Diff of the two buildlogs: -- --- b1/build.log 2024-12-03 20:25:13.818011631 +0000 +++ b2/build.log 2024-12-03 20:43:07.209454158 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Dec 3 04:34:35 -12 2024 -I: pbuilder-time-stamp: 1733243675 +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 @@ -34,52 +34,84 @@ 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/28692/tmp/hooks/D02_print_environment starting +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 - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + 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='2f97e93329824295ada80e582dac873a' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='28692' - PS1='# ' - PS2='> ' + 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' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.onRzAPlw/pbuilderrc_7Tsi --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.onRzAPlw/b1 --logfile b1/build.log pyranges_0.0.111+ds-8.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + 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 ionos11-amd64 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux + 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 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/28692/tmp/hooks/D02_print_environment finished + 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 @@ -240,7 +272,7 @@ 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 2s (22.8 MB/s) +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.) @@ -589,8 +621,8 @@ Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Dec 3 16:37:08 UTC 2024. -Universal Time is now: Tue Dec 3 16:37:08 UTC 2024. +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) ... @@ -683,7 +715,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/pyranges-0.0.111+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../pyranges_0.0.111+ds-8_source.changes +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 @@ -722,10 +758,10 @@ '/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' -> '/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/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' @@ -746,1246 +782,31205 @@ '/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 20 +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: hypothesis-6.121.0, typeguard-4.4.1, xdist-3.6.1 -created: 20/20 workers -20 workers [531 items] +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/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_chain25-method_chain25] -tests/test_change_chromosome_custom.py::test_change_chromosomes tests/data/test_data.py::test_all_data -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain43-method_chain43] -tests/test_binary.py::test_nearest[upstream-True-same] +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_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_chain1-method_chain1] +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_coverage[same] -tests/test_binary.py::test_jaccard[same] -tests/test_binary.py::test_overlap[same] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain49-method_chain49] +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_nearest[None-True-same] 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_chain7-method_chain7] +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] -[gw12] [ 0%] PASSED tests/test_change_chromosome_custom.py::test_change_chromosomes +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 -[gw12] [ 0%] PASSED tests/test_concat.py::test_concat_stranded_unstranded -tests/test_concat.py::test_concat_unstranded_unstranded -[gw12] [ 0%] PASSED tests/test_concat.py::test_concat_unstranded_unstranded -tests/test_concat.py::test_concat_unstranded_stranded -[gw12] [ 0%] PASSED tests/test_concat.py::test_concat_unstranded_stranded +[gw22] [ 0%] PASSED tests/test_concat.py::test_concat_unstranded_stranded tests/test_count_overlaps.py::test_strand_vs_strand_same -[gw12] [ 0%] PASSED 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] -[gw14] [ 1%] 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] -[gw17] [ 1%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain25-method_chain25] +[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] -[gw16] [ 1%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain31-method_chain31] +[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] -[gw11] [ 1%] 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] -[gw15] [ 2%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain43-method_chain43] +[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] -[gw18] [ 2%] 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] -[gw7] [ 2%] 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] -[gw13] [ 2%] 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] -[gw19] [ 2%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain37-method_chain37] +[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] -[gw12] [ 3%] 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_chain55-method_chain55] -[gw15] [ 3%] 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_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] -[gw11] [ 3%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain20-method_chain20] +[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] -[gw16] [ 3%] 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] -[gw14] [ 3%] 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] -[gw7] [ 3%] 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] -[gw18] [ 4%] 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] -[gw17] [ 4%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain26-method_chain26] +[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] -[gw13] [ 4%] 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] -[gw15] [ 4%] 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_chain46-method_chain46] -[gw19] [ 4%] 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] -[gw12] [ 5%] 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] -[gw16] [ 5%] 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_chain34-method_chain34] -[gw11] [ 5%] 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_chain22-method_chain22] -[gw14] [ 5%] 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_chain16-method_chain16] -[gw7] [ 5%] 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_chain10-method_chain10] -[gw17] [ 6%] 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_chain28-method_chain28] -[gw18] [ 6%] 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_chain52-method_chain52] -[gw15] [ 6%] 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] -[gw16] [ 6%] 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] -[gw11] [ 6%] PASSED 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_chain23-method_chain23] -[gw13] [ 6%] 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_chain4-method_chain4] -[gw19] [ 7%] 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_chain40-method_chain40] -[gw12] [ 7%] 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] -[gw14] [ 7%] 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] -[gw7] [ 7%] 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] -[gw17] [ 7%] 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_chain29-method_chain29] -[gw15] [ 8%] 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] -[gw18] [ 8%] 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] -[gw11] [ 8%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain23-method_chain23] +[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] -[gw13] [ 8%] 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] -[gw14] [ 8%] 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] -[gw12] [ 9%] 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_chain58-method_chain58] -[gw7] [ 9%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain11-method_chain11] +[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] -[gw16] [ 9%] 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] -[gw17] [ 9%] 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] -[gw15] [ 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_chain64-method_chain64] -[gw18] [ 9%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain53-method_chain53] +[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] -[gw19] [ 10%] 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] -[gw11] [ 10%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain24-method_chain24] +[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] -[gw14] [ 10%] 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_chain81-method_chain81] -[gw17] [ 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_chain105-method_chain105] -[gw12] [ 10%] 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] -[gw7] [ 11%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain12-method_chain12] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain89-method_chain89] -[gw15] [ 11%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain64-method_chain64] +[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] -[gw16] [ 11%] 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_chain97-method_chain97] -[gw13] [ 11%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain5-method_chain5] +[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] -[gw14] [ 11%] 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_chain82-method_chain82] -[gw11] [ 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] -[gw19] [ 12%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain41-method_chain41] +[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] -[gw15] [ 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] -[gw12] [ 12%] 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] -[gw18] [ 12%] 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_chain113-method_chain113] -[gw16] [ 12%] 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] -[gw17] [ 13%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain105-method_chain105] +[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] -[gw14] [ 13%] 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] -[gw7] [ 13%] 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] -[gw13] [ 13%] 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_chain120-method_chain120] -[gw11] [ 13%] 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] -[gw3] [ 14%] PASSED tests/test_binary.py::test_overlap[same] -tests/test_binary.py::test_overlap[opposite] -[gw15] [ 14%] 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_chain67-method_chain67] -[gw19] [ 14%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain42-method_chain42] +[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] -[gw18] [ 14%] 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] -[gw12] [ 14%] 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_chain61-method_chain61] -[gw14] [ 15%] 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] -[gw17] [ 15%] 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] -[gw15] [ 15%] 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] -[gw11] [ 15%] 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_chain76-method_chain76] -[gw13] [ 15%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain120-method_chain120] +[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] -[gw18] [ 16%] 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_chain115-method_chain115] -[gw7] [ 16%] 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_chain91-method_chain91] -[gw19] [ 16%] 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] -[gw16] [ 16%] 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] -[gw12] [ 16%] 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_chain62-method_chain62] -[gw15] [ 16%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain68-method_chain68] +[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] -[gw13] [ 17%] 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] -[gw17] [ 17%] 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_chain108-method_chain108] -[gw11] [ 17%] 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] -[gw14] [ 17%] 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_chain85-method_chain85] -[gw18] [ 17%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain115-method_chain115] +[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] -[gw19] [ 18%] 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] -[gw7] [ 18%] 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] -[gw0] [ 18%] PASSED tests/test_binary.py::test_set_intersect[False] -tests/test_binary.py::test_set_intersect[same] -[gw16] [ 18%] 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_chain100-method_chain100] -[gw10] [ 18%] PASSED tests/test_binary.py::test_jaccard[same] -tests/test_binary.py::test_join[False] -[gw12] [ 19%] 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] -[gw9] [ 19%] PASSED tests/test_binary.py::test_nearest[downstream-True-same] -[gw15] [ 19%] 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_chain70-method_chain70] -tests/test_binary.py::test_nearest[downstream-True-opposite] -[gw4] [ 19%] PASSED tests/test_binary.py::test_nearest[upstream-True-same] -tests/test_binary.py::test_nearest[upstream-True-opposite] -[gw13] [ 19%] 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] -[gw11] [ 19%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain77-method_chain77] +[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] -[gw18] [ 20%] 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] -[gw2] [ 20%] PASSED tests/test_binary.py::test_nearest[None-True-same] -[gw17] [ 20%] 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_chain109-method_chain109] -[gw7] [ 20%] 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] -tests/test_binary.py::test_nearest[None-True-opposite] -[gw19] [ 20%] 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_chain130-method_chain130] -[gw8] [ 21%] PASSED tests/test_binary.py::test_k_nearest[upstream-False-same-last] -tests/test_binary.py::test_k_nearest[upstream-False-False-last] -[gw6] [ 21%] PASSED tests/test_binary.py::test_k_nearest[downstream-False-same-last] -tests/test_binary.py::test_k_nearest[downstream-False-False-last] -[gw16] [ 21%] 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] -[gw12] [ 21%] 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_chain134-method_chain134] -[gw14] [ 21%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain85-method_chain85] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain86-method_chain86] -[gw13] [ 22%] 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_chain124-method_chain124] -[gw15] [ 22%] 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] -[gw11] [ 22%] 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_chain79-method_chain79] -[gw18] [ 22%] 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_chain118-method_chain118] -[gw7] [ 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_chain94-method_chain94] -[gw17] [ 22%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain109-method_chain109] +[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] -[gw19] [ 23%] 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_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] -[gw11] [ 23%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain79-method_chain79] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain80-method_chain80] -[gw16] [ 23%] 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] -[gw18] [ 23%] 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] -[gw15] [ 23%] 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] -[gw7] [ 24%] 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] -[gw14] [ 24%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain86-method_chain86] +[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] -[gw5] [ 24%] PASSED tests/test_binary.py::test_k_nearest[None-False-same-last] -tests/test_binary.py::test_k_nearest[None-False-False-last] -[gw12] [ 24%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain134-method_chain134] +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] -[gw13] [ 24%] 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] -[gw17] [ 25%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain110-method_chain110] +[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] -[gw19] [ 25%] 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] -[gw11] [ 25%] 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_chain141-method_chain141] -[gw15] [ 25%] 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_chain154-method_chain154] -[gw7] [ 25%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain95-method_chain95] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain96-method_chain96] -[gw18] [ 25%] 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_chain148-method_chain148] -[gw16] [ 26%] 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_chain103-method_chain103] -[gw13] [ 26%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain125-method_chain125] +[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] -[gw17] [ 26%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain111-method_chain111] -[gw19] [ 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_chain133-method_chain133] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain112-method_chain112] -[gw1] [ 26%] PASSED tests/test_binary.py::test_coverage[same] -tests/test_binary.py::test_coverage[opposite] -[gw12] [ 27%] 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] -[gw11] [ 27%] 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] -[gw14] [ 27%] 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_chain88-method_chain88] -[gw7] [ 27%] 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_chain160-method_chain160] -[gw15] [ 27%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain154-method_chain154] +[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] -[gw17] [ 28%] 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_chain178-method_chain178] -[gw13] [ 28%] 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_chain166-method_chain166] -[gw18] [ 28%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain148-method_chain148] +[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] -[gw11] [ 28%] 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_chain143-method_chain143] -[gw3] [ 28%] PASSED tests/test_binary.py::test_overlap[opposite] -tests/test_binary.py::test_intersect[False] -[gw12] [ 29%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain136-method_chain136] -[gw7] [ 29%] 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_chain137-method_chain137] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain161-method_chain161] -[gw19] [ 29%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain133-method_chain133] -[gw14] [ 29%] 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_chain184-method_chain184] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain172-method_chain172] -[gw16] [ 29%] 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] -[gw15] [ 29%] 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] -[gw17] [ 30%] 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_chain179-method_chain179] -[gw11] [ 30%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain143-method_chain143] +[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] -[gw13] [ 30%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain166-method_chain166] +[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] -[gw19] [ 30%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain172-method_chain172] +[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] -[gw18] [ 30%] 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] -[gw11] [ 31%] 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_chain145-method_chain145] -[gw7] [ 31%] 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] -[gw16] [ 31%] 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_chain190-method_chain190] -[gw13] [ 31%] 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] -[gw15] [ 31%] 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_chain157-method_chain157] -[gw17] [ 32%] 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] -[gw12] [ 32%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain137-method_chain137] +[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] -[gw14] [ 32%] 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_chain185-method_chain185] -[gw11] [ 32%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain145-method_chain145] +[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] -[gw19] [ 32%] 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] -[gw16] [ 32%] 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_chain191-method_chain191] -[gw17] [ 33%] 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_chain181-method_chain181] -[gw7] [ 33%] 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_chain163-method_chain163] -[gw15] [ 33%] 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] -[gw13] [ 33%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain168-method_chain168] +[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] -[gw18] [ 33%] 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_chain151-method_chain151] -[gw14] [ 34%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain185-method_chain185] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain186-method_chain186] -[gw11] [ 34%] 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_chain147-method_chain147] -[gw7] [ 34%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain163-method_chain163] +[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] -[gw19] [ 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_chain175-method_chain175] -[gw16] [ 34%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain191-method_chain191] -[gw17] [ 35%] 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_chain192-method_chain192] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain182-method_chain182] -[gw12] [ 35%] 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_chain139-method_chain139] -[gw13] [ 35%] 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] -[gw15] [ 35%] 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_chain159-method_chain159] -[gw7] [ 35%] 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_chain165-method_chain165] -[gw18] [ 35%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain151-method_chain151] +[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] -[gw19] [ 36%] 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] -[gw16] [ 36%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain192-method_chain192] +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] -[gw14] [ 36%] PASSED 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_chain187-method_chain187] -[gw10] [ 36%] PASSED tests/test_binary.py::test_join[False] -[gw13] [ 36%] 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_chain171-method_chain171] -tests/test_binary.py::test_join[same] -[gw15] [ 37%] 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_chain200-method_chain200] -[gw7] [ 37%] 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_chain205-method_chain205] -[gw12] [ 37%] 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] -[gw11] [ 37%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain147-method_chain147] +[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] -[gw17] [ 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_chain183-method_chain183] -[gw9] [ 38%] PASSED tests/test_binary.py::test_nearest[downstream-True-opposite] -tests/test_binary.py::test_nearest[downstream-False-False] -[gw16] [ 38%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain193-method_chain193] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain194-method_chain194] -[gw4] [ 38%] PASSED tests/test_binary.py::test_nearest[upstream-True-opposite] -[gw19] [ 38%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain176-method_chain176] -tests/test_binary.py::test_nearest[upstream-False-False] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain177-method_chain177] -[gw2] [ 38%] PASSED tests/test_binary.py::test_nearest[None-True-opposite] -tests/test_binary.py::test_nearest[None-False-False] -[gw7] [ 38%] 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] -[gw13] [ 39%] 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_chain210-method_chain210] -[gw11] [ 39%] 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] -[gw18] [ 39%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain152-method_chain152] -[gw14] [ 39%] 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_chain153-method_chain153] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain188-method_chain188] -[gw15] [ 39%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain200-method_chain200] +[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] -[gw19] [ 40%] 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_chain230-method_chain230] -[gw12] [ 40%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain140-method_chain140] +[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] -[gw16] [ 40%] 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_chain225-method_chain225] -[gw0] [ 40%] PASSED tests/test_binary.py::test_set_intersect[same] -tests/test_binary.py::test_set_union[False] -[gw17] [ 40%] 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_chain220-method_chain220] -[gw7] [ 41%] 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_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] -[gw13] [ 41%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain210-method_chain210] +[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] -[gw19] [ 41%] 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_chain231-method_chain231] -[gw12] [ 41%] 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_chain216-method_chain216] -[gw16] [ 41%] 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_chain226-method_chain226] -[gw14] [ 41%] 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_chain189-method_chain189] -[gw17] [ 42%] 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_chain221-method_chain221] -[gw18] [ 42%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain153-method_chain153] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain234-method_chain234] -[gw11] [ 42%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain196-method_chain196] +[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] -[gw13] [ 42%] 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] -[gw12] [ 42%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain216-method_chain216] +[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] -[gw7] [ 43%] 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] -[gw15] [ 43%] 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] -[gw16] [ 43%] 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_chain227-method_chain227] -[gw19] [ 43%] 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_chain232-method_chain232] -[gw17] [ 43%] 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_chain222-method_chain222] -[gw14] [ 44%] 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_chain238-method_chain238] -[gw13] [ 44%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain212-method_chain212] +[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] -[gw6] [ 44%] PASSED tests/test_binary.py::test_k_nearest[downstream-False-False-last] -tests/test_binary.py::test_k_nearest[downstream-True-opposite-last] -[gw3] [ 44%] PASSED tests/test_binary.py::test_intersect[False] -tests/test_binary.py::test_intersect[same] -[gw8] [ 44%] PASSED tests/test_binary.py::test_k_nearest[upstream-False-False-last] -[gw18] [ 45%] 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_chain235-method_chain235] -tests/test_binary.py::test_k_nearest[upstream-True-opposite-last] -[gw16] [ 45%] 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_chain228-method_chain228] -[gw7] [ 45%] 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_chain209-method_chain209] -[gw12] [ 45%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain217-method_chain217] +[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] -[gw11] [ 45%] 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] -[gw13] [ 45%] 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] -[gw17] [ 46%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain222-method_chain222] +[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] -[gw14] [ 46%] 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_chain239-method_chain239] -[gw19] [ 46%] 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_chain233-method_chain233] -[gw15] [ 46%] 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_chain203-method_chain203] -[gw16] [ 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_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] -[gw12] [ 47%] 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_chain219-method_chain219] -[gw13] [ 47%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain214-method_chain214] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain246-method_chain246] -[gw7] [ 47%] 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_chain242-method_chain242] -[gw17] [ 47%] 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_chain224-method_chain224] -[gw18] [ 47%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain235-method_chain235] +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] -[gw14] [ 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_chain240-method_chain240] -[gw19] [ 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_chain250-method_chain250] -[gw11] [ 48%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain198-method_chain198] -[gw15] [ 48%] 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] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain199-method_chain199] -[gw16] [ 48%] 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_chain254-method_chain254] -[gw12] [ 48%] 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_chain258-method_chain258] -[gw7] [ 49%] 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_chain243-method_chain243] -[gw14] [ 49%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain240-method_chain240] -[gw17] [ 49%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain224-method_chain224] +[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] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain262-method_chain262] -[gw13] [ 49%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain246-method_chain246] +[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] -[gw15] [ 49%] 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_chain266-method_chain266] -[gw12] [ 50%] 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_chain259-method_chain259] -[gw5] [ 50%] PASSED tests/test_binary.py::test_k_nearest[None-False-False-last] -[gw16] [ 50%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain254-method_chain254] -tests/test_binary.py::test_k_nearest[None-True-opposite-last] -[gw18] [ 50%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain236-method_chain236] -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_chain237-method_chain237] -[gw14] [ 50%] 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_chain273-method_chain273] -[gw17] [ 51%] 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_chain263-method_chain263] -[gw7] [ 51%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain243-method_chain243] +[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] -[gw11] [ 51%] 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_chain270-method_chain270] -[gw1] [ 51%] PASSED tests/test_binary.py::test_coverage[opposite] -[gw19] [ 51%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain250-method_chain250] -tests/test_binary.py::test_subtraction[same] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain251-method_chain251] -[gw17] [ 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_chain264-method_chain264] -[gw12] [ 52%] 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_chain260-method_chain260] -[gw7] [ 52%] PASSED 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] -[gw16] [ 52%] 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_chain256-method_chain256] -[gw13] [ 52%] 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_chain248-method_chain248] -[gw15] [ 52%] 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_chain267-method_chain267] -[gw11] [ 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_chain271-method_chain271] -[gw18] [ 53%] 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_chain276-method_chain276] -[gw14] [ 53%] 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_chain274-method_chain274] -[gw10] [ 53%] PASSED tests/test_binary.py::test_join[same] -tests/test_binary.py::test_join[opposite] -[gw17] [ 53%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain264-method_chain264] +[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] -[gw19] [ 54%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain251-method_chain251] +[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] -[gw12] [ 54%] 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_chain261-method_chain261] -[gw16] [ 54%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain256-method_chain256] +[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] -[gw15] [ 54%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain267-method_chain267] +[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] -[gw18] [ 54%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain276-method_chain276] +[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] -[gw14] [ 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_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] -[gw11] [ 55%] 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_chain272-method_chain272] -[gw13] [ 55%] 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_chain249-method_chain249] -[gw12] [ 55%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain261-method_chain261] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain285-method_chain285] -[gw7] [ 55%] 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_chain279-method_chain279] -[gw17] [ 55%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain265-method_chain265] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain282-method_chain282] -[gw14] [ 56%] 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_chain291-method_chain291] -[gw18] [ 56%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain277-method_chain277] +[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] -[gw15] [ 56%] 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_chain269-method_chain269] -[gw4] [ 56%] PASSED tests/test_binary.py::test_nearest[upstream-False-False] -[gw9] [ 56%] PASSED tests/test_binary.py::test_nearest[downstream-False-False] -[gw11] [ 57%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain272-method_chain272] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain294-method_chain294] -tests/test_binary.py::test_nearest[downstream-False-same] -tests/test_binary.py::test_nearest[upstream-False-same] -[gw16] [ 57%] 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_chain288-method_chain288] -[gw19] [ 57%] 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_chain253-method_chain253] -[gw7] [ 57%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain279-method_chain279] +[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] -[gw15] [ 57%] 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_chain303-method_chain303] -[gw14] [ 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_chain292-method_chain292] -[gw17] [ 58%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain282-method_chain282] +[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] -[gw13] [ 58%] 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_chain297-method_chain297] -[gw18] [ 58%] 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_chain300-method_chain300] -[gw16] [ 58%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain288-method_chain288] +[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] -[gw2] [ 58%] PASSED tests/test_binary.py::test_nearest[None-False-False] -tests/test_binary.py::test_nearest[None-False-same] -[gw12] [ 59%] 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_chain286-method_chain286] -[gw19] [ 59%] 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_chain306-method_chain306] -[gw3] [ 59%] PASSED tests/test_binary.py::test_intersect[same] -tests/test_binary.py::test_intersect[opposite] -[gw11] [ 59%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain294-method_chain294] +[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] -[gw14] [ 59%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain292-method_chain292] +[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] -[gw15] [ 60%] 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_chain304-method_chain304] -[gw16] [ 60%] 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_chain290-method_chain290] -[gw7] [ 60%] 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_chain281-method_chain281] -[gw17] [ 60%] 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_chain284-method_chain284] -[gw18] [ 60%] 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_chain301-method_chain301] -[gw13] [ 61%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain297-method_chain297] -[gw12] [ 61%] 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_chain287-method_chain287] +[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] -[gw14] [ 61%] 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_chain309-method_chain309] -[gw19] [ 61%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain306-method_chain306] +[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] -[gw11] [ 61%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain295-method_chain295] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain296-method_chain296] -[gw16] [ 61%] 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_chain311-method_chain311] -[gw15] [ 62%] 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_chain305-method_chain305] -[gw12] [ 62%] 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_chain317-method_chain317] -[gw17] [ 62%] 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_chain315-method_chain315] -[gw7] [ 62%] 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_chain313-method_chain313] -[gw14] [ 62%] 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_chain310-method_chain310] -[gw18] [ 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_chain302-method_chain302] -[gw13] [ 63%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain298-method_chain298] +[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] -[gw19] [ 63%] 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_chain308-method_chain308] -[gw16] [ 63%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain311-method_chain311] +[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] -[gw15] [ 63%] 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_chain321-method_chain321] -[gw11] [ 64%] 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_chain319-method_chain319] -[gw14] [ 64%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain310-method_chain310] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain323-method_chain323] -[gw12] [ 64%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain317-method_chain317] +[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] -[gw7] [ 64%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain313-method_chain313] +[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] -[gw16] [ 64%] 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_chain331-method_chain331] -[gw17] [ 64%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain315-method_chain315] +[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] -[gw18] [ 65%] 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_chain325-method_chain325] -[gw19] [ 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_chain329-method_chain329] -[gw15] [ 65%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain321-method_chain321] +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] -[gw13] [ 65%] 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_chain327-method_chain327] -[gw11] [ 65%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain319-method_chain319] +[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] -[gw0] [ 66%] PASSED tests/test_binary.py::test_set_union[False] -[gw7] [ 66%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain314-method_chain314] +[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] -tests/test_binary.py::test_set_union[same] -[gw14] [ 66%] 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_chain324-method_chain324] -[gw17] [ 66%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain316-method_chain316] +[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] -[gw12] [ 66%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain318-method_chain318] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain333-method_chain333] -[gw18] [ 67%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain325-method_chain325] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain326-method_chain326] -[gw16] [ 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_chain332-method_chain332] -[gw15] [ 67%] 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_chain339-method_chain339] -[gw14] [ 67%] 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_chain343-method_chain343] -[gw13] [ 67%] 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_chain328-method_chain328] -[gw10] [ 67%] PASSED tests/test_binary.py::test_join[opposite] -tests/test_binary.py::test_reldist -[gw11] [ 68%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain320-method_chain320] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain341-method_chain341] -[gw18] [ 68%] 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_chain345-method_chain345] -[gw17] [ 68%] 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_chain338-method_chain338] -[gw8] [ 68%] PASSED tests/test_binary.py::test_k_nearest[upstream-True-opposite-last] -[gw7] [ 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_chain336-method_chain336] -tests/test_binary.py::test_k_nearest[upstream-True-same-last] -[gw19] [ 69%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain329-method_chain329] +[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] -[gw6] [ 69%] PASSED tests/test_binary.py::test_k_nearest[downstream-True-opposite-last] -tests/test_binary.py::test_k_nearest[downstream-True-same-last] -[gw12] [ 69%] 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_chain334-method_chain334] -[gw15] [ 69%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain339-method_chain339] +[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] -[gw13] [ 69%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain328-method_chain328] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain348-method_chain348] -[gw17] [ 70%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain338-method_chain338] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain349-method_chain349] -[gw16] [ 70%] 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_chain347-method_chain347] -[gw11] [ 70%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain341-method_chain341] +[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] -[gw18] [ 70%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain345-method_chain345] -[gw7] [ 70%] 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_chain350-method_chain350] +[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] -[gw14] [ 70%] 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_chain344-method_chain344] -[gw15] [ 71%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain340-method_chain340] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain353-method_chain353] -[gw19] [ 71%] 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_chain351-method_chain351] -[gw11] [ 71%] 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_chain357-method_chain357] -[gw12] [ 71%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain334-method_chain334] +[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] -[gw17] [ 71%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain349-method_chain349] -[gw16] [ 72%] 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_chain355-method_chain355] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain356-method_chain356] -[gw13] [ 72%] 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_chain354-method_chain354] -[gw18] [ 72%] 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_chain359-method_chain359] -[gw7] [ 72%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain350-method_chain350] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain358-method_chain358] -[gw15] [ 72%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain353-method_chain353] +[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] -[gw14] [ 73%] 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_chain360-method_chain360] -[gw19] [ 73%] 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_chain362-method_chain362] -[gw4] [ 73%] PASSED tests/test_binary.py::test_nearest[upstream-False-same] -tests/test_binary.py::test_nearest[upstream-False-opposite] -[gw11] [ 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_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] -[gw3] [ 73%] PASSED tests/test_binary.py::test_intersect[opposite] -[gw12] [ 74%] 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_chain364-method_chain364] -tests/test_binary.py::test_coverage[False] -[gw16] [ 74%] 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_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] -[gw18] [ 74%] 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_chain368-method_chain368] -[gw15] [ 74%] 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_chain370-method_chain370] -[gw17] [ 74%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain355-method_chain355] +[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] -[gw9] [ 74%] PASSED tests/test_binary.py::test_nearest[downstream-False-same] -[gw7] [ 75%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain358-method_chain358] -tests/test_binary.py::test_nearest[downstream-False-opposite] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain369-method_chain369] -[gw13] [ 75%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain354-method_chain354] +[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] -[gw14] [ 75%] 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_chain371-method_chain371] -[gw11] [ 75%] 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_chain373-method_chain373] -[gw19] [ 75%] 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_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] -[gw5] [ 76%] PASSED tests/test_binary.py::test_k_nearest[None-True-opposite-last] -tests/test_binary.py::test_k_nearest[None-True-same-last] -[gw16] [ 76%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain366-method_chain366] +[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] -[gw18] [ 76%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain368-method_chain368] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain377-method_chain377] -[gw12] [ 76%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain364-method_chain364] +[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] -[gw15] [ 76%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain370-method_chain370] +[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] -[gw17] [ 77%] 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_chain379-method_chain379] -[gw13] [ 77%] 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_chain381-method_chain381] -[gw11] [ 77%] 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_chain383-method_chain383] -[gw7] [ 77%] 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_chain380-method_chain380] -[gw2] [ 77%] PASSED tests/test_binary.py::test_nearest[None-False-same] -tests/test_binary.py::test_nearest[None-False-opposite] -[gw14] [ 77%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain371-method_chain371] +[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] -[gw19] [ 78%] 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_chain384-method_chain384] -[gw12] [ 78%] 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_chain387-method_chain387] -[gw18] [ 78%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain377-method_chain377] +[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] -[gw16] [ 78%] 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_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] -[gw1] [ 78%] PASSED tests/test_binary.py::test_subtraction[same] -[gw13] [ 79%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain381-method_chain381] +[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] -[gw17] [ 79%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain379-method_chain379] -tests/test_binary.py::test_subtraction[opposite] +[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] -[gw12] [ 79%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain387-method_chain387] +[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] -[gw15] [ 79%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain378-method_chain378] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain388-method_chain388] -[gw14] [ 79%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain382-method_chain382] +[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] -[gw7] [ 80%] 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_chain392-method_chain392] -[gw18] [ 80%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain386-method_chain386] +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] -[gw16] [ 80%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain385-method_chain385] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain397-method_chain397] -[gw11] [ 80%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain383-method_chain383] +[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] -[gw19] [ 80%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain384-method_chain384] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain394-method_chain394] -[gw13] [ 80%] 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_chain398-method_chain398] -[gw17] [ 81%] 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_chain399-method_chain399] -[gw15] [ 81%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain388-method_chain388] +[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] -[gw10] [ 81%] PASSED tests/test_binary.py::test_reldist -tests/test_binary.py::test_k_nearest[downstream-False-opposite-last] -[gw11] [ 81%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain391-method_chain391] +[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] -[gw14] [ 81%] 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_chain402-method_chain402] -[gw18] [ 82%] 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_chain404-method_chain404] -[gw12] [ 82%] 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_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] -[gw15] [ 82%] 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_chain410-method_chain410] -[gw19] [ 82%] 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_chain407-method_chain407] -[gw17] [ 82%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain399-method_chain399] +[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] -[gw13] [ 83%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain398-method_chain398] +[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] -[gw7] [ 83%] 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_chain403-method_chain403] -[gw16] [ 83%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain397-method_chain397] +[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] -[gw11] [ 83%] 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_chain412-method_chain412] -[gw14] [ 83%] 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_chain413-method_chain413] -[gw18] [ 83%] 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_chain414-method_chain414] -[gw15] [ 84%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain410-method_chain410] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain416-method_chain416] -[gw13] [ 84%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain408-method_chain408] +[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] -[gw17] [ 84%] 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_chain418-method_chain418] -[gw19] [ 84%] 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_chain417-method_chain417] -[gw12] [ 84%] 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_chain415-method_chain415] -[gw7] [ 85%] 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_chain420-method_chain420] -[gw11] [ 85%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain412-method_chain412] +[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] -[gw16] [ 85%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain405-method_chain405] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain421-method_chain421] -[gw18] [ 85%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain414-method_chain414] +[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] -[gw13] [ 85%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain419-method_chain419] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain426-method_chain426] -[gw15] [ 86%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain416-method_chain416] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain425-method_chain425] -[gw12] [ 86%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain415-method_chain415] +[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] -[gw19] [ 86%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain417-method_chain417] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain428-method_chain428] -[gw14] [ 86%] 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_chain423-method_chain423] -[gw7] [ 86%] 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_chain430-method_chain430] -[gw11] [ 87%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain422-method_chain422] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain431-method_chain431] -[gw17] [ 87%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain418-method_chain418] +[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] -[gw0] [ 87%] PASSED tests/test_binary.py::test_set_union[same] -[gw13] [ 87%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain426-method_chain426] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain434-method_chain434] -tests/test_binary.py::test_overlap[False] -[gw16] [ 87%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain421-method_chain421] +[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] -[gw18] [ 87%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain424-method_chain424] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain433-method_chain433] -[gw15] [ 88%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain425-method_chain425] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain435-method_chain435] -[gw14] [ 88%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain423-method_chain423] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain438-method_chain438] -[gw19] [ 88%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain428-method_chain428] +[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] -[gw12] [ 88%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain429-method_chain429] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain436-method_chain436] -[gw13] [ 88%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain434-method_chain434] -tests/test_getset_attr.py::test_getsetattr -[gw13] [ 89%] PASSED tests/test_getset_attr.py::test_getsetattr -tests/test_stranded.py::test_unstrand -[gw13] [ 89%] PASSED tests/test_stranded.py::test_unstrand -tests/test_unary.py::test_merge[True] -[gw4] [ 89%] PASSED tests/test_binary.py::test_nearest[upstream-False-opposite] -[gw7] [ 89%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain430-method_chain430] +[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] -tests/test_binary.py::test_nearest[downstream-True-False] -[gw11] [ 89%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain431-method_chain431] +[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] -[gw15] [ 90%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain435-method_chain435] -tests/test_io.py::test_read_gff3 -[gw15] [ 90%] PASSED tests/test_io.py::test_read_gff3 -tests/test_unary.py::test_cluster_by[False] -[gw17] [ 90%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain427-method_chain427] +[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 -[gw14] [ 90%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain438-method_chain438] +[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 -[gw14] [ 90%] PASSED tests/test_io.py::test_read_bed -tests/test_unary.py::test_windows -[gw18] [ 90%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain433-method_chain433] +[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 -[gw18] [ 91%] PASSED tests/test_io.py::test_read_gtf -tests/test_unary.py::test_init[False] -[gw19] [ 91%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain437-method_chain437] +[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 -[gw19] [ 91%] PASSED tests/test_pickle.py::test_pickle -tests/test_unary.py::test_summary -[gw9] [ 91%] PASSED tests/test_binary.py::test_nearest[downstream-False-opposite] -tests/test_binary.py::test_jaccard[False] -[gw12] [ 91%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain436-method_chain436] -tests/test_stranded.py::test_stranded -[gw12] [ 92%] PASSED tests/test_stranded.py::test_stranded -[gw16] [ 92%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain432-method_chain432] -tests/test_getset_attr.py::test_getsetattr_with_str -[gw16] [ 92%] PASSED tests/test_getset_attr.py::test_getsetattr_with_str -[gw11] [ 92%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain440-method_chain440] +[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] -[gw7] [ 92%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain439-method_chain439] +[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] -[gw17] [ 93%] PASSED tests/test_genomicfeatures.py::test_introns_single -tests/test_unary.py::test_merge_by[False] -[gw2] [ 93%] PASSED tests/test_binary.py::test_nearest[None-False-opposite] -tests/test_binary.py::test_nearest[upstream-True-False] -[gw18] [ 93%] PASSED tests/test_unary.py::test_init[False] +[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 -[gw6] [ 93%] PASSED tests/test_binary.py::test_k_nearest[downstream-True-same-last] -tests/test_binary.py::test_k_nearest[downstream-True-False-last] -[gw8] [ 93%] PASSED tests/test_binary.py::test_k_nearest[upstream-True-same-last] -tests/test_binary.py::test_k_nearest[upstream-True-False-last] -[gw3] [ 93%] PASSED tests/test_binary.py::test_coverage[False] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain375-method_chain375] -[gw3] [ 94%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain375-method_chain375] -[gw10] [ 94%] PASSED tests/test_binary.py::test_k_nearest[downstream-False-opposite-last] -tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain411-method_chain411] -[gw0] [ 94%] PASSED tests/test_binary.py::test_overlap[False] -tests/test_getset_attr.py::test_getsetattr_fails -[gw0] [ 94%] PASSED tests/test_getset_attr.py::test_getsetattr_fails -[gw10] [ 94%] PASSED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain411-method_chain411] -[gw18] [ 95%] PASSED tests/test_unary.py::test_getitem -[gw1] [ 95%] PASSED tests/test_binary.py::test_subtraction[opposite] -tests/test_binary.py::test_subtraction[False] -[gw13] [ 95%] PASSED tests/test_unary.py::test_merge[True] +[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] -[gw5] [ 95%] PASSED tests/test_binary.py::test_k_nearest[None-True-same-last] +[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] -[gw19] [ 95%] PASSED tests/test_unary.py::test_summary -tests/windows/test_windows.py::test_windows -[gw19] [ 96%] PASSED tests/windows/test_windows.py::test_windows -[gw14] [ 96%] PASSED tests/test_unary.py::test_windows -tests/test_unary.py::test_init[True] -[gw4] [ 96%] PASSED tests/test_binary.py::test_nearest[downstream-True-False] -tests/test_unary.py::test_cluster[False] -[gw9] [ 96%] PASSED tests/test_binary.py::test_jaccard[False] -tests/windows/test_windows.py::test_windows2 -[gw9] [ 96%] PASSED tests/windows/test_windows.py::test_windows2 -[gw17] [ 96%] PASSED tests/test_unary.py::test_merge_by[False] -[gw2] [ 97%] PASSED tests/test_binary.py::test_nearest[upstream-True-False] -[gw7] [ 97%] PASSED tests/test_unary.py::test_cluster[True] -[gw14] [ 97%] PASSED tests/test_unary.py::test_init[True] -[gw13] [ 97%] PASSED tests/test_unary.py::test_merge[False] -[gw11] [ 97%] PASSED tests/test_unary.py::test_cluster_by[True] -[gw8] [ 98%] PASSED tests/test_binary.py::test_k_nearest[upstream-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] -[gw6] [ 98%] PASSED tests/test_binary.py::test_k_nearest[downstream-True-False-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] [ 98%] PASSED tests/test_binary.py::test_subtraction[False] -tests/test_binary.py::test_nearest[None-True-False] -[gw15] [ 98%] PASSED tests/test_unary.py::test_cluster_by[False] -tests/test_unary.py::test_merge_by[True] -[gw4] [ 98%] PASSED tests/test_unary.py::test_cluster[False] -[gw5] [ 99%] PASSED tests/test_binary.py::test_k_nearest[None-True-False-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 -[gw6] [ 99%] PASSED tests/test_binary.py::test_k_nearest[upstream-False-opposite-last] -[gw1] [ 99%] PASSED tests/test_binary.py::test_nearest[None-True-False] -[gw8] [ 99%] PASSED tests/test_binary.py::test_k_nearest[None-False-opposite-last] -[gw15] [ 99%] PASSED tests/test_unary.py::test_merge_by[True] -[gw5] [100%] PASSED 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: 21 warnings +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: 20 warnings +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: 20 warnings +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: 20 warnings +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: 20 warnings +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: 20 warnings +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: 20 warnings +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: 20 warnings +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: 20 warnings +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: 20 warnings +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: 20 warnings +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: 20 warnings +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: 20 warnings +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: 100 warnings +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: 160175 warnings -.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py: 158984 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/test_stranded.py: 6 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: 24065 warnings -.pybuild/cpython3_3.12_pyranges/build/tests/windows/test_windows.py: 2 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: 80 warnings +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: 4488 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: 6642 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: 20 warnings +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: 20 warnings +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: 20 warnings +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: 20 warnings +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: 20 warnings +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: 20 warnings +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: 20 warnings +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: 20 warnings +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: 20 warnings +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: 3140 warnings +.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: 5642 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_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_do_not_error.py: 7622 warnings -.pybuild/cpython3_3.12_pyranges/build/tests/test_binary.py: 16461 warnings -.pybuild/cpython3_3.12_pyranges/build/tests/test_unary.py: 15508 warnings +.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: 1396 warnings +.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({"+": "-", "-": "+"}) @@ -2936,61 +32931,25 @@ for _, gdf in natsorted(df.groupby(groupby)): -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -============== 531 passed, 411469 warnings in 13376.98s (3:42:56) ============== - create-stamp debian/debhelper-build-stamp - dh_testroot -O--buildsystem=pybuild - dh_prep -O--buildsystem=pybuild - dh_auto_install --destdir=debian/python3-pyranges/ -O--buildsystem=pybuild -I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/pyranges-0.0.111+ds/debian/python3-pyranges -/usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. -!! - - ******************************************************************************** - Please avoid running ``setup.py`` directly. - Instead, use pypa/build, pypa/installer or other - standards-based tools. - - See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. - ******************************************************************************** - -!! - self.initialize_options() -/usr/lib/python3.12/dist-packages/tests/conftest.py:83: SyntaxWarning: invalid escape sequence '\s' - debian/rules execute_after_dh_install -make[1]: Entering directory '/build/reproducible-path/pyranges-0.0.111+ds' -find debian/ -name *.bam* | xargs rm -rf -find debian/ -name 'hi' | xargs rm -rf -find debian/ -name '.hypothesis' | xargs rm -rf -make[1]: Leaving directory '/build/reproducible-path/pyranges-0.0.111+ds' - dh_installdocs -O--buildsystem=pybuild - dh_installchangelogs -O--buildsystem=pybuild - dh_python3 -O--buildsystem=pybuild - dh_installsystemduser -O--buildsystem=pybuild - dh_perl -O--buildsystem=pybuild - dh_link -O--buildsystem=pybuild - dh_strip_nondeterminism -O--buildsystem=pybuild - dh_compress -O--buildsystem=pybuild - dh_fixperms -O--buildsystem=pybuild - dh_missing -O--buildsystem=pybuild - dh_installdeb -O--buildsystem=pybuild - dh_gencontrol -O--buildsystem=pybuild - dh_md5sums -O--buildsystem=pybuild - dh_builddeb -O--buildsystem=pybuild -dpkg-deb: building package 'python3-pyranges' in '../python3-pyranges_0.0.111+ds-8_all.deb'. - dpkg-genbuildinfo --build=binary -O../pyranges_0.0.111+ds-8_amd64.buildinfo - dpkg-genchanges --build=binary -O../pyranges_0.0.111+ds-8_amd64.changes -dpkg-genchanges: info: binary-only upload (no source code included) - dpkg-source --after-build . -dpkg-source: info: using options from pyranges-0.0.111+ds/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ -dpkg-buildpackage: info: binary-only upload (no source included) -dpkg-genchanges: info: not including original source code in upload +=========================== 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/28692 and its subdirectories -I: Current time: Tue Dec 3 08:25:12 -12 2024 -I: pbuilder-time-stamp: 1733257512 +I: removing directory /srv/workspace/pbuilder/1718224 and its subdirectories