999 10005019 + 3218848 Actual Chromosome Start End Strand Distance 0 chr1 149159 150036 - 6794729 1 chr1 1083624 1092889 - 5851876 2 chr1 1447905 1455463 + 5322233 3 chr1 1447905 1455463 + 8065811 4 chr1 3306323 3306324 + 3471372 5 chr1 3306323 3306324 + 6214950 6 chr1 3865112 3873752 - 3071013 7 chr1 4869654 4871133 + 1906563 8 chr1 4869654 4871133 + 4650141 9 chr1 9999999 10005019 + 475767 10 chr1 9999999 10005019 + 3218848 Expected Chromosome Start End Strand Distance 0 chr1 149159 150036 - 6794729 1 chr1 1083624 1092889 - 5851876 2 chr1 1447905 1455463 + 5322233 3 chr1 1447905 1455463 + 8065811 4 chr1 3306323 3306324 + 3471372 5 chr1 3306323 3306324 + 6214950 6 chr1 3865112 3873752 - 3071013 7 chr1 4869654 4871133 + 1906563 8 chr1 4869654 4871133 + 4650141 9 chr1 9999999 10005019 + 475767 10 chr1 9999999 10005019 + 3218848 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=11, step=1) Expected index RangeIndex(start=0, stop=11, step=1) index equal [ True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp__xrbtqv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp__xrbtqv/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 2 chr1 1447905 1455463 + 1447904 3 chr1 1447905 1455463 + 5489302 4 chr1 3306323 3306324 + 3306322 5 chr1 3306323 3306324 + 3638441 7 chr1 4869654 4871133 + 2073632 8 chr1 4869654 4871133 + 4869653 9 chr1 9999999 10005019 + 3047555 10 chr1 9999999 10005019 + 3050811 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3306323 | 3306324 | a | 0 | ... | | chr1 | 3306323 | 3306324 | a | 0 | ... | | chr1 | 1447905 | 1455463 | a | 0 | ... | | chr1 | 1447905 | 1455463 | a | 0 | ... | | chr1 | 9999999 | 10005019 | a | 0 | ... | | chr1 | 9999999 | 10005019 | a | 0 | ... | | chr1 | 4869654 | 4871133 | a | 0 | ... | | chr1 | 4869654 | 4871133 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1447905 1455463 + 1447904 3 chr1 1447905 1455463 + 5489302 0 chr1 3306323 3306324 + 3306322 1 chr1 3306323 3306324 + 3638441 6 chr1 4869654 4871133 + 2073632 7 chr1 4869654 4871133 + 4869653 4 chr1 9999999 10005019 + 3047555 5 chr1 9999999 10005019 + 3050811 df2 Chromosome Start End Strand Distance 2 chr1 1447905 1455463 + 1447904 3 chr1 1447905 1455463 + 5489302 4 chr1 3306323 3306324 + 3306322 5 chr1 3306323 3306324 + 3638441 7 chr1 4869654 4871133 + 2073632 8 chr1 4869654 4871133 + 4869653 9 chr1 9999999 10005019 + 3047555 10 chr1 9999999 10005019 + 3050811 Actual Chromosome Start End Strand Distance 0 chr1 1447905 1455463 + 1447904 1 chr1 1447905 1455463 + 5489302 2 chr1 3306323 3306324 + 3306322 3 chr1 3306323 3306324 + 3638441 4 chr1 4869654 4871133 + 2073632 5 chr1 4869654 4871133 + 4869653 6 chr1 9999999 10005019 + 3047555 7 chr1 9999999 10005019 + 3050811 Expected Chromosome Start End Strand Distance 0 chr1 1447905 1455463 + 1447904 1 chr1 1447905 1455463 + 5489302 2 chr1 3306323 3306324 + 3306322 3 chr1 3306323 3306324 + 3638441 4 chr1 4869654 4871133 + 2073632 5 chr1 4869654 4871133 + 4869653 6 chr1 9999999 10005019 + 3047555 7 chr1 9999999 10005019 + 3050811 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0uwrtj0m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0uwrtj0m/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 8 2 chr1 1 2 - 0 3 chr1 1 2 - 8 4 chr1 1 2 - 0 5 chr1 1 2 - 8 6 chr1 7 8 - 2 7 chr1 7 8 - 6 8 chr1 12 13 - 3 9 chr1 12 13 - 11 10 chr1 21 22 - 12 11 chr1 21 22 - 20 12 chr1 21 22 - 12 13 chr1 21 22 - 20 14 chr1 21 22 - 12 15 chr1 21 22 - 20 16 chr1 21 22 - 12 17 chr1 21 22 - 20 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 12 | 13 | a | 0 | ... | | chr1 | 12 | 13 | a | 0 | ... | | chr1 | 7 | 8 | a | 0 | ... | | chr1 | 7 | 8 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 21 | 22 | a | 0 | ... | | chr1 | 21 | 22 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 18 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 1 2 - 0 6 chr1 1 2 - 0 16 chr1 1 2 - 0 5 chr1 1 2 - 8 7 chr1 1 2 - 8 17 chr1 1 2 - 8 2 chr1 7 8 - 2 3 chr1 7 8 - 6 0 chr1 12 13 - 3 1 chr1 12 13 - 11 8 chr1 21 22 - 12 10 chr1 21 22 - 12 12 chr1 21 22 - 12 14 chr1 21 22 - 12 9 chr1 21 22 - 20 11 chr1 21 22 - 20 13 chr1 21 22 - 20 15 chr1 21 22 - 20 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 2 chr1 1 2 - 0 4 chr1 1 2 - 0 1 chr1 1 2 - 8 3 chr1 1 2 - 8 5 chr1 1 2 - 8 6 chr1 7 8 - 2 7 chr1 7 8 - 6 8 chr1 12 13 - 3 9 chr1 12 13 - 11 10 chr1 21 22 - 12 12 chr1 21 22 - 12 14 chr1 21 22 - 12 16 chr1 21 22 - 12 11 chr1 21 22 - 20 13 chr1 21 22 - 20 15 chr1 21 22 - 20 17 chr1 21 22 - 20 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 8 4 chr1 1 2 - 8 5 chr1 1 2 - 8 6 chr1 7 8 - 2 7 chr1 7 8 - 6 8 chr1 12 13 - 3 9 chr1 12 13 - 11 10 chr1 21 22 - 12 11 chr1 21 22 - 12 12 chr1 21 22 - 12 13 chr1 21 22 - 12 14 chr1 21 22 - 20 15 chr1 21 22 - 20 16 chr1 21 22 - 20 17 chr1 21 22 - 20 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 8 4 chr1 1 2 - 8 5 chr1 1 2 - 8 6 chr1 7 8 - 2 7 chr1 7 8 - 6 8 chr1 12 13 - 3 9 chr1 12 13 - 11 10 chr1 21 22 - 12 11 chr1 21 22 - 12 12 chr1 21 22 - 12 13 chr1 21 22 - 12 14 chr1 21 22 - 20 15 chr1 21 22 - 20 16 chr1 21 22 - 20 17 chr1 21 22 - 20 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=18, step=1) Expected index RangeIndex(start=0, stop=18, step=1) index equal [ True True True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyjj_vevn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyjj_vevn/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 8 2 chr1 1 2 - 0 3 chr1 1 2 - 8 4 chr1 1 2 - 0 5 chr1 1 2 - 8 6 chr1 12 13 - 3 7 chr1 12 13 - 11 8 chr1 21 22 - 12 9 chr1 21 22 - 20 10 chr1 21 22 - 12 11 chr1 21 22 - 20 12 chr1 21 22 - 12 13 chr1 21 22 - 20 14 chr1 21 22 - 12 15 chr1 21 22 - 20 16 chr1 4169063 4169064 - 4169054 17 chr1 4169063 4169064 - 4169062 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 12 | 13 | a | 0 | ... | | chr1 | 12 | 13 | a | 0 | ... | | chr1 | 4169063 | 4169064 | a | 0 | ... | | chr1 | 4169063 | 4169064 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 21 | 22 | a | 0 | ... | | chr1 | 21 | 22 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 18 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 1 2 - 0 6 chr1 1 2 - 0 16 chr1 1 2 - 0 5 chr1 1 2 - 8 7 chr1 1 2 - 8 17 chr1 1 2 - 8 0 chr1 12 13 - 3 1 chr1 12 13 - 11 8 chr1 21 22 - 12 10 chr1 21 22 - 12 12 chr1 21 22 - 12 14 chr1 21 22 - 12 9 chr1 21 22 - 20 11 chr1 21 22 - 20 13 chr1 21 22 - 20 15 chr1 21 22 - 20 2 chr1 4169063 4169064 - 4169054 3 chr1 4169063 4169064 - 4169062 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 2 chr1 1 2 - 0 4 chr1 1 2 - 0 1 chr1 1 2 - 8 3 chr1 1 2 - 8 5 chr1 1 2 - 8 6 chr1 12 13 - 3 7 chr1 12 13 - 11 8 chr1 21 22 - 12 10 chr1 21 22 - 12 12 chr1 21 22 - 12 14 chr1 21 22 - 12 9 chr1 21 22 - 20 11 chr1 21 22 - 20 13 chr1 21 22 - 20 15 chr1 21 22 - 20 16 chr1 4169063 4169064 - 4169054 17 chr1 4169063 4169064 - 4169062 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 8 4 chr1 1 2 - 8 5 chr1 1 2 - 8 6 chr1 12 13 - 3 7 chr1 12 13 - 11 8 chr1 21 22 - 12 9 chr1 21 22 - 12 10 chr1 21 22 - 12 11 chr1 21 22 - 12 12 chr1 21 22 - 20 13 chr1 21 22 - 20 14 chr1 21 22 - 20 15 chr1 21 22 - 20 16 chr1 4169063 4169064 - 4169054 17 chr1 4169063 4169064 - 4169062 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 8 4 chr1 1 2 - 8 5 chr1 1 2 - 8 6 chr1 12 13 - 3 7 chr1 12 13 - 11 8 chr1 21 22 - 12 9 chr1 21 22 - 12 10 chr1 21 22 - 12 11 chr1 21 22 - 12 12 chr1 21 22 - 20 13 chr1 21 22 - 20 14 chr1 21 22 - 20 15 chr1 21 22 - 20 16 chr1 4169063 4169064 - 4169054 17 chr1 4169063 4169064 - 4169062 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=18, step=1) Expected index RangeIndex(start=0, stop=18, step=1) index equal [ True True True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx3zlik43/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx3zlik43/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_co4fllt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_co4fllt/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwltpme_d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwltpme_d/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9qjlg5_3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9qjlg5_3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 2 3 - 1 2 chr1 9817571 9817572 - 9817568 3 chr1 9817571 9817572 - 9817570 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 2 3 - 1 2 chr1 9817571 9817572 - 9817568 3 chr1 9817571 9817572 - 9817570 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=3, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpue150atr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpue150atr/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 2 3 - 1 2 chr1 9817571 9817572 - 9817568 3 chr1 9817571 9817572 - 9817570 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 2 3 - 1 2 chr1 9817571 9817572 - 9817568 3 chr1 9817571 9817572 - 9817570 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=3, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg1f5an1c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg1f5an1c/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 2 3 - 1 2 chr1 9817571 9817572 - 9817568 3 chr1 9817571 9817572 - 9817570 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 2 3 - 1 2 chr1 9817571 9817572 - 9817568 3 chr1 9817571 9817572 - 9817570 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=3, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmppecohn_i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppecohn_i/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_28u9jg6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_28u9jg6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqn68tv1p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqn68tv1p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5jgryh0e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5jgryh0e/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 3 4 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3 | 4 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1 2 - 0 0 chr1 3 4 - 2 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 3 4 - 2 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 3 4 - 2 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 3 4 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmph_slefk7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph_slefk7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 2 5584 - 1 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 2 | 5584 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 2 5584 - 1 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 2 5584 - 1 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 2 5584 - 1 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 2 5584 - 1 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2viort89/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2viort89/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 9494 - 0 1 chr1 2 3 - 1 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 9494 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 9494 - 0 1 chr1 2 3 - 1 df2 Chromosome Start End Strand Distance 0 chr1 1 9494 - 0 1 chr1 2 3 - 1 Actual Chromosome Start End Strand Distance 0 chr1 1 9494 - 0 1 chr1 2 3 - 1 Expected Chromosome Start End Strand Distance 0 chr1 1 9494 - 0 1 chr1 2 3 - 1 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxshppf_k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxshppf_k/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmprud4uhoh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprud4uhoh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 12 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 12 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 12 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 12 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 12 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp700r0hge/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp700r0hge/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 9495 - 1 1 chr1 9817571 9827064 - 9817570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 9495 | a | 0 | ... | | chr1 | 9817571 | 9827064 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 9495 - 1 1 chr1 9817571 9827064 - 9817570 df2 Chromosome Start End Strand Distance 0 chr1 2 9495 - 1 1 chr1 9817571 9827064 - 9817570 Actual Chromosome Start End Strand Distance 0 chr1 2 9495 - 1 1 chr1 9817571 9827064 - 9817570 Expected Chromosome Start End Strand Distance 0 chr1 2 9495 - 1 1 chr1 9817571 9827064 - 9817570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9nhswmc6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9nhswmc6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk57cqbrd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk57cqbrd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpye880hxx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpye880hxx/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy_woolbx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy_woolbx/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 2 chr1 1 2 - 0 3 chr1 1 2 - 6624348 4 chr1 1 2 - 0 5 chr1 1 2 - 6624348 6 chr1 1 2 - 0 7 chr1 1 2 - 6624348 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 2 chr1 1 2 - 0 4 chr1 1 2 - 0 1 chr1 1 2 - 6624348 3 chr1 1 2 - 6624348 5 chr1 1 2 - 6624348 df2 Chromosome Start End Strand Distance 2 chr1 1 2 - 0 4 chr1 1 2 - 0 6 chr1 1 2 - 0 3 chr1 1 2 - 6624348 5 chr1 1 2 - 6624348 7 chr1 1 2 - 6624348 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 6624348 4 chr1 1 2 - 6624348 5 chr1 1 2 - 6624348 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 6624348 4 chr1 1 2 - 6624348 5 chr1 1 2 - 6624348 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg8natn1t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg8natn1t/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 2 3 - 1 2 chr1 9817571 9817572 - 9817568 3 chr1 9817571 9817572 - 9817570 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 2 3 - 1 2 chr1 9817571 9817572 - 9817568 3 chr1 9817571 9817572 - 9817570 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=3, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc2cwn3_x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc2cwn3_x/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 2 3 - 1 2 chr1 9817571 9817572 - 9817568 3 chr1 9817571 9817572 - 9817570 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 2 3 - 1 2 chr1 9817571 9817572 - 9817568 3 chr1 9817571 9817572 - 9817570 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=3, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_seu3yyf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_seu3yyf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 2 3 - 1 2 chr1 9817571 9817572 - 9817568 3 chr1 9817571 9817572 - 9817570 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 2 3 - 1 2 chr1 9817571 9817572 - 9817568 3 chr1 9817571 9817572 - 9817570 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=3, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdrr8dt14/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdrr8dt14/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2gjuscy6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2gjuscy6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 2 3 - 1 2 chr1 9817571 9817572 - 9817568 3 chr1 9817571 9817572 - 9817570 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 2 3 - 1 2 chr1 9817571 9817572 - 9817568 3 chr1 9817571 9817572 - 9817570 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=3, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpisz7y11d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpisz7y11d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6qf1baxs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6qf1baxs/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 2 3 - 1 2 chr1 9817571 9817572 - 9817568 3 chr1 9817571 9817572 - 9817570 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 2 3 - 1 2 chr1 9817571 9817572 - 9817568 3 chr1 9817571 9817572 - 9817570 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=3, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp64j8afx4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp64j8afx4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4vc5h642/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4vc5h642/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 2 3 - 1 2 chr1 9817571 9817572 - 9817568 3 chr1 9817571 9817572 - 9817570 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 2 3 - 1 2 chr1 9817571 9817572 - 9817568 3 chr1 9817571 9817572 - 9817570 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=3, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4mg67c0g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4mg67c0g/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwpgl0zre/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwpgl0zre/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp82cxrmq8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp82cxrmq8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4ldf2wsj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4ldf2wsj/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaq65bypl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaq65bypl/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuimac8qt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuimac8qt/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 9817571 9817572 + 9817570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9817571 | 9817572 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 9817571 9817572 + 9817570 df2 Chromosome Start End Strand Distance 1 chr1 9817571 9817572 + 9817570 Actual Chromosome Start End Strand Distance 0 chr1 9817571 9817572 + 9817570 Expected Chromosome Start End Strand Distance 0 chr1 9817571 9817572 + 9817570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3qfzihjt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3qfzihjt/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 2 3 - 1 2 chr1 9817571 9817572 - 9817568 3 chr1 9817571 9817572 - 9817570 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 2 3 - 1 2 chr1 9817571 9817572 - 9817568 3 chr1 9817571 9817572 - 9817570 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=3, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn6fysgq0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn6fysgq0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 2 3 - 1 2 chr1 9817571 9817572 - 9817568 3 chr1 9817571 9817572 - 9817570 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 2 3 - 1 2 chr1 9817571 9817572 - 9817568 3 chr1 9817571 9817572 - 9817570 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=3, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmplyp0hbzp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplyp0hbzp/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 2 3 - 1 2 chr1 9817571 9817572 - 9817568 3 chr1 9817571 9817572 - 9817570 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 2 3 - 1 2 chr1 9817571 9817572 - 9817568 3 chr1 9817571 9817572 - 9817570 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=3, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8sc51pzu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8sc51pzu/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 9817571 9817572 + 9817570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9817571 | 9817572 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 9817571 9817572 + 9817570 df2 Chromosome Start End Strand Distance 1 chr1 9817571 9817572 + 9817570 Actual Chromosome Start End Strand Distance 0 chr1 9817571 9817572 + 9817570 Expected Chromosome Start End Strand Distance 0 chr1 9817571 9817572 + 9817570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpomo08xwj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpomo08xwj/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 2 3 - 1 2 chr1 9817571 9817572 - 9817568 3 chr1 9817571 9817572 - 9817570 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 2 3 - 1 2 chr1 9817571 9817572 - 9817568 3 chr1 9817571 9817572 - 9817570 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=3, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp57d0wic1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp57d0wic1/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyqley2_j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyqley2_j/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkzh4a89n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkzh4a89n/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvp23p6uh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvp23p6uh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy0w4xqcg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy0w4xqcg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmprmt13pj8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprmt13pj8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 9817571 9817572 + 9817570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9817571 | 9817572 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 9817571 9817572 + 9817570 df2 Chromosome Start End Strand Distance 1 chr1 9817571 9817572 + 9817570 Actual Chromosome Start End Strand Distance 0 chr1 9817571 9817572 + 9817570 Expected Chromosome Start End Strand Distance 0 chr1 9817571 9817572 + 9817570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8yi5evpf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8yi5evpf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 2 3 - 1 2 chr1 9817571 9817572 - 9817568 3 chr1 9817571 9817572 - 9817570 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 2 3 - 1 2 chr1 9817571 9817572 - 9817568 3 chr1 9817571 9817572 - 9817570 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817568 2 chr1 9817571 9817572 - 9817570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=3, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcf9cm7ab/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcf9cm7ab/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 5 6 + 4 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 5 | 6 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 5 6 + 4 df2 Chromosome Start End Strand Distance 1 chr1 5 6 + 4 Actual Chromosome Start End Strand Distance 0 chr1 5 6 + 4 Expected Chromosome Start End Strand Distance 0 chr1 5 6 + 4 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvam7zqfr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvam7zqfr/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnq040egg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnq040egg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 9817571 | 9817572 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 1 1 chr1 9817571 9817572 - 9817570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7cwm6myv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7cwm6myv/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 9817571 9817572 + 9817570 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9817571 | 9817572 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 9817571 9817572 + 9817570 df2 Chromosome Start End Strand Distance 1 chr1 9817571 9817572 + 9817570 Actual Chromosome Start End Strand Distance 0 chr1 9817571 9817572 + 9817570 Expected Chromosome Start End Strand Distance 0 chr1 9817571 9817572 + 9817570 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiv9fs_1i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiv9fs_1i/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1 2 - 0 3 chr1 1 2 - 2 0 chr1 2 3 - 1 1 chr1 2 3 - 1 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 3 chr1 2 3 - 1 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=3, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5u9cvlan/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5u9cvlan/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3na2hr0h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3na2hr0h/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1 2 - 0 3 chr1 1 2 - 2 0 chr1 2 3 - 1 1 chr1 2 3 - 1 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 3 chr1 2 3 - 1 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=3, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg76oy68l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg76oy68l/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 2 3 - 1 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1 2 - 0 0 chr1 2 3 - 1 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 2 3 - 1 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 2 3 - 1 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 2 3 - 1 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpszzooz9z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpszzooz9z/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 2 3 - 1 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1 2 - 0 0 chr1 2 3 - 1 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 2 3 - 1 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 2 3 - 1 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 2 3 - 1 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbesz089j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbesz089j/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 2 3 - 1 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 1 2 - 0 0 chr1 2 3 - 1 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 2 3 - 1 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 2 3 - 1 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 2 3 - 1 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf9hu3neo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf9hu3neo/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqzqojp_o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqzqojp_o/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2lfn621v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2lfn621v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfs9ctzbq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfs9ctzbq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0b3zhar8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0b3zhar8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1 2 - 0 3 chr1 1 2 - 2 0 chr1 2 3 - 1 1 chr1 2 3 - 1 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 3 chr1 2 3 - 1 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=3, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpib_038hp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpib_038hp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9659a7xk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9659a7xk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4ns7rg7x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4ns7rg7x/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsqoed2u4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsqoed2u4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmptk2tzlfr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptk2tzlfr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpscprhgaa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpscprhgaa/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6bj3hiya/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6bj3hiya/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmppiykdxx5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppiykdxx5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_frziguw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_frziguw/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9llrdln_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9llrdln_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1 2 - 0 3 chr1 1 2 - 2 0 chr1 2 3 - 1 1 chr1 2 3 - 1 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 3 chr1 2 3 - 1 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=3, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxxj_d7xh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxxj_d7xh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 1 2 - 0 3 chr1 1 2 - 2 4 chr1 1 2 - 0 5 chr1 1 2 - 2 6 chr1 1 2 - 0 7 chr1 1 2 - 2 8 chr1 1 2 - 0 9 chr1 1 2 - 2 10 chr1 2 3 - 1 11 chr1 902006 902007 - 902003 12 chr1 902006 902007 - 902005 13 chr1 8640421 8640422 - 8640418 14 chr1 8640421 8640422 - 8640420 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 902006 | 902007 | a | 0 | ... | | chr1 | 902006 | 902007 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 8640421 | 8640422 | a | 0 | ... | | chr1 | 8640421 | 8640422 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 16 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 1 2 - 0 6 chr1 1 2 - 0 8 chr1 1 2 - 0 10 chr1 1 2 - 0 12 chr1 1 2 - 0 5 chr1 1 2 - 2 7 chr1 1 2 - 2 9 chr1 1 2 - 2 11 chr1 1 2 - 2 13 chr1 1 2 - 2 0 chr1 2 3 - 1 1 chr1 2 3 - 1 2 chr1 902006 902007 - 902003 3 chr1 902006 902007 - 902005 14 chr1 8640421 8640422 - 8640418 15 chr1 8640421 8640422 - 8640420 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 2 chr1 1 2 - 0 4 chr1 1 2 - 0 6 chr1 1 2 - 0 8 chr1 1 2 - 0 1 chr1 1 2 - 2 3 chr1 1 2 - 2 5 chr1 1 2 - 2 7 chr1 1 2 - 2 9 chr1 1 2 - 2 10 chr1 2 3 - 1 11 chr1 902006 902007 - 902003 12 chr1 902006 902007 - 902005 13 chr1 8640421 8640422 - 8640418 14 chr1 8640421 8640422 - 8640420 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 2 6 chr1 1 2 - 2 7 chr1 1 2 - 2 8 chr1 1 2 - 2 9 chr1 1 2 - 2 10 chr1 2 3 - 1 11 chr1 2 3 - 1 12 chr1 902006 902007 - 902003 13 chr1 902006 902007 - 902005 14 chr1 8640421 8640422 - 8640418 15 chr1 8640421 8640422 - 8640420 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 2 6 chr1 1 2 - 2 7 chr1 1 2 - 2 8 chr1 1 2 - 2 9 chr1 1 2 - 2 10 chr1 2 3 - 1 11 chr1 902006 902007 - 902003 12 chr1 902006 902007 - 902005 13 chr1 8640421 8640422 - 8640418 14 chr1 8640421 8640422 - 8640420 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=16, step=1) Expected index RangeIndex(start=0, stop=15, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwye0illv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwye0illv/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7pw3t00r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7pw3t00r/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnwt8ys37/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnwt8ys37/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn5_pqo2p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn5_pqo2p/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1v9_epf6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1v9_epf6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbv1i1d0e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbv1i1d0e/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 1 2 - 0 3 chr1 1 2 - 2 4 chr1 1 2 - 0 5 chr1 1 2 - 2 6 chr1 1 2 - 0 7 chr1 1 2 - 2 8 chr1 1 2 - 0 9 chr1 1 2 - 2 10 chr1 2 3 - 1 11 chr1 902006 902007 - 902003 12 chr1 902006 902007 - 902005 13 chr1 8640421 8640422 - 8640418 14 chr1 8640421 8640422 - 8640420 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 902006 | 902007 | a | 0 | ... | | chr1 | 902006 | 902007 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 8640421 | 8640422 | a | 0 | ... | | chr1 | 8640421 | 8640422 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 16 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 1 2 - 0 6 chr1 1 2 - 0 8 chr1 1 2 - 0 10 chr1 1 2 - 0 12 chr1 1 2 - 0 5 chr1 1 2 - 2 7 chr1 1 2 - 2 9 chr1 1 2 - 2 11 chr1 1 2 - 2 13 chr1 1 2 - 2 0 chr1 2 3 - 1 1 chr1 2 3 - 1 2 chr1 902006 902007 - 902003 3 chr1 902006 902007 - 902005 14 chr1 8640421 8640422 - 8640418 15 chr1 8640421 8640422 - 8640420 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 2 chr1 1 2 - 0 4 chr1 1 2 - 0 6 chr1 1 2 - 0 8 chr1 1 2 - 0 1 chr1 1 2 - 2 3 chr1 1 2 - 2 5 chr1 1 2 - 2 7 chr1 1 2 - 2 9 chr1 1 2 - 2 10 chr1 2 3 - 1 11 chr1 902006 902007 - 902003 12 chr1 902006 902007 - 902005 13 chr1 8640421 8640422 - 8640418 14 chr1 8640421 8640422 - 8640420 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 2 6 chr1 1 2 - 2 7 chr1 1 2 - 2 8 chr1 1 2 - 2 9 chr1 1 2 - 2 10 chr1 2 3 - 1 11 chr1 2 3 - 1 12 chr1 902006 902007 - 902003 13 chr1 902006 902007 - 902005 14 chr1 8640421 8640422 - 8640418 15 chr1 8640421 8640422 - 8640420 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 2 6 chr1 1 2 - 2 7 chr1 1 2 - 2 8 chr1 1 2 - 2 9 chr1 1 2 - 2 10 chr1 2 3 - 1 11 chr1 902006 902007 - 902003 12 chr1 902006 902007 - 902005 13 chr1 8640421 8640422 - 8640418 14 chr1 8640421 8640422 - 8640420 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=16, step=1) Expected index RangeIndex(start=0, stop=15, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxzq9_g25/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxzq9_g25/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr1 1 2 - 0 8 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr1 1 2 - 0 8 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmps87luys8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps87luys8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8fwgybzz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8fwgybzz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2f1vhvoz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2f1vhvoz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 1 2 - 0 3 chr1 1 2 - 2 4 chr1 1 2 - 0 5 chr1 1 2 - 2 6 chr1 1 2 - 0 7 chr1 1 2 - 2 8 chr1 1 2 - 0 9 chr1 1 2 - 2 10 chr1 2 3 - 1 11 chr1 902006 902007 - 902003 12 chr1 902006 902007 - 902005 13 chr1 8640421 8640422 - 8640418 14 chr1 8640421 8640422 - 8640420 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 902006 | 902007 | a | 0 | ... | | chr1 | 902006 | 902007 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 8640421 | 8640422 | a | 0 | ... | | chr1 | 8640421 | 8640422 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 16 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 1 2 - 0 6 chr1 1 2 - 0 8 chr1 1 2 - 0 10 chr1 1 2 - 0 12 chr1 1 2 - 0 5 chr1 1 2 - 2 7 chr1 1 2 - 2 9 chr1 1 2 - 2 11 chr1 1 2 - 2 13 chr1 1 2 - 2 0 chr1 2 3 - 1 1 chr1 2 3 - 1 2 chr1 902006 902007 - 902003 3 chr1 902006 902007 - 902005 14 chr1 8640421 8640422 - 8640418 15 chr1 8640421 8640422 - 8640420 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 2 chr1 1 2 - 0 4 chr1 1 2 - 0 6 chr1 1 2 - 0 8 chr1 1 2 - 0 1 chr1 1 2 - 2 3 chr1 1 2 - 2 5 chr1 1 2 - 2 7 chr1 1 2 - 2 9 chr1 1 2 - 2 10 chr1 2 3 - 1 11 chr1 902006 902007 - 902003 12 chr1 902006 902007 - 902005 13 chr1 8640421 8640422 - 8640418 14 chr1 8640421 8640422 - 8640420 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 2 6 chr1 1 2 - 2 7 chr1 1 2 - 2 8 chr1 1 2 - 2 9 chr1 1 2 - 2 10 chr1 2 3 - 1 11 chr1 2 3 - 1 12 chr1 902006 902007 - 902003 13 chr1 902006 902007 - 902005 14 chr1 8640421 8640422 - 8640418 15 chr1 8640421 8640422 - 8640420 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 2 6 chr1 1 2 - 2 7 chr1 1 2 - 2 8 chr1 1 2 - 2 9 chr1 1 2 - 2 10 chr1 2 3 - 1 11 chr1 902006 902007 - 902003 12 chr1 902006 902007 - 902005 13 chr1 8640421 8640422 - 8640418 14 chr1 8640421 8640422 - 8640420 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=16, step=1) Expected index RangeIndex(start=0, stop=15, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz077ghre/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz077ghre/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmptqx1zdeo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptqx1zdeo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfm1ulph9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfm1ulph9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8n61_pmo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8n61_pmo/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 5 chr1 902006 902007 + 902005 6 chr1 9119356 9119357 + 9119355 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9119356 | 9119357 | a | 0 | ... | | chr1 | 902006 | 902007 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 1 chr1 902006 902007 + 902005 0 chr1 9119356 9119357 + 9119355 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 5 chr1 902006 902007 + 902005 6 chr1 9119356 9119357 + 9119355 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 902006 902007 + 902005 5 chr1 9119356 9119357 + 9119355 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 902006 902007 + 902005 5 chr1 9119356 9119357 + 9119355 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0dxq1eeo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0dxq1eeo/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 5 chr1 902006 902007 + 902005 6 chr1 9119356 9119357 + 9119355 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9119356 | 9119357 | a | 0 | ... | | chr1 | 902006 | 902007 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 1 chr1 902006 902007 + 902005 0 chr1 9119356 9119357 + 9119355 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 5 chr1 902006 902007 + 902005 6 chr1 9119356 9119357 + 9119355 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 902006 902007 + 902005 5 chr1 9119356 9119357 + 9119355 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 902006 902007 + 902005 5 chr1 9119356 9119357 + 9119355 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8kgdcvuh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8kgdcvuh/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 5 chr1 902006 902007 + 902005 6 chr1 9119356 9119357 + 9119355 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9119356 | 9119357 | a | 0 | ... | | chr1 | 902006 | 902007 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 1 chr1 902006 902007 + 902005 0 chr1 9119356 9119357 + 9119355 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 5 chr1 902006 902007 + 902005 6 chr1 9119356 9119357 + 9119355 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 902006 902007 + 902005 5 chr1 9119356 9119357 + 9119355 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 902006 902007 + 902005 5 chr1 9119356 9119357 + 9119355 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr_am15cl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr_am15cl/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 5 chr1 902006 902007 + 902005 6 chr1 9119356 9119357 + 9119355 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9119356 | 9119357 | a | 0 | ... | | chr1 | 902006 | 902007 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 1 chr1 902006 902007 + 902005 0 chr1 9119356 9119357 + 9119355 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 5 chr1 902006 902007 + 902005 6 chr1 9119356 9119357 + 9119355 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 902006 902007 + 902005 5 chr1 9119356 9119357 + 9119355 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 902006 902007 + 902005 5 chr1 9119356 9119357 + 9119355 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcp851hl1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcp851hl1/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 5 chr1 902006 902007 + 902005 6 chr1 9119356 9119357 + 9119355 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9119356 | 9119357 | a | 0 | ... | | chr1 | 902006 | 902007 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 1 chr1 902006 902007 + 902005 0 chr1 9119356 9119357 + 9119355 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 5 chr1 902006 902007 + 902005 6 chr1 9119356 9119357 + 9119355 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 902006 902007 + 902005 5 chr1 9119356 9119357 + 9119355 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 902006 902007 + 902005 5 chr1 9119356 9119357 + 9119355 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu5qj7qjj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu5qj7qjj/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 5 chr1 902006 902007 + 902005 6 chr1 9119356 9119357 + 9119355 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9119356 | 9119357 | a | 0 | ... | | chr1 | 902006 | 902007 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 1 chr1 902006 902007 + 902005 0 chr1 9119356 9119357 + 9119355 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 5 chr1 902006 902007 + 902005 6 chr1 9119356 9119357 + 9119355 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 902006 902007 + 902005 5 chr1 9119356 9119357 + 9119355 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 902006 902007 + 902005 5 chr1 9119356 9119357 + 9119355 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2cth619c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2cth619c/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 5 chr1 902006 902007 + 902005 6 chr1 9119356 9119357 + 9119355 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9119356 | 9119357 | a | 0 | ... | | chr1 | 902006 | 902007 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 1 chr1 902006 902007 + 902005 0 chr1 9119356 9119357 + 9119355 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 5 chr1 902006 902007 + 902005 6 chr1 9119356 9119357 + 9119355 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 902006 902007 + 902005 5 chr1 9119356 9119357 + 9119355 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 902006 902007 + 902005 5 chr1 9119356 9119357 + 9119355 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpditgq4po/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpditgq4po/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 5 chr1 902006 902007 + 902005 6 chr1 9119356 9119357 + 9119355 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9119356 | 9119357 | a | 0 | ... | | chr1 | 902006 | 902007 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 1 2 + 0 5 chr1 1 2 + 0 1 chr1 902006 902007 + 902005 0 chr1 9119356 9119357 + 9119355 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 5 chr1 902006 902007 + 902005 6 chr1 9119356 9119357 + 9119355 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 902006 902007 + 902005 5 chr1 9119356 9119357 + 9119355 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 1 chr1 1 2 + 0 2 chr1 1 2 + 0 3 chr1 1 2 + 0 4 chr1 902006 902007 + 902005 5 chr1 9119356 9119357 + 9119355 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4i4kyl6c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4i4kyl6c/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 1 2 - 0 3 chr1 1 2 - 2 4 chr1 1 2 - 0 5 chr1 1 2 - 2 6 chr1 1 2 - 0 7 chr1 1 2 - 2 8 chr1 1 2 - 0 9 chr1 1 2 - 2 10 chr1 2 3 - 1 11 chr1 902006 902007 - 902003 12 chr1 902006 902007 - 902005 13 chr1 8640421 8640422 - 8640418 14 chr1 8640421 8640422 - 8640420 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 902006 | 902007 | a | 0 | ... | | chr1 | 902006 | 902007 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 8640421 | 8640422 | a | 0 | ... | | chr1 | 8640421 | 8640422 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 16 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 1 2 - 0 6 chr1 1 2 - 0 8 chr1 1 2 - 0 10 chr1 1 2 - 0 12 chr1 1 2 - 0 5 chr1 1 2 - 2 7 chr1 1 2 - 2 9 chr1 1 2 - 2 11 chr1 1 2 - 2 13 chr1 1 2 - 2 0 chr1 2 3 - 1 1 chr1 2 3 - 1 2 chr1 902006 902007 - 902003 3 chr1 902006 902007 - 902005 14 chr1 8640421 8640422 - 8640418 15 chr1 8640421 8640422 - 8640420 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 2 chr1 1 2 - 0 4 chr1 1 2 - 0 6 chr1 1 2 - 0 8 chr1 1 2 - 0 1 chr1 1 2 - 2 3 chr1 1 2 - 2 5 chr1 1 2 - 2 7 chr1 1 2 - 2 9 chr1 1 2 - 2 10 chr1 2 3 - 1 11 chr1 902006 902007 - 902003 12 chr1 902006 902007 - 902005 13 chr1 8640421 8640422 - 8640418 14 chr1 8640421 8640422 - 8640420 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 2 6 chr1 1 2 - 2 7 chr1 1 2 - 2 8 chr1 1 2 - 2 9 chr1 1 2 - 2 10 chr1 2 3 - 1 11 chr1 2 3 - 1 12 chr1 902006 902007 - 902003 13 chr1 902006 902007 - 902005 14 chr1 8640421 8640422 - 8640418 15 chr1 8640421 8640422 - 8640420 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 2 6 chr1 1 2 - 2 7 chr1 1 2 - 2 8 chr1 1 2 - 2 9 chr1 1 2 - 2 10 chr1 2 3 - 1 11 chr1 902006 902007 - 902003 12 chr1 902006 902007 - 902005 13 chr1 8640421 8640422 - 8640418 14 chr1 8640421 8640422 - 8640420 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=16, step=1) Expected index RangeIndex(start=0, stop=15, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd9zdodof/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd9zdodof/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 2 3 - 1 6 chr1 902006 902007 - 902005 7 chr1 8640421 8640422 - 8640420 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 902006 | 902007 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 8640421 | 8640422 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 0 chr1 2 3 - 1 1 chr1 902006 902007 - 902005 7 chr1 8640421 8640422 - 8640420 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 2 3 - 1 6 chr1 902006 902007 - 902005 7 chr1 8640421 8640422 - 8640420 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 2 3 - 1 6 chr1 902006 902007 - 902005 7 chr1 8640421 8640422 - 8640420 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 2 3 - 1 6 chr1 902006 902007 - 902005 7 chr1 8640421 8640422 - 8640420 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpznz5jgsm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpznz5jgsm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 5 chr1 2 3 - 1 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 df2 Chromosome Start End Strand Distance 5 chr1 2 3 - 1 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 1 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 1 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp__i37az4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp__i37az4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpghmqaiql/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpghmqaiql/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo_is7uyx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo_is7uyx/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 2 3 - 1 6 chr1 902006 902007 - 902005 7 chr1 8640421 8640422 - 8640420 8 chr1 9119356 9119357 - 9119355 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 9119356 | 9119357 | a | 0 | ... | | chr1 | 902006 | 902007 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 8640421 | 8640422 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr1 1 2 - 0 0 chr1 2 3 - 1 2 chr1 902006 902007 - 902005 8 chr1 8640421 8640422 - 8640420 1 chr1 9119356 9119357 - 9119355 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 2 3 - 1 6 chr1 902006 902007 - 902005 7 chr1 8640421 8640422 - 8640420 8 chr1 9119356 9119357 - 9119355 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 2 3 - 1 6 chr1 902006 902007 - 902005 7 chr1 8640421 8640422 - 8640420 8 chr1 9119356 9119357 - 9119355 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 2 3 - 1 6 chr1 902006 902007 - 902005 7 chr1 8640421 8640422 - 8640420 8 chr1 9119356 9119357 - 9119355 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=9, step=1) index equal [ True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0gcbfqof/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0gcbfqof/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 8 chr1 9119356 9119357 + 9119355 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9119356 | 9119357 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 9119356 9119357 + 9119355 df2 Chromosome Start End Strand Distance 8 chr1 9119356 9119357 + 9119355 Actual Chromosome Start End Strand Distance 0 chr1 9119356 9119357 + 9119355 Expected Chromosome Start End Strand Distance 0 chr1 9119356 9119357 + 9119355 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcmif7mey/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcmif7mey/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 8 chr1 9119356 9119357 + 9119355 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9119356 | 9119357 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 9119356 9119357 + 9119355 df2 Chromosome Start End Strand Distance 8 chr1 9119356 9119357 + 9119355 Actual Chromosome Start End Strand Distance 0 chr1 9119356 9119357 + 9119355 Expected Chromosome Start End Strand Distance 0 chr1 9119356 9119357 + 9119355 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3sb3hbh9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3sb3hbh9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa2hdmbe5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa2hdmbe5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmph3a3k23v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph3a3k23v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp06nz8r02/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp06nz8r02/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0maklr8p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0maklr8p/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 1 2 - 0 3 chr1 1 2 - 2 4 chr1 1 2 - 0 5 chr1 1 2 - 2 6 chr1 1 2 - 0 7 chr1 1 2 - 2 8 chr1 1 2 - 0 9 chr1 1 2 - 2 10 chr1 2 3 - 1 11 chr1 902006 902007 - 902003 12 chr1 902006 902007 - 902005 13 chr1 8640421 8640422 - 8640418 14 chr1 8640421 8640422 - 8640420 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 902006 | 902007 | a | 0 | ... | | chr1 | 902006 | 902007 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 8640421 | 8640422 | a | 0 | ... | | chr1 | 8640421 | 8640422 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 16 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 1 2 - 0 6 chr1 1 2 - 0 8 chr1 1 2 - 0 10 chr1 1 2 - 0 12 chr1 1 2 - 0 5 chr1 1 2 - 2 7 chr1 1 2 - 2 9 chr1 1 2 - 2 11 chr1 1 2 - 2 13 chr1 1 2 - 2 0 chr1 2 3 - 1 1 chr1 2 3 - 1 2 chr1 902006 902007 - 902003 3 chr1 902006 902007 - 902005 14 chr1 8640421 8640422 - 8640418 15 chr1 8640421 8640422 - 8640420 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 2 chr1 1 2 - 0 4 chr1 1 2 - 0 6 chr1 1 2 - 0 8 chr1 1 2 - 0 1 chr1 1 2 - 2 3 chr1 1 2 - 2 5 chr1 1 2 - 2 7 chr1 1 2 - 2 9 chr1 1 2 - 2 10 chr1 2 3 - 1 11 chr1 902006 902007 - 902003 12 chr1 902006 902007 - 902005 13 chr1 8640421 8640422 - 8640418 14 chr1 8640421 8640422 - 8640420 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 2 6 chr1 1 2 - 2 7 chr1 1 2 - 2 8 chr1 1 2 - 2 9 chr1 1 2 - 2 10 chr1 2 3 - 1 11 chr1 2 3 - 1 12 chr1 902006 902007 - 902003 13 chr1 902006 902007 - 902005 14 chr1 8640421 8640422 - 8640418 15 chr1 8640421 8640422 - 8640420 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 2 6 chr1 1 2 - 2 7 chr1 1 2 - 2 8 chr1 1 2 - 2 9 chr1 1 2 - 2 10 chr1 2 3 - 1 11 chr1 902006 902007 - 902003 12 chr1 902006 902007 - 902005 13 chr1 8640421 8640422 - 8640418 14 chr1 8640421 8640422 - 8640420 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=16, step=1) Expected index RangeIndex(start=0, stop=15, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq9w9f4lr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq9w9f4lr/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 2 3 - 1 6 chr1 902006 902007 - 902005 7 chr1 8640421 8640422 - 8640420 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 902006 | 902007 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 8640421 | 8640422 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 0 chr1 2 3 - 1 1 chr1 902006 902007 - 902005 7 chr1 8640421 8640422 - 8640420 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 2 3 - 1 6 chr1 902006 902007 - 902005 7 chr1 8640421 8640422 - 8640420 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 2 3 - 1 6 chr1 902006 902007 - 902005 7 chr1 8640421 8640422 - 8640420 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 2 3 - 1 6 chr1 902006 902007 - 902005 7 chr1 8640421 8640422 - 8640420 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjfl8fv4b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjfl8fv4b/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 1 2 - 0 3 chr1 1 2 - 2 4 chr1 1 2 - 0 5 chr1 1 2 - 2 6 chr1 1 2 - 0 7 chr1 1 2 - 2 8 chr1 1 2 - 0 9 chr1 1 2 - 2 10 chr1 2 3 - 1 11 chr1 902006 902007 - 902003 12 chr1 902006 902007 - 902005 13 chr1 8640421 8640422 - 8640418 14 chr1 8640421 8640422 - 8640420 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 902006 | 902007 | a | 0 | ... | | chr1 | 902006 | 902007 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 8640421 | 8640422 | a | 0 | ... | | chr1 | 8640421 | 8640422 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 16 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 1 2 - 0 6 chr1 1 2 - 0 8 chr1 1 2 - 0 10 chr1 1 2 - 0 12 chr1 1 2 - 0 5 chr1 1 2 - 2 7 chr1 1 2 - 2 9 chr1 1 2 - 2 11 chr1 1 2 - 2 13 chr1 1 2 - 2 0 chr1 2 3 - 1 1 chr1 2 3 - 1 2 chr1 902006 902007 - 902003 3 chr1 902006 902007 - 902005 14 chr1 8640421 8640422 - 8640418 15 chr1 8640421 8640422 - 8640420 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 2 chr1 1 2 - 0 4 chr1 1 2 - 0 6 chr1 1 2 - 0 8 chr1 1 2 - 0 1 chr1 1 2 - 2 3 chr1 1 2 - 2 5 chr1 1 2 - 2 7 chr1 1 2 - 2 9 chr1 1 2 - 2 10 chr1 2 3 - 1 11 chr1 902006 902007 - 902003 12 chr1 902006 902007 - 902005 13 chr1 8640421 8640422 - 8640418 14 chr1 8640421 8640422 - 8640420 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 2 6 chr1 1 2 - 2 7 chr1 1 2 - 2 8 chr1 1 2 - 2 9 chr1 1 2 - 2 10 chr1 2 3 - 1 11 chr1 2 3 - 1 12 chr1 902006 902007 - 902003 13 chr1 902006 902007 - 902005 14 chr1 8640421 8640422 - 8640418 15 chr1 8640421 8640422 - 8640420 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 2 6 chr1 1 2 - 2 7 chr1 1 2 - 2 8 chr1 1 2 - 2 9 chr1 1 2 - 2 10 chr1 2 3 - 1 11 chr1 902006 902007 - 902003 12 chr1 902006 902007 - 902005 13 chr1 8640421 8640422 - 8640418 14 chr1 8640421 8640422 - 8640420 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=16, step=1) Expected index RangeIndex(start=0, stop=15, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsvcwgamk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsvcwgamk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 2 3 - 1 6 chr1 902006 902007 - 902005 7 chr1 8640421 8640422 - 8640420 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 902006 | 902007 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 8640421 | 8640422 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 0 chr1 2 3 - 1 1 chr1 902006 902007 - 902005 7 chr1 8640421 8640422 - 8640420 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 2 3 - 1 6 chr1 902006 902007 - 902005 7 chr1 8640421 8640422 - 8640420 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 2 3 - 1 6 chr1 902006 902007 - 902005 7 chr1 8640421 8640422 - 8640420 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 2 3 - 1 6 chr1 902006 902007 - 902005 7 chr1 8640421 8640422 - 8640420 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmppgt05kax/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppgt05kax/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 2 3 - 1 6 chr1 902006 902007 - 902005 7 chr1 8640421 8640422 - 8640420 8 chr1 9119356 9119357 - 9119355 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 9119356 | 9119357 | a | 0 | ... | | chr1 | 902006 | 902007 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 8640421 | 8640422 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr1 1 2 - 0 0 chr1 2 3 - 1 2 chr1 902006 902007 - 902005 8 chr1 8640421 8640422 - 8640420 1 chr1 9119356 9119357 - 9119355 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 2 3 - 1 6 chr1 902006 902007 - 902005 7 chr1 8640421 8640422 - 8640420 8 chr1 9119356 9119357 - 9119355 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 2 3 - 1 6 chr1 902006 902007 - 902005 7 chr1 8640421 8640422 - 8640420 8 chr1 9119356 9119357 - 9119355 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 2 3 - 1 6 chr1 902006 902007 - 902005 7 chr1 8640421 8640422 - 8640420 8 chr1 9119356 9119357 - 9119355 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=9, step=1) index equal [ True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5s9j34h3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5s9j34h3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 1 2 - 0 3 chr1 1 2 - 2 4 chr1 1 2 - 0 5 chr1 1 2 - 2 6 chr1 1 2 - 0 7 chr1 1 2 - 2 8 chr1 1 2 - 0 9 chr1 1 2 - 2 10 chr1 2 3 - 1 11 chr1 902006 902007 - 902003 12 chr1 902006 902007 - 902005 13 chr1 8640421 8640422 - 8640418 14 chr1 8640421 8640422 - 8640420 15 chr1 9119356 9119357 - 9119353 16 chr1 9119356 9119357 - 9119355 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 9119356 | 9119357 | a | 0 | ... | | chr1 | 9119356 | 9119357 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 8640421 | 8640422 | a | 0 | ... | | chr1 | 8640421 | 8640422 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 18 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr1 1 2 - 0 8 chr1 1 2 - 0 10 chr1 1 2 - 0 12 chr1 1 2 - 0 14 chr1 1 2 - 0 7 chr1 1 2 - 2 9 chr1 1 2 - 2 11 chr1 1 2 - 2 13 chr1 1 2 - 2 15 chr1 1 2 - 2 0 chr1 2 3 - 1 1 chr1 2 3 - 1 4 chr1 902006 902007 - 902003 5 chr1 902006 902007 - 902005 16 chr1 8640421 8640422 - 8640418 17 chr1 8640421 8640422 - 8640420 2 chr1 9119356 9119357 - 9119353 3 chr1 9119356 9119357 - 9119355 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 2 chr1 1 2 - 0 4 chr1 1 2 - 0 6 chr1 1 2 - 0 8 chr1 1 2 - 0 1 chr1 1 2 - 2 3 chr1 1 2 - 2 5 chr1 1 2 - 2 7 chr1 1 2 - 2 9 chr1 1 2 - 2 10 chr1 2 3 - 1 11 chr1 902006 902007 - 902003 12 chr1 902006 902007 - 902005 13 chr1 8640421 8640422 - 8640418 14 chr1 8640421 8640422 - 8640420 15 chr1 9119356 9119357 - 9119353 16 chr1 9119356 9119357 - 9119355 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 2 6 chr1 1 2 - 2 7 chr1 1 2 - 2 8 chr1 1 2 - 2 9 chr1 1 2 - 2 10 chr1 2 3 - 1 11 chr1 2 3 - 1 12 chr1 902006 902007 - 902003 13 chr1 902006 902007 - 902005 14 chr1 8640421 8640422 - 8640418 15 chr1 8640421 8640422 - 8640420 16 chr1 9119356 9119357 - 9119353 17 chr1 9119356 9119357 - 9119355 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 2 6 chr1 1 2 - 2 7 chr1 1 2 - 2 8 chr1 1 2 - 2 9 chr1 1 2 - 2 10 chr1 2 3 - 1 11 chr1 902006 902007 - 902003 12 chr1 902006 902007 - 902005 13 chr1 8640421 8640422 - 8640418 14 chr1 8640421 8640422 - 8640420 15 chr1 9119356 9119357 - 9119353 16 chr1 9119356 9119357 - 9119355 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=18, step=1) Expected index RangeIndex(start=0, stop=17, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzqdd5i2b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzqdd5i2b/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 2 3 - 1 6 chr1 902006 902007 - 902005 7 chr1 8640421 8640422 - 8640420 8 chr1 9119356 9119357 - 9119355 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 9119356 | 9119357 | a | 0 | ... | | chr1 | 902006 | 902007 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 8640421 | 8640422 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr1 1 2 - 0 0 chr1 2 3 - 1 2 chr1 902006 902007 - 902005 8 chr1 8640421 8640422 - 8640420 1 chr1 9119356 9119357 - 9119355 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 2 3 - 1 6 chr1 902006 902007 - 902005 7 chr1 8640421 8640422 - 8640420 8 chr1 9119356 9119357 - 9119355 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 2 3 - 1 6 chr1 902006 902007 - 902005 7 chr1 8640421 8640422 - 8640420 8 chr1 9119356 9119357 - 9119355 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 2 3 - 1 6 chr1 902006 902007 - 902005 7 chr1 8640421 8640422 - 8640420 8 chr1 9119356 9119357 - 9119355 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=9, step=1) index equal [ True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpet7ob6l_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpet7ob6l_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqqemgy3k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqqemgy3k/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 1 2 - 0 3 chr1 1 2 - 2 4 chr1 1 2 - 0 5 chr1 1 2 - 2 6 chr1 1 2 - 0 7 chr1 1 2 - 2 8 chr1 1 2 - 0 9 chr1 1 2 - 2 10 chr1 2 3 - 1 11 chr1 902006 902007 - 902003 12 chr1 902006 902007 - 902005 13 chr1 8640421 8640422 - 8640418 14 chr1 8640421 8640422 - 8640420 15 chr1 9119356 9119357 - 9119353 16 chr1 9119356 9119357 - 9119355 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 9119356 | 9119357 | a | 0 | ... | | chr1 | 9119356 | 9119357 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 8640421 | 8640422 | a | 0 | ... | | chr1 | 8640421 | 8640422 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 18 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr1 1 2 - 0 8 chr1 1 2 - 0 10 chr1 1 2 - 0 12 chr1 1 2 - 0 14 chr1 1 2 - 0 7 chr1 1 2 - 2 9 chr1 1 2 - 2 11 chr1 1 2 - 2 13 chr1 1 2 - 2 15 chr1 1 2 - 2 0 chr1 2 3 - 1 1 chr1 2 3 - 1 4 chr1 902006 902007 - 902003 5 chr1 902006 902007 - 902005 16 chr1 8640421 8640422 - 8640418 17 chr1 8640421 8640422 - 8640420 2 chr1 9119356 9119357 - 9119353 3 chr1 9119356 9119357 - 9119355 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 2 chr1 1 2 - 0 4 chr1 1 2 - 0 6 chr1 1 2 - 0 8 chr1 1 2 - 0 1 chr1 1 2 - 2 3 chr1 1 2 - 2 5 chr1 1 2 - 2 7 chr1 1 2 - 2 9 chr1 1 2 - 2 10 chr1 2 3 - 1 11 chr1 902006 902007 - 902003 12 chr1 902006 902007 - 902005 13 chr1 8640421 8640422 - 8640418 14 chr1 8640421 8640422 - 8640420 15 chr1 9119356 9119357 - 9119353 16 chr1 9119356 9119357 - 9119355 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 2 6 chr1 1 2 - 2 7 chr1 1 2 - 2 8 chr1 1 2 - 2 9 chr1 1 2 - 2 10 chr1 2 3 - 1 11 chr1 2 3 - 1 12 chr1 902006 902007 - 902003 13 chr1 902006 902007 - 902005 14 chr1 8640421 8640422 - 8640418 15 chr1 8640421 8640422 - 8640420 16 chr1 9119356 9119357 - 9119353 17 chr1 9119356 9119357 - 9119355 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 2 6 chr1 1 2 - 2 7 chr1 1 2 - 2 8 chr1 1 2 - 2 9 chr1 1 2 - 2 10 chr1 2 3 - 1 11 chr1 902006 902007 - 902003 12 chr1 902006 902007 - 902005 13 chr1 8640421 8640422 - 8640418 14 chr1 8640421 8640422 - 8640420 15 chr1 9119356 9119357 - 9119353 16 chr1 9119356 9119357 - 9119355 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=18, step=1) Expected index RangeIndex(start=0, stop=17, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr5et42jy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr5et42jy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv32er_2g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv32er_2g/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 1 2 - 0 3 chr1 1 2 - 2 4 chr1 1 2 - 0 5 chr1 1 2 - 2 6 chr1 1 2 - 0 7 chr1 1 2 - 2 8 chr1 1 2 - 0 9 chr1 1 2 - 2 10 chr1 1 2 - 0 11 chr1 1 2 - 2 12 chr1 2 3 - 1 13 chr1 902006 902007 - 902003 14 chr1 902006 902007 - 902005 15 chr1 9119356 9119357 - 9119353 16 chr1 9119356 9119357 - 9119355 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 9119356 | 9119357 | a | 0 | ... | | chr1 | 9119356 | 9119357 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 18 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 6 chr1 1 2 - 0 8 chr1 1 2 - 0 10 chr1 1 2 - 0 12 chr1 1 2 - 0 14 chr1 1 2 - 0 16 chr1 1 2 - 0 7 chr1 1 2 - 2 9 chr1 1 2 - 2 11 chr1 1 2 - 2 13 chr1 1 2 - 2 15 chr1 1 2 - 2 17 chr1 1 2 - 2 0 chr1 2 3 - 1 1 chr1 2 3 - 1 4 chr1 902006 902007 - 902003 5 chr1 902006 902007 - 902005 2 chr1 9119356 9119357 - 9119353 3 chr1 9119356 9119357 - 9119355 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 2 chr1 1 2 - 0 4 chr1 1 2 - 0 6 chr1 1 2 - 0 8 chr1 1 2 - 0 10 chr1 1 2 - 0 1 chr1 1 2 - 2 3 chr1 1 2 - 2 5 chr1 1 2 - 2 7 chr1 1 2 - 2 9 chr1 1 2 - 2 11 chr1 1 2 - 2 12 chr1 2 3 - 1 13 chr1 902006 902007 - 902003 14 chr1 902006 902007 - 902005 15 chr1 9119356 9119357 - 9119353 16 chr1 9119356 9119357 - 9119355 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 2 7 chr1 1 2 - 2 8 chr1 1 2 - 2 9 chr1 1 2 - 2 10 chr1 1 2 - 2 11 chr1 1 2 - 2 12 chr1 2 3 - 1 13 chr1 2 3 - 1 14 chr1 902006 902007 - 902003 15 chr1 902006 902007 - 902005 16 chr1 9119356 9119357 - 9119353 17 chr1 9119356 9119357 - 9119355 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 2 7 chr1 1 2 - 2 8 chr1 1 2 - 2 9 chr1 1 2 - 2 10 chr1 1 2 - 2 11 chr1 1 2 - 2 12 chr1 2 3 - 1 13 chr1 902006 902007 - 902003 14 chr1 902006 902007 - 902005 15 chr1 9119356 9119357 - 9119353 16 chr1 9119356 9119357 - 9119355 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=18, step=1) Expected index RangeIndex(start=0, stop=17, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmptuzbsaex/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptuzbsaex/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 1 2 - 0 3 chr1 1 2 - 2 4 chr1 1 2 - 0 5 chr1 1 2 - 2 6 chr1 1 2 - 0 7 chr1 1 2 - 2 8 chr1 1 2 - 0 9 chr1 1 2 - 2 10 chr1 1 2 - 0 11 chr1 1 2 - 2 12 chr1 1 2 - 0 13 chr1 1 2 - 2 14 chr1 902006 902007 - 902003 15 chr1 902006 902007 - 902005 16 chr1 9119356 9119357 - 9119353 17 chr1 9119356 9119357 - 9119355 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 9119356 | 9119357 | a | 0 | ... | | chr1 | 9119356 | 9119357 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 18 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 6 chr1 1 2 - 0 8 chr1 1 2 - 0 10 chr1 1 2 - 0 12 chr1 1 2 - 0 14 chr1 1 2 - 0 16 chr1 1 2 - 0 1 chr1 1 2 - 2 7 chr1 1 2 - 2 9 chr1 1 2 - 2 11 chr1 1 2 - 2 13 chr1 1 2 - 2 15 chr1 1 2 - 2 17 chr1 1 2 - 2 4 chr1 902006 902007 - 902003 5 chr1 902006 902007 - 902005 2 chr1 9119356 9119357 - 9119353 3 chr1 9119356 9119357 - 9119355 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 2 chr1 1 2 - 0 4 chr1 1 2 - 0 6 chr1 1 2 - 0 8 chr1 1 2 - 0 10 chr1 1 2 - 0 12 chr1 1 2 - 0 1 chr1 1 2 - 2 3 chr1 1 2 - 2 5 chr1 1 2 - 2 7 chr1 1 2 - 2 9 chr1 1 2 - 2 11 chr1 1 2 - 2 13 chr1 1 2 - 2 14 chr1 902006 902007 - 902003 15 chr1 902006 902007 - 902005 16 chr1 9119356 9119357 - 9119353 17 chr1 9119356 9119357 - 9119355 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr1 1 2 - 2 8 chr1 1 2 - 2 9 chr1 1 2 - 2 10 chr1 1 2 - 2 11 chr1 1 2 - 2 12 chr1 1 2 - 2 13 chr1 1 2 - 2 14 chr1 902006 902007 - 902003 15 chr1 902006 902007 - 902005 16 chr1 9119356 9119357 - 9119353 17 chr1 9119356 9119357 - 9119355 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr1 1 2 - 2 8 chr1 1 2 - 2 9 chr1 1 2 - 2 10 chr1 1 2 - 2 11 chr1 1 2 - 2 12 chr1 1 2 - 2 13 chr1 1 2 - 2 14 chr1 902006 902007 - 902003 15 chr1 902006 902007 - 902005 16 chr1 9119356 9119357 - 9119353 17 chr1 9119356 9119357 - 9119355 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=18, step=1) Expected index RangeIndex(start=0, stop=18, step=1) index equal [ True True True True True True True True True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpckver0lb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpckver0lb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 1 2 - 0 3 chr1 1 2 - 2 4 chr1 1 2 - 0 5 chr1 1 2 - 2 6 chr1 1 2 - 0 7 chr1 1 2 - 2 8 chr1 1 2 - 0 9 chr1 1 2 - 2 10 chr1 1 2 - 0 11 chr1 1 2 - 2 12 chr1 1 2 - 0 13 chr1 1 2 - 2 14 chr1 2 3 - 1 15 chr1 9119356 9119357 - 9119353 16 chr1 9119356 9119357 - 9119355 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 9119356 | 9119357 | a | 0 | ... | | chr1 | 9119356 | 9119357 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 18 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 6 chr1 1 2 - 0 8 chr1 1 2 - 0 10 chr1 1 2 - 0 12 chr1 1 2 - 0 14 chr1 1 2 - 0 16 chr1 1 2 - 0 1 chr1 1 2 - 2 7 chr1 1 2 - 2 9 chr1 1 2 - 2 11 chr1 1 2 - 2 13 chr1 1 2 - 2 15 chr1 1 2 - 2 17 chr1 1 2 - 2 4 chr1 2 3 - 1 5 chr1 2 3 - 1 2 chr1 9119356 9119357 - 9119353 3 chr1 9119356 9119357 - 9119355 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 2 chr1 1 2 - 0 4 chr1 1 2 - 0 6 chr1 1 2 - 0 8 chr1 1 2 - 0 10 chr1 1 2 - 0 12 chr1 1 2 - 0 1 chr1 1 2 - 2 3 chr1 1 2 - 2 5 chr1 1 2 - 2 7 chr1 1 2 - 2 9 chr1 1 2 - 2 11 chr1 1 2 - 2 13 chr1 1 2 - 2 14 chr1 2 3 - 1 15 chr1 9119356 9119357 - 9119353 16 chr1 9119356 9119357 - 9119355 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr1 1 2 - 2 8 chr1 1 2 - 2 9 chr1 1 2 - 2 10 chr1 1 2 - 2 11 chr1 1 2 - 2 12 chr1 1 2 - 2 13 chr1 1 2 - 2 14 chr1 2 3 - 1 15 chr1 2 3 - 1 16 chr1 9119356 9119357 - 9119353 17 chr1 9119356 9119357 - 9119355 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr1 1 2 - 2 8 chr1 1 2 - 2 9 chr1 1 2 - 2 10 chr1 1 2 - 2 11 chr1 1 2 - 2 12 chr1 1 2 - 2 13 chr1 1 2 - 2 14 chr1 2 3 - 1 15 chr1 9119356 9119357 - 9119353 16 chr1 9119356 9119357 - 9119355 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=18, step=1) Expected index RangeIndex(start=0, stop=17, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd_uywuod/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd_uywuod/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 1 2 - 0 3 chr1 1 2 - 2 4 chr1 1 2 - 0 5 chr1 1 2 - 2 6 chr1 1 2 - 0 7 chr1 1 2 - 2 8 chr1 1 2 - 0 9 chr1 1 2 - 2 10 chr1 1 2 - 0 11 chr1 1 2 - 2 12 chr1 1 2 - 0 13 chr1 1 2 - 2 14 chr1 1 2 - 0 15 chr1 1 2 - 2 16 chr1 2 3 - 1 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 18 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 2 chr1 1 2 - 0 6 chr1 1 2 - 0 8 chr1 1 2 - 0 10 chr1 1 2 - 0 12 chr1 1 2 - 0 14 chr1 1 2 - 0 16 chr1 1 2 - 0 1 chr1 1 2 - 2 3 chr1 1 2 - 2 7 chr1 1 2 - 2 9 chr1 1 2 - 2 11 chr1 1 2 - 2 13 chr1 1 2 - 2 15 chr1 1 2 - 2 17 chr1 1 2 - 2 4 chr1 2 3 - 1 5 chr1 2 3 - 1 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 2 chr1 1 2 - 0 4 chr1 1 2 - 0 6 chr1 1 2 - 0 8 chr1 1 2 - 0 10 chr1 1 2 - 0 12 chr1 1 2 - 0 14 chr1 1 2 - 0 1 chr1 1 2 - 2 3 chr1 1 2 - 2 5 chr1 1 2 - 2 7 chr1 1 2 - 2 9 chr1 1 2 - 2 11 chr1 1 2 - 2 13 chr1 1 2 - 2 15 chr1 1 2 - 2 16 chr1 2 3 - 1 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr1 1 2 - 0 8 chr1 1 2 - 2 9 chr1 1 2 - 2 10 chr1 1 2 - 2 11 chr1 1 2 - 2 12 chr1 1 2 - 2 13 chr1 1 2 - 2 14 chr1 1 2 - 2 15 chr1 1 2 - 2 16 chr1 2 3 - 1 17 chr1 2 3 - 1 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr1 1 2 - 0 8 chr1 1 2 - 2 9 chr1 1 2 - 2 10 chr1 1 2 - 2 11 chr1 1 2 - 2 12 chr1 1 2 - 2 13 chr1 1 2 - 2 14 chr1 1 2 - 2 15 chr1 1 2 - 2 16 chr1 2 3 - 1 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=18, step=1) Expected index RangeIndex(start=0, stop=17, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmywtkk00/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmywtkk00/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 1 2 - 0 3 chr1 1 2 - 2 4 chr1 1 2 - 0 5 chr1 1 2 - 2 6 chr1 1 2 - 0 7 chr1 1 2 - 2 8 chr1 1 2 - 0 9 chr1 1 2 - 2 10 chr1 1 2 - 0 11 chr1 1 2 - 2 12 chr1 1 2 - 0 13 chr1 1 2 - 2 14 chr1 1 2 - 0 15 chr1 1 2 - 2 16 chr1 2 3 - 1 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 18 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 2 chr1 1 2 - 0 6 chr1 1 2 - 0 8 chr1 1 2 - 0 10 chr1 1 2 - 0 12 chr1 1 2 - 0 14 chr1 1 2 - 0 16 chr1 1 2 - 0 1 chr1 1 2 - 2 3 chr1 1 2 - 2 7 chr1 1 2 - 2 9 chr1 1 2 - 2 11 chr1 1 2 - 2 13 chr1 1 2 - 2 15 chr1 1 2 - 2 17 chr1 1 2 - 2 4 chr1 2 3 - 1 5 chr1 2 3 - 1 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 2 chr1 1 2 - 0 4 chr1 1 2 - 0 6 chr1 1 2 - 0 8 chr1 1 2 - 0 10 chr1 1 2 - 0 12 chr1 1 2 - 0 14 chr1 1 2 - 0 1 chr1 1 2 - 2 3 chr1 1 2 - 2 5 chr1 1 2 - 2 7 chr1 1 2 - 2 9 chr1 1 2 - 2 11 chr1 1 2 - 2 13 chr1 1 2 - 2 15 chr1 1 2 - 2 16 chr1 2 3 - 1 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr1 1 2 - 0 8 chr1 1 2 - 2 9 chr1 1 2 - 2 10 chr1 1 2 - 2 11 chr1 1 2 - 2 12 chr1 1 2 - 2 13 chr1 1 2 - 2 14 chr1 1 2 - 2 15 chr1 1 2 - 2 16 chr1 2 3 - 1 17 chr1 2 3 - 1 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 6 chr1 1 2 - 0 7 chr1 1 2 - 0 8 chr1 1 2 - 2 9 chr1 1 2 - 2 10 chr1 1 2 - 2 11 chr1 1 2 - 2 12 chr1 1 2 - 2 13 chr1 1 2 - 2 14 chr1 1 2 - 2 15 chr1 1 2 - 2 16 chr1 2 3 - 1 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=18, step=1) Expected index RangeIndex(start=0, stop=17, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp01vvweah/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp01vvweah/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqsqj9twx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqsqj9twx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9rg2if4i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9rg2if4i/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 1 2 - 0 3 chr1 1 2 - 2 4 chr1 1 2 - 0 5 chr1 1 2 - 2 6 chr1 1 2 - 0 7 chr1 1 2 - 2 8 chr1 2 3 - 1 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 4 chr1 1 2 - 0 6 chr1 1 2 - 0 8 chr1 1 2 - 0 1 chr1 1 2 - 2 5 chr1 1 2 - 2 7 chr1 1 2 - 2 9 chr1 1 2 - 2 2 chr1 2 3 - 1 3 chr1 2 3 - 1 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 2 chr1 1 2 - 0 4 chr1 1 2 - 0 6 chr1 1 2 - 0 1 chr1 1 2 - 2 3 chr1 1 2 - 2 5 chr1 1 2 - 2 7 chr1 1 2 - 2 8 chr1 2 3 - 1 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 2 5 chr1 1 2 - 2 6 chr1 1 2 - 2 7 chr1 1 2 - 2 8 chr1 2 3 - 1 9 chr1 2 3 - 1 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 2 5 chr1 1 2 - 2 6 chr1 1 2 - 2 7 chr1 1 2 - 2 8 chr1 2 3 - 1 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=9, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp26i774cp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp26i774cp/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=4, step=1) index equal [ True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsqdi20i1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsqdi20i1/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcem6mwaf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcem6mwaf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpghxamuj_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpghxamuj_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp88oi9o7w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp88oi9o7w/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5tclvom8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5tclvom8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjlmuvhcb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjlmuvhcb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpymiv1tsr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpymiv1tsr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvfov5nve/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvfov5nve/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp34ksl4g_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp34ksl4g_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 2 3 - 1 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 1 chr1 2 3 - 1 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 2 3 - 1 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 2 3 - 1 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 2 3 - 1 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmps42ztr29/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps42ztr29/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 1 2 - 0 3 chr1 1 2 - 2 4 chr1 1 2 - 0 5 chr1 1 2 - 2 6 chr1 1 2 - 0 7 chr1 1 2 - 2 8 chr1 2 3 - 1 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 4 chr1 1 2 - 0 6 chr1 1 2 - 0 8 chr1 1 2 - 0 1 chr1 1 2 - 2 5 chr1 1 2 - 2 7 chr1 1 2 - 2 9 chr1 1 2 - 2 2 chr1 2 3 - 1 3 chr1 2 3 - 1 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 2 chr1 1 2 - 0 4 chr1 1 2 - 0 6 chr1 1 2 - 0 1 chr1 1 2 - 2 3 chr1 1 2 - 2 5 chr1 1 2 - 2 7 chr1 1 2 - 2 8 chr1 2 3 - 1 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 2 5 chr1 1 2 - 2 6 chr1 1 2 - 2 7 chr1 1 2 - 2 8 chr1 2 3 - 1 9 chr1 2 3 - 1 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 2 5 chr1 1 2 - 2 6 chr1 1 2 - 2 7 chr1 1 2 - 2 8 chr1 2 3 - 1 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=9, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpninwgzh2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpninwgzh2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpstrcy_fw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpstrcy_fw/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 1 2 - 0 3 chr1 1 2 - 2 4 chr1 1 2 - 0 5 chr1 1 2 - 2 6 chr1 1 2 - 0 7 chr1 1 2 - 2 8 chr1 1 2 - 0 9 chr1 1 2 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 2 chr1 1 2 - 0 4 chr1 1 2 - 0 6 chr1 1 2 - 0 8 chr1 1 2 - 0 1 chr1 1 2 - 2 3 chr1 1 2 - 2 5 chr1 1 2 - 2 7 chr1 1 2 - 2 9 chr1 1 2 - 2 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 2 chr1 1 2 - 0 4 chr1 1 2 - 0 6 chr1 1 2 - 0 8 chr1 1 2 - 0 1 chr1 1 2 - 2 3 chr1 1 2 - 2 5 chr1 1 2 - 2 7 chr1 1 2 - 2 9 chr1 1 2 - 2 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 2 6 chr1 1 2 - 2 7 chr1 1 2 - 2 8 chr1 1 2 - 2 9 chr1 1 2 - 2 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 5 chr1 1 2 - 2 6 chr1 1 2 - 2 7 chr1 1 2 - 2 8 chr1 1 2 - 2 9 chr1 1 2 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=10, step=1) index equal [ True True True True True True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp579flo20/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp579flo20/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu8_rt1q6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu8_rt1q6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 2 1 chr1 1 2 + 2 2 chr1 1 2 + 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 2 1 chr1 1 2 + 2 2 chr1 1 2 + 2 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 2 1 chr1 1 2 + 2 2 chr1 1 2 + 2 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 2 1 chr1 1 2 + 2 2 chr1 1 2 + 2 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 2 1 chr1 1 2 + 2 2 chr1 1 2 + 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp49633tkg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp49633tkg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 1 2 - 0 3 chr1 1 2 - 2 4 chr1 1 2 - 0 5 chr1 1 2 - 2 6 chr1 1 2 - 0 7 chr1 1 2 - 2 8 chr1 2 3 - 1 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 4 chr1 1 2 - 0 6 chr1 1 2 - 0 8 chr1 1 2 - 0 1 chr1 1 2 - 2 5 chr1 1 2 - 2 7 chr1 1 2 - 2 9 chr1 1 2 - 2 2 chr1 2 3 - 1 3 chr1 2 3 - 1 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 2 chr1 1 2 - 0 4 chr1 1 2 - 0 6 chr1 1 2 - 0 1 chr1 1 2 - 2 3 chr1 1 2 - 2 5 chr1 1 2 - 2 7 chr1 1 2 - 2 8 chr1 2 3 - 1 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 2 5 chr1 1 2 - 2 6 chr1 1 2 - 2 7 chr1 1 2 - 2 8 chr1 2 3 - 1 9 chr1 2 3 - 1 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 2 5 chr1 1 2 - 2 6 chr1 1 2 - 2 7 chr1 1 2 - 2 8 chr1 2 3 - 1 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=10, step=1) Expected index RangeIndex(start=0, stop=9, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn92hehck/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn92hehck/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 2 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 2 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 2 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt8ffsvxu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt8ffsvxu/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 2 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 2 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 2 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2f72tw7i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2f72tw7i/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmphvi9fjmb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphvi9fjmb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8t6uptl7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8t6uptl7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk6s3dob_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk6s3dob_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 2 3 - 1 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 1 chr1 2 3 - 1 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 2 3 - 1 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 2 3 - 1 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 2 3 - 1 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnwqrrvb7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnwqrrvb7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm7eaa1pb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm7eaa1pb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 2 3 - 1 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 1 chr1 2 3 - 1 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 2 3 - 1 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 2 3 - 1 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 2 3 - 1 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmc92f2hr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmc92f2hr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5u4yi263/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5u4yi263/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1fivt584/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1fivt584/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpta0avjia/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpta0avjia/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 2 3 - 1 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 1 2 - 0 1 chr1 2 3 - 1 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 2 3 - 1 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 2 3 - 1 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 0 4 chr1 2 3 - 1 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg3rs1eoq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg3rs1eoq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 1 2 - 0 3 chr1 1 2 - 2 4 chr1 1 2 - 0 5 chr1 1 2 - 2 6 chr1 2 3 - 1 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 4 chr1 1 2 - 0 6 chr1 1 2 - 0 1 chr1 1 2 - 2 5 chr1 1 2 - 2 7 chr1 1 2 - 2 2 chr1 2 3 - 1 3 chr1 2 3 - 1 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 2 chr1 1 2 - 0 4 chr1 1 2 - 0 1 chr1 1 2 - 2 3 chr1 1 2 - 2 5 chr1 1 2 - 2 6 chr1 2 3 - 1 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 2 4 chr1 1 2 - 2 5 chr1 1 2 - 2 6 chr1 2 3 - 1 7 chr1 2 3 - 1 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 0 3 chr1 1 2 - 2 4 chr1 1 2 - 2 5 chr1 1 2 - 2 6 chr1 2 3 - 1 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=7, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8w3qlbsz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8w3qlbsz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 1 2 - 0 3 chr1 1 2 - 2 4 chr1 2 3 - 1 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 4 chr1 1 2 - 0 1 chr1 1 2 - 2 5 chr1 1 2 - 2 2 chr1 2 3 - 1 3 chr1 2 3 - 1 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 2 chr1 1 2 - 0 1 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 2 3 - 1 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 2 3 - 1 5 chr1 2 3 - 1 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 2 chr1 1 2 - 2 3 chr1 1 2 - 2 4 chr1 2 3 - 1 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=5, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4w8a2krj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4w8a2krj/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 3 chr1 2 3 - 1 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 3 chr1 2 3 - 1 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=3, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa4fcy9lk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa4fcy9lk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 1 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 1 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 1 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd44ce7x_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd44ce7x_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 3 - 1 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 df2 Chromosome Start End Strand Distance 0 chr1 2 3 - 1 Actual Chromosome Start End Strand Distance 0 chr1 2 3 - 1 Expected Chromosome Start End Strand Distance 0 chr1 2 3 - 1 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmptqdah8q9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptqdah8q9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmphgw5scd1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphgw5scd1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9sb7oufh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9sb7oufh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwx0xs41n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwx0xs41n/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu2dj2i0l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu2dj2i0l/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzzzxqw13/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzzzxqw13/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_4ispb_a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_4ispb_a/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 2 1 chr1 2 3 + 1 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 2 1 chr1 2 3 + 1 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 2 1 chr1 2 3 + 1 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 2 1 chr1 2 3 + 1 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 2 1 chr1 2 3 + 1 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvv3d0pk2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvv3d0pk2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 2 3 + 1 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 2 3 + 1 df2 Chromosome Start End Strand Distance 1 chr1 2 3 + 1 Actual Chromosome Start End Strand Distance 0 chr1 2 3 + 1 Expected Chromosome Start End Strand Distance 0 chr1 2 3 + 1 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpchnwjhun/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpchnwjhun/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn9f148qf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn9f148qf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp46wdyi7e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp46wdyi7e/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 3 chr1 2 3 - 1 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 3 chr1 2 3 - 1 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=3, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmphvna79b7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphvna79b7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 3 chr1 2 3 - 1 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 3 chr1 2 3 - 1 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=3, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3kfv3uu7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3kfv3uu7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpti589h9w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpti589h9w/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 3 chr1 2 3 - 1 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 3 chr1 2 3 - 1 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=3, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1b0j3b7z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1b0j3b7z/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 3 chr1 2 3 - 1 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 3 chr1 2 3 - 1 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=3, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmptqfw9tmj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptqfw9tmj/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 2 3 - 1 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 2 3 - 1 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 2 3 - 1 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 2 3 - 1 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 2 3 - 1 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8_9exlm0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8_9exlm0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgfb9io6d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgfb9io6d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6ghou33y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6ghou33y/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc7rc3au7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc7rc3au7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2avzqlne/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2avzqlne/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmtnncjws/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmtnncjws/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 3 chr1 2 3 - 1 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 3 chr1 2 3 - 1 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=3, step=1) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpunatsps1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpunatsps1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxkd_j86y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxkd_j86y/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 1 | 2 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | | chr1 | 2 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 4 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 3 chr1 2 3 - 1 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 3 chr1 2 3 - 1 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 1 chr1 1 2 - 2 2 chr1 2 3 - 1 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=4, step=1) Expected index RangeIndex(start=0, stop=3, step=1) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr11 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr16 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr18 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr18 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr18 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr10 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr18 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr8 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrY than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr10 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr18 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr8 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrY than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr10 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr18 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr8 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrY than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr10 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr8 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr15 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr15 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr3 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr22 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr22 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr22 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr22 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr22 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr17 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr13 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr13 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr13 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr13 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr13 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr13 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr13 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr13 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr8 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr13 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr8 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr13 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr8 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr17 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr3 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr4 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr16 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr18 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrY than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr18 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrY than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr13 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr15 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr3 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr8 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrM than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrM than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrM than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr21 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr9 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrX than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr21 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr9 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrX than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr9 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr21 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr9 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrX than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr21 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr9 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrX than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr19 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr14 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr14 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr21 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr9 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr14 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr14 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr21 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr9 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr15 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr15 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrY than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr8 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr8 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr8 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr8 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr8 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr12 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr12 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrY than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrY than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrY than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrY than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrY than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr22 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr22 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr17 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr22 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr6 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr19 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr19 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr19 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. =============================== warnings summary =============================== tests/conftest.py:83 /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/conftest.py:83: SyntaxWarning: invalid escape sequence '\s' sep="\s+", pyranges/__init__.py:18: 43 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/__init__.py:18: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html import pkg_resources tests/test_binary.py:118: 42 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:118: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:139: 42 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:139: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:160: 42 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:160: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:187: 42 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:187: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:212: 42 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:212: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:291: 42 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:291: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:329: 42 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:329: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:368: 42 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:368: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:392: 42 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:392: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:426: 42 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:426: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:516: 42 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:516: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_binary.py:579: 42 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py:579: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) pyranges/methods/init.py:60: 210 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_change_chromosome_custom.py: 2 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_concat.py: 8 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_count_overlaps.py: 1 warning .pybuild/cpython3_3.12_pyranges/build/tests/data/test_data.py: 9 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py: 159634 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py: 158789 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_getset_attr.py: 3 warnings .pybuild/cpython3_3.12_pyranges/build/tests/windows/test_windows.py: 2 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_io.py: 4 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_pickle.py: 1 warning .pybuild/cpython3_3.12_pyranges/build/tests/test_stranded.py: 6 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py: 358 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py: 24070 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/init.py:60: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. return {k: v for k, v in df.groupby(grpby_key)} pyranges/methods/init.py:189: 168 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_change_chromosome_custom.py: 1 warning .pybuild/cpython3_3.12_pyranges/build/tests/test_concat.py: 7 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py: 4411 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py: 2000 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_stranded.py: 2 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py: 6289 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/init.py:189: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. empty_removed = df.groupby("Chromosome") tests/test_do_not_error.py:46: 42 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py:46: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:35: 42 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:35: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:100: 42 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:100: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:163: 42 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:163: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:205: 42 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:205: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:234: 42 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:234: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:272: 42 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:272: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) tests/test_unary.py:287: 42 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:287: HypothesisDeprecationWarning: The return_value health check is deprecated, because this is always an error. @settings( tests/test_unary.py:315: 42 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:315: HypothesisDeprecationWarning: `HealthCheck.all()` is deprecated; use `list(HealthCheck)` instead. The `hypothesis codemod` command-line tool can automatically refactor your code to fix this warning. suppress_health_check=HealthCheck.all()) .pybuild/cpython3_3.12_pyranges/build/tests/test_concat.py::test_concat_unstranded_stranded /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:47: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[NaN, NaN, NaN, '+', '-'] Categories (3, object): ['+', '-', '.']' has dtype incompatible with category, please explicitly cast to a compatible dtype first. v.loc[:, "Strand"] = type_v.cat.add_categories(["."]) .pybuild/cpython3_3.12_pyranges/build/tests/test_concat.py::test_concat_stranded_unstranded /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/concat.py:47: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['+', '+', '-', NaN, NaN] Categories (3, object): ['+', '-', '.']' has dtype incompatible with category, please explicitly cast to a compatible dtype first. v.loc[:, "Strand"] = type_v.cat.add_categories(["."]) .pybuild/cpython3_3.12_pyranges/build/tests/test_concat.py: 1 warning .pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py: 2999 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_stranded.py: 2 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py: 119 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py: 5289 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/methods/init.py:187: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. empty_removed = df.groupby(["Chromosome", "Strand"]) .pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py: 8341 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py: 14699 warnings .pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py: 16620 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/tostring2.py:31: FutureWarning: The behavior of DataFrame concatenation with empty or all-NA entries is deprecated. In a future version, this will no longer exclude empty or all-NA columns when determining the result dtypes. To retain the old behavior, exclude the relevant entries before the concat operation. df = pd.concat([plus, minus]) .pybuild/cpython3_3.12_pyranges/build/tests/test_do_not_error.py: 1471 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/pyranges.py:3779: FutureWarning: The behavior of Series.replace (and DataFrame.replace) with CategoricalDtype is deprecated. In a future version, replace will only be used for cases that preserve the categories. To change the categories, use ser.cat.rename_categories instead. other.Strand = other.Strand.replace({"+": "-", "-": "+"}) .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1217804. 1221351. 1223357. 1223968. 1227319. 1228946. 1232031.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000078808.16' 'ENSG00000078808.16' 'ENSG00000078808.16' 'ENSG00000078808.16' 'ENSG00000078808.16' 'ENSG00000078808.16']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1336515. 1337055. 1338183. 1338436. 1338653. 1339812. 1340190. 1340365. 1340503. 1342156. 1342484. 1342758. 1349350.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000107404.19' 'ENSG00000107404.19' 'ENSG00000107404.19' 'ENSG00000107404.19' 'ENSG00000107404.19' 'ENSG00000107404.19' 'ENSG00000107404.19' 'ENSG00000107404.19' 'ENSG00000107404.19' 'ENSG00000107404.19' 'ENSG00000107404.19' 'ENSG00000107404.19']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1311924. 1312147. 1313592. 1315697. 1317450. 1321096. 1321984. 1323287. 1324691.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000127054.20' 'ENSG00000127054.20' 'ENSG00000127054.20' 'ENSG00000127054.20' 'ENSG00000127054.20' 'ENSG00000127054.20' 'ENSG00000127054.20' 'ENSG00000127054.20']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1293708. 1293933. 1294199. 1294628. 1295008. 1295554. 1295938. 1296109. 1296280. 1296633. 1297933. 1298265. 1298421. 1299905. 1300068. 1300202. 1300692. 1302046. 1302975. 1305929. 1307156. 1307383. 1308018. 1309609.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18' 'ENSG00000131584.18']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1084506. 1085310. 1086012. 1087636. 1092294. 1092813. 1106127. 1106871. 1115075. 1116361.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000131591.17' 'ENSG00000131591.17' 'ENSG00000131591.17' 'ENSG00000131591.17' 'ENSG00000131591.17' 'ENSG00000131591.17' 'ENSG00000131591.17' 'ENSG00000131591.17' 'ENSG00000131591.17']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1472089. 1477350. 1478745. 1479108. 1480936. 1482303. 1482662. 1485171. 1486235. 1486668. 1487914. 1490671. 1497848.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000160072.19' 'ENSG00000160072.19' 'ENSG00000160072.19' 'ENSG00000160072.19' 'ENSG00000160072.19' 'ENSG00000160072.19' 'ENSG00000160072.19' 'ENSG00000160072.19' 'ENSG00000160072.19' 'ENSG00000160072.19' 'ENSG00000160072.19' 'ENSG00000160072.19']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1255487. 1256335. 1257130. 1257310. 1262390. 1263569. 1264830. 1266290. 1267992. 1271637. 1273885.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000160087.20' 'ENSG00000160087.20' 'ENSG00000160087.20' 'ENSG00000160087.20' 'ENSG00000160087.20' 'ENSG00000160087.20' 'ENSG00000160087.20' 'ENSG00000160087.20' 'ENSG00000160087.20' 'ENSG00000160087.20']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1173926. 1174321. 1174489. 1175034. 1179333. 1179853. 1180340. 1180884. 1181815. 1182446. 1183047. 1184091. 1185864. 1196488. 1196716. 1197186. 1197935.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13' 'ENSG00000162571.13']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1281610. 1282010. 1282319. 1284090. 1285664. 1286278. 1286975. 1287299. 1287836. 1288037. 1290388. 1290555. 1290694. 1290953. 1291140. 1292029.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000162572.20' 'ENSG00000162572.20' 'ENSG00000162572.20' 'ENSG00000162572.20' 'ENSG00000162572.20' 'ENSG00000162572.20' 'ENSG00000162572.20' 'ENSG00000162572.20' 'ENSG00000162572.20' 'ENSG00000162572.20' 'ENSG00000162572.20' 'ENSG00000162572.20' 'ENSG00000162572.20' 'ENSG00000162572.20' 'ENSG00000162572.20']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1353946. 1354106. 1354509. 1355752. 1356704. 1358794. 1361777.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000162576.16' 'ENSG00000162576.16' 'ENSG00000162576.16' 'ENSG00000162576.16' 'ENSG00000162576.16' 'ENSG00000162576.16']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1331536. 1331938. 1332806. 1333124. 1333379. 1335306.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000169962.4' 'ENSG00000169962.4' 'ENSG00000169962.4' 'ENSG00000169962.4' 'ENSG00000169962.4']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1308720. 1308972. 1309851. 1311071. 1311677.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000169972.11' 'ENSG00000169972.11' 'ENSG00000169972.11' 'ENSG00000169972.11']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1373902. 1375495.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000175756.13']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1235041.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 818202. 819837.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000177757.2']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1435146. 1435821. 1437484. 1442882.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000179403.11' 'ENSG00000179403.11' 'ENSG00000179403.11']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1242646. 1243552. 1244275. 1244724. 1246722.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000184163.3' 'ENSG00000184163.3' 'ENSG00000184163.3' 'ENSG00000184163.3']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 65433. 65573. 71585.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000186092.6' 'ENSG00000186092.6']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1211832. 1212138. 1212704. 1213785. 1214138.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000186827.10' 'ENSG00000186827.10' 'ENSG00000186827.10' 'ENSG00000186827.10']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1203968. 1204236. 1204486. 1205680. 1206691.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000186891.13' 'ENSG00000186891.13' 'ENSG00000186891.13' 'ENSG00000186891.13']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 966614. 966803. 970423. 970601. 971006. 971208. 971523. 972150. 972424. 973010. 973326. 973640. 974051. 974364. 975108. 975865.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000187583.10' 'ENSG00000187583.10' 'ENSG00000187583.10' 'ENSG00000187583.10' 'ENSG00000187583.10' 'ENSG00000187583.10' 'ENSG00000187583.10' 'ENSG00000187583.10' 'ENSG00000187583.10' 'ENSG00000187583.10' 'ENSG00000187583.10' 'ENSG00000187583.10' 'ENSG00000187583.10' 'ENSG00000187583.10' 'ENSG00000187583.10']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1001281. 1008279. 1013576. 1014540.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000187608.9' 'ENSG00000187608.9' 'ENSG00000187608.9']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 924948. 925189. 925800. 926013. 930336. 931089. 935896. 939129. 939460. 940462. 941306. 943058. 943377. 944581.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000187634.11' 'ENSG00000187634.11' 'ENSG00000187634.11' 'ENSG00000187634.11' 'ENSG00000187634.11' 'ENSG00000187634.11' 'ENSG00000187634.11' 'ENSG00000187634.11' 'ENSG00000187634.11' 'ENSG00000187634.11' 'ENSG00000187634.11' 'ENSG00000187634.11' 'ENSG00000187634.11']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 976269. 976641. 981029. 981173. 982093.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000187642.9' 'ENSG00000187642.9' 'ENSG00000187642.9' 'ENSG00000187642.9']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 960800. 961750. 962478. 962917. 963253. 963504. 964008. 964180. 964530. 965715.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000187961.13' 'ENSG00000187961.13' 'ENSG00000187961.13' 'ENSG00000187961.13' 'ENSG00000187961.13' 'ENSG00000187961.13' 'ENSG00000187961.13' 'ENSG00000187961.13' 'ENSG00000187961.13']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1020373. 1022462. 1034703. 1035324. 1040880. 1041397. 1041702. 1042162. 1043457. 1043732. 1044023. 1044257. 1044439. 1045277. 1045523. 1045876. 1046088. 1046349. 1046735. 1046957. 1047454. 1047687. 1047895. 1048365. 1049059. 1049451. 1049795. 1050037. 1050329. 1050591. 1050837. 1051043. 1051369. 1051645. 1051815. 1053977. 1054551. 1056118.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14' 'ENSG00000188157.14']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 999432. 1000172.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000188290.10']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 944800. 945146. 945422. 945653. 946286. 947060. 948232. 948603. 951238. 952139. 952600. 953288. 953892. 954523. 956013. 956215. 957025. 959081. 959309.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10' 'ENSG00000188976.10']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1512473. 1516088. 1517412. 1517775. 1518990. 1520306. 1520617.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000197785.13' 'ENSG00000197785.13' 'ENSG00000197785.13' 'ENSG00000197785.13' 'ENSG00000197785.13' 'ENSG00000197785.13' 'ENSG00000197785.13']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 634922.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1169087.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1426385. 1427787.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000205116.3']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1176396. 1179555.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000205231.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1167952.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1167198.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1450758. 1452122. 1452434. 1454500. 1455519. 1455916. 1456349. 1457180. 1459231. 1460917. 1462708. 1470158.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000215915.9' 'ENSG00000215915.9' 'ENSG00000215915.9' 'ENSG00000215915.9' 'ENSG00000215915.9' 'ENSG00000215915.9' 'ENSG00000215915.9' 'ENSG00000215915.9' 'ENSG00000215915.9' 'ENSG00000215915.9' 'ENSG00000215915.9']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1059846. 1060393. 1061117. 1063201. 1063566. 1064401. 1064589. 1065475. 1066456. 1066667. 1067646. 1068003. 1068724. 1069355.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000217801.9' 'ENSG00000217801.9' 'ENSG00000217801.9' 'ENSG00000217801.9' 'ENSG00000217801.9' 'ENSG00000217801.9' 'ENSG00000217801.9' 'ENSG00000217801.9' 'ENSG00000217801.9' 'ENSG00000217801.9' 'ENSG00000217801.9' 'ENSG00000217801.9' 'ENSG00000217801.9']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1387582. 1387869. 1388743. 1388830. 1389047. 1389473. 1390371. 1390563. 1392803. 1393460. 1395537. 1398366. 1398956. 1399328.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000221978.11' 'ENSG00000221978.11' 'ENSG00000221978.11' 'ENSG00000221978.11' 'ENSG00000221978.11' 'ENSG00000221978.11' 'ENSG00000221978.11' 'ENSG00000221978.11' 'ENSG00000221978.11' 'ENSG00000221978.11' 'ENSG00000221978.11' 'ENSG00000221978.11' 'ENSG00000221978.11']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 157887.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 758336.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1379032.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 921016.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1137110. 1141032. 1144056.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000223823.1' 'ENSG00000223823.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 12227. 12721. 13052. 14409.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000223972.5' 'ENSG00000223972.5' 'ENSG00000223972.5']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1325102. 1325595. 1327032. 1328897.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000224051.6' 'ENSG00000224051.6' 'ENSG00000224051.6']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1402046.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1012190. 1013193.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000224969.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1430954. 1431843. 1434573.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000225285.1' 'ENSG00000225285.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 630683.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 827522.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1420564. 1422691.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000225905.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 629433.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 14501. 15038. 15947. 16765. 17055. 17368. 17742. 18061. 18366. 24891. 29570.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000227232.5' 'ENSG00000227232.5' 'ENSG00000227232.5' 'ENSG00000227232.5' 'ENSG00000227232.5' 'ENSG00000227232.5' 'ENSG00000227232.5' 'ENSG00000227232.5' 'ENSG00000227232.5' 'ENSG00000227232.5']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 729804. 733364. 735613. 743350. 744391. 744825. 746818. 756141. 759123. 765247. 766387. 768613. 769712. 773107. 774280. 778626.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000228327.3' 'ENSG00000228327.3' 'ENSG00000228327.3' 'ENSG00000228327.3' 'ENSG00000228327.3' 'ENSG00000228327.3' 'ENSG00000228327.3' 'ENSG00000228327.3' 'ENSG00000228327.3' 'ENSG00000228327.3' 'ENSG00000228327.3' 'ENSG00000228327.3' 'ENSG00000228327.3' 'ENSG00000228327.3' 'ENSG00000228327.3']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 259025. 261634. 268204. 268816. 289370. 297502. 357586. 358183. 359681.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000228463.10' 'ENSG00000228463.10' 'ENSG00000228463.10' 'ENSG00000228463.10' 'ENSG00000228463.10' 'ENSG00000228463.10' 'ENSG00000228463.10' 'ENSG00000228463.10']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 825552. 826923. 827775. 827853. 829104. 831677. 842020. 847806. 849602. 850351. 852515. 852766. 859446.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000228794.8' 'ENSG00000228794.8' 'ENSG00000228794.8' 'ENSG00000228794.8' 'ENSG00000228794.8' 'ENSG00000228794.8' 'ENSG00000228794.8' 'ENSG00000228794.8' 'ENSG00000228794.8' 'ENSG00000228794.8' 'ENSG00000228794.8' 'ENSG00000228794.8']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 633438.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 724360. 724903.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000229376.3']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 761154. 761989.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000229905.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 586358. 586955. 588453. 594756. 598551. 601577. 608056. 612864. 627823. 628223. 629006. 631204. 633129. 698959. 702340. 703789. 711922. 720206. 724564. 732212. 733064. 827796.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10' 'ENSG00000230021.10']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 801163. 805891. 808623. 810170. 817712.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000230092.7' 'ENSG00000230092.7' 'ENSG00000230092.7' 'ENSG00000230092.7']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 868675. 869575. 870201. 875155. 876903.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000230368.2' 'ENSG00000230368.2' 'ENSG00000230368.2' 'ENSG00000230368.2']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1275299. 1279393. 1280420.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000230415.1' 'ENSG00000230415.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 911473. 914948.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000230699.2']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1008229.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 489387. 489906.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000233653.3']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 134836.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 874349.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1419549. 1420592. 1421769.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000235098.8' 'ENSG00000235098.8']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 587729. 594768.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000235146.2']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 358957. 360168. 366052.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000236601.2' 'ENSG00000236601.2']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 348366.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 365692. 366151. 368450. 373323. 379972. 476945. 485208. 489553. 494898. 495049. 495476. 496605. 497299. 498305. 499369. 501620. 502243. 502955. 505103. 514423. 517266. 522928.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12' 'ENSG00000237094.12']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1072575. 1074307.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000237330.2']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 779092. 782191. 783363. 784977. 787672. 793041. 795582. 801876. 803667. 804222. 805270. 806459. 807465. 810060.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000237491.8' 'ENSG00000237491.8' 'ENSG00000237491.8' 'ENSG00000237491.8' 'ENSG00000237491.8' 'ENSG00000237491.8' 'ENSG00000237491.8' 'ENSG00000237491.8' 'ENSG00000237491.8' 'ENSG00000237491.8' 'ENSG00000237491.8' 'ENSG00000237491.8' 'ENSG00000237491.8']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 35174. 35481. 36081.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000237613.2' 'ENSG00000237613.2']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 632616.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 91629. 92240. 111357. 112804. 120932. 129223. 133723.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000238009.6' 'ENSG00000238009.6' 'ENSG00000238009.6' 'ENSG00000238009.6' 'ENSG00000238009.6' 'ENSG00000238009.6']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 139847. 140339.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000239906.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 90050. 91105.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000239945.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 57653. 58856. 64116.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000240361.2' 'ENSG00000240361.2']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 633741.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1317899. 1318689.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000240731.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 914444. 914971.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000241180.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 160690. 161525.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000241599.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 143011. 149707. 155831. 164791. 165942. 168165. 168767. 169264. 172688. 173862.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000241860.6' 'ENSG00000241860.6' 'ENSG00000241860.6' 'ENSG00000241860.6' 'ENSG00000241860.6' 'ENSG00000241860.6' 'ENSG00000241860.6' 'ENSG00000241860.6' 'ENSG00000241860.6']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1402601. 1407019. 1407313.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000242485.5' 'ENSG00000242485.5']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1055215. 1056116.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000242590.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 30039. 30667. 31109.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000243485.5' 'ENSG00000243485.5']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 634376.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 491989. 493241.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000250575.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1251334.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1405752.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 53312.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 675265.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 135895.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 440232.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 137965.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1170343.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 904957. 915976.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000272438.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1410618.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 998051.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1062808. 1063288.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000273443.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 187958.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1296170.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 17436.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 516479.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 632413.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 185350. 185559. 186469. 187287. 187577. 187890. 188266. 188584. 188902. 195411.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000279457.4' 'ENSG00000279457.4' 'ENSG00000279457.4' 'ENSG00000279457.4' 'ENSG00000279457.4' 'ENSG00000279457.4' 'ENSG00000279457.4' 'ENSG00000279457.4' 'ENSG00000279457.4']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 182746. 183216. 183571. 183901. 184174.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000279928.2' 'ENSG00000279928.2' 'ENSG00000279928.2' 'ENSG00000279928.2']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 874591. 875155. 875625. 876611. 877234.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000283040.1' 'ENSG00000283040.1' 'ENSG00000283040.1' 'ENSG00000283040.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1312566.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 30503.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1339708.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 686673.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 451697.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1503661. 1509452.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000284740.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 782050.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py:37: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '[ nan 1098113. 1104598.]' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. x.loc[:, "Start"] = x.Start.shift() .pybuild/cpython3_3.12_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/pyranges/genomicfeatures.py:600: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '['ENSG00000285812.1']' has dtype incompatible with int32, please explicitly cast to a compatible dtype first. introns.loc[:, "by_id"] = original_ids[id_column].values .pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py: 2000 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:153: FutureWarning: A value is trying to be set on a copy of a DataFrame or Series through chained assignment using an inplace method. The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy. For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[col].method(value) instead, to perform the operation inplace on the original object. result_df.Cluster.replace(cluster_ids, inplace=True) .pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py: 2000 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py:178: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. for _, gdf in natsorted(df.groupby(groupby)): -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========================== short test summary info ============================ FAILED tests/test_binary.py::test_k_nearest[None-True-same-last] - ValueError... ========= 1 failed, 530 passed, 410640 warnings in 1019.76s (0:16:59) ========== E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.12_pyranges/build; python3.12 -m pytest -v -n 42 dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.12 returned exit code 13 make: *** [debian/rules:22: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package I: user script /srv/workspace/pbuilder/1718224/tmp/hooks/C01_cleanup starting debug output: disk usage on i-capture-the-hostname at Tue Jan 6 03:06:05 UTC 2026 Filesystem Size Used Avail Use% Mounted on tmpfs 40G 0 40G 0% /dev/shm I: user script /srv/workspace/pbuilder/1718224/tmp/hooks/C01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1718224 and its subdirectories