Diff of the two buildlogs: -- --- b1/build.log 2025-11-07 21:06:16.228392928 +0000 +++ b2/build.log 2025-11-07 21:07:16.236463110 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Nov 7 09:03:34 -12 2025 -I: pbuilder-time-stamp: 1762549414 +I: Current time: Fri Dec 11 17:29:19 +14 2026 +I: pbuilder-time-stamp: 1796959759 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -26,53 +26,85 @@ dpkg-source: info: applying perl-5.42-precedence.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3047937/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/265301/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +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 Dec 11 03:29 /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/265301/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/265301/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='arm64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='arm64' + 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]="3" [2]="3" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 nocheck' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='acc613420a4c4b8a86ed40375effe990' - 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='3047937' - PS1='# ' - PS2='> ' + INVOCATION_ID=156e913eab614f7ca187fa701821634e + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=265301 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.QI36Vapd/pbuilderrc_jnns --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.QI36Vapd/b1 --logfile b1/build.log bioperl_1.7.8-2.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + 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.QI36Vapd/pbuilderrc_v92o --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.QI36Vapd/b2 --logfile b2/build.log bioperl_1.7.8-2.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3047937/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/265301/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -460,7 +492,7 @@ Get: 252 http://deb.debian.org/debian forky/main arm64 libxml-simple-perl all 2.25-2 [69.8 kB] Get: 253 http://deb.debian.org/debian forky/main arm64 libyaml-perl all 1.31-1 [64.8 kB] Get: 254 http://deb.debian.org/debian forky/main arm64 rename all 2.02-1 [21.8 kB] -Fetched 46.6 MB in 1s (83.0 MB/s) +Fetched 46.6 MB in 0s (130 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:arm64. (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 ... 19964 files and directories currently installed.) @@ -1524,7 +1556,11 @@ Solving dependencies... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/reproducible-path/bioperl-1.7.8/ && 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 > ../bioperl_1.7.8-2_source.changes +I: user script /srv/workspace/pbuilder/265301/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/265301/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/bioperl-1.7.8/ && 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 > ../bioperl_1.7.8-2_source.changes dpkg-buildpackage: info: source package bioperl dpkg-buildpackage: info: source version 1.7.8-2 dpkg-buildpackage: info: source distribution unstable @@ -1551,514 +1587,514 @@ dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/bioperl-1.7.8' -cp lib/Bio/AlignIO/meme.pm blib/lib/Bio/AlignIO/meme.pm -cp lib/Bio/AlignIO/largemultifasta.pm blib/lib/Bio/AlignIO/largemultifasta.pm -cp lib/Bio/Annotation/DBLink.pm blib/lib/Bio/Annotation/DBLink.pm -cp lib/Bio/AnalysisParserI.pm blib/lib/Bio/AnalysisParserI.pm -cp lib/Bio/AlignIO/nexus.pm blib/lib/Bio/AlignIO/nexus.pm -cp lib/Bio/Annotation/OntologyTerm.pm blib/lib/Bio/Annotation/OntologyTerm.pm cp lib/Bio/AlignIO/fasta.pm blib/lib/Bio/AlignIO/fasta.pm -cp lib/Bio/AlignIO/prodom.pm blib/lib/Bio/AlignIO/prodom.pm -cp lib/Bio/AlignIO/selex.pm blib/lib/Bio/AlignIO/selex.pm -cp lib/Bio/AnalysisI.pm blib/lib/Bio/AnalysisI.pm -cp lib/Bio/Annotation/Collection.pm blib/lib/Bio/Annotation/Collection.pm -cp lib/Bio/AlignIO/arp.pm blib/lib/Bio/AlignIO/arp.pm -cp lib/Bio/AlignIO/pfam.pm blib/lib/Bio/AlignIO/pfam.pm -cp lib/Bio/Annotation/Reference.pm blib/lib/Bio/Annotation/Reference.pm -cp lib/Bio/AlignIO/psi.pm blib/lib/Bio/AlignIO/psi.pm -cp lib/Bio/Annotation/Relation.pm blib/lib/Bio/Annotation/Relation.pm -cp lib/Bio/AnalysisResultI.pm blib/lib/Bio/AnalysisResultI.pm -cp lib/Bio/AlignIO/clustalw.pm blib/lib/Bio/AlignIO/clustalw.pm +cp lib/Bio/AlignIO.pm blib/lib/Bio/AlignIO.pm cp lib/Bio/AlignIO/mase.pm blib/lib/Bio/AlignIO/mase.pm -cp lib/Bio/Annotation/Comment.pm blib/lib/Bio/Annotation/Comment.pm -cp lib/Bio/AlignIO/emboss.pm blib/lib/Bio/AlignIO/emboss.pm -cp lib/Bio/Align/DNAStatistics.pm blib/lib/Bio/Align/DNAStatistics.pm -cp lib/Bio/AnnotatableI.pm blib/lib/Bio/AnnotatableI.pm -cp lib/Bio/AlignIO/proda.pm blib/lib/Bio/AlignIO/proda.pm +cp lib/Bio/Annotation/AnnotationFactory.pm blib/lib/Bio/Annotation/AnnotationFactory.pm cp lib/Bio/Align/PairwiseStatistics.pm blib/lib/Bio/Align/PairwiseStatistics.pm +cp lib/Bio/AlignIO/msf.pm blib/lib/Bio/AlignIO/msf.pm cp lib/Bio/AlignIO/Handler/GenericAlignHandler.pm blib/lib/Bio/AlignIO/Handler/GenericAlignHandler.pm -cp lib/Bio/AlignIO/maf.pm blib/lib/Bio/AlignIO/maf.pm -cp lib/Bio/AlignIO/po.pm blib/lib/Bio/AlignIO/po.pm +cp lib/Bio/Annotation/Reference.pm blib/lib/Bio/Annotation/Reference.pm cp lib/Bio/Align/ProteinStatistics.pm blib/lib/Bio/Align/ProteinStatistics.pm +cp lib/Bio/AlignIO/nexus.pm blib/lib/Bio/AlignIO/nexus.pm +cp lib/Bio/AlignIO/maf.pm blib/lib/Bio/AlignIO/maf.pm +cp lib/Bio/AlignIO/prodom.pm blib/lib/Bio/AlignIO/prodom.pm +cp lib/Bio/AlignIO/bl2seq.pm blib/lib/Bio/AlignIO/bl2seq.pm +cp lib/Bio/Annotation/DBLink.pm blib/lib/Bio/Annotation/DBLink.pm +cp lib/Bio/AlignIO/clustalw.pm blib/lib/Bio/AlignIO/clustalw.pm +cp lib/Bio/Annotation/Relation.pm blib/lib/Bio/Annotation/Relation.pm +cp lib/Bio/Annotation/OntologyTerm.pm blib/lib/Bio/Annotation/OntologyTerm.pm +cp lib/Bio/Align/Utilities.pm blib/lib/Bio/Align/Utilities.pm +cp lib/Bio/AlignIO/largemultifasta.pm blib/lib/Bio/AlignIO/largemultifasta.pm +cp lib/Bio/AlignIO/arp.pm blib/lib/Bio/AlignIO/arp.pm +cp lib/Bio/AlignIO/proda.pm blib/lib/Bio/AlignIO/proda.pm +cp lib/Bio/AnalysisParserI.pm blib/lib/Bio/AnalysisParserI.pm cp lib/Bio/AlignIO/xmfa.pm blib/lib/Bio/AlignIO/xmfa.pm cp lib/Bio/Align/StatisticsI.pm blib/lib/Bio/Align/StatisticsI.pm -cp lib/Bio/AlignIO/phylip.pm blib/lib/Bio/AlignIO/phylip.pm cp lib/Bio/Align/AlignI.pm blib/lib/Bio/Align/AlignI.pm -cp lib/Bio/Align/Utilities.pm blib/lib/Bio/Align/Utilities.pm -cp lib/Bio/AlignIO/mega.pm blib/lib/Bio/AlignIO/mega.pm -cp lib/Bio/AlignIO/msf.pm blib/lib/Bio/AlignIO/msf.pm +cp lib/Bio/Align/DNAStatistics.pm blib/lib/Bio/Align/DNAStatistics.pm +cp lib/Bio/AlignIO/phylip.pm blib/lib/Bio/AlignIO/phylip.pm cp lib/Bio/AlignIO/metafasta.pm blib/lib/Bio/AlignIO/metafasta.pm -cp lib/Bio/AlignIO.pm blib/lib/Bio/AlignIO.pm -cp lib/Bio/AlignIO/bl2seq.pm blib/lib/Bio/AlignIO/bl2seq.pm -cp lib/Bio/Annotation/AnnotationFactory.pm blib/lib/Bio/Annotation/AnnotationFactory.pm -cp lib/Bio/DB/GFF/Util/Binning.pm blib/lib/Bio/DB/GFF/Util/Binning.pm -cp lib/Bio/DB/SeqI.pm blib/lib/Bio/DB/SeqI.pm -cp lib/Bio/DB/FileCache.pm blib/lib/Bio/DB/FileCache.pm -cp lib/Bio/DB/UpdateableSeqI.pm blib/lib/Bio/DB/UpdateableSeqI.pm -cp lib/Bio/DB/GenericWebAgent.pm blib/lib/Bio/DB/GenericWebAgent.pm -cp lib/Bio/DB/QueryI.pm blib/lib/Bio/DB/QueryI.pm -cp lib/Bio/DB/Taxonomy/silva.pm blib/lib/Bio/DB/Taxonomy/silva.pm -cp lib/Bio/DB/Taxonomy/greengenes.pm blib/lib/Bio/DB/Taxonomy/greengenes.pm -cp lib/Bio/CodonUsage/Table.pm blib/lib/Bio/CodonUsage/Table.pm -cp lib/Bio/DB/Flat/BDB/genbank.pm blib/lib/Bio/DB/Flat/BDB/genbank.pm -cp lib/Bio/DB/ReferenceI.pm blib/lib/Bio/DB/ReferenceI.pm -cp lib/Bio/DB/InMemoryCache.pm blib/lib/Bio/DB/InMemoryCache.pm -cp lib/Bio/Annotation/Tree.pm blib/lib/Bio/Annotation/Tree.pm -cp lib/Bio/DB/Taxonomy/flatfile.pm blib/lib/Bio/DB/Taxonomy/flatfile.pm +cp lib/Bio/AlignIO/selex.pm blib/lib/Bio/AlignIO/selex.pm +cp lib/Bio/Annotation/Comment.pm blib/lib/Bio/Annotation/Comment.pm +cp lib/Bio/AlignIO/po.pm blib/lib/Bio/AlignIO/po.pm +cp lib/Bio/Annotation/Collection.pm blib/lib/Bio/Annotation/Collection.pm +cp lib/Bio/AlignIO/meme.pm blib/lib/Bio/AlignIO/meme.pm +cp lib/Bio/AnalysisI.pm blib/lib/Bio/AnalysisI.pm +cp lib/Bio/AnalysisResultI.pm blib/lib/Bio/AnalysisResultI.pm +cp lib/Bio/AlignIO/pfam.pm blib/lib/Bio/AlignIO/pfam.pm +cp lib/Bio/AlignIO/emboss.pm blib/lib/Bio/AlignIO/emboss.pm +cp lib/Bio/AlignIO/mega.pm blib/lib/Bio/AlignIO/mega.pm +cp lib/Bio/AlignIO/psi.pm blib/lib/Bio/AlignIO/psi.pm +cp lib/Bio/AnnotatableI.pm blib/lib/Bio/AnnotatableI.pm +cp lib/Bio/Annotation/TypeManager.pm blib/lib/Bio/Annotation/TypeManager.pm +cp lib/Bio/DB/Qual.pm blib/lib/Bio/DB/Qual.pm cp lib/Bio/DB/Flat.pm blib/lib/Bio/DB/Flat.pm -cp lib/Bio/Annotation/TagTree.pm blib/lib/Bio/Annotation/TagTree.pm -cp lib/Bio/DB/Flat/BinarySearch.pm blib/lib/Bio/DB/Flat/BinarySearch.pm cp lib/Bio/DB/IndexedBase.pm blib/lib/Bio/DB/IndexedBase.pm -cp lib/Bio/CodonUsage/IO.pm blib/lib/Bio/CodonUsage/IO.pm -cp lib/Bio/Annotation/TypeManager.pm blib/lib/Bio/Annotation/TypeManager.pm -cp lib/Bio/DB/GFF/Util/Rearrange.pm blib/lib/Bio/DB/GFF/Util/Rearrange.pm -cp lib/Bio/DB/Taxonomy/list.pm blib/lib/Bio/DB/Taxonomy/list.pm +cp lib/Bio/DB/Failover.pm blib/lib/Bio/DB/Failover.pm +cp lib/Bio/DB/FileCache.pm blib/lib/Bio/DB/FileCache.pm cp lib/Bio/DB/Taxonomy.pm blib/lib/Bio/DB/Taxonomy.pm -cp lib/Bio/DB/Flat/BDB/swiss.pm blib/lib/Bio/DB/Flat/BDB/swiss.pm -cp lib/Bio/Annotation/StructuredValue.pm blib/lib/Bio/Annotation/StructuredValue.pm -cp lib/Bio/DB/Flat/BDB.pm blib/lib/Bio/DB/Flat/BDB.pm -cp lib/Bio/AnnotationI.pm blib/lib/Bio/AnnotationI.pm -cp lib/Bio/DB/Fasta.pm blib/lib/Bio/DB/Fasta.pm -cp lib/Bio/Annotation/Target.pm blib/lib/Bio/Annotation/Target.pm cp lib/Bio/DB/Registry.pm blib/lib/Bio/DB/Registry.pm +cp lib/Bio/DB/Flat/BDB/swiss.pm blib/lib/Bio/DB/Flat/BDB/swiss.pm +cp lib/Bio/DB/ReferenceI.pm blib/lib/Bio/DB/ReferenceI.pm +cp lib/Bio/DB/Query/WebQuery.pm blib/lib/Bio/DB/Query/WebQuery.pm cp lib/Bio/DB/LocationI.pm blib/lib/Bio/DB/LocationI.pm cp lib/Bio/DB/RandomAccessI.pm blib/lib/Bio/DB/RandomAccessI.pm +cp lib/Bio/AnnotationI.pm blib/lib/Bio/AnnotationI.pm +cp lib/Bio/DB/Flat/BinarySearch.pm blib/lib/Bio/DB/Flat/BinarySearch.pm +cp lib/Bio/DB/GFF/Util/Binning.pm blib/lib/Bio/DB/GFF/Util/Binning.pm cp lib/Bio/Annotation/SimpleValue.pm blib/lib/Bio/Annotation/SimpleValue.pm -cp lib/Bio/AnnotationCollectionI.pm blib/lib/Bio/AnnotationCollectionI.pm -cp lib/Bio/DB/Qual.pm blib/lib/Bio/DB/Qual.pm -cp lib/Bio/DB/Failover.pm blib/lib/Bio/DB/Failover.pm -cp lib/Bio/DB/Query/WebQuery.pm blib/lib/Bio/DB/Query/WebQuery.pm +cp lib/Bio/DB/GenericWebAgent.pm blib/lib/Bio/DB/GenericWebAgent.pm +cp lib/Bio/Annotation/Tree.pm blib/lib/Bio/Annotation/Tree.pm cp lib/Bio/DB/Flat/BDB/fasta.pm blib/lib/Bio/DB/Flat/BDB/fasta.pm +cp lib/Bio/DB/Flat/BDB.pm blib/lib/Bio/DB/Flat/BDB.pm +cp lib/Bio/CodonUsage/Table.pm blib/lib/Bio/CodonUsage/Table.pm +cp lib/Bio/DB/Taxonomy/list.pm blib/lib/Bio/DB/Taxonomy/list.pm +cp lib/Bio/DB/SeqI.pm blib/lib/Bio/DB/SeqI.pm cp lib/Bio/DB/Flat/BDB/embl.pm blib/lib/Bio/DB/Flat/BDB/embl.pm +cp lib/Bio/DB/InMemoryCache.pm blib/lib/Bio/DB/InMemoryCache.pm +cp lib/Bio/DB/Taxonomy/silva.pm blib/lib/Bio/DB/Taxonomy/silva.pm +cp lib/Bio/Annotation/TagTree.pm blib/lib/Bio/Annotation/TagTree.pm +cp lib/Bio/Annotation/StructuredValue.pm blib/lib/Bio/Annotation/StructuredValue.pm +cp lib/Bio/CodonUsage/IO.pm blib/lib/Bio/CodonUsage/IO.pm +cp lib/Bio/DB/QueryI.pm blib/lib/Bio/DB/QueryI.pm +cp lib/Bio/DB/Taxonomy/flatfile.pm blib/lib/Bio/DB/Taxonomy/flatfile.pm +cp lib/Bio/DB/Taxonomy/greengenes.pm blib/lib/Bio/DB/Taxonomy/greengenes.pm +cp lib/Bio/DB/GFF/Util/Rearrange.pm blib/lib/Bio/DB/GFF/Util/Rearrange.pm +cp lib/Bio/DB/Flat/BDB/genbank.pm blib/lib/Bio/DB/Flat/BDB/genbank.pm +cp lib/Bio/DB/Fasta.pm blib/lib/Bio/DB/Fasta.pm +cp lib/Bio/DB/UpdateableSeqI.pm blib/lib/Bio/DB/UpdateableSeqI.pm +cp lib/Bio/AnnotationCollectionI.pm blib/lib/Bio/AnnotationCollectionI.pm cp lib/Bio/DB/DBFetch.pm blib/lib/Bio/DB/DBFetch.pm -cp lib/Bio/Factory/SequenceProcessorI.pm blib/lib/Bio/Factory/SequenceProcessorI.pm +cp lib/Bio/Annotation/Target.pm blib/lib/Bio/Annotation/Target.pm +cp lib/Bio/Factory/TreeFactoryI.pm blib/lib/Bio/Factory/TreeFactoryI.pm +cp lib/Bio/Factory/FTLocationFactory.pm blib/lib/Bio/Factory/FTLocationFactory.pm +cp lib/Bio/Index/EMBL.pm blib/lib/Bio/Index/EMBL.pm +cp lib/Bio/HandlerBaseI.pm blib/lib/Bio/HandlerBaseI.pm +cp lib/Bio/IdentifiableI.pm blib/lib/Bio/IdentifiableI.pm +cp lib/Bio/Factory/ObjectBuilderI.pm blib/lib/Bio/Factory/ObjectBuilderI.pm +cp lib/Bio/DBLinkContainerI.pm blib/lib/Bio/DBLinkContainerI.pm cp lib/Bio/FeatureHolderI.pm blib/lib/Bio/FeatureHolderI.pm -cp lib/Bio/Das/FeatureTypeI.pm blib/lib/Bio/Das/FeatureTypeI.pm cp lib/Bio/Factory/ObjectFactoryI.pm blib/lib/Bio/Factory/ObjectFactoryI.pm -cp lib/Bio/Factory/SequenceStreamI.pm blib/lib/Bio/Factory/SequenceStreamI.pm -cp lib/Bio/Event/EventHandlerI.pm blib/lib/Bio/Event/EventHandlerI.pm -cp lib/Bio/DescribableI.pm blib/lib/Bio/DescribableI.pm -cp lib/Bio/Factory/ObjectFactory.pm blib/lib/Bio/Factory/ObjectFactory.pm -cp lib/Bio/Index/Fasta.pm blib/lib/Bio/Index/Fasta.pm +cp lib/Bio/Index/Abstract.pm blib/lib/Bio/Index/Abstract.pm +cp lib/Bio/LocatableSeq.pm blib/lib/Bio/LocatableSeq.pm cp lib/Bio/IdCollectionI.pm blib/lib/Bio/IdCollectionI.pm -cp lib/Bio/Event/EventGeneratorI.pm blib/lib/Bio/Event/EventGeneratorI.pm -cp lib/Bio/DBLinkContainerI.pm blib/lib/Bio/DBLinkContainerI.pm -cp lib/Bio/Index/EMBL.pm blib/lib/Bio/Index/EMBL.pm -cp lib/Bio/IdentifiableI.pm blib/lib/Bio/IdentifiableI.pm -cp lib/Bio/Index/GenBank.pm blib/lib/Bio/Index/GenBank.pm +cp lib/Bio/Event/EventHandlerI.pm blib/lib/Bio/Event/EventHandlerI.pm cp lib/Bio/Index/Blast.pm blib/lib/Bio/Index/Blast.pm -cp lib/Bio/HandlerBaseI.pm blib/lib/Bio/HandlerBaseI.pm -cp lib/Bio/Factory/FTLocationFactory.pm blib/lib/Bio/Factory/FTLocationFactory.pm +cp lib/Bio/DescribableI.pm blib/lib/Bio/DescribableI.pm cp lib/Bio/Index/SwissPfam.pm blib/lib/Bio/Index/SwissPfam.pm -cp lib/Bio/Index/Swissprot.pm blib/lib/Bio/Index/Swissprot.pm -cp lib/Bio/Index/Fastq.pm blib/lib/Bio/Index/Fastq.pm -cp lib/Bio/Index/Abstract.pm blib/lib/Bio/Index/Abstract.pm -cp lib/Bio/Factory/ApplicationFactoryI.pm blib/lib/Bio/Factory/ApplicationFactoryI.pm -cp lib/Bio/Factory/SeqAnalysisParserFactoryI.pm blib/lib/Bio/Factory/SeqAnalysisParserFactoryI.pm cp lib/Bio/Factory/SequenceFactoryI.pm blib/lib/Bio/Factory/SequenceFactoryI.pm -cp lib/Bio/Factory/TreeFactoryI.pm blib/lib/Bio/Factory/TreeFactoryI.pm -cp lib/Bio/Index/Qual.pm blib/lib/Bio/Index/Qual.pm -cp lib/Bio/LocatableSeq.pm blib/lib/Bio/LocatableSeq.pm +cp lib/Bio/DasI.pm blib/lib/Bio/DasI.pm +cp lib/Bio/Index/Fasta.pm blib/lib/Bio/Index/Fasta.pm +cp lib/Bio/Factory/ApplicationFactoryI.pm blib/lib/Bio/Factory/ApplicationFactoryI.pm cp lib/Bio/Factory/SeqAnalysisParserFactory.pm blib/lib/Bio/Factory/SeqAnalysisParserFactory.pm -cp lib/Bio/Factory/DriverFactory.pm blib/lib/Bio/Factory/DriverFactory.pm -cp lib/Bio/Index/BlastTable.pm blib/lib/Bio/Index/BlastTable.pm cp lib/Bio/Das/SegmentI.pm blib/lib/Bio/Das/SegmentI.pm -cp lib/Bio/DB/WebDBSeqI.pm blib/lib/Bio/DB/WebDBSeqI.pm -cp lib/Bio/Factory/LocationFactoryI.pm blib/lib/Bio/Factory/LocationFactoryI.pm +cp lib/Bio/Factory/SequenceProcessorI.pm blib/lib/Bio/Factory/SequenceProcessorI.pm cp lib/Bio/Index/AbstractSeq.pm blib/lib/Bio/Index/AbstractSeq.pm +cp lib/Bio/Factory/SeqAnalysisParserFactoryI.pm blib/lib/Bio/Factory/SeqAnalysisParserFactoryI.pm +cp lib/Bio/Factory/DriverFactory.pm blib/lib/Bio/Factory/DriverFactory.pm +cp lib/Bio/DB/WebDBSeqI.pm blib/lib/Bio/DB/WebDBSeqI.pm +cp lib/Bio/Index/Qual.pm blib/lib/Bio/Index/Qual.pm +cp lib/Bio/Das/FeatureTypeI.pm blib/lib/Bio/Das/FeatureTypeI.pm +cp lib/Bio/Index/Swissprot.pm blib/lib/Bio/Index/Swissprot.pm +cp lib/Bio/Event/EventGeneratorI.pm blib/lib/Bio/Event/EventGeneratorI.pm +cp lib/Bio/Index/Fastq.pm blib/lib/Bio/Index/Fastq.pm +cp lib/Bio/Index/BlastTable.pm blib/lib/Bio/Index/BlastTable.pm +cp lib/Bio/Factory/ObjectFactory.pm blib/lib/Bio/Factory/ObjectFactory.pm +cp lib/Bio/Index/GenBank.pm blib/lib/Bio/Index/GenBank.pm +cp lib/Bio/Factory/SequenceStreamI.pm blib/lib/Bio/Factory/SequenceStreamI.pm cp lib/Bio/Factory/AnalysisI.pm blib/lib/Bio/Factory/AnalysisI.pm -cp lib/Bio/Factory/ObjectBuilderI.pm blib/lib/Bio/Factory/ObjectBuilderI.pm -cp lib/Bio/DasI.pm blib/lib/Bio/DasI.pm -cp lib/Bio/Matrix/Mlagan.pm blib/lib/Bio/Matrix/Mlagan.pm -cp lib/Bio/Matrix/IO/mlagan.pm blib/lib/Bio/Matrix/IO/mlagan.pm -cp lib/Bio/Matrix/PSM/PsmHeaderI.pm blib/lib/Bio/Matrix/PSM/PsmHeaderI.pm -cp lib/Bio/Location/WidestCoordPolicy.pm blib/lib/Bio/Location/WidestCoordPolicy.pm -cp lib/Bio/Location/AvWithinCoordPolicy.pm blib/lib/Bio/Location/AvWithinCoordPolicy.pm -cp lib/Bio/Matrix/PhylipDist.pm blib/lib/Bio/Matrix/PhylipDist.pm -cp lib/Bio/Location/Fuzzy.pm blib/lib/Bio/Location/Fuzzy.pm -cp lib/Bio/Matrix/PSM/InstanceSite.pm blib/lib/Bio/Matrix/PSM/InstanceSite.pm -cp lib/Bio/Matrix/PSM/IO/mast.pm blib/lib/Bio/Matrix/PSM/IO/mast.pm +cp lib/Bio/Factory/LocationFactoryI.pm blib/lib/Bio/Factory/LocationFactoryI.pm +cp lib/Bio/Matrix/PSM/IO/meme.pm blib/lib/Bio/Matrix/PSM/IO/meme.pm +cp lib/Bio/Ontology/DocumentRegistry.pm blib/lib/Bio/Ontology/DocumentRegistry.pm +cp lib/Bio/Matrix/IO/phylip.pm blib/lib/Bio/Matrix/IO/phylip.pm +cp lib/Bio/Matrix/PSM/Psm.pm blib/lib/Bio/Matrix/PSM/Psm.pm +cp lib/Bio/Location/NarrowestCoordPolicy.pm blib/lib/Bio/Location/NarrowestCoordPolicy.pm +cp lib/Bio/Matrix/IO.pm blib/lib/Bio/Matrix/IO.pm cp lib/Bio/Matrix/Generic.pm blib/lib/Bio/Matrix/Generic.pm cp lib/Bio/Matrix/MatrixI.pm blib/lib/Bio/Matrix/MatrixI.pm -cp lib/Bio/Location/NarrowestCoordPolicy.pm blib/lib/Bio/Location/NarrowestCoordPolicy.pm -cp lib/Bio/Matrix/PSM/IO/transfac.pm blib/lib/Bio/Matrix/PSM/IO/transfac.pm +cp lib/Bio/Matrix/PhylipDist.pm blib/lib/Bio/Matrix/PhylipDist.pm +cp lib/Bio/Matrix/PSM/InstanceSite.pm blib/lib/Bio/Matrix/PSM/InstanceSite.pm cp lib/Bio/Matrix/PSM/IO/psiblast.pm blib/lib/Bio/Matrix/PSM/IO/psiblast.pm -cp lib/Bio/Location/Simple.pm blib/lib/Bio/Location/Simple.pm cp lib/Bio/Matrix/IO/scoring.pm blib/lib/Bio/Matrix/IO/scoring.pm -cp lib/Bio/Location/CoordinatePolicyI.pm blib/lib/Bio/Location/CoordinatePolicyI.pm -cp lib/Bio/Location/FuzzyLocationI.pm blib/lib/Bio/Location/FuzzyLocationI.pm -cp lib/Bio/Matrix/PSM/IO/meme.pm blib/lib/Bio/Matrix/PSM/IO/meme.pm -cp lib/Bio/LocationI.pm blib/lib/Bio/LocationI.pm -cp lib/Bio/Matrix/Scoring.pm blib/lib/Bio/Matrix/Scoring.pm -cp lib/Bio/Matrix/PSM/PsmHeader.pm blib/lib/Bio/Matrix/PSM/PsmHeader.pm -cp lib/Bio/Matrix/IO/phylip.pm blib/lib/Bio/Matrix/IO/phylip.pm -cp lib/Bio/Matrix/PSM/Psm.pm blib/lib/Bio/Matrix/PSM/Psm.pm -cp lib/Bio/Matrix/PSM/InstanceSiteI.pm blib/lib/Bio/Matrix/PSM/InstanceSiteI.pm -cp lib/Bio/Matrix/PSM/IO/masta.pm blib/lib/Bio/Matrix/PSM/IO/masta.pm +cp lib/Bio/Matrix/PSM/IO/transfac.pm blib/lib/Bio/Matrix/PSM/IO/transfac.pm +cp lib/Bio/Location/Atomic.pm blib/lib/Bio/Location/Atomic.pm cp lib/Bio/Matrix/PSM/IO.pm blib/lib/Bio/Matrix/PSM/IO.pm -cp lib/Bio/Matrix/IO.pm blib/lib/Bio/Matrix/IO.pm +cp lib/Bio/Matrix/PSM/InstanceSiteI.pm blib/lib/Bio/Matrix/PSM/InstanceSiteI.pm +cp lib/Bio/Location/Simple.pm blib/lib/Bio/Location/Simple.pm +cp lib/Bio/Matrix/IO/mlagan.pm blib/lib/Bio/Matrix/IO/mlagan.pm +cp lib/Bio/Matrix/Mlagan.pm blib/lib/Bio/Matrix/Mlagan.pm +cp lib/Bio/Matrix/Scoring.pm blib/lib/Bio/Matrix/Scoring.pm cp lib/Bio/Location/SplitLocationI.pm blib/lib/Bio/Location/SplitLocationI.pm -cp lib/Bio/Matrix/PSM/SiteMatrixI.pm blib/lib/Bio/Matrix/PSM/SiteMatrixI.pm -cp lib/Bio/Location/Atomic.pm blib/lib/Bio/Location/Atomic.pm -cp lib/Bio/Matrix/PSM/PsmI.pm blib/lib/Bio/Matrix/PSM/PsmI.pm cp lib/Bio/Matrix/PSM/ProtPsm.pm blib/lib/Bio/Matrix/PSM/ProtPsm.pm -cp lib/Bio/Matrix/PSM/ProtMatrix.pm blib/lib/Bio/Matrix/PSM/ProtMatrix.pm +cp lib/Bio/Location/FuzzyLocationI.pm blib/lib/Bio/Location/FuzzyLocationI.pm +cp lib/Bio/Matrix/PSM/IO/mast.pm blib/lib/Bio/Matrix/PSM/IO/mast.pm +cp lib/Bio/Matrix/PSM/IO/masta.pm blib/lib/Bio/Matrix/PSM/IO/masta.pm +cp lib/Bio/Matrix/PSM/PsmI.pm blib/lib/Bio/Matrix/PSM/PsmI.pm +cp lib/Bio/Location/Fuzzy.pm blib/lib/Bio/Location/Fuzzy.pm cp lib/Bio/Location/Split.pm blib/lib/Bio/Location/Split.pm +cp lib/Bio/Location/AvWithinCoordPolicy.pm blib/lib/Bio/Location/AvWithinCoordPolicy.pm +cp lib/Bio/Matrix/PSM/ProtMatrix.pm blib/lib/Bio/Matrix/PSM/ProtMatrix.pm +cp lib/Bio/Matrix/PSM/PsmHeaderI.pm blib/lib/Bio/Matrix/PSM/PsmHeaderI.pm +cp lib/Bio/Location/CoordinatePolicyI.pm blib/lib/Bio/Location/CoordinatePolicyI.pm +cp lib/Bio/Location/WidestCoordPolicy.pm blib/lib/Bio/Location/WidestCoordPolicy.pm +cp lib/Bio/Matrix/PSM/PsmHeader.pm blib/lib/Bio/Matrix/PSM/PsmHeader.pm +cp lib/Bio/LocationI.pm blib/lib/Bio/LocationI.pm cp lib/Bio/Matrix/PSM/SiteMatrix.pm blib/lib/Bio/Matrix/PSM/SiteMatrix.pm -cp lib/Bio/Ontology/DocumentRegistry.pm blib/lib/Bio/Ontology/DocumentRegistry.pm -cp lib/Bio/Ontology/RelationshipType.pm blib/lib/Bio/Ontology/RelationshipType.pm -cp lib/Bio/OntologyIO/soflat.pm blib/lib/Bio/OntologyIO/soflat.pm -cp lib/Bio/OntologyIO/dagflat.pm blib/lib/Bio/OntologyIO/dagflat.pm -cp lib/Bio/Ontology/InterProTerm.pm blib/lib/Bio/Ontology/InterProTerm.pm -cp lib/Bio/OntologyIO/InterProParser.pm blib/lib/Bio/OntologyIO/InterProParser.pm +cp lib/Bio/Matrix/PSM/SiteMatrixI.pm blib/lib/Bio/Matrix/PSM/SiteMatrixI.pm +cp lib/Bio/Range.pm blib/lib/Bio/Range.pm cp lib/Bio/Ontology/OntologyI.pm blib/lib/Bio/Ontology/OntologyI.pm +cp lib/Bio/Ontology/GOterm.pm blib/lib/Bio/Ontology/GOterm.pm +cp lib/Bio/OntologyIO/dagflat.pm blib/lib/Bio/OntologyIO/dagflat.pm +cp lib/Bio/OntologyIO/goflat.pm blib/lib/Bio/OntologyIO/goflat.pm cp lib/Bio/Ontology/Term.pm blib/lib/Bio/Ontology/Term.pm -cp lib/Bio/Root/Exception.pm blib/lib/Bio/Root/Exception.pm -cp lib/Bio/RangeI.pm blib/lib/Bio/RangeI.pm -cp lib/Bio/OntologyIO.pm blib/lib/Bio/OntologyIO.pm -cp lib/Bio/PrimarySeq.pm blib/lib/Bio/PrimarySeq.pm -cp lib/Bio/Ontology/OntologyStore.pm blib/lib/Bio/Ontology/OntologyStore.pm cp lib/Bio/Ontology/TermI.pm blib/lib/Bio/Ontology/TermI.pm -cp lib/Bio/Ontology/GOterm.pm blib/lib/Bio/Ontology/GOterm.pm -cp lib/Bio/OntologyIO/Handlers/InterProHandler.pm blib/lib/Bio/OntologyIO/Handlers/InterProHandler.pm -cp lib/Bio/Ontology/RelationshipFactory.pm blib/lib/Bio/Ontology/RelationshipFactory.pm +cp lib/Bio/Root/Exception.pm blib/lib/Bio/Root/Exception.pm cp lib/Bio/Ontology/TermFactory.pm blib/lib/Bio/Ontology/TermFactory.pm +cp lib/Bio/Ontology/OBOEngine.pm blib/lib/Bio/Ontology/OBOEngine.pm +cp lib/Bio/OntologyIO/soflat.pm blib/lib/Bio/OntologyIO/soflat.pm +cp lib/Bio/Ontology/InterProTerm.pm blib/lib/Bio/Ontology/InterProTerm.pm cp lib/Bio/Ontology/PathI.pm blib/lib/Bio/Ontology/PathI.pm -cp lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm blib/lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm -cp lib/Bio/OntologyIO/obo.pm blib/lib/Bio/OntologyIO/obo.pm -cp lib/Bio/Ontology/OntologyEngineI.pm blib/lib/Bio/Ontology/OntologyEngineI.pm -cp lib/Bio/Range.pm blib/lib/Bio/Range.pm -cp lib/Bio/Ontology/Path.pm blib/lib/Bio/Ontology/Path.pm -cp lib/Bio/Ontology/RelationshipI.pm blib/lib/Bio/Ontology/RelationshipI.pm -cp lib/Bio/Ontology/OBOterm.pm blib/lib/Bio/Ontology/OBOterm.pm -cp lib/Bio/OntologyIO/goflat.pm blib/lib/Bio/OntologyIO/goflat.pm cp lib/Bio/Ontology/Relationship.pm blib/lib/Bio/Ontology/Relationship.pm +cp lib/Bio/PrimarySeqI.pm blib/lib/Bio/PrimarySeqI.pm cp lib/Bio/OntologyIO/simplehierarchy.pm blib/lib/Bio/OntologyIO/simplehierarchy.pm -cp lib/Bio/Ontology/SimpleOntologyEngine.pm blib/lib/Bio/Ontology/SimpleOntologyEngine.pm +cp lib/Bio/OntologyIO.pm blib/lib/Bio/OntologyIO.pm +cp lib/Bio/Ontology/Ontology.pm blib/lib/Bio/Ontology/Ontology.pm +cp lib/Bio/Ontology/OBOterm.pm blib/lib/Bio/Ontology/OBOterm.pm +cp lib/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm blib/lib/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm +cp lib/Bio/Ontology/OntologyEngineI.pm blib/lib/Bio/Ontology/OntologyEngineI.pm +cp lib/Bio/OntologyIO/Handlers/InterProHandler.pm blib/lib/Bio/OntologyIO/Handlers/InterProHandler.pm +cp lib/Bio/OntologyIO/InterProParser.pm blib/lib/Bio/OntologyIO/InterProParser.pm cp lib/Bio/OntologyIO/Handlers/BaseSAXHandler.pm blib/lib/Bio/OntologyIO/Handlers/BaseSAXHandler.pm +cp lib/Bio/RangeI.pm blib/lib/Bio/RangeI.pm cp lib/Bio/ParameterBaseI.pm blib/lib/Bio/ParameterBaseI.pm +cp lib/Bio/OntologyIO/obo.pm blib/lib/Bio/OntologyIO/obo.pm +cp lib/Bio/Ontology/RelationshipFactory.pm blib/lib/Bio/Ontology/RelationshipFactory.pm +cp lib/Bio/Ontology/SimpleOntologyEngine.pm blib/lib/Bio/Ontology/SimpleOntologyEngine.pm +cp lib/Bio/Ontology/Path.pm blib/lib/Bio/Ontology/Path.pm +cp lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm blib/lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm +cp lib/Bio/PrimarySeq.pm blib/lib/Bio/PrimarySeq.pm +cp lib/Bio/Ontology/OntologyStore.pm blib/lib/Bio/Ontology/OntologyStore.pm +cp lib/Bio/Ontology/RelationshipType.pm blib/lib/Bio/Ontology/RelationshipType.pm cp lib/Bio/PullParserI.pm blib/lib/Bio/PullParserI.pm -cp lib/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm blib/lib/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm -cp lib/Bio/Ontology/OBOEngine.pm blib/lib/Bio/Ontology/OBOEngine.pm -cp lib/Bio/Ontology/Ontology.pm blib/lib/Bio/Ontology/Ontology.pm -cp lib/Bio/PrimarySeqI.pm blib/lib/Bio/PrimarySeqI.pm +cp lib/Bio/Ontology/RelationshipI.pm blib/lib/Bio/Ontology/RelationshipI.pm +cp lib/Bio/Search/Hit/PullHitI.pm blib/lib/Bio/Search/Hit/PullHitI.pm +cp lib/Bio/Root/Test.pm blib/lib/Bio/Root/Test.pm cp lib/Bio/Search/HSP/GenericHSP.pm blib/lib/Bio/Search/HSP/GenericHSP.pm -cp lib/Bio/Search/Hit/BlastHit.pm blib/lib/Bio/Search/Hit/BlastHit.pm -cp lib/Bio/Search/Hit/BlastPullHit.pm blib/lib/Bio/Search/Hit/BlastPullHit.pm -cp lib/Bio/Search/Iteration/IterationI.pm blib/lib/Bio/Search/Iteration/IterationI.pm -cp lib/Bio/Search/HSP/HSPI.pm blib/lib/Bio/Search/HSP/HSPI.pm -cp lib/Bio/Root/Version.pm blib/lib/Bio/Root/Version.pm -cp lib/Bio/Search/HSP/ModelHSP.pm blib/lib/Bio/Search/HSP/ModelHSP.pm -cp lib/Bio/Search/BlastStatistics.pm blib/lib/Bio/Search/BlastStatistics.pm -cp lib/Bio/Search/Processor.pm blib/lib/Bio/Search/Processor.pm -cp lib/Bio/Root/RootI.pm blib/lib/Bio/Root/RootI.pm -cp lib/Bio/Root/Root.pm blib/lib/Bio/Root/Root.pm -cp lib/Bio/Search/BlastUtils.pm blib/lib/Bio/Search/BlastUtils.pm +cp lib/Bio/Search/HSP/WABAHSP.pm blib/lib/Bio/Search/HSP/WABAHSP.pm cp lib/Bio/Search/Hit/Fasta.pm blib/lib/Bio/Search/Hit/Fasta.pm -cp lib/Bio/Search/GenericStatistics.pm blib/lib/Bio/Search/GenericStatistics.pm +cp lib/Bio/Search/HSP/PsiBlastHSP.pm blib/lib/Bio/Search/HSP/PsiBlastHSP.pm +cp lib/Bio/Search/Hit/GenericHit.pm blib/lib/Bio/Search/Hit/GenericHit.pm +cp lib/Bio/Search/Iteration/GenericIteration.pm blib/lib/Bio/Search/Iteration/GenericIteration.pm cp lib/Bio/Search/Hit/HitFactory.pm blib/lib/Bio/Search/Hit/HitFactory.pm -cp lib/Bio/Search/DatabaseI.pm blib/lib/Bio/Search/DatabaseI.pm -cp lib/Bio/Search/Hit/PsiBlastHit.pm blib/lib/Bio/Search/Hit/PsiBlastHit.pm -cp lib/Bio/Search/Hit/HitI.pm blib/lib/Bio/Search/Hit/HitI.pm +cp lib/Bio/Search/Processor.pm blib/lib/Bio/Search/Processor.pm +cp lib/Bio/Root/HTTPget.pm blib/lib/Bio/Root/HTTPget.pm +cp lib/Bio/Search/BlastUtils.pm blib/lib/Bio/Search/BlastUtils.pm cp lib/Bio/Search/HSP/FastaHSP.pm blib/lib/Bio/Search/HSP/FastaHSP.pm -cp lib/Bio/Root/Utilities.pm blib/lib/Bio/Root/Utilities.pm cp lib/Bio/Search/HSP/HSPFactory.pm blib/lib/Bio/Search/HSP/HSPFactory.pm +cp lib/Bio/Search/Hit/BlastPullHit.pm blib/lib/Bio/Search/Hit/BlastPullHit.pm cp lib/Bio/Search/Hit/ModelHit.pm blib/lib/Bio/Search/Hit/ModelHit.pm -cp lib/Bio/Search/HSP/BlastHSP.pm blib/lib/Bio/Search/HSP/BlastHSP.pm -cp lib/Bio/Search/HSP/BlastPullHSP.pm blib/lib/Bio/Search/HSP/BlastPullHSP.pm -cp lib/Bio/Search/Iteration/GenericIteration.pm blib/lib/Bio/Search/Iteration/GenericIteration.pm -cp lib/Bio/Root/Test.pm blib/lib/Bio/Root/Test.pm -cp lib/Bio/Search/HSP/WABAHSP.pm blib/lib/Bio/Search/HSP/WABAHSP.pm cp lib/Bio/Root/Storable.pm blib/lib/Bio/Root/Storable.pm +cp lib/Bio/Search/Hit/BlastHit.pm blib/lib/Bio/Search/Hit/BlastHit.pm cp lib/Bio/Search/HSP/PullHSPI.pm blib/lib/Bio/Search/HSP/PullHSPI.pm -cp lib/Bio/Search/GenericDatabase.pm blib/lib/Bio/Search/GenericDatabase.pm +cp lib/Bio/Root/Root.pm blib/lib/Bio/Root/Root.pm +cp lib/Bio/Search/HSP/BlastHSP.pm blib/lib/Bio/Search/HSP/BlastHSP.pm +cp lib/Bio/Search/GenericStatistics.pm blib/lib/Bio/Search/GenericStatistics.pm +cp lib/Bio/Root/Version.pm blib/lib/Bio/Root/Version.pm +cp lib/Bio/Root/Utilities.pm blib/lib/Bio/Root/Utilities.pm +cp lib/Bio/Search/BlastStatistics.pm blib/lib/Bio/Search/BlastStatistics.pm cp lib/Bio/Root/TestObject.pm blib/lib/Bio/Root/TestObject.pm -cp lib/Bio/Search/Hit/GenericHit.pm blib/lib/Bio/Search/Hit/GenericHit.pm +cp lib/Bio/Search/HSP/HSPI.pm blib/lib/Bio/Search/HSP/HSPI.pm +cp lib/Bio/Search/HSP/BlastPullHSP.pm blib/lib/Bio/Search/HSP/BlastPullHSP.pm cp lib/Bio/Search/HSP/PSLHSP.pm blib/lib/Bio/Search/HSP/PSLHSP.pm -cp lib/Bio/Search/Hit/PullHitI.pm blib/lib/Bio/Search/Hit/PullHitI.pm -cp lib/Bio/Root/HTTPget.pm blib/lib/Bio/Root/HTTPget.pm +cp lib/Bio/Search/Hit/HitI.pm blib/lib/Bio/Search/Hit/HitI.pm +cp lib/Bio/Search/HSP/ModelHSP.pm blib/lib/Bio/Search/HSP/ModelHSP.pm cp lib/Bio/Root/IO.pm blib/lib/Bio/Root/IO.pm -cp lib/Bio/Search/HSP/PsiBlastHSP.pm blib/lib/Bio/Search/HSP/PsiBlastHSP.pm -cp lib/Bio/SearchIO/FastHitEventBuilder.pm blib/lib/Bio/SearchIO/FastHitEventBuilder.pm -cp lib/Bio/Search/Result/ResultFactory.pm blib/lib/Bio/Search/Result/ResultFactory.pm -cp lib/Bio/SearchIO/Writer/GbrowseGFF.pm blib/lib/Bio/SearchIO/Writer/GbrowseGFF.pm -cp lib/Bio/SearchIO/Writer/HTMLResultWriter.pm blib/lib/Bio/SearchIO/Writer/HTMLResultWriter.pm -cp lib/Bio/SearchIO/blast.pm blib/lib/Bio/SearchIO/blast.pm -cp lib/Bio/Search/Tiling/TilingI.pm blib/lib/Bio/Search/Tiling/TilingI.pm +cp lib/Bio/Root/RootI.pm blib/lib/Bio/Root/RootI.pm +cp lib/Bio/Search/Hit/PsiBlastHit.pm blib/lib/Bio/Search/Hit/PsiBlastHit.pm +cp lib/Bio/Search/DatabaseI.pm blib/lib/Bio/Search/DatabaseI.pm +cp lib/Bio/Search/Iteration/IterationI.pm blib/lib/Bio/Search/Iteration/IterationI.pm +cp lib/Bio/Search/GenericDatabase.pm blib/lib/Bio/Search/GenericDatabase.pm +cp lib/Bio/Search/Result/CrossMatchResult.pm blib/lib/Bio/Search/Result/CrossMatchResult.pm +cp lib/Bio/SearchIO/Writer/HSPTableWriter.pm blib/lib/Bio/SearchIO/Writer/HSPTableWriter.pm cp lib/Bio/SearchIO/axt.pm blib/lib/Bio/SearchIO/axt.pm -cp lib/Bio/Search/StatisticsI.pm blib/lib/Bio/Search/StatisticsI.pm -cp lib/Bio/Search/Result/GenericResult.pm blib/lib/Bio/Search/Result/GenericResult.pm -cp lib/Bio/Search/Result/INFERNALResult.pm blib/lib/Bio/Search/Result/INFERNALResult.pm -cp lib/Bio/Search/Result/BlastResult.pm blib/lib/Bio/Search/Result/BlastResult.pm -cp lib/Bio/SearchIO/EventHandlerI.pm blib/lib/Bio/SearchIO/EventHandlerI.pm cp lib/Bio/Search/Tiling/MapTileUtils.pm blib/lib/Bio/Search/Tiling/MapTileUtils.pm +cp lib/Bio/Search/Result/WABAResult.pm blib/lib/Bio/Search/Result/WABAResult.pm +cp lib/Bio/Search/Result/ResultFactory.pm blib/lib/Bio/Search/Result/ResultFactory.pm +cp lib/Bio/Search/SearchUtils.pm blib/lib/Bio/Search/SearchUtils.pm +cp lib/Bio/Search/Result/ResultI.pm blib/lib/Bio/Search/Result/ResultI.pm +cp lib/Bio/SearchIO/FastHitEventBuilder.pm blib/lib/Bio/SearchIO/FastHitEventBuilder.pm cp lib/Bio/SearchIO/IteratedSearchResultEventBuilder.pm blib/lib/Bio/SearchIO/IteratedSearchResultEventBuilder.pm -cp lib/Bio/SearchIO/blasttable.pm blib/lib/Bio/SearchIO/blasttable.pm -cp lib/Bio/SearchIO.pm blib/lib/Bio/SearchIO.pm cp lib/Bio/SearchIO/cross_match.pm blib/lib/Bio/SearchIO/cross_match.pm -cp lib/Bio/Search/Result/CrossMatchResult.pm blib/lib/Bio/Search/Result/CrossMatchResult.pm -cp lib/Bio/Search/Tiling/MapTiling.pm blib/lib/Bio/Search/Tiling/MapTiling.pm -cp lib/Bio/SearchIO/Writer/ResultTableWriter.pm blib/lib/Bio/SearchIO/Writer/ResultTableWriter.pm +cp lib/Bio/Search/Result/BlastResult.pm blib/lib/Bio/Search/Result/BlastResult.pm cp lib/Bio/SearchIO/SearchResultEventBuilder.pm blib/lib/Bio/SearchIO/SearchResultEventBuilder.pm -cp lib/Bio/Search/Result/ResultI.pm blib/lib/Bio/Search/Result/ResultI.pm -cp lib/Bio/Search/Result/PullResultI.pm blib/lib/Bio/Search/Result/PullResultI.pm -cp lib/Bio/Search/SearchUtils.pm blib/lib/Bio/Search/SearchUtils.pm -cp lib/Bio/SearchIO/SearchWriterI.pm blib/lib/Bio/SearchIO/SearchWriterI.pm -cp lib/Bio/Search/Result/BlastPullResult.pm blib/lib/Bio/Search/Result/BlastPullResult.pm -cp lib/Bio/SearchIO/Writer/TextResultWriter.pm blib/lib/Bio/SearchIO/Writer/TextResultWriter.pm -cp lib/Bio/SearchIO/Writer/HitTableWriter.pm blib/lib/Bio/SearchIO/Writer/HitTableWriter.pm +cp lib/Bio/SearchIO/blasttable.pm blib/lib/Bio/SearchIO/blasttable.pm +cp lib/Bio/SearchIO/blast.pm blib/lib/Bio/SearchIO/blast.pm +cp lib/Bio/SearchIO/Writer/HTMLResultWriter.pm blib/lib/Bio/SearchIO/Writer/HTMLResultWriter.pm cp lib/Bio/SearchIO/blast_pull.pm blib/lib/Bio/SearchIO/blast_pull.pm -cp lib/Bio/Search/Result/WABAResult.pm blib/lib/Bio/Search/Result/WABAResult.pm +cp lib/Bio/SearchIO/Writer/HitTableWriter.pm blib/lib/Bio/SearchIO/Writer/HitTableWriter.pm +cp lib/Bio/Search/Tiling/MapTiling.pm blib/lib/Bio/Search/Tiling/MapTiling.pm +cp lib/Bio/SearchIO/Writer/GbrowseGFF.pm blib/lib/Bio/SearchIO/Writer/GbrowseGFF.pm +cp lib/Bio/Search/StatisticsI.pm blib/lib/Bio/Search/StatisticsI.pm +cp lib/Bio/Search/Result/BlastPullResult.pm blib/lib/Bio/Search/Result/BlastPullResult.pm +cp lib/Bio/SearchIO/SearchWriterI.pm blib/lib/Bio/SearchIO/SearchWriterI.pm cp lib/Bio/SearchIO/erpin.pm blib/lib/Bio/SearchIO/erpin.pm -cp lib/Bio/SearchIO/Writer/HSPTableWriter.pm blib/lib/Bio/SearchIO/Writer/HSPTableWriter.pm -cp lib/Bio/Seq/LargeSeqI.pm blib/lib/Bio/Seq/LargeSeqI.pm -cp lib/Bio/SeqFeature/Computation.pm blib/lib/Bio/SeqFeature/Computation.pm -cp lib/Bio/Seq.pm blib/lib/Bio/Seq.pm -cp lib/Bio/SeqFeature/AnnotationAdaptor.pm blib/lib/Bio/SeqFeature/AnnotationAdaptor.pm -cp lib/Bio/Seq/SimulatedRead.pm blib/lib/Bio/Seq/SimulatedRead.pm -cp lib/Bio/Seq/EncodedSeq.pm blib/lib/Bio/Seq/EncodedSeq.pm -cp lib/Bio/SearchIO/exonerate.pm blib/lib/Bio/SearchIO/exonerate.pm -cp lib/Bio/Seq/QualI.pm blib/lib/Bio/Seq/QualI.pm -cp lib/Bio/SearchIO/infernal.pm blib/lib/Bio/SearchIO/infernal.pm -cp lib/Bio/SearchIO/wise.pm blib/lib/Bio/SearchIO/wise.pm +cp lib/Bio/SearchIO/EventHandlerI.pm blib/lib/Bio/SearchIO/EventHandlerI.pm +cp lib/Bio/Search/Result/GenericResult.pm blib/lib/Bio/Search/Result/GenericResult.pm +cp lib/Bio/SearchIO/Writer/TextResultWriter.pm blib/lib/Bio/SearchIO/Writer/TextResultWriter.pm +cp lib/Bio/SearchIO/Writer/ResultTableWriter.pm blib/lib/Bio/SearchIO/Writer/ResultTableWriter.pm +cp lib/Bio/Search/Result/PullResultI.pm blib/lib/Bio/Search/Result/PullResultI.pm +cp lib/Bio/Search/Tiling/TilingI.pm blib/lib/Bio/Search/Tiling/TilingI.pm +cp lib/Bio/Search/Result/INFERNALResult.pm blib/lib/Bio/Search/Result/INFERNALResult.pm +cp lib/Bio/SearchIO.pm blib/lib/Bio/SearchIO.pm +cp lib/Bio/Seq/BaseSeqProcessor.pm blib/lib/Bio/Seq/BaseSeqProcessor.pm cp lib/Bio/SearchIO/waba.pm blib/lib/Bio/SearchIO/waba.pm -cp lib/Bio/Seq/PrimaryQual.pm blib/lib/Bio/Seq/PrimaryQual.pm cp lib/Bio/SeqFeature/CollectionI.pm blib/lib/Bio/SeqFeature/CollectionI.pm +cp lib/Bio/Seq/SeqFastaSpeedFactory.pm blib/lib/Bio/Seq/SeqFastaSpeedFactory.pm cp lib/Bio/SearchIO/megablast.pm blib/lib/Bio/SearchIO/megablast.pm -cp lib/Bio/Seq/PrimedSeq.pm blib/lib/Bio/Seq/PrimedSeq.pm -cp lib/Bio/SearchIO/fasta.pm blib/lib/Bio/SearchIO/fasta.pm -cp lib/Bio/SearchIO/sim4.pm blib/lib/Bio/SearchIO/sim4.pm cp lib/Bio/Seq/TraceI.pm blib/lib/Bio/Seq/TraceI.pm +cp lib/Bio/SearchIO/rnamotif.pm blib/lib/Bio/SearchIO/rnamotif.pm +cp lib/Bio/SeqAnalysisParserI.pm blib/lib/Bio/SeqAnalysisParserI.pm +cp lib/Bio/Seq/LargeSeqI.pm blib/lib/Bio/Seq/LargeSeqI.pm +cp lib/Bio/Seq/SimulatedRead.pm blib/lib/Bio/Seq/SimulatedRead.pm +cp lib/Bio/SearchIO/wise.pm blib/lib/Bio/SearchIO/wise.pm +cp lib/Bio/SearchIO/fasta.pm blib/lib/Bio/SearchIO/fasta.pm +cp lib/Bio/SearchIO/infernal.pm blib/lib/Bio/SearchIO/infernal.pm +cp lib/Bio/SeqFeature/Computation.pm blib/lib/Bio/SeqFeature/Computation.pm +cp lib/Bio/SeqFeature/Gene/Exon.pm blib/lib/Bio/SeqFeature/Gene/Exon.pm +cp lib/Bio/SearchIO/gmap_f9.pm blib/lib/Bio/SearchIO/gmap_f9.pm cp lib/Bio/Seq/SeqBuilder.pm blib/lib/Bio/Seq/SeqBuilder.pm -cp lib/Bio/Seq/LargePrimarySeq.pm blib/lib/Bio/Seq/LargePrimarySeq.pm -cp lib/Bio/Seq/BaseSeqProcessor.pm blib/lib/Bio/Seq/BaseSeqProcessor.pm -cp lib/Bio/Seq/LargeSeq.pm blib/lib/Bio/Seq/LargeSeq.pm -cp lib/Bio/Seq/RichSeq.pm blib/lib/Bio/Seq/RichSeq.pm -cp lib/Bio/SeqFeature/Amplicon.pm blib/lib/Bio/SeqFeature/Amplicon.pm -cp lib/Bio/SeqFeature/Collection.pm blib/lib/Bio/SeqFeature/Collection.pm -cp lib/Bio/Seq/Meta/Array.pm blib/lib/Bio/Seq/Meta/Array.pm +cp lib/Bio/Seq/RichSeqI.pm blib/lib/Bio/Seq/RichSeqI.pm +cp lib/Bio/SeqFeature/AnnotationAdaptor.pm blib/lib/Bio/SeqFeature/AnnotationAdaptor.pm +cp lib/Bio/Seq.pm blib/lib/Bio/Seq.pm cp lib/Bio/Seq/LargeLocatableSeq.pm blib/lib/Bio/Seq/LargeLocatableSeq.pm -cp lib/Bio/SeqFeature/Gene/Exon.pm blib/lib/Bio/SeqFeature/Gene/Exon.pm -cp lib/Bio/SeqFeature/FeaturePair.pm blib/lib/Bio/SeqFeature/FeaturePair.pm -cp lib/Bio/Seq/Meta.pm blib/lib/Bio/Seq/Meta.pm cp lib/Bio/Seq/Quality.pm blib/lib/Bio/Seq/Quality.pm -cp lib/Bio/Seq/RichSeqI.pm blib/lib/Bio/Seq/RichSeqI.pm -cp lib/Bio/Seq/SeqFastaSpeedFactory.pm blib/lib/Bio/Seq/SeqFastaSpeedFactory.pm -cp lib/Bio/SeqAnalysisParserI.pm blib/lib/Bio/SeqAnalysisParserI.pm +cp lib/Bio/Seq/RichSeq.pm blib/lib/Bio/Seq/RichSeq.pm cp lib/Bio/Seq/SequenceTrace.pm blib/lib/Bio/Seq/SequenceTrace.pm -cp lib/Bio/Seq/MetaI.pm blib/lib/Bio/Seq/MetaI.pm +cp lib/Bio/SeqFeature/Amplicon.pm blib/lib/Bio/SeqFeature/Amplicon.pm +cp lib/Bio/Seq/Meta.pm blib/lib/Bio/Seq/Meta.pm +cp lib/Bio/Seq/PrimaryQual.pm blib/lib/Bio/Seq/PrimaryQual.pm +cp lib/Bio/Seq/QualI.pm blib/lib/Bio/Seq/QualI.pm +cp lib/Bio/SeqFeature/FeaturePair.pm blib/lib/Bio/SeqFeature/FeaturePair.pm cp lib/Bio/Seq/SeqFactory.pm blib/lib/Bio/Seq/SeqFactory.pm -cp lib/Bio/SearchIO/rnamotif.pm blib/lib/Bio/SearchIO/rnamotif.pm -cp lib/Bio/SearchIO/gmap_f9.pm blib/lib/Bio/SearchIO/gmap_f9.pm +cp lib/Bio/SearchIO/exonerate.pm blib/lib/Bio/SearchIO/exonerate.pm +cp lib/Bio/SearchIO/sim4.pm blib/lib/Bio/SearchIO/sim4.pm cp lib/Bio/SearchIO/psl.pm blib/lib/Bio/SearchIO/psl.pm -cp lib/Bio/SeqFeature/Generic.pm blib/lib/Bio/SeqFeature/Generic.pm -cp lib/Bio/SeqFeature/Gene/Intron.pm blib/lib/Bio/SeqFeature/Gene/Intron.pm -cp lib/Bio/SeqFeature/Gene/NC_Feature.pm blib/lib/Bio/SeqFeature/Gene/NC_Feature.pm +cp lib/Bio/SeqFeature/Collection.pm blib/lib/Bio/SeqFeature/Collection.pm +cp lib/Bio/Seq/LargeSeq.pm blib/lib/Bio/Seq/LargeSeq.pm +cp lib/Bio/Seq/Meta/Array.pm blib/lib/Bio/Seq/Meta/Array.pm +cp lib/Bio/Seq/PrimedSeq.pm blib/lib/Bio/Seq/PrimedSeq.pm +cp lib/Bio/Seq/MetaI.pm blib/lib/Bio/Seq/MetaI.pm +cp lib/Bio/Seq/LargePrimarySeq.pm blib/lib/Bio/Seq/LargePrimarySeq.pm +cp lib/Bio/Seq/EncodedSeq.pm blib/lib/Bio/Seq/EncodedSeq.pm +cp lib/Bio/SeqIO/ace.pm blib/lib/Bio/SeqIO/ace.pm +cp lib/Bio/SeqFeature/Tools/TypeMapper.pm blib/lib/Bio/SeqFeature/Tools/TypeMapper.pm cp lib/Bio/SeqFeatureI.pm blib/lib/Bio/SeqFeatureI.pm -cp lib/Bio/SeqIO.pm blib/lib/Bio/SeqIO.pm -cp lib/Bio/SeqFeature/Tools/IDHandler.pm blib/lib/Bio/SeqFeature/Tools/IDHandler.pm +cp lib/Bio/SeqFeature/Gene/TranscriptI.pm blib/lib/Bio/SeqFeature/Gene/TranscriptI.pm +cp lib/Bio/SeqFeature/Gene/UTR.pm blib/lib/Bio/SeqFeature/Gene/UTR.pm +cp lib/Bio/SeqFeature/Tools/Unflattener.pm blib/lib/Bio/SeqFeature/Tools/Unflattener.pm +cp lib/Bio/SeqIO/bsml.pm blib/lib/Bio/SeqIO/bsml.pm +cp lib/Bio/SeqFeature/Gene/NC_Feature.pm blib/lib/Bio/SeqFeature/Gene/NC_Feature.pm cp lib/Bio/SeqFeature/Gene/Transcript.pm blib/lib/Bio/SeqFeature/Gene/Transcript.pm -cp lib/Bio/SeqFeature/Lite.pm blib/lib/Bio/SeqFeature/Lite.pm -cp lib/Bio/SeqFeature/Primer.pm blib/lib/Bio/SeqFeature/Primer.pm -cp lib/Bio/SeqIO/embl.pm blib/lib/Bio/SeqIO/embl.pm -cp lib/Bio/SeqIO/Handler/GenericRichSeqHandler.pm blib/lib/Bio/SeqIO/Handler/GenericRichSeqHandler.pm -cp lib/Bio/SeqFeature/Gene/GeneStructureI.pm blib/lib/Bio/SeqFeature/Gene/GeneStructureI.pm -cp lib/Bio/SeqFeature/Tools/TypeMapper.pm blib/lib/Bio/SeqFeature/Tools/TypeMapper.pm -cp lib/Bio/SeqFeature/Tools/FeatureNamer.pm blib/lib/Bio/SeqFeature/Tools/FeatureNamer.pm -cp lib/Bio/SeqIO/MultiFile.pm blib/lib/Bio/SeqIO/MultiFile.pm +cp lib/Bio/SeqFeature/Gene/GeneStructure.pm blib/lib/Bio/SeqFeature/Gene/GeneStructure.pm cp lib/Bio/SeqFeature/SimilarityPair.pm blib/lib/Bio/SeqFeature/SimilarityPair.pm -cp lib/Bio/SeqFeature/Tools/Unflattener.pm blib/lib/Bio/SeqFeature/Tools/Unflattener.pm cp lib/Bio/SeqIO/fastq.pm blib/lib/Bio/SeqIO/fastq.pm +cp lib/Bio/SeqFeature/Tools/IDHandler.pm blib/lib/Bio/SeqFeature/Tools/IDHandler.pm +cp lib/Bio/SeqIO/embldriver.pm blib/lib/Bio/SeqIO/embldriver.pm +cp lib/Bio/SeqFeature/Gene/Poly_A_site.pm blib/lib/Bio/SeqFeature/Gene/Poly_A_site.pm +cp lib/Bio/SeqFeature/Similarity.pm blib/lib/Bio/SeqFeature/Similarity.pm +cp lib/Bio/SeqIO.pm blib/lib/Bio/SeqIO.pm +cp lib/Bio/SeqFeature/Generic.pm blib/lib/Bio/SeqFeature/Generic.pm cp lib/Bio/SeqIO/bsml_sax.pm blib/lib/Bio/SeqIO/bsml_sax.pm -cp lib/Bio/SeqFeature/PositionProxy.pm blib/lib/Bio/SeqFeature/PositionProxy.pm -cp lib/Bio/SeqFeature/TypedSeqFeatureI.pm blib/lib/Bio/SeqFeature/TypedSeqFeatureI.pm -cp lib/Bio/SeqFeature/Gene/GeneStructure.pm blib/lib/Bio/SeqFeature/Gene/GeneStructure.pm -cp lib/Bio/SeqIO/FTHelper.pm blib/lib/Bio/SeqIO/FTHelper.pm cp lib/Bio/SeqFeature/Gene/ExonI.pm blib/lib/Bio/SeqFeature/Gene/ExonI.pm +cp lib/Bio/SeqIO/embl.pm blib/lib/Bio/SeqIO/embl.pm +cp lib/Bio/SeqIO/Handler/GenericRichSeqHandler.pm blib/lib/Bio/SeqIO/Handler/GenericRichSeqHandler.pm +cp lib/Bio/SeqFeature/Gene/GeneStructureI.pm blib/lib/Bio/SeqFeature/Gene/GeneStructureI.pm +cp lib/Bio/SeqI.pm blib/lib/Bio/SeqI.pm +cp lib/Bio/SeqFeature/Lite.pm blib/lib/Bio/SeqFeature/Lite.pm cp lib/Bio/SeqFeature/SubSeq.pm blib/lib/Bio/SeqFeature/SubSeq.pm -cp lib/Bio/SeqFeature/Gene/TranscriptI.pm blib/lib/Bio/SeqFeature/Gene/TranscriptI.pm +cp lib/Bio/SeqIO/fasta.pm blib/lib/Bio/SeqIO/fasta.pm +cp lib/Bio/SeqFeature/PositionProxy.pm blib/lib/Bio/SeqFeature/PositionProxy.pm cp lib/Bio/SeqIO/asciitree.pm blib/lib/Bio/SeqIO/asciitree.pm +cp lib/Bio/SeqIO/FTHelper.pm blib/lib/Bio/SeqIO/FTHelper.pm +cp lib/Bio/SeqFeature/Tools/FeatureNamer.pm blib/lib/Bio/SeqFeature/Tools/FeatureNamer.pm +cp lib/Bio/SeqIO/MultiFile.pm blib/lib/Bio/SeqIO/MultiFile.pm cp lib/Bio/SeqFeature/Gene/Promoter.pm blib/lib/Bio/SeqFeature/Gene/Promoter.pm -cp lib/Bio/SeqIO/fasta.pm blib/lib/Bio/SeqIO/fasta.pm -cp lib/Bio/SeqIO/bsml.pm blib/lib/Bio/SeqIO/bsml.pm -cp lib/Bio/SeqI.pm blib/lib/Bio/SeqI.pm -cp lib/Bio/SeqFeature/Similarity.pm blib/lib/Bio/SeqFeature/Similarity.pm -cp lib/Bio/SeqIO/ace.pm blib/lib/Bio/SeqIO/ace.pm -cp lib/Bio/SeqIO/embldriver.pm blib/lib/Bio/SeqIO/embldriver.pm -cp lib/Bio/SeqFeature/Gene/UTR.pm blib/lib/Bio/SeqFeature/Gene/UTR.pm -cp lib/Bio/SeqFeature/Gene/Poly_A_site.pm blib/lib/Bio/SeqFeature/Gene/Poly_A_site.pm -cp lib/Bio/SeqIO/largefasta.pm blib/lib/Bio/SeqIO/largefasta.pm -cp lib/Bio/Tools/Analysis/SimpleAnalysisBase.pm blib/lib/Bio/Tools/Analysis/SimpleAnalysisBase.pm -cp lib/Bio/SeqIO/gbdriver.pm blib/lib/Bio/SeqIO/gbdriver.pm -cp lib/Bio/SeqUtils.pm blib/lib/Bio/SeqUtils.pm -cp lib/Bio/Tools/Blat.pm blib/lib/Bio/Tools/Blat.pm -cp lib/Bio/Tools/AnalysisResult.pm blib/lib/Bio/Tools/AnalysisResult.pm +cp lib/Bio/SeqFeature/Primer.pm blib/lib/Bio/SeqFeature/Primer.pm +cp lib/Bio/SeqFeature/Gene/Intron.pm blib/lib/Bio/SeqFeature/Gene/Intron.pm +cp lib/Bio/SeqFeature/TypedSeqFeatureI.pm blib/lib/Bio/SeqFeature/TypedSeqFeatureI.pm cp lib/Bio/SeqIO/tigrxml.pm blib/lib/Bio/SeqIO/tigrxml.pm -cp lib/Bio/SeqIO/table.pm blib/lib/Bio/SeqIO/table.pm -cp lib/Bio/SeqIO/game/seqHandler.pm blib/lib/Bio/SeqIO/game/seqHandler.pm -cp lib/Bio/SeqIO/game/featHandler.pm blib/lib/Bio/SeqIO/game/featHandler.pm -cp lib/Bio/SeqIO/swissdriver.pm blib/lib/Bio/SeqIO/swissdriver.pm -cp lib/Bio/SeqIO/tab.pm blib/lib/Bio/SeqIO/tab.pm -cp lib/Bio/SeqIO/pir.pm blib/lib/Bio/SeqIO/pir.pm -cp lib/Bio/SeqIO/swiss.pm blib/lib/Bio/SeqIO/swiss.pm -cp lib/Bio/SeqIO/tinyseq/tinyseqHandler.pm blib/lib/Bio/SeqIO/tinyseq/tinyseqHandler.pm -cp lib/Bio/SeqIO/msout.pm blib/lib/Bio/SeqIO/msout.pm -cp lib/Bio/SeqIO/gcg.pm blib/lib/Bio/SeqIO/gcg.pm -cp lib/Bio/SimpleAlign.pm blib/lib/Bio/SimpleAlign.pm +cp lib/Bio/SeqIO/largefasta.pm blib/lib/Bio/SeqIO/largefasta.pm cp lib/Bio/SeqIO/gbxml.pm blib/lib/Bio/SeqIO/gbxml.pm +cp lib/Bio/SeqIO/raw.pm blib/lib/Bio/SeqIO/raw.pm +cp lib/Bio/SeqIO/game/featHandler.pm blib/lib/Bio/SeqIO/game/featHandler.pm cp lib/Bio/SeqIO/game/gameWriter.pm blib/lib/Bio/SeqIO/game/gameWriter.pm -cp lib/Bio/SeqIO/game/gameHandler.pm blib/lib/Bio/SeqIO/game/gameHandler.pm -cp lib/Bio/SeqIO/tigr.pm blib/lib/Bio/SeqIO/tigr.pm -cp lib/Bio/SeqIO/kegg.pm blib/lib/Bio/SeqIO/kegg.pm -cp lib/Bio/SeqIO/locuslink.pm blib/lib/Bio/SeqIO/locuslink.pm +cp lib/Bio/SeqIO/qual.pm blib/lib/Bio/SeqIO/qual.pm cp lib/Bio/Species.pm blib/lib/Bio/Species.pm -cp lib/Bio/Tools/Alignment/Trim.pm blib/lib/Bio/Tools/Alignment/Trim.pm -cp lib/Bio/SimpleAnalysisI.pm blib/lib/Bio/SimpleAnalysisI.pm +cp lib/Bio/SeqIO/tigr.pm blib/lib/Bio/SeqIO/tigr.pm +cp lib/Bio/SeqIO/swiss.pm blib/lib/Bio/SeqIO/swiss.pm +cp lib/Bio/SeqIO/game/seqHandler.pm blib/lib/Bio/SeqIO/game/seqHandler.pm cp lib/Bio/SeqIO/phd.pm blib/lib/Bio/SeqIO/phd.pm cp lib/Bio/Tools/AmpliconSearch.pm blib/lib/Bio/Tools/AmpliconSearch.pm -cp lib/Bio/SeqIO/metafasta.pm blib/lib/Bio/SeqIO/metafasta.pm -cp lib/Bio/SeqIO/qual.pm blib/lib/Bio/SeqIO/qual.pm -cp lib/Bio/SeqIO/raw.pm blib/lib/Bio/SeqIO/raw.pm +cp lib/Bio/SeqIO/tab.pm blib/lib/Bio/SeqIO/tab.pm cp lib/Bio/SeqIO/seqxml.pm blib/lib/Bio/SeqIO/seqxml.pm -cp lib/Bio/SeqIO/genbank.pm blib/lib/Bio/SeqIO/genbank.pm +cp lib/Bio/SeqUtils.pm blib/lib/Bio/SeqUtils.pm +cp lib/Bio/SeqIO/game/gameSubs.pm blib/lib/Bio/SeqIO/game/gameSubs.pm cp lib/Bio/Tools/Alignment/Consed.pm blib/lib/Bio/Tools/Alignment/Consed.pm -cp lib/Bio/SeqIO/scf.pm blib/lib/Bio/SeqIO/scf.pm -cp lib/Bio/Taxon.pm blib/lib/Bio/Taxon.pm -cp lib/Bio/SeqIO/tinyseq.pm blib/lib/Bio/SeqIO/tinyseq.pm +cp lib/Bio/SeqIO/genbank.pm blib/lib/Bio/SeqIO/genbank.pm +cp lib/Bio/Tools/Alignment/Trim.pm blib/lib/Bio/Tools/Alignment/Trim.pm +cp lib/Bio/SimpleAnalysisI.pm blib/lib/Bio/SimpleAnalysisI.pm +cp lib/Bio/Tools/Blat.pm blib/lib/Bio/Tools/Blat.pm +cp lib/Bio/SeqIO/game/gameHandler.pm blib/lib/Bio/SeqIO/game/gameHandler.pm +cp lib/Bio/SeqIO/gbdriver.pm blib/lib/Bio/SeqIO/gbdriver.pm cp lib/Bio/SeqIO/game.pm blib/lib/Bio/SeqIO/game.pm +cp lib/Bio/Tools/Analysis/SimpleAnalysisBase.pm blib/lib/Bio/Tools/Analysis/SimpleAnalysisBase.pm +cp lib/Bio/Tools/AnalysisResult.pm blib/lib/Bio/Tools/AnalysisResult.pm +cp lib/Bio/SeqIO/locuslink.pm blib/lib/Bio/SeqIO/locuslink.pm +cp lib/Bio/SeqIO/table.pm blib/lib/Bio/SeqIO/table.pm +cp lib/Bio/SeqIO/msout.pm blib/lib/Bio/SeqIO/msout.pm +cp lib/Bio/SeqIO/tinyseq.pm blib/lib/Bio/SeqIO/tinyseq.pm cp lib/Bio/SeqIO/mbsout.pm blib/lib/Bio/SeqIO/mbsout.pm -cp lib/Bio/SeqIO/game/gameSubs.pm blib/lib/Bio/SeqIO/game/gameSubs.pm -cp lib/Bio/Tools/Phylo/Phylip/ProtDist.pm blib/lib/Bio/Tools/Phylo/Phylip/ProtDist.pm -cp lib/Bio/Tools/Phylo/Molphy.pm blib/lib/Bio/Tools/Phylo/Molphy.pm +cp lib/Bio/SeqIO/tinyseq/tinyseqHandler.pm blib/lib/Bio/SeqIO/tinyseq/tinyseqHandler.pm +cp lib/Bio/SeqIO/gcg.pm blib/lib/Bio/SeqIO/gcg.pm +cp lib/Bio/SeqIO/scf.pm blib/lib/Bio/SeqIO/scf.pm +cp lib/Bio/SeqIO/kegg.pm blib/lib/Bio/SeqIO/kegg.pm +cp lib/Bio/Taxon.pm blib/lib/Bio/Taxon.pm +cp lib/Bio/SeqIO/swissdriver.pm blib/lib/Bio/SeqIO/swissdriver.pm +cp lib/Bio/SimpleAlign.pm blib/lib/Bio/SimpleAlign.pm +cp lib/Bio/SeqIO/pir.pm blib/lib/Bio/SeqIO/pir.pm +cp lib/Bio/SeqIO/metafasta.pm blib/lib/Bio/SeqIO/metafasta.pm +cp lib/Bio/Tools/Genscan.pm blib/lib/Bio/Tools/Genscan.pm cp lib/Bio/Tools/EPCR.pm blib/lib/Bio/Tools/EPCR.pm +cp lib/Bio/Tools/Primer3.pm blib/lib/Bio/Tools/Primer3.pm +cp lib/Bio/Tools/Profile.pm blib/lib/Bio/Tools/Profile.pm +cp lib/Bio/Tools/GFF.pm blib/lib/Bio/Tools/GFF.pm +cp lib/Bio/Tools/Primer/Pair.pm blib/lib/Bio/Tools/Primer/Pair.pm cp lib/Bio/Tools/ECnumber.pm blib/lib/Bio/Tools/ECnumber.pm -cp lib/Bio/Tools/PrositeScan.pm blib/lib/Bio/Tools/PrositeScan.pm -cp lib/Bio/Tools/FootPrinter.pm blib/lib/Bio/Tools/FootPrinter.pm -cp lib/Bio/Tools/GuessSeqFormat.pm blib/lib/Bio/Tools/GuessSeqFormat.pm -cp lib/Bio/Tools/Fgenesh.pm blib/lib/Bio/Tools/Fgenesh.pm -cp lib/Bio/Tools/Prints.pm blib/lib/Bio/Tools/Prints.pm -cp lib/Bio/Tools/Phylo/Molphy/Result.pm blib/lib/Bio/Tools/Phylo/Molphy/Result.pm +cp lib/Bio/Tools/EMBOSS/Palindrome.pm blib/lib/Bio/Tools/EMBOSS/Palindrome.pm cp lib/Bio/Tools/Phylo/Gerp.pm blib/lib/Bio/Tools/Phylo/Gerp.pm -cp lib/Bio/Tools/Primer/Pair.pm blib/lib/Bio/Tools/Primer/Pair.pm -cp lib/Bio/Tools/Glimmer.pm blib/lib/Bio/Tools/Glimmer.pm -cp lib/Bio/Tools/Pseudowise.pm blib/lib/Bio/Tools/Pseudowise.pm -cp lib/Bio/Tools/Genemark.pm blib/lib/Bio/Tools/Genemark.pm -cp lib/Bio/Tools/Eponine.pm blib/lib/Bio/Tools/Eponine.pm -cp lib/Bio/Tools/Primer3.pm blib/lib/Bio/Tools/Primer3.pm -cp lib/Bio/Tools/CodonTable.pm blib/lib/Bio/Tools/CodonTable.pm -cp lib/Bio/Tools/Coil.pm blib/lib/Bio/Tools/Coil.pm cp lib/Bio/Tools/Primer/Feature.pm blib/lib/Bio/Tools/Primer/Feature.pm -cp lib/Bio/Tools/Profile.pm blib/lib/Bio/Tools/Profile.pm -cp lib/Bio/Tools/Primer/Assessor/Base.pm blib/lib/Bio/Tools/Primer/Assessor/Base.pm -cp lib/Bio/Tools/Est2Genome.pm blib/lib/Bio/Tools/Est2Genome.pm -cp lib/Bio/Tools/Primer/AssessorI.pm blib/lib/Bio/Tools/Primer/AssessorI.pm -cp lib/Bio/Tools/Match.pm blib/lib/Bio/Tools/Match.pm +cp lib/Bio/Tools/Phylo/Phylip/ProtDist.pm blib/lib/Bio/Tools/Phylo/Phylip/ProtDist.pm +cp lib/Bio/Tools/ESTScan.pm blib/lib/Bio/Tools/ESTScan.pm +cp lib/Bio/Tools/Promoterwise.pm blib/lib/Bio/Tools/Promoterwise.pm +cp lib/Bio/Tools/Glimmer.pm blib/lib/Bio/Tools/Glimmer.pm cp lib/Bio/Tools/OddCodes.pm blib/lib/Bio/Tools/OddCodes.pm -cp lib/Bio/Tools/Genscan.pm blib/lib/Bio/Tools/Genscan.pm +cp lib/Bio/Tools/Primer/Assessor/Base.pm blib/lib/Bio/Tools/Primer/Assessor/Base.pm +cp lib/Bio/Tools/Geneid.pm blib/lib/Bio/Tools/Geneid.pm +cp lib/Bio/Tools/Genewise.pm blib/lib/Bio/Tools/Genewise.pm +cp lib/Bio/Tools/IUPAC.pm blib/lib/Bio/Tools/IUPAC.pm +cp lib/Bio/Tools/CodonTable.pm blib/lib/Bio/Tools/CodonTable.pm +cp lib/Bio/Tools/Eponine.pm blib/lib/Bio/Tools/Eponine.pm cp lib/Bio/Tools/Lucy.pm blib/lib/Bio/Tools/Lucy.pm +cp lib/Bio/Tools/Phylo/Molphy.pm blib/lib/Bio/Tools/Phylo/Molphy.pm +cp lib/Bio/Tools/MZEF.pm blib/lib/Bio/Tools/MZEF.pm +cp lib/Bio/Tools/Coil.pm blib/lib/Bio/Tools/Coil.pm +cp lib/Bio/Tools/Pseudowise.pm blib/lib/Bio/Tools/Pseudowise.pm cp lib/Bio/Tools/Genomewise.pm blib/lib/Bio/Tools/Genomewise.pm -cp lib/Bio/Tools/IUPAC.pm blib/lib/Bio/Tools/IUPAC.pm +cp lib/Bio/Tools/Fgenesh.pm blib/lib/Bio/Tools/Fgenesh.pm +cp lib/Bio/Tools/GuessSeqFormat.pm blib/lib/Bio/Tools/GuessSeqFormat.pm +cp lib/Bio/Tools/Grail.pm blib/lib/Bio/Tools/Grail.pm +cp lib/Bio/Tools/Est2Genome.pm blib/lib/Bio/Tools/Est2Genome.pm cp lib/Bio/Tools/Prediction/Gene.pm blib/lib/Bio/Tools/Prediction/Gene.pm -cp lib/Bio/Tools/MZEF.pm blib/lib/Bio/Tools/MZEF.pm -cp lib/Bio/Tools/ESTScan.pm blib/lib/Bio/Tools/ESTScan.pm -cp lib/Bio/Tools/GFF.pm blib/lib/Bio/Tools/GFF.pm -cp lib/Bio/Tools/Promoterwise.pm blib/lib/Bio/Tools/Promoterwise.pm +cp lib/Bio/Tools/Genemark.pm blib/lib/Bio/Tools/Genemark.pm +cp lib/Bio/Tools/PrositeScan.pm blib/lib/Bio/Tools/PrositeScan.pm +cp lib/Bio/Tools/Primer/AssessorI.pm blib/lib/Bio/Tools/Primer/AssessorI.pm +cp lib/Bio/Tools/Prints.pm blib/lib/Bio/Tools/Prints.pm cp lib/Bio/Tools/Prediction/Exon.pm blib/lib/Bio/Tools/Prediction/Exon.pm -cp lib/Bio/Tools/Grail.pm blib/lib/Bio/Tools/Grail.pm -cp lib/Bio/Tools/EMBOSS/Palindrome.pm blib/lib/Bio/Tools/EMBOSS/Palindrome.pm -cp lib/Bio/Tools/Geneid.pm blib/lib/Bio/Tools/Geneid.pm -cp lib/Bio/Tools/Genewise.pm blib/lib/Bio/Tools/Genewise.pm -cp lib/Bio/Tree/DistanceFactory.pm blib/lib/Bio/Tree/DistanceFactory.pm -cp lib/Bio/Tools/SeqStats.pm blib/lib/Bio/Tools/SeqStats.pm +cp lib/Bio/Tools/Match.pm blib/lib/Bio/Tools/Match.pm +cp lib/Bio/Tools/Phylo/Molphy/Result.pm blib/lib/Bio/Tools/Phylo/Molphy/Result.pm +cp lib/Bio/Tools/FootPrinter.pm blib/lib/Bio/Tools/FootPrinter.pm +cp lib/Bio/Tools/Run/GenericParameters.pm blib/lib/Bio/Tools/Run/GenericParameters.pm +cp lib/Bio/Tools/SeqPattern.pm blib/lib/Bio/Tools/SeqPattern.pm +cp lib/Bio/Tools/Spidey/Exon.pm blib/lib/Bio/Tools/Spidey/Exon.pm +cp lib/Bio/Tree/RandomFactory.pm blib/lib/Bio/Tree/RandomFactory.pm +cp lib/Bio/Tools/Sim4/Exon.pm blib/lib/Bio/Tools/Sim4/Exon.pm +cp lib/Bio/Tree/NodeI.pm blib/lib/Bio/Tree/NodeI.pm +cp lib/Bio/Tools/Run/Phylo/PhyloBase.pm blib/lib/Bio/Tools/Run/Phylo/PhyloBase.pm +cp lib/Bio/Tree/Tree.pm blib/lib/Bio/Tree/Tree.pm cp lib/Bio/Tools/Run/WrapperBase.pm blib/lib/Bio/Tools/Run/WrapperBase.pm -cp lib/Bio/Tools/Run/AnalysisFactory.pm blib/lib/Bio/Tools/Run/AnalysisFactory.pm -cp lib/Bio/Tools/isPcr.pm blib/lib/Bio/Tools/isPcr.pm -cp lib/Bio/Tools/RepeatMasker.pm blib/lib/Bio/Tools/RepeatMasker.pm -cp lib/Bio/Tree/NodeNHX.pm blib/lib/Bio/Tree/NodeNHX.pm cp lib/Bio/Tools/ipcress.pm blib/lib/Bio/Tools/ipcress.pm cp lib/Bio/Tools/Run/ParametersI.pm blib/lib/Bio/Tools/Run/ParametersI.pm -cp lib/Bio/Tools/Run/Phylo/PhyloBase.pm blib/lib/Bio/Tools/Run/Phylo/PhyloBase.pm -cp lib/Bio/Tools/SeqPattern.pm blib/lib/Bio/Tools/SeqPattern.pm -cp lib/Bio/Tree/RandomFactory.pm blib/lib/Bio/Tree/RandomFactory.pm -cp lib/Bio/Tools/QRNA.pm blib/lib/Bio/Tools/QRNA.pm -cp lib/Bio/Tools/SeqPattern/Backtranslate.pm blib/lib/Bio/Tools/SeqPattern/Backtranslate.pm -cp lib/Bio/Tools/Seg.pm blib/lib/Bio/Tools/Seg.pm cp lib/Bio/Tools/RandomDistFunctions.pm blib/lib/Bio/Tools/RandomDistFunctions.pm -cp lib/Bio/Tools/TandemRepeatsFinder.pm blib/lib/Bio/Tools/TandemRepeatsFinder.pm -cp lib/Bio/Tools/Signalp/ExtendedSignalp.pm blib/lib/Bio/Tools/Signalp/ExtendedSignalp.pm -cp lib/Bio/Tools/Spidey/Results.pm blib/lib/Bio/Tools/Spidey/Results.pm +cp lib/Bio/Tools/SeqStats.pm blib/lib/Bio/Tools/SeqStats.pm +cp lib/Bio/Tools/Run/AnalysisFactory.pm blib/lib/Bio/Tools/Run/AnalysisFactory.pm +cp lib/Bio/Tools/Sim4/Results.pm blib/lib/Bio/Tools/Sim4/Results.pm +cp lib/Bio/Tools/Signalp.pm blib/lib/Bio/Tools/Signalp.pm +cp lib/Bio/Tools/Seg.pm blib/lib/Bio/Tools/Seg.pm +cp lib/Bio/Tools/QRNA.pm blib/lib/Bio/Tools/QRNA.pm cp lib/Bio/Tools/TargetP.pm blib/lib/Bio/Tools/TargetP.pm -cp lib/Bio/Tools/SeqWords.pm blib/lib/Bio/Tools/SeqWords.pm -cp lib/Bio/Tools/Run/Analysis.pm blib/lib/Bio/Tools/Run/Analysis.pm +cp lib/Bio/Tools/Tmhmm.pm blib/lib/Bio/Tools/Tmhmm.pm cp lib/Bio/Tree/Node.pm blib/lib/Bio/Tree/Node.pm -cp lib/Bio/Tools/pICalculator.pm blib/lib/Bio/Tools/pICalculator.pm -cp lib/Bio/Tools/Signalp.pm blib/lib/Bio/Tools/Signalp.pm -cp lib/Bio/Tools/Sim4/Results.pm blib/lib/Bio/Tools/Sim4/Results.pm -cp lib/Bio/Tools/Sim4/Exon.pm blib/lib/Bio/Tools/Sim4/Exon.pm cp lib/Bio/Tools/Sigcleave.pm blib/lib/Bio/Tools/Sigcleave.pm -cp lib/Bio/Tools/Tmhmm.pm blib/lib/Bio/Tools/Tmhmm.pm -cp lib/Bio/Tools/tRNAscanSE.pm blib/lib/Bio/Tools/tRNAscanSE.pm -cp lib/Bio/Tools/Run/WrapperBase/CommandExts.pm blib/lib/Bio/Tools/Run/WrapperBase/CommandExts.pm +cp lib/Bio/Tree/NodeNHX.pm blib/lib/Bio/Tree/NodeNHX.pm cp lib/Bio/Tree/AnnotatableNode.pm blib/lib/Bio/Tree/AnnotatableNode.pm -cp lib/Bio/Tools/Run/GenericParameters.pm blib/lib/Bio/Tools/Run/GenericParameters.pm -cp lib/Bio/Tree/Tree.pm blib/lib/Bio/Tree/Tree.pm -cp lib/Bio/Tools/Spidey/Exon.pm blib/lib/Bio/Tools/Spidey/Exon.pm +cp lib/Bio/Tools/Spidey/Results.pm blib/lib/Bio/Tools/Spidey/Results.pm +cp lib/Bio/Tools/Signalp/ExtendedSignalp.pm blib/lib/Bio/Tools/Signalp/ExtendedSignalp.pm cp lib/Bio/Tree/Compatible.pm blib/lib/Bio/Tree/Compatible.pm +cp lib/Bio/Tree/DistanceFactory.pm blib/lib/Bio/Tree/DistanceFactory.pm +cp lib/Bio/Tools/SeqPattern/Backtranslate.pm blib/lib/Bio/Tools/SeqPattern/Backtranslate.pm +cp lib/Bio/Tools/pICalculator.pm blib/lib/Bio/Tools/pICalculator.pm +cp lib/Bio/Tools/TandemRepeatsFinder.pm blib/lib/Bio/Tools/TandemRepeatsFinder.pm +cp lib/Bio/Tools/RepeatMasker.pm blib/lib/Bio/Tools/RepeatMasker.pm +cp lib/Bio/Tools/SeqWords.pm blib/lib/Bio/Tools/SeqWords.pm +cp lib/Bio/Tools/isPcr.pm blib/lib/Bio/Tools/isPcr.pm +cp lib/Bio/Tools/tRNAscanSE.pm blib/lib/Bio/Tools/tRNAscanSE.pm +cp lib/Bio/Tools/Run/WrapperBase/CommandExts.pm blib/lib/Bio/Tools/Run/WrapperBase/CommandExts.pm +cp lib/Bio/Tools/Run/Analysis.pm blib/lib/Bio/Tools/Run/Analysis.pm cp lib/Bio/Tree/Statistics.pm blib/lib/Bio/Tree/Statistics.pm -cp lib/Bio/Tree/NodeI.pm blib/lib/Bio/Tree/NodeI.pm -cp lib/Bio/TreeIO/nhx.pm blib/lib/Bio/TreeIO/nhx.pm cp lib/Bio/TreeIO.pm blib/lib/Bio/TreeIO.pm -cp lib/Bio/UpdateableSeqI.pm blib/lib/Bio/UpdateableSeqI.pm cp lib/Bio/TreeIO/nexus.pm blib/lib/Bio/TreeIO/nexus.pm +cp lib/Bio/TreeIO/tabtree.pm blib/lib/Bio/TreeIO/tabtree.pm +cp lib/Bio/WebAgent.pm blib/lib/Bio/WebAgent.pm +cp lib/Bio/TreeIO/cluster.pm blib/lib/Bio/TreeIO/cluster.pm cp lib/BioPerl.pm blib/lib/BioPerl.pm +cp lib/Bio/TreeIO/nhx.pm blib/lib/Bio/TreeIO/nhx.pm cp lib/Bio/Tree/TreeI.pm blib/lib/Bio/Tree/TreeI.pm -cp lib/Bio/TreeIO/TreeEventBuilder.pm blib/lib/Bio/TreeIO/TreeEventBuilder.pm cp lib/Bio/TreeIO/phyloxml.pm blib/lib/Bio/TreeIO/phyloxml.pm +cp lib/Bio/TreeIO/pag.pm blib/lib/Bio/TreeIO/pag.pm cp lib/Bio/Tree/TreeFunctionsI.pm blib/lib/Bio/Tree/TreeFunctionsI.pm -cp lib/Bio/WebAgent.pm blib/lib/Bio/WebAgent.pm -cp lib/Bio/TreeIO/cluster.pm blib/lib/Bio/TreeIO/cluster.pm +cp lib/Bio/TreeIO/NewickParser.pm blib/lib/Bio/TreeIO/NewickParser.pm cp lib/Bio/TreeIO/lintree.pm blib/lib/Bio/TreeIO/lintree.pm -cp lib/Bio/TreeIO/pag.pm blib/lib/Bio/TreeIO/pag.pm +cp lib/Bio/TreeIO/TreeEventBuilder.pm blib/lib/Bio/TreeIO/TreeEventBuilder.pm +cp lib/Bio/UpdateableSeqI.pm blib/lib/Bio/UpdateableSeqI.pm cp lib/Bio/TreeIO/newick.pm blib/lib/Bio/TreeIO/newick.pm -cp lib/Bio/TreeIO/NewickParser.pm blib/lib/Bio/TreeIO/NewickParser.pm -cp lib/Bio/TreeIO/tabtree.pm blib/lib/Bio/TreeIO/tabtree.pm cp bin/bp_aacomp blib/script/bp_aacomp -"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_aacomp cp bin/bp_bioflat_index blib/script/bp_bioflat_index cp bin/bp_biogetseq blib/script/bp_biogetseq +cp bin/bp_dbsplit blib/script/bp_dbsplit +"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_aacomp "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_bioflat_index +cp bin/bp_extract_feature_seq blib/script/bp_extract_feature_seq "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_biogetseq -cp bin/bp_dbsplit blib/script/bp_dbsplit +cp bin/bp_fastam9_to_table blib/script/bp_fastam9_to_table "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_dbsplit -cp bin/bp_extract_feature_seq blib/script/bp_extract_feature_seq +"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_fastam9_to_table "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_extract_feature_seq -cp bin/bp_fastam9_to_table blib/script/bp_fastam9_to_table cp bin/bp_fetch blib/script/bp_fetch -"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_fastam9_to_table cp bin/bp_filter_search blib/script/bp_filter_search -"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_fetch -"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_filter_search cp bin/bp_find-blast-matches blib/script/bp_find-blast-matches -cp bin/bp_gccalc blib/script/bp_gccalc +"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_filter_search "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_find-blast-matches +cp bin/bp_gccalc blib/script/bp_gccalc +"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_fetch "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_gccalc cp bin/bp_genbank2gff3 blib/script/bp_genbank2gff3 +"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_genbank2gff3 cp bin/bp_index blib/script/bp_index "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_index -"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_genbank2gff3 cp bin/bp_local_taxonomydb_query blib/script/bp_local_taxonomydb_query "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_local_taxonomydb_query cp bin/bp_make_mrna_protein blib/script/bp_make_mrna_protein "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_make_mrna_protein cp bin/bp_mask_by_search blib/script/bp_mask_by_search -"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_mask_by_search cp bin/bp_mrtrans blib/script/bp_mrtrans +"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_mask_by_search "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_mrtrans cp bin/bp_mutate blib/script/bp_mutate -"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_mutate cp bin/bp_nexus2nh blib/script/bp_nexus2nh -cp bin/bp_nrdb blib/script/bp_nrdb "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_nexus2nh +cp bin/bp_nrdb blib/script/bp_nrdb +"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_mutate "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_nrdb cp bin/bp_oligo_count blib/script/bp_oligo_count "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_oligo_count @@ -2068,11 +2104,11 @@ "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_process_sgd cp bin/bp_revtrans-motif blib/script/bp_revtrans-motif cp bin/bp_search2alnblocks blib/script/bp_search2alnblocks -"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_search2alnblocks "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_revtrans-motif +"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_search2alnblocks cp bin/bp_search2gff blib/script/bp_search2gff -"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_search2gff cp bin/bp_search2table blib/script/bp_search2table +"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_search2gff "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_search2table cp bin/bp_search2tribe blib/script/bp_search2tribe "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_search2tribe @@ -2081,8 +2117,8 @@ cp bin/bp_seqconvert blib/script/bp_seqconvert "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seqconvert cp bin/bp_seqcut blib/script/bp_seqcut -cp bin/bp_seqpart blib/script/bp_seqpart "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seqcut +cp bin/bp_seqpart blib/script/bp_seqpart "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seqpart cp bin/bp_seqret blib/script/bp_seqret "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seqret @@ -2092,11 +2128,11 @@ cp bin/bp_sreformat blib/script/bp_sreformat "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_split_seq "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_sreformat -cp bin/bp_taxid4species blib/script/bp_taxid4species -"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_taxid4species cp bin/bp_taxonomy2tree blib/script/bp_taxonomy2tree -"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_taxonomy2tree +cp bin/bp_taxid4species blib/script/bp_taxid4species cp bin/bp_translate_seq blib/script/bp_translate_seq +"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_taxonomy2tree +"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_taxid4species "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_translate_seq cp bin/bp_tree2pag blib/script/bp_tree2pag "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_tree2pag @@ -2119,15588 +2155,7 @@ Manifying 33 pod documents Manifying 15 pod documents make[1]: Leaving directory '/build/reproducible-path/bioperl-1.7.8' - dh_auto_test - make -j12 test TEST_VERBOSE=1 -make[1]: Entering directory '/build/reproducible-path/bioperl-1.7.8' -PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, 'blib/lib', 'blib/arch')" t/*.t t/Align/*.t t/AlignIO/*.t t/Annotation/*.t t/LocalDB/*.t t/LocalDB/Index/*.t t/LocalDB/Taxonomy/*.t t/Matrix/*.t t/Matrix/IO/*.t t/Ontology/*.t t/Ontology/IO/*.t t/RemoteDB/*.t t/Root/*.t t/SearchIO/*.t t/SearchIO/Writer/*.t t/Seq/*.t t/SeqFeature/*.t t/SeqIO/*.t t/SeqTools/*.t t/Tools/*.t t/Tools/Alignment/*.t t/Tools/EMBOSS/*.t t/Tools/Phylo/*.t t/Tools/Phylo/Phylip/*.t t/Tools/Signalp/*.t t/Tools/Spidey/*.t t/Tree/*.t t/Tree/TreeIO/*.t -t/00-compile.t ...................... -1..511 -ok 1 - Bio/Align/AlignI.pm loaded ok -ok 2 - Bio/Align/DNAStatistics.pm loaded ok -ok 3 - Bio/Align/PairwiseStatistics.pm loaded ok -ok 4 - Bio/Align/ProteinStatistics.pm loaded ok -ok 5 - Bio/Align/StatisticsI.pm loaded ok -ok 6 - Bio/Align/Utilities.pm loaded ok -ok 7 - Bio/AlignIO.pm loaded ok -ok 8 - Bio/AlignIO/Handler/GenericAlignHandler.pm loaded ok -ok 9 - Bio/AlignIO/arp.pm loaded ok -ok 10 - Bio/AlignIO/bl2seq.pm loaded ok -ok 11 - Bio/AlignIO/clustalw.pm loaded ok -ok 12 - Bio/AlignIO/emboss.pm loaded ok -ok 13 - Bio/AlignIO/fasta.pm loaded ok -ok 14 - Bio/AlignIO/largemultifasta.pm loaded ok -ok 15 - Bio/AlignIO/maf.pm loaded ok -ok 16 - Bio/AlignIO/mase.pm loaded ok -ok 17 - Bio/AlignIO/mega.pm loaded ok -ok 18 - Bio/AlignIO/meme.pm loaded ok -ok 19 - Bio/AlignIO/metafasta.pm loaded ok -ok 20 - Bio/AlignIO/msf.pm loaded ok -ok 21 - Bio/AlignIO/nexus.pm loaded ok -ok 22 - Bio/AlignIO/pfam.pm loaded ok -ok 23 - Bio/AlignIO/phylip.pm loaded ok -ok 24 - Bio/AlignIO/po.pm loaded ok -ok 25 - Bio/AlignIO/proda.pm loaded ok -ok 26 - Bio/AlignIO/prodom.pm loaded ok -ok 27 - Bio/AlignIO/psi.pm loaded ok -ok 28 - Bio/AlignIO/selex.pm loaded ok -ok 29 - Bio/AlignIO/xmfa.pm loaded ok -ok 30 - Bio/AnalysisI.pm loaded ok -ok 31 - Bio/AnalysisParserI.pm loaded ok -ok 32 - Bio/AnalysisResultI.pm loaded ok -ok 33 - Bio/AnnotatableI.pm loaded ok -ok 34 - Bio/Annotation/AnnotationFactory.pm loaded ok -ok 35 - Bio/Annotation/Collection.pm loaded ok -ok 36 - Bio/Annotation/Comment.pm loaded ok -ok 37 - Bio/Annotation/DBLink.pm loaded ok -ok 38 - Bio/Annotation/OntologyTerm.pm loaded ok -ok 39 - Bio/Annotation/Reference.pm loaded ok -ok 40 - Bio/Annotation/Relation.pm loaded ok -ok 41 - Bio/Annotation/SimpleValue.pm loaded ok -ok 42 - Bio/Annotation/StructuredValue.pm loaded ok -ok 43 - Bio/Annotation/TagTree.pm loaded ok -ok 44 - Bio/Annotation/Target.pm loaded ok -ok 45 - Bio/Annotation/Tree.pm loaded ok -ok 46 - Bio/Annotation/TypeManager.pm loaded ok -ok 47 - Bio/AnnotationCollectionI.pm loaded ok -ok 48 - Bio/AnnotationI.pm loaded ok -ok 49 - Bio/CodonUsage/IO.pm loaded ok -ok 50 - Bio/CodonUsage/Table.pm loaded ok -ok 51 - Bio/DB/DBFetch.pm loaded ok -ok 52 - Bio/DB/Failover.pm loaded ok -ok 53 - Bio/DB/Fasta.pm loaded ok -ok 54 - Bio/DB/FileCache.pm loaded ok -ok 55 - Bio/DB/Flat.pm loaded ok -ok 56 - Bio/DB/Flat/BDB.pm loaded ok -ok 57 - Bio/DB/Flat/BDB/embl.pm loaded ok -ok 58 - Bio/DB/Flat/BDB/fasta.pm loaded ok -ok 59 - Bio/DB/Flat/BDB/genbank.pm loaded ok -ok 60 - Bio/DB/Flat/BDB/swiss.pm loaded ok -ok 61 - Bio/DB/Flat/BinarySearch.pm loaded ok -ok 62 - Bio/DB/GFF/Util/Binning.pm loaded ok -ok 63 - Bio/DB/GFF/Util/Rearrange.pm loaded ok -ok 64 - Bio/DB/GenericWebAgent.pm loaded ok -ok 65 - Bio/DB/InMemoryCache.pm loaded ok -ok 66 - Bio/DB/IndexedBase.pm loaded ok -ok 67 - Bio/DB/LocationI.pm loaded ok -ok 68 - Bio/DB/Qual.pm loaded ok -ok 69 - Bio/DB/Query/WebQuery.pm loaded ok -ok 70 - Bio/DB/QueryI.pm loaded ok -ok 71 - Bio/DB/RandomAccessI.pm loaded ok -ok 72 - Bio/DB/ReferenceI.pm loaded ok -ok 73 - Bio/DB/Registry.pm loaded ok -ok 74 - Bio/DB/SeqI.pm loaded ok -ok 75 - Bio/DB/Taxonomy.pm loaded ok -ok 76 - Bio/DB/Taxonomy/flatfile.pm loaded ok -ok 77 - Bio/DB/Taxonomy/greengenes.pm loaded ok -ok 78 - Bio/DB/Taxonomy/list.pm loaded ok -ok 79 - Bio/DB/Taxonomy/silva.pm loaded ok -ok 80 - Bio/DB/UpdateableSeqI.pm loaded ok -ok 81 - Bio/DB/WebDBSeqI.pm loaded ok -ok 82 - Bio/DBLinkContainerI.pm loaded ok -ok 83 - Bio/Das/FeatureTypeI.pm loaded ok -ok 84 - Bio/Das/SegmentI.pm loaded ok -ok 85 - Bio/DasI.pm loaded ok -ok 86 - Bio/DescribableI.pm loaded ok -ok 87 - Bio/Event/EventGeneratorI.pm loaded ok -ok 88 - Bio/Event/EventHandlerI.pm loaded ok -ok 89 - Bio/Factory/AnalysisI.pm loaded ok -ok 90 - Bio/Factory/ApplicationFactoryI.pm loaded ok -ok 91 - Bio/Factory/DriverFactory.pm loaded ok -ok 92 - Bio/Factory/FTLocationFactory.pm loaded ok -ok 93 - Bio/Factory/LocationFactoryI.pm loaded ok -ok 94 - Bio/Factory/ObjectBuilderI.pm loaded ok -ok 95 - Bio/Factory/ObjectFactory.pm loaded ok -ok 96 - Bio/Factory/ObjectFactoryI.pm loaded ok -ok 97 - Bio/Factory/SeqAnalysisParserFactory.pm loaded ok -ok 98 - Bio/Factory/SeqAnalysisParserFactoryI.pm loaded ok -ok 99 - Bio/Factory/SequenceFactoryI.pm loaded ok -ok 100 - Bio/Factory/SequenceProcessorI.pm loaded ok -ok 101 - Bio/Factory/SequenceStreamI.pm loaded ok -ok 102 - Bio/Factory/TreeFactoryI.pm loaded ok -ok 103 - Bio/FeatureHolderI.pm loaded ok -ok 104 - Bio/HandlerBaseI.pm loaded ok -ok 105 - Bio/IdCollectionI.pm loaded ok -ok 106 - Bio/IdentifiableI.pm loaded ok -ok 107 - Bio/Index/Abstract.pm loaded ok -ok 108 - Bio/Index/AbstractSeq.pm loaded ok -ok 109 - Bio/Index/Blast.pm loaded ok -ok 110 - Bio/Index/BlastTable.pm loaded ok -ok 111 - Bio/Index/EMBL.pm loaded ok -ok 112 - Bio/Index/Fasta.pm loaded ok -ok 113 - Bio/Index/Fastq.pm loaded ok -ok 114 - Bio/Index/GenBank.pm loaded ok -ok 115 - Bio/Index/Qual.pm loaded ok -ok 116 - Bio/Index/SwissPfam.pm loaded ok -ok 117 - Bio/Index/Swissprot.pm loaded ok -ok 118 - Bio/LocatableSeq.pm loaded ok -ok 119 - Bio/Location/Atomic.pm loaded ok -ok 120 - Bio/Location/AvWithinCoordPolicy.pm loaded ok -ok 121 - Bio/Location/CoordinatePolicyI.pm loaded ok -ok 122 - Bio/Location/Fuzzy.pm loaded ok -ok 123 - Bio/Location/FuzzyLocationI.pm loaded ok -ok 124 - Bio/Location/NarrowestCoordPolicy.pm loaded ok -ok 125 - Bio/Location/Simple.pm loaded ok -ok 126 - Bio/Location/Split.pm loaded ok -ok 127 - Bio/Location/SplitLocationI.pm loaded ok -ok 128 - Bio/Location/WidestCoordPolicy.pm loaded ok -ok 129 - Bio/LocationI.pm loaded ok -ok 130 - Bio/Matrix/Generic.pm loaded ok -ok 131 - Bio/Matrix/IO.pm loaded ok -ok 132 - Bio/Matrix/IO/mlagan.pm loaded ok -ok 133 - Bio/Matrix/IO/phylip.pm loaded ok -ok 134 - Bio/Matrix/IO/scoring.pm loaded ok -ok 135 - Bio/Matrix/MatrixI.pm loaded ok -ok 136 - Bio/Matrix/Mlagan.pm loaded ok -ok 137 - Bio/Matrix/PSM/IO.pm loaded ok -ok 138 - Bio/Matrix/PSM/IO/mast.pm loaded ok -ok 139 - Bio/Matrix/PSM/IO/masta.pm loaded ok -ok 140 - Bio/Matrix/PSM/IO/meme.pm loaded ok -ok 141 - Bio/Matrix/PSM/IO/psiblast.pm loaded ok -ok 142 - Bio/Matrix/PSM/IO/transfac.pm loaded ok -ok 143 - Bio/Matrix/PSM/InstanceSite.pm loaded ok -ok 144 - Bio/Matrix/PSM/InstanceSiteI.pm loaded ok -ok 145 - Bio/Matrix/PSM/ProtMatrix.pm loaded ok -ok 146 - Bio/Matrix/PSM/ProtPsm.pm loaded ok -ok 147 - Bio/Matrix/PSM/Psm.pm loaded ok -ok 148 - Bio/Matrix/PSM/PsmHeader.pm loaded ok -ok 149 - Bio/Matrix/PSM/PsmHeaderI.pm loaded ok -ok 150 - Bio/Matrix/PSM/PsmI.pm loaded ok -ok 151 - Bio/Matrix/PSM/SiteMatrix.pm loaded ok -ok 152 - Bio/Matrix/PSM/SiteMatrixI.pm loaded ok -ok 153 - Bio/Matrix/PhylipDist.pm loaded ok -ok 154 - Bio/Matrix/Scoring.pm loaded ok -ok 155 - Bio/Ontology/DocumentRegistry.pm loaded ok -ok 156 - Bio/Ontology/GOterm.pm loaded ok -ok 157 - Bio/Ontology/InterProTerm.pm loaded ok -ok 158 - Bio/Ontology/OBOEngine.pm loaded ok -ok 159 - Bio/Ontology/OBOterm.pm loaded ok -ok 160 - Bio/Ontology/Ontology.pm loaded ok -ok 161 - Bio/Ontology/OntologyEngineI.pm loaded ok -ok 162 - Bio/Ontology/OntologyI.pm loaded ok -ok 163 - Bio/Ontology/OntologyStore.pm loaded ok -ok 164 - Bio/Ontology/Path.pm loaded ok -ok 165 - Bio/Ontology/PathI.pm loaded ok -ok 166 - Bio/Ontology/Relationship.pm loaded ok -ok 167 - Bio/Ontology/RelationshipFactory.pm loaded ok -ok 168 - Bio/Ontology/RelationshipI.pm loaded ok -ok 169 - Bio/Ontology/RelationshipType.pm loaded ok -ok 170 - Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm loaded ok -ok 171 - Bio/Ontology/SimpleOntologyEngine.pm loaded ok -ok 172 - Bio/Ontology/Term.pm loaded ok -ok 173 - Bio/Ontology/TermFactory.pm loaded ok -ok 174 - Bio/Ontology/TermI.pm loaded ok -ok 175 - Bio/OntologyIO.pm loaded ok -ok 176 - Bio/OntologyIO/Handlers/BaseSAXHandler.pm loaded ok -ok 177 - Bio/OntologyIO/Handlers/InterProHandler.pm loaded ok -ok 178 - Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm loaded ok -ok 179 - Bio/OntologyIO/InterProParser.pm loaded ok -ok 180 - Bio/OntologyIO/dagflat.pm loaded ok -ok 181 - Bio/OntologyIO/goflat.pm loaded ok -ok 182 - Bio/OntologyIO/obo.pm loaded ok -ok 183 - Bio/OntologyIO/simplehierarchy.pm loaded ok -ok 184 - Bio/OntologyIO/soflat.pm loaded ok -ok 185 - Bio/ParameterBaseI.pm loaded ok -ok 186 - Bio/PrimarySeq.pm loaded ok -ok 187 - Bio/PrimarySeqI.pm loaded ok -ok 188 - Bio/PullParserI.pm loaded ok -ok 189 - Bio/Range.pm loaded ok -ok 190 - Bio/RangeI.pm loaded ok -ok 191 - Bio/Root/Exception.pm loaded ok -ok 192 - Bio/Root/HTTPget.pm loaded ok -ok 193 - Bio/Root/IO.pm loaded ok -ok 194 - Bio/Root/Root.pm loaded ok -ok 195 - Bio/Root/RootI.pm loaded ok -ok 196 - Bio/Root/Storable.pm loaded ok -ok 197 - Bio/Root/Test.pm loaded ok -ok 198 - Bio/Root/TestObject.pm loaded ok -ok 199 - Bio/Root/Utilities.pm loaded ok -ok 200 - Bio/Root/Version.pm loaded ok -ok 201 - Bio/Search/BlastStatistics.pm loaded ok -ok 202 - Bio/Search/BlastUtils.pm loaded ok -ok 203 - Bio/Search/DatabaseI.pm loaded ok -ok 204 - Bio/Search/GenericDatabase.pm loaded ok -ok 205 - Bio/Search/GenericStatistics.pm loaded ok -ok 206 - Bio/Search/HSP/BlastHSP.pm loaded ok -ok 207 - Bio/Search/HSP/BlastPullHSP.pm loaded ok -ok 208 - Bio/Search/HSP/FastaHSP.pm loaded ok -ok 209 - Bio/Search/HSP/GenericHSP.pm loaded ok -ok 210 - Bio/Search/HSP/HSPFactory.pm loaded ok -ok 211 - Bio/Search/HSP/HSPI.pm loaded ok -ok 212 - Bio/Search/HSP/ModelHSP.pm loaded ok -ok 213 - Bio/Search/HSP/PSLHSP.pm loaded ok -ok 214 - Bio/Search/HSP/PsiBlastHSP.pm loaded ok -ok 215 - Bio/Search/HSP/PullHSPI.pm loaded ok -ok 216 - Bio/Search/HSP/WABAHSP.pm loaded ok -ok 217 - Bio/Search/Hit/BlastHit.pm loaded ok -ok 218 - Bio/Search/Hit/BlastPullHit.pm loaded ok -ok 219 - Bio/Search/Hit/Fasta.pm loaded ok -ok 220 - Bio/Search/Hit/GenericHit.pm loaded ok -ok 221 - Bio/Search/Hit/HitFactory.pm loaded ok -ok 222 - Bio/Search/Hit/HitI.pm loaded ok -ok 223 - Bio/Search/Hit/ModelHit.pm loaded ok -ok 224 - Bio/Search/Hit/PsiBlastHit.pm loaded ok -ok 225 - Bio/Search/Hit/PullHitI.pm loaded ok -ok 226 - Bio/Search/Iteration/GenericIteration.pm loaded ok -ok 227 - Bio/Search/Iteration/IterationI.pm loaded ok -ok 228 - Bio/Search/Processor.pm loaded ok -ok 229 - Bio/Search/Result/BlastPullResult.pm loaded ok -ok 230 - Bio/Search/Result/BlastResult.pm loaded ok -ok 231 - Bio/Search/Result/CrossMatchResult.pm loaded ok -ok 232 - Bio/Search/Result/GenericResult.pm loaded ok -ok 233 - Bio/Search/Result/INFERNALResult.pm loaded ok -ok 234 - Bio/Search/Result/PullResultI.pm loaded ok -ok 235 - Bio/Search/Result/ResultFactory.pm loaded ok -ok 236 - Bio/Search/Result/ResultI.pm loaded ok -ok 237 - Bio/Search/Result/WABAResult.pm loaded ok -ok 238 - Bio/Search/SearchUtils.pm loaded ok -ok 239 - Bio/Search/StatisticsI.pm loaded ok -ok 240 - Bio/Search/Tiling/MapTileUtils.pm loaded ok -ok 241 - Bio/Search/Tiling/MapTiling.pm loaded ok -ok 242 - Bio/Search/Tiling/TilingI.pm loaded ok -ok 243 - Bio/SearchIO.pm loaded ok -ok 244 - Bio/SearchIO/EventHandlerI.pm loaded ok -ok 245 - Bio/SearchIO/FastHitEventBuilder.pm loaded ok -ok 246 - Bio/SearchIO/IteratedSearchResultEventBuilder.pm loaded ok -ok 247 - Bio/SearchIO/SearchResultEventBuilder.pm loaded ok -ok 248 - Bio/SearchIO/SearchWriterI.pm loaded ok -ok 249 - Bio/SearchIO/Writer/GbrowseGFF.pm loaded ok -ok 250 - Bio/SearchIO/Writer/HSPTableWriter.pm loaded ok -ok 251 - Bio/SearchIO/Writer/HTMLResultWriter.pm loaded ok -ok 252 - Bio/SearchIO/Writer/HitTableWriter.pm loaded ok -ok 253 - Bio/SearchIO/Writer/ResultTableWriter.pm loaded ok -ok 254 - Bio/SearchIO/Writer/TextResultWriter.pm loaded ok -ok 255 - Bio/SearchIO/axt.pm loaded ok -ok 256 - Bio/SearchIO/blast.pm loaded ok -ok 257 - Bio/SearchIO/blast_pull.pm loaded ok -ok 258 - Bio/SearchIO/blasttable.pm loaded ok -ok 259 - Bio/SearchIO/cross_match.pm loaded ok -ok 260 - Bio/SearchIO/erpin.pm loaded ok -ok 261 - Bio/SearchIO/exonerate.pm loaded ok -ok 262 - Bio/SearchIO/fasta.pm loaded ok -ok 263 - Bio/SearchIO/gmap_f9.pm loaded ok -ok 264 - Bio/SearchIO/infernal.pm loaded ok -ok 265 - Bio/SearchIO/megablast.pm loaded ok -ok 266 - Bio/SearchIO/psl.pm loaded ok -ok 267 - Bio/SearchIO/rnamotif.pm loaded ok -ok 268 - Bio/SearchIO/sim4.pm loaded ok -ok 269 - Bio/SearchIO/waba.pm loaded ok -ok 270 - Bio/SearchIO/wise.pm loaded ok -ok 271 - Bio/Seq.pm loaded ok -ok 272 - Bio/Seq/BaseSeqProcessor.pm loaded ok -ok 273 - Bio/Seq/EncodedSeq.pm loaded ok -ok 274 - Bio/Seq/LargeLocatableSeq.pm loaded ok -ok 275 - Bio/Seq/LargePrimarySeq.pm loaded ok -ok 276 - Bio/Seq/LargeSeq.pm loaded ok -ok 277 - Bio/Seq/LargeSeqI.pm loaded ok -ok 278 - Bio/Seq/Meta.pm loaded ok -ok 279 - Bio/Seq/Meta/Array.pm loaded ok -ok 280 - Bio/Seq/MetaI.pm loaded ok -ok 281 - Bio/Seq/PrimaryQual.pm loaded ok -ok 282 - Bio/Seq/PrimedSeq.pm loaded ok -ok 283 - Bio/Seq/QualI.pm loaded ok -ok 284 - Bio/Seq/Quality.pm loaded ok -ok 285 - Bio/Seq/RichSeq.pm loaded ok -ok 286 - Bio/Seq/RichSeqI.pm loaded ok -ok 287 - Bio/Seq/SeqBuilder.pm loaded ok -ok 288 - Bio/Seq/SeqFactory.pm loaded ok -ok 289 - Bio/Seq/SeqFastaSpeedFactory.pm loaded ok -ok 290 - Bio/Seq/SequenceTrace.pm loaded ok -ok 291 - Bio/Seq/SimulatedRead.pm loaded ok -ok 292 - Bio/Seq/TraceI.pm loaded ok -ok 293 - Bio/SeqAnalysisParserI.pm loaded ok -ok 294 - Bio/SeqFeature/Amplicon.pm loaded ok -ok 295 - Bio/SeqFeature/AnnotationAdaptor.pm loaded ok -ok 296 - Bio/SeqFeature/Collection.pm loaded ok -ok 297 - Bio/SeqFeature/CollectionI.pm loaded ok -ok 298 - Bio/SeqFeature/Computation.pm loaded ok -ok 299 - Bio/SeqFeature/FeaturePair.pm loaded ok -ok 300 - Bio/SeqFeature/Gene/Exon.pm loaded ok -ok 301 - Bio/SeqFeature/Gene/ExonI.pm loaded ok -ok 302 - Bio/SeqFeature/Gene/GeneStructure.pm loaded ok -ok 303 - Bio/SeqFeature/Gene/GeneStructureI.pm loaded ok -ok 304 - Bio/SeqFeature/Gene/Intron.pm loaded ok -ok 305 - Bio/SeqFeature/Gene/NC_Feature.pm loaded ok -ok 306 - Bio/SeqFeature/Gene/Poly_A_site.pm loaded ok -ok 307 - Bio/SeqFeature/Gene/Promoter.pm loaded ok -ok 308 - Bio/SeqFeature/Gene/Transcript.pm loaded ok -ok 309 - Bio/SeqFeature/Gene/TranscriptI.pm loaded ok -ok 310 - Bio/SeqFeature/Gene/UTR.pm loaded ok -ok 311 - Bio/SeqFeature/Generic.pm loaded ok -ok 312 - Bio/SeqFeature/Lite.pm loaded ok -ok 313 - Bio/SeqFeature/PositionProxy.pm loaded ok -ok 314 - Bio/SeqFeature/Primer.pm loaded ok -ok 315 - Bio/SeqFeature/Similarity.pm loaded ok -ok 316 - Bio/SeqFeature/SimilarityPair.pm loaded ok -ok 317 - Bio/SeqFeature/SubSeq.pm loaded ok -ok 318 - Bio/SeqFeature/Tools/FeatureNamer.pm loaded ok -ok 319 - Bio/SeqFeature/Tools/IDHandler.pm loaded ok -ok 320 - Bio/SeqFeature/Tools/TypeMapper.pm loaded ok -ok 321 - Bio/SeqFeature/Tools/Unflattener.pm loaded ok -ok 322 - Bio/SeqFeature/TypedSeqFeatureI.pm loaded ok -ok 323 - Bio/SeqFeatureI.pm loaded ok -ok 324 - Bio/SeqI.pm loaded ok -ok 325 - Bio/SeqIO.pm loaded ok -ok 326 - Bio/SeqIO/FTHelper.pm loaded ok -ok 327 - Bio/SeqIO/Handler/GenericRichSeqHandler.pm loaded ok -ok 328 - Bio/SeqIO/MultiFile.pm loaded ok -ok 329 - Bio/SeqIO/ace.pm loaded ok -ok 330 - Bio/SeqIO/asciitree.pm loaded ok -ok 331 - Bio/SeqIO/bsml.pm loaded ok -ok 332 - Bio/SeqIO/bsml_sax.pm loaded ok -ok 333 - Bio/SeqIO/embl.pm loaded ok -ok 334 - Bio/SeqIO/embldriver.pm loaded ok -ok 335 - Bio/SeqIO/fasta.pm loaded ok -ok 336 - Bio/SeqIO/fastq.pm loaded ok -ok 337 - Bio/SeqIO/game.pm loaded ok -ok 338 - Bio/SeqIO/game/featHandler.pm loaded ok -ok 339 - Bio/SeqIO/game/gameHandler.pm loaded ok -ok 340 - Bio/SeqIO/game/gameSubs.pm loaded ok -ok 341 - Bio/SeqIO/game/gameWriter.pm loaded ok -ok 342 - Bio/SeqIO/game/seqHandler.pm loaded ok -ok 343 - Bio/SeqIO/gbdriver.pm loaded ok -ok 344 - Bio/SeqIO/gbxml.pm loaded ok -ok 345 - Bio/SeqIO/gcg.pm loaded ok -ok 346 - Bio/SeqIO/genbank.pm loaded ok -ok 347 - Bio/SeqIO/kegg.pm loaded ok -ok 348 - Bio/SeqIO/largefasta.pm loaded ok -ok 349 - Bio/SeqIO/locuslink.pm loaded ok -ok 350 - Bio/SeqIO/mbsout.pm loaded ok -ok 351 - Bio/SeqIO/metafasta.pm loaded ok -ok 352 - Bio/SeqIO/msout.pm loaded ok -ok 353 - Bio/SeqIO/phd.pm loaded ok -ok 354 - Bio/SeqIO/pir.pm loaded ok -ok 355 - Bio/SeqIO/qual.pm loaded ok -ok 356 - Bio/SeqIO/raw.pm loaded ok -ok 357 - Bio/SeqIO/scf.pm loaded ok -ok 358 - Bio/SeqIO/seqxml.pm loaded ok -ok 359 - Bio/SeqIO/swiss.pm loaded ok -ok 360 - Bio/SeqIO/swissdriver.pm loaded ok -ok 361 - Bio/SeqIO/tab.pm loaded ok -ok 362 - Bio/SeqIO/table.pm loaded ok -ok 363 - Bio/SeqIO/tigr.pm loaded ok -ok 364 - Bio/SeqIO/tigrxml.pm loaded ok -ok 365 - Bio/SeqIO/tinyseq.pm loaded ok -ok 366 - Bio/SeqIO/tinyseq/tinyseqHandler.pm loaded ok -ok 367 - Bio/SeqUtils.pm loaded ok -ok 368 - Bio/SimpleAlign.pm loaded ok -ok 369 - Bio/SimpleAnalysisI.pm loaded ok -ok 370 - Bio/Species.pm loaded ok -ok 371 - Bio/Taxon.pm loaded ok -ok 372 - Bio/Tools/Alignment/Consed.pm loaded ok -ok 373 - Bio/Tools/Alignment/Trim.pm loaded ok -ok 374 - Bio/Tools/AmpliconSearch.pm loaded ok -ok 375 - Bio/Tools/Analysis/SimpleAnalysisBase.pm loaded ok -ok 376 - Bio/Tools/AnalysisResult.pm loaded ok -ok 377 - Bio/Tools/Blat.pm loaded ok -ok 378 - Bio/Tools/CodonTable.pm loaded ok -ok 379 - Bio/Tools/Coil.pm loaded ok -ok 380 - Bio/Tools/ECnumber.pm loaded ok -ok 381 - Bio/Tools/EMBOSS/Palindrome.pm loaded ok -ok 382 - Bio/Tools/EPCR.pm loaded ok -ok 383 - Bio/Tools/ESTScan.pm loaded ok -ok 384 - Bio/Tools/Eponine.pm loaded ok -ok 385 - Bio/Tools/Est2Genome.pm loaded ok -ok 386 - Bio/Tools/Fgenesh.pm loaded ok -ok 387 - Bio/Tools/FootPrinter.pm loaded ok -ok 388 - Bio/Tools/GFF.pm loaded ok -ok 389 - Bio/Tools/Geneid.pm loaded ok -ok 390 - Bio/Tools/Genemark.pm loaded ok -ok 391 - Bio/Tools/Genewise.pm loaded ok -ok 392 - Bio/Tools/Genomewise.pm loaded ok -ok 393 - Bio/Tools/Genscan.pm loaded ok -ok 394 - Bio/Tools/Glimmer.pm loaded ok -ok 395 - Bio/Tools/Grail.pm loaded ok -ok 396 - Bio/Tools/GuessSeqFormat.pm loaded ok -ok 397 - Bio/Tools/IUPAC.pm loaded ok -ok 398 - Bio/Tools/Lucy.pm loaded ok -ok 399 - Bio/Tools/MZEF.pm loaded ok -ok 400 - Bio/Tools/Match.pm loaded ok -ok 401 - Bio/Tools/OddCodes.pm loaded ok -ok 402 - Bio/Tools/Phylo/Gerp.pm loaded ok -ok 403 - Bio/Tools/Phylo/Molphy.pm loaded ok -ok 404 - Bio/Tools/Phylo/Molphy/Result.pm loaded ok -ok 405 - Bio/Tools/Phylo/Phylip/ProtDist.pm loaded ok -ok 406 - Bio/Tools/Prediction/Exon.pm loaded ok -ok 407 - Bio/Tools/Prediction/Gene.pm loaded ok -ok 408 - Bio/Tools/Primer/Assessor/Base.pm loaded ok -ok 409 - Bio/Tools/Primer/AssessorI.pm loaded ok -ok 410 - Bio/Tools/Primer/Feature.pm loaded ok -ok 411 - Bio/Tools/Primer/Pair.pm loaded ok -ok 412 - Bio/Tools/Primer3.pm loaded ok -ok 413 - Bio/Tools/Prints.pm loaded ok -ok 414 - Bio/Tools/Profile.pm loaded ok -ok 415 - Bio/Tools/Promoterwise.pm loaded ok -ok 416 - Bio/Tools/PrositeScan.pm loaded ok -ok 417 - Bio/Tools/Pseudowise.pm loaded ok -ok 418 - Bio/Tools/QRNA.pm loaded ok -ok 419 - Bio/Tools/RandomDistFunctions.pm loaded ok -ok 420 - Bio/Tools/RepeatMasker.pm loaded ok -ok 421 - Bio/Tools/Run/Analysis.pm loaded ok -ok 422 - Bio/Tools/Run/AnalysisFactory.pm loaded ok -ok 423 - Bio/Tools/Run/GenericParameters.pm loaded ok -ok 424 - Bio/Tools/Run/ParametersI.pm loaded ok -ok 425 - Bio/Tools/Run/Phylo/PhyloBase.pm loaded ok -ok 426 - Bio/Tools/Run/WrapperBase.pm loaded ok -ok 427 - Bio/Tools/Run/WrapperBase/CommandExts.pm loaded ok -ok 428 - Bio/Tools/Seg.pm loaded ok -ok 429 - Bio/Tools/SeqPattern.pm loaded ok -ok 430 - Bio/Tools/SeqPattern/Backtranslate.pm loaded ok -ok 431 - Bio/Tools/SeqStats.pm loaded ok -ok 432 - Bio/Tools/SeqWords.pm loaded ok -ok 433 - Bio/Tools/Sigcleave.pm loaded ok -ok 434 - Bio/Tools/Signalp.pm loaded ok -ok 435 - Bio/Tools/Signalp/ExtendedSignalp.pm loaded ok -ok 436 - Bio/Tools/Sim4/Exon.pm loaded ok -ok 437 - Bio/Tools/Sim4/Results.pm loaded ok -ok 438 - Bio/Tools/Spidey/Exon.pm loaded ok -ok 439 - Bio/Tools/Spidey/Results.pm loaded ok -ok 440 - Bio/Tools/TandemRepeatsFinder.pm loaded ok -ok 441 - Bio/Tools/TargetP.pm loaded ok -ok 442 - Bio/Tools/Tmhmm.pm loaded ok -ok 443 - Bio/Tools/ipcress.pm loaded ok -ok 444 - Bio/Tools/isPcr.pm loaded ok -ok 445 - Bio/Tools/pICalculator.pm loaded ok -ok 446 - Bio/Tools/tRNAscanSE.pm loaded ok -ok 447 - Bio/Tree/AnnotatableNode.pm loaded ok -ok 448 - Bio/Tree/Compatible.pm loaded ok -ok 449 - Bio/Tree/DistanceFactory.pm loaded ok -ok 450 - Bio/Tree/Node.pm loaded ok -ok 451 - Bio/Tree/NodeI.pm loaded ok -ok 452 - Bio/Tree/NodeNHX.pm loaded ok -ok 453 - Bio/Tree/RandomFactory.pm loaded ok -ok 454 - Bio/Tree/Statistics.pm loaded ok -ok 455 - Bio/Tree/Tree.pm loaded ok -ok 456 - Bio/Tree/TreeFunctionsI.pm loaded ok -ok 457 - Bio/Tree/TreeI.pm loaded ok -ok 458 - Bio/TreeIO.pm loaded ok -ok 459 - Bio/TreeIO/NewickParser.pm loaded ok -ok 460 - Bio/TreeIO/TreeEventBuilder.pm loaded ok -ok 461 - Bio/TreeIO/cluster.pm loaded ok -ok 462 - Bio/TreeIO/lintree.pm loaded ok -ok 463 - Bio/TreeIO/newick.pm loaded ok -ok 464 - Bio/TreeIO/nexus.pm loaded ok -ok 465 - Bio/TreeIO/nhx.pm loaded ok -ok 466 - Bio/TreeIO/pag.pm loaded ok -ok 467 - Bio/TreeIO/phyloxml.pm loaded ok -ok 468 - Bio/TreeIO/tabtree.pm loaded ok -ok 469 - Bio/UpdateableSeqI.pm loaded ok -ok 470 - Bio/WebAgent.pm loaded ok -ok 471 - BioPerl.pm loaded ok -ok 472 - bin/bp_aacomp compiled ok -ok 473 - bin/bp_bioflat_index compiled ok -ok 474 - bin/bp_biogetseq compiled ok -ok 475 - bin/bp_dbsplit compiled ok -ok 476 - bin/bp_extract_feature_seq compiled ok -ok 477 - bin/bp_fastam9_to_table compiled ok -ok 478 - bin/bp_fetch compiled ok -ok 479 - bin/bp_filter_search compiled ok -ok 480 - bin/bp_find-blast-matches compiled ok -ok 481 - bin/bp_gccalc compiled ok -ok 482 - bin/bp_genbank2gff3 compiled ok -ok 483 - bin/bp_index compiled ok -ok 484 - bin/bp_local_taxonomydb_query compiled ok -ok 485 - bin/bp_make_mrna_protein compiled ok -ok 486 - bin/bp_mask_by_search compiled ok -ok 487 - bin/bp_mrtrans compiled ok -ok 488 - bin/bp_mutate compiled ok -ok 489 - bin/bp_nexus2nh compiled ok -ok 490 - bin/bp_nrdb compiled ok -ok 491 - bin/bp_oligo_count compiled ok -ok 492 - bin/bp_process_gadfly compiled ok -ok 493 - bin/bp_process_sgd compiled ok -ok 494 - bin/bp_revtrans-motif compiled ok -ok 495 - bin/bp_search2alnblocks compiled ok -ok 496 - bin/bp_search2gff compiled ok -ok 497 - bin/bp_search2table compiled ok -ok 498 - bin/bp_search2tribe compiled ok -ok 499 - bin/bp_seq_length compiled ok -ok 500 - bin/bp_seqconvert compiled ok -ok 501 - bin/bp_seqcut compiled ok -ok 502 - bin/bp_seqpart compiled ok -ok 503 - bin/bp_seqret compiled ok -ok 504 - bin/bp_seqretsplit compiled ok -ok 505 - bin/bp_split_seq compiled ok -ok 506 - bin/bp_sreformat compiled ok -ok 507 - bin/bp_taxid4species compiled ok -ok 508 - bin/bp_taxonomy2tree compiled ok -ok 509 - bin/bp_translate_seq compiled ok -ok 510 - bin/bp_tree2pag compiled ok -ok 511 - bin/bp_unflatten_seq compiled ok -ok -t/Align/AlignStats.t ................ -1..45 -ok 1 - use Bio::Align::DNAStatistics; -ok 2 - use Bio::Align::ProteinStatistics; -ok 3 - use Bio::AlignIO; -ok 4 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 38 - An object of class 'Bio::Matrix::PhylipDist' isa 'Bio::Matrix::PhylipDist' -ok 39 -ok 40 -ok 41 -ok 42 - An object of class 'Bio::Seq' isa 'Bio::PrimarySeqI' -ok 43 -ok 44 - Warn if seqs don't overlap -ok 45 -ok -t/Align/AlignUtil.t ................. -1..47 -ok 1 - use Bio::Align::Utilities; -ok 2 - use Bio::AlignIO; -ok 3 - use Bio::SeqIO; -ok 4 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 -ok 43 -ok 44 -ok 45 -ok 46 -ok 47 -ok -t/Align/SimpleAlign.t ............... -1..206 -ok 1 - use Bio::SimpleAlign; -ok 2 - use Bio::AlignIO; -ok 3 - use Bio::SeqFeature::Generic; -ok 4 - use Bio::Location::Simple; -ok 5 - use Bio::Location::Split; -ok 6 - An object of class 'Bio::AlignIO::pfam' isa 'Bio::AlignIO' -ok 7 - pfam input test -ok 8 - match_line -ok 9 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 10 - num_sequences -ok 11 - num_sequences -ok 12 - select_noncont -ok 13 - select_noncont -ok 14 - num_sequences -ok 15 - select_noncont -ok 16 - select_noncont -ok 17 - select_noncont_by_name -ok 18 - select_noncont_by_name -ok 19 - select_noncont_by_name -ok 20 - select_noncont_by_name -ok 21 - each_seq -ok 22 - get_nse -ok 23 - id -ok 24 - num_gaps -ok 25 - each_alphabetically -ok 26 - column_from_residue_number -ok 27 - display_name get/set -ok 28 - display_name get -ok 29 - consensus_string -ok 30 - consensus_string -ok 31 - consensus_string -ok 32 -ok 33 - each_seq_with_id -ok 34 - is_flush -ok 35 - id get/set -ok 36 - length -ok 37 - num_residues -ok 38 - num_sequences -ok 39 - overall_percentage_identity -ok 40 - overall_percentage_identity (align) -ok 41 - overall_percentage_identity (short) -ok 42 - overall_percentage_identity (long) -ok 43 - average_percentage_identity -ok 44 -ok 45 - set_displayname_count -ok 46 -ok 47 - set_displayname_flat -ok 48 -ok 49 - set_displayname_normal -ok 50 -ok 51 -ok 52 - uppercase, map_chars -ok 53 - match_line -ok 54 - remove_seqs -ok 55 - remove_seqs -ok 56 - add_seq -ok 57 - add_seq -ok 58 - get_seq_by_pos -ok 59 - get_seq_by_pos -ok 60 -ok 61 -ok 62 -ok 63 - purge -ok 64 - purge -ok 65 - IO::String consensus_iupac -ok 66 - IO::String write_aln normal -ok 67 - IO::String write_aln slice -ok 68 - IO::String write_aln slice -ok 69 - IO::String write_aln slice -ok 70 - IO::String write_aln slice -ok 71 - IO::String write_aln slice -ok 72 -ok 73 - remove_columns by position -ok 74 - remove_columns by position (wrong order) -ok 75 - cigar_line -ok 76 - cigar_line -ok 77 - cigar_line -ok 78 - cigar_line -ok 79 - sort_alphabetically - before -ok 80 -ok 81 - sort_alphabetically - after -ok 82 - remove_gaps -ok 83 - remove_gaps all_gaps_only -ok 84 - set_new_reference -ok 85 - set_new_reference -ok 86 - uniq_seq -ok 87 - bug 2099 -ok 88 - bug 2099 -ok 89 - bug 2793 -ok 90 - bug 2793 -ok 91 - bug 2793 -ok 92 - bug 2793 -ok 93 - Bad sequence, bad! -ok 94 - An object of class 'Bio::SimpleAlign' isa 'Bio::AnnotatableI' -ok 95 - added 3 seqs -ok 96 - first 2 features added -ok 97 - 3rd feature added -ok 98 -ok 99 - slice 1 len -ok 100 - correct masked seq -ok 101 - correct masked seq -ok 102 - correct masked seq -ok 103 -ok 104 - slice 2 len -ok 105 - correct masked seq -ok 106 - correct masked seq -ok 107 - correct masked seq -ok 108 -ok 109 - slice 3 len -ok 110 - correct masked seq -ok 111 - correct masked seq -ok 112 - correct masked seq -ok 113 -ok 114 - slice 4 len -ok 115 - correct masked seq -ok 116 - correct masked seq -ok 117 - correct masked seq -ok 118 - initial display id ok -ok 119 - safe display id ok -ok 120 - restored display id ok -ok 121 - sort by list ok -ok 122 -ok 123 -ok 124 -ok 125 -ok 126 -ok 127 -ok 128 - BIC:GGATCCATT[C/C]CTACT -ok 129 - BIC:GGAT[C/-][C/-]ATT[C/C]CT[A/C]CT -ok 130 - BIC:G[G/C]ATCCATT[C/G]CTACT -ok 131 - BIC:GGATCCATT[C/G]CTACT -ok 132 - BIC:GGATCCATT[C/G]CTAC[T/A] -ok 133 - BIC:GGATCCATT[C/G]CTA[C/G][T/A] -ok 134 - BIC:GGATCCATT[C/G]CTACT -ok 135 - BIC:GGATCCATT{C.C}CTACT -ok 136 - BIC:GGAT{C.-}{C.-}ATT{C.C}CT{A.C}CT -ok 137 - BIC:G{G.C}ATCCATT{C.G}CTACT -ok 138 - BIC:GGATCCATT{C.G}CTACT -ok 139 - BIC:GGATCCATT{C.G}CTAC{T.A} -ok 140 - BIC:GGATCCATT{C.G}CTA{C.G}{T.A} -ok 141 - BIC:GGATCCATT{C.G}CTACT -ok 142 -ok 143 -ok 144 -ok 145 -ok 146 -ok 147 -ok 148 -ok 149 -ok 150 -ok 151 -ok 152 -ok 153 -ok 154 -ok 155 -ok 156 -ok 157 -ok 158 -ok 159 -ok 160 -ok 161 -ok 162 -ok 163 -ok 164 -ok 165 -ok 166 -ok 167 -ok 168 -ok 169 -ok 170 -ok 171 -ok 172 -ok 173 -ok 174 -ok 175 -ok 176 -ok 177 -ok 178 -ok 179 -ok 180 -ok 181 -ok 182 -ok 183 -ok 184 -ok 185 -ok 186 -ok 187 -ok 188 -ok 189 -ok 190 -ok 191 -ok 192 -ok 193 -ok 194 -ok 195 -ok 196 -ok 197 -ok 198 -ok 199 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign' -ok 200 - consensus string looks ok -ok 201 - conservation length -ok 202 - conservation scores -ok 203 - looks like correct unmasked alignment (from clustalw) -ok 204 - looks like correct masked alignment (from clustalw) -ok 205 -ok 206 - align after looks ok -ok -t/Align/TreeBuild.t ................. -1..13 -ok 1 - use Bio::Align::DNAStatistics; -ok 2 - use Bio::Align::ProteinStatistics; -ok 3 - use Bio::Align::Utilities; -ok 4 - use Bio::AlignIO; -ok 5 - use Bio::Tree::DistanceFactory; -ok 6 - use Bio::TreeIO; -ok 7 - 'SimpleAlign object parsed out' isa 'Bio::SimpleAlign' -ok 8 - 'Protein distance matrix retrieved' isa 'Bio::Matrix::MatrixI' -ok 9 - 'Tree object gotten back' isa 'Bio::Tree::TreeI' -ok 10 - NJ calculated Branch length -ok 11 - NJ calculated Branch length -ok 12 - Make sure two nodes are sister -ok 13 - 10 replicates formulated -ok -t/Align/Utilities.t ................. -1..14 -ok 1 - use Bio::Align::Utilities; -ok 2 - use Bio::SimpleAlign; -ok 3 - use Bio::PrimarySeq; -ok 4 - use Bio::LocatableSeq; -ok 5 - use Bio::AlignIO; -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok -t/AlignIO/AlignIO.t ................. -1..27 -ok 1 - use Bio::AlignIO; -ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::AnnotatableI' -ok 3 - input filehandle method test : metafasta -ok 4 - input filehandle method test : msf -ok 5 - input filehandle method test : fasta -ok 6 - input filehandle method test : phylip -ok 7 - input filehandle method test : mase -ok 8 - input filehandle method test : po -ok 9 - input filehandle method test : clustalw -ok 10 - input filehandle method test : arp -ok 11 - input filehandle method test : nexus -ok 12 - input filehandle method test : pfam -ok 13 - input filehandle method test : selex -ok 14 - input filehandle method test : psi -ok 15 - input filehandle method test : xmfa -ok 16 - input filehandle method test : prodom -ok 17 - filehandle output test : metafasta -ok 18 - filehandle output test : msf -ok 19 - filehandle output test : fasta -ok 20 - filehandle output test : phylip -ok 21 - filehandle output test : po -ok 22 - filehandle output test : clustalw -ok 23 - filehandle output test : nexus -ok 24 - filehandle output test : pfam -ok 25 - filehandle output test : selex -ok 26 - filehandle output test : psi -ok 27 - filehandle output test : xmfa -ok -t/AlignIO/arp.t ..................... -1..48 -ok 1 - use Bio::AlignIO::arp; -ok 2 - An object of class 'Bio::AlignIO::arp' isa 'Bio::AlignIO' -ok 3 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 4 - ARP get_nse() -ok 5 -ok 6 - ARP num_sequences() -ok 7 - ARP id() -ok 8 - ARP description() -ok 9 - An object of class 'Bio::Annotation::Collection' isa 'Bio::AnnotationCollectionI' -ok 10 - An object of class 'Bio::Annotation::TagTree' isa 'Bio::AnnotationI' -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 - An object of class 'Bio::AlignIO::arp' isa 'Bio::AlignIO' -ok 16 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 17 - ARP get_nse() -ok 18 - ARP num_sequences() -ok 19 - ARP id() -ok 20 - ARP description() -ok 21 - An object of class 'Bio::Annotation::Collection' isa 'Bio::AnnotationCollectionI' -ok 22 - An object of class 'Bio::Annotation::TagTree' isa 'Bio::AnnotationI' -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 28 - ARP get_nse() -ok 29 - ARP num_sequences() -ok 30 - ARP id() -ok 31 - ARP description() -ok 32 - An object of class 'Bio::Annotation::Collection' isa 'Bio::AnnotationCollectionI' -ok 33 - An object of class 'Bio::Annotation::TagTree' isa 'Bio::AnnotationI' -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 39 - ARP get_nse() -ok 40 - ARP num_sequences() -ok 41 - ARP id() -ok 42 - ARP description() -ok 43 - An object of class 'Bio::Annotation::Collection' isa 'Bio::AnnotationCollectionI' -ok 44 - An object of class 'Bio::Annotation::TagTree' isa 'Bio::AnnotationI' -ok 45 -ok 46 -ok 47 -ok 48 -ok -t/AlignIO/bl2seq.t .................. -1..7 -ok 1 - use Bio::AlignIO::bl2seq; -ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 3 - BLAST bl2seq format test -ok 4 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 5 -ok 6 -ok 7 -ok -t/AlignIO/clustalw.t ................ -1..6 -ok 1 - use Bio::AlignIO::clustalw; -ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 3 - clustalw consensus_string test -ok 4 - clustalw output test -ok 5 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 6 - clustalw input test -ok -t/AlignIO/emboss.t .................. -1..37 -ok 1 - use Bio::AlignIO::emboss; -ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 11 -ok 12 -ok 13 -ok 14 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 15 -ok 16 -ok 17 -ok 18 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 19 -ok 20 -ok 21 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok -t/AlignIO/fasta.t ................... -1..12 -ok 1 - use Bio::AlignIO::fasta; -ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 3 - fasta input test -ok 4 - fasta input test -ok 5 - fasta input test for description -ok 6 - fasta input test for id -ok 7 - fasta input test, captures formatted start/end -ok 8 - fasta input test for end -ok 9 - fasta input test for description -ok 10 - fasta output test -ok 11 - filehandle input test -ok 12 - filehandle output test -ok -t/AlignIO/largemultifasta.t ......... -1..7 -ok 1 - use Bio::AlignIO::largemultifasta; -ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 3 - fasta input test -ok 4 - fasta input test for description -ok 5 - fasta input test for id -ok 6 - fasta input test for description -ok 7 - fasta output test -ok -t/AlignIO/maf.t ..................... -1..11 -ok 1 - use Bio::AlignIO::maf; -ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 3 - maf input test -ok 4 -ok 5 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 6 - maf input test -ok 7 -ok 8 - maf input test -ok 9 -ok 10 - maf input test -ok 11 -ok -t/AlignIO/mase.t .................... -1..3 -ok 1 - use Bio::AlignIO::mase; -ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 3 - mase input test -ok -t/AlignIO/mega.t .................... -1..6 -ok 1 - use Bio::AlignIO::mega; -ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 3 -ok 4 -ok 5 -ok 6 - mega output test -ok -t/AlignIO/meme.t .................... -1..20 -ok 1 - use Bio::AlignIO::meme; -ok 2 - An object of class 'Bio::AlignIO::meme' isa 'Bio::AlignIO' -ok 3 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 - An object of class 'Bio::AlignIO::meme' isa 'Bio::AlignIO' -ok 9 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 - An object of class 'Bio::AlignIO::meme' isa 'Bio::AlignIO' -ok 16 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 17 -ok 18 -ok 19 -ok 20 -ok -t/AlignIO/metafasta.t ............... -1..4 -ok 1 - use Bio::AlignIO::metafasta; -ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 3 - consensus_string on metafasta -ok 4 - symbol_chars() using metafasta -ok -t/AlignIO/msf.t ..................... -1..4 -ok 1 - use Bio::AlignIO::msf; -ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 3 - msf input test -ok 4 - msf output test -ok -t/AlignIO/nexus.t ................... -1..43 -ok 1 - use Bio::AlignIO::nexus; -ok 2 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' -ok 3 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 4 -ok 5 - nexus output test -ok 6 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' -ok 7 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 8 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' -ok 9 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 10 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' -ok 11 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 12 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' -ok 13 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 14 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' -ok 15 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 16 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' -ok 17 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 18 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' -ok 19 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 20 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' -ok 21 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 22 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' -ok 23 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 24 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' -ok 25 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 26 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' -ok 27 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 28 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' -ok 29 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 30 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' -ok 31 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 32 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' -ok 33 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 34 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' -ok 35 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 36 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' -ok 37 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 38 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' -ok 39 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 40 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' -ok 41 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 42 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' -ok 43 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok -t/AlignIO/pfam.t .................... -1..5 -ok 1 - use Bio::AlignIO::pfam; -ok 2 - An object of class 'Bio::AlignIO::pfam' isa 'Bio::AlignIO' -ok 3 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 4 -ok 5 - pfam output test -ok -t/AlignIO/phylip.t .................. -1..20 -ok 1 - use Bio::AlignIO::phylip; -ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 3 -ok 4 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 5 -ok 6 -ok 7 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 8 -ok 9 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 10 -ok 11 - phylip output test -ok 12 -ok 13 -ok 14 -ok 15 -not ok 16 # TODO problems with default strand -# Failed (TODO) test at t/AlignIO/phylip.t line 77. -# got: undef -# expected: '0' -ok 17 - newline between header and sequences is parsed correctly -ok 18 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign' -ok 19 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign' -ok 20 -ok -t/AlignIO/po.t ...................... -1..11 -ok 1 - use Bio::AlignIO::po; -ok 2 - An object of class 'Bio::AlignIO::po' isa 'Bio::AlignIO' -ok 3 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 4 -ok 5 - An object of class 'Bio::AlignIO::clustalw' isa 'Bio::AlignIO' -ok 6 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 7 - po output test -ok 8 - An object of class 'Bio::AlignIO::po' isa 'Bio::AlignIO' -ok 9 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 10 -ok 11 -ok -t/AlignIO/prodom.t .................. -1..3 -ok 1 - use Bio::AlignIO::prodom; -ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 3 - prodom input test -ok -t/AlignIO/psi.t ..................... -1..5 -ok 1 - use Bio::AlignIO::psi; -ok 2 - An object of class 'Bio::AlignIO::psi' isa 'Bio::AlignIO' -ok 3 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 4 -ok 5 -ok -t/AlignIO/selex.t ................... -1..4 -ok 1 - use Bio::AlignIO::selex; -ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 3 - selex format test -ok 4 - selex output test -ok -t/AlignIO/xmfa.t .................... -1..30 -ok 1 - use Bio::AlignIO::xmfa; -ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 3 - xmfa input test -ok 4 - xmfa input test for start -ok 5 - xmfa input test for end -ok 6 - xmfa strand test -ok 7 - xmfa input test for id -ok 8 - xmfa input test for id -ok 9 - xmfa input test -ok 10 - xmfa input test for start -ok 11 - xmfa input test for end -ok 12 - xmfa strand test -ok 13 - xmfa input test for id -ok 14 - xmfa input test for id -ok 15 - xmfa input test -ok 16 - xmfa input test for start -ok 17 - xmfa input test for end -ok 18 - xmfa strand test -ok 19 - xmfa input test for id -ok 20 - xmfa input test for id -ok 21 - xmfa alignment score -ok 22 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 23 - xmfa input test -ok 24 - xmfa strand -ok 25 - xmfa input test for description -ok 26 - xmfa input test for id -ok 27 - xmfa input test for end -ok 28 - xmfa input test for end -ok 29 - xmfa alignment score -ok 30 - xmfa output test -ok -t/Annotation/Annotation.t ........... -1..148 -ok 1 - use Bio::Annotation::Collection; -ok 2 - use Bio::Annotation::DBLink; -ok 3 - use Bio::Annotation::Comment; -ok 4 - use Bio::Annotation::Reference; -ok 5 - use Bio::Annotation::SimpleValue; -ok 6 - use Bio::Annotation::Target; -ok 7 - use Bio::Annotation::AnnotationFactory; -ok 8 - use Bio::Annotation::StructuredValue; -ok 9 - use Bio::Annotation::TagTree; -ok 10 - use Bio::Annotation::Tree; -ok 11 - An object of class 'Bio::Annotation::SimpleValue' isa 'Bio::AnnotationI' -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 - An object of class 'Bio::Annotation::DBLink' isa 'Bio::AnnotationI' -ok 19 -ok 20 -ok 21 -ok 22 - An object of class 'Bio::Annotation::Collection' isa 'Bio::AnnotationCollectionI' -ok 23 -ok 24 -ok 25 - An object of class 'Bio::Annotation::Target' isa 'Bio::AnnotationI' -ok 26 -ok 27 - An object of class 'Bio::Annotation::Reference' isa 'Bio::AnnotationI' -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 -ok 43 -ok 44 -ok 45 -ok 46 -ok 47 -ok 48 -ok 49 -ok 50 - An object of class 'Bio::Annotation::StructuredValue' isa 'Bio::AnnotationI' -ok 51 -ok 52 -ok 53 -ok 54 -ok 55 -ok 56 -ok 57 -ok 58 -ok 59 -ok 60 -ok 61 -ok 62 -ok 63 -ok 64 -ok 65 - An object of class 'Bio::Annotation::Collection' isa 'Bio::AnnotationCollectionI' -ok 66 -ok 67 -ok 68 -ok 69 -ok 70 - An object of class 'Bio::Annotation::StructuredValue' isa 'Bio::Annotation::StructuredValue' -ok 71 -ok 72 -ok 73 -ok 74 -ok 75 - use Bio::Annotation::OntologyTerm; -ok 76 - An object of class 'Bio::Ontology::Term' isa 'Bio::Ontology::Term' -ok 77 -ok 78 -ok 79 -ok 80 -ok 81 -ok 82 - An object of class 'Bio::Annotation::AnnotationFactory' isa 'Bio::Factory::ObjectFactoryI' -ok 83 - An object of class 'Bio::Annotation::SimpleValue' isa 'Bio::Annotation::SimpleValue' -ok 84 -ok 85 - An object of class 'Bio::Annotation::OntologyTerm' isa 'Bio::Annotation::OntologyTerm' -ok 86 - Bio::Annotation::Comment -ok 87 - An object of class 'Bio::Annotation::Comment' isa 'Bio::Annotation::Comment' -ok 88 -ok 89 - Bio::Annotation::Comment -ok 90 - An object of class 'Bio::Annotation::Comment' isa 'Bio::Annotation::Comment' -ok 91 - Bio::Annotation::Comment -ok 92 - An object of class 'Bio::Annotation::Comment' isa 'Bio::Annotation::Comment' -ok 93 -ok 94 - An object of class 'Bio::Annotation::Target' isa 'Bio::Annotation::Target' -ok 95 -ok 96 -ok 97 - An object of class 'Bio::Annotation::Tree' isa 'Bio::AnnotationI' -ok 98 - tree_id() -ok 99 - tagname() -ok 100 -ok 101 - add tree to AlignI -ok 102 - get seq from node id -ok 103 -ok 104 - An object of class 'Bio::Annotation::Tree' isa 'Bio::Annotation::Tree' -ok 105 - An object of class 'Bio::Annotation::TagTree' isa 'Bio::AnnotationI' -ok 106 - default itext -ok 107 - roundtrip -ok 108 - itext -ok 109 - spxr -ok 110 - indent -ok 111 - xml -ok 112 - An object of class 'Data::Stag::StagImpl' isa 'Data::Stag::StagI' -ok 113 -ok 114 - child changes -ok 115 - An object of class 'Data::Stag::StagImpl' isa 'Data::Stag::StagI' -ok 116 -ok 117 - child changes -ok 118 - An object of class 'Data::Stag::StagImpl' isa 'Data::Stag::StagI' -ok 119 -ok 120 - child changes -ok 121 - child changes in parent node -ok 122 - no tags -ok 123 - before Stag node -ok 124 - after Stag node -ok 125 - both stag nodes -ok 126 - different instances -ok 127 - before TagTree -ok 128 - after TagTree -ok 129 - both stag nodes -ok 130 - different instances -ok 131 - before TagTree -ok 132 - after TagTree -ok 133 - stag nodes -ok 134 - same instance -ok 135 - before TagTree -ok 136 - after TagTree -ok 137 - stag nodes -ok 138 - different instance -ok 139 - An object of class 'Bio::Annotation::TagTree' isa 'Bio::AnnotationI' -ok 140 - An object of class 'Data::Stag::StagImpl' isa 'Data::Stag::StagI' -ok 141 - child changes -ok 142 - An object of class 'Data::Stag::StagImpl' isa 'Data::Stag::StagI' -ok 143 - child changes -ok 144 - An object of class 'Data::Stag::StagImpl' isa 'Data::Stag::StagI' -ok 145 - child changes -ok 146 -ok 147 -ok 148 - An object of class 'Bio::Annotation::TagTree' isa 'Bio::Annotation::TagTree' -ok -t/Annotation/AnnotationAdaptor.t .... -1..23 -ok 1 - use Bio::SeqFeature::Generic; -ok 2 - use Bio::SeqFeature::AnnotationAdaptor; -ok 3 - use Bio::Annotation::DBLink; -ok 4 - use Bio::Annotation::Comment; -ok 5 - use Bio::Annotation::SimpleValue; -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok -t/author-mojibake.t ................. skipped: these tests are for testing by the author -t/author-pod-syntax.t ............... skipped: these tests are for testing by the author -Subroutine new redefined at /build/reproducible-path/bioperl-1.7.8/blib/lib/Bio/DB/IndexedBase.pm line 1121. -Subroutine next_seq redefined at /build/reproducible-path/bioperl-1.7.8/blib/lib/Bio/DB/IndexedBase.pm line 1130. -Subroutine TIEHANDLE redefined at /build/reproducible-path/bioperl-1.7.8/blib/lib/Bio/DB/IndexedBase.pm line 1139. -Subroutine READLINE redefined at /build/reproducible-path/bioperl-1.7.8/blib/lib/Bio/DB/IndexedBase.pm line 1144. -t/LocalDB/Fasta.t ................... -1..109 -ok 1 - Index a directory -ok 2 -ok 3 - An object of class 'Bio::DB::Fasta' isa 'Bio::DB::Fasta' -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 - An object of class 'Bio::PrimarySeq::Fasta' isa 'Bio::PrimarySeq::Fasta' -ok 29 - An object of class 'Bio::PrimarySeq::Fasta' isa 'Bio::PrimarySeqI' -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 - bug 3126 -ok 38 -ok 39 -ok 40 - An object of class 'Bio::PrimarySeq::Fasta' isa 'Bio::PrimarySeq::Fasta' -ok 41 - An object of class 'Bio::PrimarySeq::Fasta' isa 'Bio::PrimarySeqI' -ok 42 -ok 43 -ok 44 -ok 45 - An object of class 'Bio::PrimarySeq::Fasta' isa 'Bio::PrimarySeq::Fasta' -ok 46 - An object of class 'Bio::PrimarySeq::Fasta' isa 'Bio::PrimarySeqI' -ok 47 -ok 48 -ok 49 - use Class::Unload; -ok 50 - Re-open an existing index -ok 51 -ok 52 - Tied hash access -ok 53 -ok 54 -ok 55 -ok 56 -ok 57 - Writing with SeqIO -ok 58 -ok 59 -ok 60 - Index a single file -ok 61 -ok 62 -ok 63 -ok 64 -ok 65 -ok 66 -ok 67 -ok 68 -ok 69 -ok 70 -ok 71 -ok 72 - An object of class 'Bio::DB::Indexed::Stream' isa 'Bio::DB::Indexed::Stream' -ok 73 -ok 74 - An object of class 'Bio::PrimarySeq::Fasta' isa 'Bio::PrimarySeq::Fasta' -ok 75 -ok 76 -ok 77 -ok 78 -ok 79 -ok 80 -ok 81 -ok 82 -ok 83 -ok 84 -ok 85 -ok 86 -ok 87 -ok 88 -ok 89 -ok 90 - Make single ID -ok 91 -ok 92 -ok 93 - An object of class 'Bio::PrimarySeq::Fasta' isa 'Bio::PrimarySeqI' -ok 94 - Make multiple IDs, bug \#3389 -ok 95 -ok 96 -ok 97 - An object of class 'Bio::PrimarySeq::Fasta' isa 'Bio::PrimarySeqI' -ok 98 - Index a set of files -ok 99 -ok 100 -ok 101 -ok 102 -ok 103 - threw Regexp ((?^:FASTA header doesn't match)) -ok 104 - threw Regexp ((?^:Blank lines can only precede header lines)) -ok 105 -ok 106 - length is correct in sequences past spaces -ok 107 -ok 108 - subseq is correct -ok 109 - subseq is correct -ok -t/LocalDB/Flat.t .................... -1..27 -ok 1 - use Bio::DB::Flat; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok -t/LocalDB/Index/Blast.t ............. -1..5 -ok 1 - use Cwd; -ok 2 - use Bio::SearchIO; -ok 3 - use Bio::Index::Blast; -# Subtest: BLASTP - 1..12 - ok 1 - ok 2 - ok 3 - ok 4 - ok 5 - ok 6 - ok 7 - ok 8 - ok 9 - ok 10 - ok 11 - ok 12 -ok 4 - BLASTP -# Subtest: RPS-BLAST - 1..11 - ok 1 - ok 2 - ok 3 - ok 4 - ok 5 - ok 6 - ok 7 - ok 8 - ok 9 - ok 10 - ok 11 -ok 5 - RPS-BLAST -ok -t/LocalDB/Index/BlastTable.t ........ -1..27 -ok 1 - use Cwd; -ok 2 - use Bio::SearchIO; -ok 3 - use Bio::Index::BlastTable; -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok -t/LocalDB/Index/Index.t ............. -1..65 -ok 1 - use Bio::Index::Fasta; -ok 2 - use Bio::Index::Qual; -ok 3 - use Bio::Index::SwissPfam; -ok 4 - use Bio::Index::EMBL; -ok 5 - use Bio::Index::GenBank; -ok 6 - use Bio::Index::Swissprot; -ok 7 - use Bio::DB::InMemoryCache; -ok 8 - use Bio::DB::InMemoryCache; -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 - An object of class 'Bio::Seq' isa 'Bio::PrimarySeqI' -ok 18 -ok 19 -ok 20 -ok 21 - An object of class 'Bio::Seq' isa 'Bio::SeqI' -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 -ok 43 -ok 44 -ok 45 -ok 46 -ok 47 -ok 48 -ok 49 -ok 50 -ok 51 -ok 52 -ok 53 -ok 54 -ok 55 -ok 56 -ok 57 -ok 58 -ok 59 -ok 60 -ok 61 -ok 62 -ok 63 -ok 64 -ok 65 -ok -t/LocalDB/Qual.t .................... -1..56 -ok 1 - use Bio::Root::IO; -ok 2 - use File::Copy; -ok 3 -ok 4 -ok 5 - An object of class 'Bio::DB::Qual' isa 'Bio::DB::Qual' -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 - An object of class 'Bio::Seq::PrimaryQual::Qual' isa 'Bio::Seq::PrimaryQual::Qual' -ok 23 - An object of class 'Bio::Seq::PrimaryQual::Qual' isa 'Bio::Seq::QualI' -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 - An object of class 'Bio::Seq::PrimaryQual::Qual' isa 'Bio::Seq::PrimaryQual::Qual' -ok 38 - An object of class 'Bio::Seq::PrimaryQual::Qual' isa 'Bio::Seq::QualI' -ok 39 -ok 40 -ok 41 -ok 42 - An object of class 'Bio::Seq::PrimaryQual::Qual' isa 'Bio::Seq::PrimaryQual::Qual' -ok 43 - An object of class 'Bio::Seq::PrimaryQual::Qual' isa 'Bio::Seq::PrimaryQual' -ok 44 -ok 45 -ok 46 -ok 47 -ok 48 - An object of class 'Bio::DB::Indexed::Stream' isa 'Bio::DB::Indexed::Stream' -ok 49 -ok 50 - An object of class 'Bio::Seq::PrimaryQual::Qual' isa 'Bio::Seq::PrimaryQual' -ok 51 -ok 52 - An object of class 'Bio::Seq::PrimaryQual::Qual' isa 'Bio::Seq::PrimaryQual' -ok 53 -ok 54 -ok 55 -ok 56 -ok -t/LocalDB/Registry.t ................ -1..14 -ok 1 - use Bio::DB::Registry; -ok 2 - use Bio::DB::Flat; -ok 3 -ok 4 -ok 5 -ok 6 # skip Network tests have not been requested -ok 7 # skip Network tests have not been requested -ok 8 # skip Network tests have not been requested -ok 9 # skip Network tests have not been requested -ok 10 # skip Network tests have not been requested -ok 11 # skip Network tests have not been requested -ok 12 # skip Network tests have not been requested -ok 13 # skip Network tests have not been requested -ok 14 # skip Network tests have not been requested -ok -t/LocalDB/Taxonomy/greengenes.t ..... -1..38 -ok 1 - use Bio::DB::Taxonomy; -ok 2 - use Bio::Tree::Tree; -ok 3 -ok 4 - An object of class 'Bio::DB::Taxonomy::greengenes' isa 'Bio::DB::Taxonomy::greengenes' -ok 5 - An object of class 'Bio::DB::Taxonomy::greengenes' isa 'Bio::DB::Taxonomy::list' -ok 6 - An object of class 'Bio::DB::Taxonomy::greengenes' isa 'Bio::DB::Taxonomy' -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok -t/LocalDB/Taxonomy/silva.t .......... -1..42 -ok 1 - use Bio::DB::Taxonomy; -ok 2 - use Bio::Tree::Tree; -ok 3 -ok 4 - An object of class 'Bio::DB::Taxonomy::silva' isa 'Bio::DB::Taxonomy::silva' -ok 5 - An object of class 'Bio::DB::Taxonomy::silva' isa 'Bio::DB::Taxonomy::list' -ok 6 - An object of class 'Bio::DB::Taxonomy::silva' isa 'Bio::DB::Taxonomy' -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 -ok -t/Matrix/InstanceSite.t ............. -1..6 -ok 1 - use Bio::Matrix::PSM::InstanceSite; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok -t/Matrix/IO/masta.t ................. -1..16 -ok 1 - use Bio::Matrix::PSM::IO; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok -t/Matrix/IO/psm.t ................... -1..63 -ok 1 - use Bio::Matrix::PSM::IO; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 -ok 43 -ok 44 -ok 45 -ok 46 -ok 47 -ok 48 -ok 49 -ok 50 -ok 51 -ok 52 -ok 53 -ok 54 -ok 55 -ok 56 -ok 57 -ok 58 -ok 59 -ok 60 -ok 61 -ok 62 -ok 63 -ok -t/Matrix/Matrix.t ................... -1..77 -ok 1 - use Bio::Matrix::Generic; -ok 2 - use Bio::Matrix::IO; -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 - An object of class 'Bio::Matrix::Scoring' isa 'Bio::Matrix::Scoring' -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 - An object of class 'Bio::Matrix::Scoring' isa 'Bio::Matrix::Scoring' -ok 43 -ok 44 -ok 45 -ok 46 -ok 47 -ok 48 -ok 49 -ok 50 -ok 51 -ok 52 -ok 53 -ok 54 -ok 55 -ok 56 -ok 57 -ok 58 -ok 59 -ok 60 -ok 61 -ok 62 -ok 63 -ok 64 -ok 65 -ok 66 -ok 67 -ok 68 -ok 69 -ok 70 -ok 71 -ok 72 -ok 73 -ok 74 -ok 75 -ok 76 -ok 77 -ok -t/Matrix/ProtMatrix.t ............... -1..14 -ok 1 - use Bio::Matrix::PSM::ProtMatrix; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok -t/Matrix/ProtPsm.t .................. -1..14 -ok 1 - use Bio::Matrix::PSM::IO; -ok 2 -ok 3 -ok 4 -ok 5 # skip TODO: Module incomplete -ok 6 # skip TODO: Module incomplete -ok 7 # skip TODO: Module incomplete -ok 8 # skip TODO: Module incomplete -ok 9 # skip TODO: Module incomplete -ok 10 # skip TODO: Module incomplete -ok 11 # skip TODO: Module incomplete -ok 12 # skip TODO: Module incomplete -ok 13 # skip TODO: Module incomplete -ok 14 # skip TODO: Module incomplete -ok -t/Matrix/SiteMatrix.t ............... -1..14 -ok 1 - use Bio::Matrix::PSM::SiteMatrix; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok -t/Ontology/GOterm.t ................. -1..62 -ok 1 - use Bio::Ontology::GOterm; -ok 2 - use Bio::Ontology::Ontology; -ok 3 - use Bio::Annotation::DBLink; -ok 4 - An object of class 'Bio::Ontology::GOterm' isa 'Bio::Ontology::GOterm' -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 -ok 43 -ok 44 -ok 45 -ok 46 -ok 47 -ok 48 -ok 49 -ok 50 -ok 51 -ok 52 -ok 53 -ok 54 -ok 55 -ok 56 -ok 57 -ok 58 -ok 59 -ok 60 -ok 61 -ok 62 -ok -t/Ontology/GraphAdaptor.t ........... -1..28 -ok 1 - use Bio::Ontology::SimpleGOEngine::GraphAdaptor; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok -t/Ontology/IO/go.t .................. -1..102 -ok 1 - use Bio::OntologyIO; -ok 2 -ok 3 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::OntologyI' -ok 4 -ok 5 - An object of class 'Bio::Ontology::OBOEngine' isa 'Bio::Ontology::OntologyEngineI' -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 -ok 43 -ok 44 -ok 45 -ok 46 -ok 47 -ok 48 -ok 49 -ok 50 -ok 51 -ok 52 -ok 53 -ok 54 -ok 55 -ok 56 -ok 57 -ok 58 -ok 59 -ok 60 -ok 61 -ok 62 -ok 63 -ok 64 -ok 65 -ok 66 -ok 67 -ok 68 -ok 69 -ok 70 -ok 71 -ok 72 -ok 73 -ok 74 -ok 75 -ok 76 -ok 77 -ok 78 -ok 79 -ok 80 -ok 81 -ok 82 -ok 83 -ok 84 -ok 85 -ok 86 -ok 87 -ok 88 -ok 89 -ok 90 -ok 91 -ok 92 -ok 93 -ok 94 -ok 95 -ok 96 -ok 97 -ok 98 -ok 99 -ok 100 -ok 101 -ok 102 -ok -t/Ontology/IO/interpro.t ............ -1..69 -ok 1 - use Bio::OntologyIO; -ok 2 - An object of class 'Bio::OntologyIO::InterProParser' isa 'Bio::OntologyIO::InterProParser' -ok 3 -ok 4 - get_dbxrefs on leaf terms is non-empty -ok 5 - get_dbxrefs(member_list) on leaf terms is non-empty -ok 6 - get_dbxrefs(sec_list) on leaf terms is non-empty -ok 7 - get_dbxrefs(class_list) on leaf terms is non-empty -ok 8 - get_dbxrefs(pub_list) on leaf terms is non-empty -ok 9 - get_dbxrefs(example_list) on leaf terms is non-empty -ok 10 - get_dbxrefs(external_doc_list) on leaf terms is non-empty -ok 11 - get_members on leaf terms is non-empty -ok 12 - class_list on leaf terms is non-empty -ok 13 - get_examples on leaf terms is non-empty -ok 14 - get_external_documents on leaf terms is non-empty -ok 15 - get_references on leaf terms is non-empty -ok 16 - protein_count on leaf terms is non-empty -ok 17 - to_string looks reasonable -ok 18 - There are 8 root InterPro terms -ok 19 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' -ok 20 - term Integrins alpha chain in ontology InterPro -ok 21 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' -ok 22 - term Cdc20/Fizzy in ontology InterPro -ok 23 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' -ok 24 - term Binding Site in ontology InterPro -ok 25 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' -ok 26 - term Conserved Site in ontology InterPro -ok 27 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' -ok 28 - term Helix-turn-helix, AraC type in ontology InterPro -ok 29 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' -ok 30 - term post-translational modification in ontology InterPro -ok 31 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' -ok 32 - term Active Site in ontology InterPro -ok 33 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' -ok 34 - term Repeat in ontology InterPro -ok 35 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' -ok 36 - term Kringle in ontology InterPro -ok 37 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' -ok 38 - term Region in ontology InterPro -ok 39 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' -ok 40 - term Active Site in ontology InterPro -ok 41 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' -ok 42 - term Binding Site in ontology InterPro -ok 43 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' -ok 44 - term Conserved Site in ontology InterPro -ok 45 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' -ok 46 - term Domain in ontology InterPro -ok 47 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' -ok 48 - term Family in ontology InterPro -ok 49 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' -ok 50 - term Region in ontology InterPro -ok 51 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' -ok 52 - term Repeat in ontology InterPro -ok 53 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' -ok 54 - term post-translational modification in ontology InterPro -ok 55 -ok 56 -ok 57 -ok 58 -ok 59 -ok 60 -ok 61 - Integrins alpha chain term has one parent -ok 62 - Integrins alpha chain term has one ancestor -ok 63 - Cdc20/Fizzy term has one parent -ok 64 - Cdc20/Fizzy term has one ancestor -ok 65 - Helix-turn-helix, AraC type term has one parent -ok 66 - Helix-turn-helix, AraC type term has one ancestor -ok 67 - Kringle term has one parent -ok 68 - Kringle term has one ancestor -ok 69 - secondary accession map has 2 keys -ok -t/Ontology/IO/obo.t ................. -1..92 -ok 1 - use Bio::OntologyIO; -ok 2 - use Bio::Ontology::RelationshipType; -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 -ok 43 -ok 44 -ok 45 -ok 46 - 'got a ontology IO handler' isa 'Bio::OntologyIO' -ok 47 - 'got ontology parser2' isa 'Bio::Ontology::Ontology' -ok 48 - 'got OBO engine object' isa 'Bio::Ontology::OBOEngine' -ok 49 - 'got ontology parser2' isa 'Bio::Ontology::Ontology' -ok 50 - 'got OBO engine object' isa 'Bio::Ontology::OBOEngine' -ok 51 - 'got ontology parser2' isa 'Bio::Ontology::Ontology' -ok 52 - 'got OBO engine object' isa 'Bio::Ontology::OBOEngine' -ok 53 - Gene ontology -ok 54 - biological process -ok 55 - molecular function -ok 56 - Got root -ok 57 - Got root -ok 58 - Got regulates -# from gene_ontology -ok 59 - Got -# positively regulates from gene_ontology -ok 60 - Got -# regulates from biological_process -ok 61 - Got -# positively regulates from biological_process -ok 62 - Got predicates for gene_ontology -ok 63 - Got predicates for biological_process -ok 64 - Got regulates predicate -ok 65 - Got positively regulates predicate -ok 66 - Got relationships for biological_process -ok 67 - Got relationships for molecular_function -ok 68 - Got is a relationship from -# molecular_function -ok 69 - 'Got term object' isa 'Bio::Ontology::Term' -ok 70 - Got term id -ok 71 - Got term name -ok 72 - 'Got regulated object' isa 'Bio::Ontology::Term' -ok 73 - Got regulated term1 id -ok 74 - 'Got term1 object' isa 'Bio::Ontology::Term' -ok 75 - Got back the child -ok 76 - 'Got term object' isa 'Bio::Ontology::Term' -ok 77 - Got term id -ok 78 - Got term name -ok 79 - 'Got regulated object' isa 'Bio::Ontology::Term' -ok 80 - Got regulated term1 id -ok 81 - Got identical regulation -ok 82 - 'Got term1 object' isa 'Bio::Ontology::Term' -ok 83 - Got back the child -ok 84 - 'got a ontology IO handler' isa 'Bio::OntologyIO' -ok 85 -ok 86 -ok 87 -ok 88 -ok 89 -ok 90 -ok 91 -ok 92 -ok -t/Ontology/Ontology.t ............... -1..55 -ok 1 - use Bio::OntologyIO; -ok 2 - use Bio::Ontology::RelationshipType; -ok 3 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 -ok 43 -ok 44 -ok 45 -ok 46 -ok 47 -ok 48 -ok 49 -ok 50 -ok 51 -ok 52 -ok 53 - Interpro XML file interpro.xml can be parsed -ok 54 - Interpro XML file interpro_sample.xml can be parsed -ok 55 - Interpro XML file interpro_relationship.xml can be parsed -ok -t/Ontology/OntologyEngine.t ......... -1..31 -ok 1 - use Bio::Ontology::Term; -ok 2 - use Bio::Ontology::Relationship; -ok 3 - use Bio::Ontology::RelationshipType; -ok 4 - use Bio::Ontology::SimpleOntologyEngine; -ok 5 - use Bio::Ontology::Ontology; -ok 6 - An object of class 'Bio::Ontology::SimpleOntologyEngine' isa 'Bio::Ontology::OntologyEngineI' -ok 7 -ok 8 - adding a relationship with an undef object term fails -ok 9 - adding a relationship with an undef object term fails -ok 10 - adding a relationship with an undef subject term fails -ok 11 - adding a relationship with an undef subject term fails -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok -t/Ontology/OntologyStore.t .......... skipped: Network tests have not been requested -t/Ontology/Relationship.t ........... -1..12 -ok 1 - use Bio::Ontology::Relationship; -ok 2 - use Bio::Ontology::GOterm; -ok 3 - use Bio::Ontology::RelationshipType; -ok 4 - An object of class 'Bio::Ontology::RelationshipType' isa 'Bio::Ontology::RelationshipType' -ok 5 - An object of class 'Bio::Ontology::GOterm' isa 'Bio::Ontology::GOterm' -ok 6 - An object of class 'Bio::Ontology::GOterm' isa 'Bio::Ontology::GOterm' -ok 7 - An object of class 'Bio::Ontology::Relationship' isa 'Bio::Ontology::Relationship' -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok -t/Ontology/RelationshipType.t ....... -1..23 -ok 1 - use Bio::Ontology::RelationshipType; -ok 2 - use Bio::Ontology::Ontology; -ok 3 - An object of class 'Bio::Ontology::RelationshipType' isa 'Bio::Ontology::RelationshipType' -ok 4 - An object of class 'Bio::Ontology::RelationshipType' isa 'Bio::Ontology::TermI' -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok -t/Ontology/Term.t ................... -1..54 -ok 1 - use Bio::Ontology::Term; -ok 2 - use Bio::Ontology::TermFactory; -ok 3 - use Bio::Annotation::DBLink; -ok 4 - An object of class 'Bio::Ontology::Term' isa 'Bio::Ontology::TermI' -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 -ok 43 -ok 44 - An object of class 'Bio::Ontology::Term' isa 'Bio::Ontology::TermI' -ok 45 -ok 46 - An object of class 'Bio::Ontology::GOterm' isa 'Bio::Ontology::TermI' -ok 47 - An object of class 'Bio::Ontology::GOterm' isa 'Bio::Ontology::GOterm' -ok 48 -ok 49 -ok 50 - An object of class 'Bio::Annotation::OntologyTerm' isa 'Bio::Ontology::TermI' -ok 51 - An object of class 'Bio::Annotation::OntologyTerm' isa 'Bio::AnnotationI' -ok 52 -ok 53 -ok 54 -ok -t/RemoteDB/SeqRead_fail.t ........... skipped: Network tests have not been requested -t/RemoteDB/Taxonomy.t ............... -1..152 -ok 1 - use Bio::DB::Taxonomy; -ok 2 - use Bio::Tree::Tree; -ok 3 -ok 4 - An object of class 'Bio::DB::Taxonomy::flatfile' isa 'Bio::DB::Taxonomy::flatfile' -ok 5 - An object of class 'Bio::DB::Taxonomy::flatfile' isa 'Bio::DB::Taxonomy' -ok 6 - removal of temporary index files: no -directory -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 - removal of temporary index files: test_output_dir() -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 - Bio::DB::Taxonomy::flatfile: common names -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 -ok 43 -ok 44 -ok 45 -ok 46 -ok 47 -ok 48 -ok 49 -ok 50 -ok 51 -ok 52 -ok 53 -ok 54 -ok 55 -ok 56 -ok 57 -ok 58 -ok 59 -ok 60 -ok 61 -ok 62 - An object of class 'Bio::DB::Taxonomy::list' isa 'Bio::DB::Taxonomy::list' -ok 63 - An object of class 'Bio::DB::Taxonomy::list' isa 'Bio::DB::Taxonomy' -ok 64 -ok 65 -ok 66 -ok 67 -ok 68 - Ranks -ok 69 -ok 70 -ok 71 - Ranks -ok 72 -ok 73 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' -ok 74 -ok 75 -ok 76 -ok 77 -ok 78 -ok 79 -ok 80 -ok 81 -ok 82 -ok 83 -ok 84 -ok 85 -ok 86 -ok 87 -ok 88 -ok 89 -ok 90 # skip The optional module Bio::DB::Taxonomy::entrez (or dependencies thereof) was not installed -ok 91 # skip The optional module Bio::DB::Taxonomy::entrez (or dependencies thereof) was not installed -ok 92 # skip The optional module Bio::DB::Taxonomy::entrez (or dependencies thereof) was not installed -ok 93 # skip The optional module Bio::DB::Taxonomy::entrez (or dependencies thereof) was not installed -ok 94 # skip The optional module Bio::DB::Taxonomy::entrez (or dependencies thereof) was not installed -ok 95 # skip The optional module Bio::DB::Taxonomy::entrez (or dependencies thereof) was not installed -ok 96 # skip The optional module Bio::DB::Taxonomy::entrez (or dependencies thereof) was not installed -ok 97 # skip The optional module Bio::DB::Taxonomy::entrez (or dependencies thereof) was not installed -ok 98 # skip The optional module Bio::DB::Taxonomy::entrez (or dependencies thereof) was not installed -ok 99 -ok 100 -ok 101 -ok 102 -ok 103 -ok 104 -ok 105 -ok 106 -ok 107 -ok 108 -ok 109 -ok 110 - List context -ok 111 - 'Scalar context' isa 'SCALAR' -ok 112 -ok 113 -ok 114 -ok 115 -ok 116 -ok 117 -ok 118 -ok 119 - DB with ambiguous names -ok 120 -ok 121 -ok 122 -ok 123 -ok 124 -ok 125 -ok 126 -ok 127 -ok 128 -ok 129 -ok 130 -ok 131 -ok 132 -ok 133 -ok 134 -ok 135 -ok 136 -ok 137 -ok 138 -ok 139 -ok 140 -ok 141 -ok 142 -ok 143 -ok 144 -ok 145 -ok 146 -ok 147 -ok 148 -ok 149 -ok 150 -ok 151 -ok 152 -ok -t/Root/Exception.t .................. -1..7 -ok 1 - use Bio::Root::TestObject; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok -t/Root/HTTPget.t .................... skipped: Network tests have not been requested -t/Root/IO.t ......................... -1..154 -ok 1 - use Bio::Root::IO; -ok 2 -ok 3 - An object of class 'Bio::Root::IO' isa 'Bio::Root::IO' -ok 4 - Throw -ok 5 - threw Regexp ((?^:Testing throw)) -ok 6 - Warn -ok 7 - threw Regexp ((?^:Testing throw)) -ok 8 - Stack trace -ok 9 -ok 10 - Verbosity -ok 11 -ok 12 -ok 13 -ok 14 - executable file -ok 15 - non-executable file -ok 16 - executable dir -ok 17 -ok 18 -ok 19 -ok 20 - Read from file -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 - Write to file -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 - Read+write to file -ok 36 -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 -ok 43 -ok 44 -ok 45 -ok 46 - Read from File::Temp handle -ok 47 - An object of class 'Bio::Root::IO' isa 'Bio::Root::IO' -ok 48 - is a write handle -ok 49 - no warnings in ->close() -ok 50 -ok 51 - Exclusive arguments -ok 52 - threw Regexp ((?^:Input file given twice)) -ok 53 - threw Regexp ((?^:File or filehandle provided with -string)) -ok 54 - threw Regexp ((?^:Providing both a file and a filehandle for reading)) -ok 55 - threw Regexp ((?^:File or filehandle provided with -string)) -ok 56 - threw Regexp ((?^:File or filehandle provided with -string)) -ok 57 - Same file -ok 58 - Pushback -ok 59 -ok 60 -ok 61 -ok 62 -ok 63 -ok 64 -ok 65 -ok 66 -ok 67 -ok 68 -ok 69 -ok 70 -ok 71 - _print -ok 72 -ok 73 - _insert at middle of file -ok 74 -ok 75 -ok 76 -ok 77 -ok 78 -ok 79 - _insert in empty file -ok 80 -ok 81 -ok 82 -ok 83 -ok 84 -ok 85 -ok 86 -ok 87 -ok 88 -ok 89 -ok 90 -ok 91 -ok 92 -ok 93 -ok 94 -ok 95 -ok 96 -ok 97 -ok 98 -ok 99 -ok 100 -ok 101 -ok 102 -ok 103 -ok 104 -ok 105 -ok 106 -ok 107 -ok 108 -ok 109 # TODO Sporadic test failures when running using PerlIO::eol on Linux w/Windows line endings: # -ok 110 -ok 111 -ok 112 # TODO Sporadic test failures when running using PerlIO::eol on Linux w/Windows line endings: # -ok 113 -ok 114 -ok 115 # TODO Sporadic test failures when running using PerlIO::eol on Linux w/Windows line endings: # -ok 116 -ok 117 -ok 118 # TODO Sporadic test failures when running using PerlIO::eol on Linux w/Windows line endings: # -ok 119 -ok 120 -ok 121 -ok 122 - Bio::Root::IO->new can handle a Path::Class object -ok 123 - An object of class 'Bio::Root::IO' isa 'Bio::Root::IO' -ok 124 - Read string -ok 125 -ok 126 -ok 127 -ok 128 -ok 129 -ok 130 -ok 131 -ok 132 -ok 133 -ok 134 -ok 135 -ok 136 - An object of class 'Bio::Root::IO' isa 'Bio::Root::IO' -ok 137 - A reference of type 'GLOB' isa 'GLOB' -ok 138 -ok 139 -ok 140 - auto UNLINK => 1 -ok 141 -ok 142 -ok 143 - tempfile deleted -ok 144 - A reference of type 'GLOB' isa 'GLOB' -ok 145 -ok 146 - UNLINK => 0 -ok 147 -ok 148 -ok 149 - A reference of type 'GLOB' isa 'GLOB' -ok 150 - tempfile suffix -ok 151 -ok 152 - A reference of type 'GLOB' isa 'GLOB' -ok 153 - tempfile() in scalar context -ok 154 -ok -t/Root/RootI.t ...................... -1..43 -ok 1 - use Bio::Root::Root; -ok 2 -ok 3 - An object of class 'Bio::Root::Root' isa 'Bio::Root::RootI' -ok 4 - threw Regexp ((?^:Testing throw)) -ok 5 - threw Regexp ((?^:EXCEPTION: Bio::Root::NotImplemented)) -ok 6 - threw Regexp ((?^:EXCEPTION )) -ok 7 - threw Regexp ((?^:Testing throw)) -ok 8 -ok 9 - threw Regexp ((?^:Testing throw)) -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 - arg callable since method was created -ok 16 - mal-formed arg callable since method was created with good name -ok 17 - Bio::Foo2->can('t3') -ok 18 - Methods don't pollute original Bio::Root::Root namespace -ok 19 - Bio::Foo2->can('test_4') -ok 20 - Methods don't pollute original Bio::Root::Root namespace -ok 21 - Bio::Foo3->can('t5') -ok 22 - arg not in method list not created -ok 23 - Bio::Foo3->can('t5') -ok 24 - Methods don't pollute original Bio::Root::Root namespace -ok 25 - verbose was set correctly -ok 26 - synonym was set correctly -ok 27 - real method of synonym was set correctly -ok 28 - mal-formed arg correctly resolved to created method -ok 29 - synonym of set method was set correctly -ok 30 - Bio::Foo4->can('t7') -ok 31 - Methods don't pollute original Bio::Root::Root namespace -ok 32 - Bio::Foo4->can('test7') -ok 33 - Methods don't pollute original Bio::Root::Root namespace -ok 34 - Bio::Foo4->can('test_8') -ok 35 - Methods don't pollute original Bio::Root::Root namespace -ok 36 - Bio::Foo4->can('t8') -ok 37 - Methods don't pollute original Bio::Root::Root namespace -ok 38 - clone -ok 39 - clone -ok 40 - clone -ok 41 - clone changed, original didn't -ok 42 - parameters passed to clone() modify object -ok 43 - original is not modified -ok -t/Root/RootIO.t ..................... skipped: Network tests have not been requested -t/Root/Storable.t ................... -1..35 -ok 1 - use Bio::Root::Storable; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok - ---------------------- WARNING --------------------- -MSG: find_exe: Multiple paths to 'gzip' found. Using /usr/bin/gzip. ---------------------------------------------------- - ---------------------- WARNING --------------------- -MSG: find_exe: Multiple paths to 'gzip' found. Using /usr/bin/gzip. ---------------------------------------------------- - ---------------------- WARNING --------------------- -MSG: find_exe: Multiple paths to 'gunzip' found. Using /usr/bin/gunzip. ---------------------------------------------------- - ---------------------- WARNING --------------------- -MSG: find_exe: Multiple paths to 'gzip' found. Using /usr/bin/gzip. ---------------------------------------------------- - ---------------------- WARNING --------------------- -MSG: find_exe: Multiple paths to 'gunzip' found. Using /usr/bin/gunzip. ---------------------------------------------------- -t/Root/Utilities.t .................. -1..56 -ok 1 - use Bio::Root::Utilities; -ok 2 - An object of class 'Bio::Root::Utilities' isa 'Bio::Root::Utilities' -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 - file_date() -ok 38 - unix (\n or 012 or ^J) -ok 39 - date format -ok 40 - date format -ok 41 - date format -ok 42 - date format -ok 43 - date format -ok 44 -ok 45 -ok 46 -ok 47 -ok 48 -ok 49 -ok 50 -ok 51 -ok 52 -ok 53 -ok 54 -ok 55 -ok 56 -ok -t/SearchIO/axt.t .................... -1..19 -ok 1 - use Bio::SearchIO; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok -t/SearchIO/blast.t .................. -1..1389 -ok 1 - use Bio::SearchIO; -ok 2 - Bio::SearchIO->new can handle a Path::Class object -ok 3 - An object of class 'Bio::SearchIO::blast' isa 'Bio::Root::IO' -ok 4 - Bio::SearchIO->new can handle a Path::Class object -ok 5 - An object of class 'Bio::SearchIO::blast' isa 'Bio::Root::IO' -ok 6 -ok 7 - database_name() -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 -ok 43 -ok 44 -ok 45 -ok 46 -ok 47 -ok 48 -ok 49 -ok 50 -ok 51 -ok 52 -ok 53 -ok 54 -ok 55 -ok 56 -ok 57 -ok 58 -ok 59 -ok 60 -ok 61 -ok 62 -ok 63 -ok 64 -ok 65 -ok 66 -ok 67 -ok 68 -ok 69 -ok 70 -ok 71 -ok 72 -ok 73 -ok 74 -ok 75 -ok 76 -ok 77 -ok 78 -ok 79 -ok 80 -ok 81 -ok 82 -ok 83 -ok 84 -ok 85 -ok 86 -ok 87 -ok 88 -ok 89 -ok 90 -ok 91 -ok 92 -ok 93 -ok 94 -ok 95 -ok 96 -ok 97 -ok 98 -ok 99 -ok 100 -ok 101 -ok 102 -ok 103 -ok 104 -ok 105 -ok 106 -ok 107 -ok 108 -ok 109 -ok 110 -ok 111 -ok 112 -ok 113 -ok 114 -ok 115 -ok 116 -ok 117 -ok 118 -ok 119 -ok 120 -ok 121 -ok 122 -ok 123 -ok 124 -ok 125 -ok 126 -ok 127 -ok 128 -ok 129 -ok 130 -ok 131 -ok 132 -ok 133 -ok 134 -ok 135 -ok 136 -ok 137 -ok 138 -ok 139 -ok 140 -ok 141 -ok 142 -ok 143 -ok 144 -ok 145 -ok 146 -ok 147 -ok 148 -ok 149 -ok 150 -ok 151 -ok 152 -ok 153 -ok 154 -ok 155 -ok 156 -ok 157 -ok 158 -ok 159 -ok 160 -ok 161 -ok 162 -ok 163 -ok 164 -ok 165 -ok 166 -ok 167 -ok 168 -ok 169 -ok 170 -ok 171 -ok 172 -ok 173 -ok 174 -ok 175 -ok 176 -ok 177 -ok 178 -ok 179 -ok 180 -ok 181 -ok 182 -ok 183 -ok 184 -ok 185 -ok 186 -ok 187 -ok 188 -ok 189 -ok 190 -ok 191 -ok 192 -ok 193 -ok 194 -ok 195 -ok 196 -ok 197 -ok 198 -ok 199 -ok 200 -ok 201 -ok 202 -ok 203 -ok 204 -ok 205 -ok 206 -ok 207 -ok 208 -ok 209 -ok 210 -ok 211 -ok 212 -ok 213 -ok 214 -ok 215 -ok 216 -ok 217 -ok 218 -ok 219 -ok 220 -ok 221 -ok 222 -ok 223 -ok 224 -ok 225 -ok 226 -ok 227 -ok 228 -ok 229 -ok 230 -ok 231 -ok 232 -ok 233 -ok 234 -ok 235 -ok 236 -ok 237 -ok 238 -ok 239 -ok 240 -ok 241 -ok 242 -ok 243 -ok 244 -ok 245 -ok 246 -ok 247 -ok 248 -ok 249 -ok 250 -ok 251 -ok 252 -ok 253 -ok 254 -ok 255 -ok 256 -ok 257 -ok 258 -ok 259 -ok 260 -ok 261 -ok 262 -ok 263 -ok 264 -ok 265 -ok 266 -ok 267 -ok 268 -ok 269 -ok 270 -ok 271 -ok 272 -ok 273 -ok 274 -ok 275 -ok 276 -ok 277 -ok 278 -ok 279 -ok 280 -ok 281 -ok 282 -ok 283 -ok 284 -ok 285 -ok 286 -ok 287 -ok 288 -ok 289 -ok 290 -ok 291 -ok 292 -ok 293 -ok 294 -ok 295 -ok 296 -ok 297 -ok 298 -ok 299 -ok 300 -ok 301 -ok 302 -ok 303 -ok 304 -ok 305 -ok 306 -ok 307 -ok 308 -ok 309 -ok 310 -ok 311 -ok 312 -ok 313 -ok 314 -ok 315 -ok 316 -ok 317 -ok 318 -ok 319 -ok 320 -ok 321 -ok 322 -ok 323 -ok 324 -ok 325 -ok 326 -ok 327 -ok 328 -ok 329 -ok 330 -ok 331 -ok 332 -ok 333 -ok 334 -ok 335 -ok 336 -ok 337 -ok 338 -ok 339 -ok 340 -ok 341 -ok 342 -ok 343 -ok 344 -ok 345 -ok 346 -ok 347 -ok 348 -ok 349 -ok 350 -ok 351 -ok 352 -ok 353 -ok 354 -ok 355 -ok 356 -ok 357 -ok 358 -ok 359 -ok 360 -ok 361 -ok 362 -ok 363 -ok 364 -ok 365 -ok 366 -ok 367 -ok 368 -ok 369 -ok 370 -ok 371 -ok 372 -ok 373 -ok 374 -ok 375 -ok 376 -ok 377 -ok 378 -ok 379 -ok 380 -ok 381 -ok 382 -ok 383 -ok 384 -ok 385 -ok 386 -ok 387 -ok 388 -ok 389 -ok 390 -ok 391 -ok 392 -ok 393 -ok 394 -ok 395 -ok 396 -ok 397 -ok 398 -ok 399 -ok 400 -ok 401 -ok 402 -ok 403 -ok 404 -ok 405 -ok 406 -ok 407 -ok 408 -ok 409 -ok 410 -ok 411 -ok 412 -ok 413 -ok 414 -not ok 415 # TODO frac_identical & frac_conserved are still too wrong -# Failed (TODO) test at t/SearchIO/blast.t line 667. -# '0.852' -# > -# '0.9' -not ok 416 # TODO frac_identical & frac_conserved are still too wrong -# Failed (TODO) test at t/SearchIO/blast.t line 668. -# '1.599' -# <= -# '1' -ok 417 -ok 418 -ok 419 -ok 420 -ok 421 -ok 422 -ok 423 -ok 424 -ok 425 -ok 426 -ok 427 -ok 428 -ok 429 -ok 430 -ok 431 -ok 432 -ok 433 -ok 434 -ok 435 -ok 436 -ok 437 -ok 438 -ok 439 -ok 440 -ok 441 -ok 442 -ok 443 -ok 444 -ok 445 -ok 446 -ok 447 -ok 448 -ok 449 -ok 450 -ok 451 -ok 452 -ok 453 -ok 454 -ok 455 -ok 456 -ok 457 -ok 458 -ok 459 -ok 460 -ok 461 -ok 462 -ok 463 -ok 464 -ok 465 -ok 466 -ok 467 -ok 468 -ok 469 -ok 470 -ok 471 -ok 472 -ok 473 -ok 474 -ok 475 -ok 476 -ok 477 -ok 478 -ok 479 -ok 480 -ok 481 -ok 482 -ok 483 -ok 484 -ok 485 -ok 486 -ok 487 -ok 488 -ok 489 -ok 490 -ok 491 -ok 492 -ok 493 -ok 494 -ok 495 -ok 496 -ok 497 -ok 498 -ok 499 -ok 500 -ok 501 -ok 502 -ok 503 -ok 504 -ok 505 -ok 506 -ok 507 -ok 508 -ok 509 -ok 510 -ok 511 -ok 512 -ok 513 -ok 514 -ok 515 -ok 516 -ok 517 -ok 518 -ok 519 -ok 520 -ok 521 -ok 522 -ok 523 -ok 524 -ok 525 -ok 526 -ok 527 -ok 528 -ok 529 -ok 530 -ok 531 -ok 532 -ok 533 -ok 534 -ok 535 -ok 536 -ok 537 -ok 538 -ok 539 -ok 540 -ok 541 -ok 542 -ok 543 -ok 544 -ok 545 -ok 546 -ok 547 -ok 548 -ok 549 -ok 550 -ok 551 -ok 552 -ok 553 -ok 554 -ok 555 -ok 556 -ok 557 -ok 558 -ok 559 -ok 560 -ok 561 -ok 562 -ok 563 -ok 564 -ok 565 -ok 566 -ok 567 -ok 568 -ok 569 -ok 570 -ok 571 -ok 572 -ok 573 -ok 574 -ok 575 -ok 576 -ok 577 -ok 578 -ok 579 -ok 580 -ok 581 -ok 582 -ok 583 -ok 584 -ok 585 -ok 586 -ok 587 -ok 588 -ok 589 -ok 590 -ok 591 -ok 592 -ok 593 -ok 594 -ok 595 -ok 596 -ok 597 - Multiblast query test -ok 598 -ok 599 - Multiblast query test -ok 600 -ok 601 - Multiblast query test -ok 602 -ok 603 - Multiblast query test -ok 604 -ok 605 -ok 606 -ok 607 -ok 608 -ok 609 -ok 610 -ok 611 -ok 612 -ok 613 -ok 614 -ok 615 -ok 616 -ok 617 -ok 618 -ok 619 -ok 620 -ok 621 -ok 622 -ok 623 -ok 624 -ok 625 -ok 626 -ok 627 -ok 628 -ok 629 -ok 630 -ok 631 -ok 632 -ok 633 -ok 634 -ok 635 -ok 636 -ok 637 -ok 638 -ok 639 -ok 640 -ok 641 -ok 642 -ok 643 -ok 644 -ok 645 -ok 646 -ok 647 -ok 648 -ok 649 -ok 650 -ok 651 -ok 652 -ok 653 -ok 654 -ok 655 -ok 656 -ok 657 -ok 658 -ok 659 -ok 660 -ok 661 -ok 662 -ok 663 -ok 664 -ok 665 -ok 666 -ok 667 -ok 668 -ok 669 -ok 670 -ok 671 -ok 672 -ok 673 -ok 674 -ok 675 -ok 676 -ok 677 -ok 678 -ok 679 -ok 680 -ok 681 -ok 682 -ok 683 -ok 684 -ok 685 -ok 686 -ok 687 -ok 688 -ok 689 -ok 690 -ok 691 -ok 692 -ok 693 -ok 694 -ok 695 -ok 696 -ok 697 -ok 698 -ok 699 -ok 700 -ok 701 -ok 702 -ok 703 -ok 704 -ok 705 -ok 706 -ok 707 -ok 708 -ok 709 -ok 710 -ok 711 -ok 712 -ok 713 -ok 714 -ok 715 -ok 716 -ok 717 -ok 718 -ok 719 -ok 720 -ok 721 -ok 722 -ok 723 -ok 724 -ok 725 -ok 726 -ok 727 -ok 728 -ok 729 -ok 730 -ok 731 -ok 732 -ok 733 -ok 734 -ok 735 -ok 736 -ok 737 -ok 738 -ok 739 -ok 740 -ok 741 -ok 742 -ok 743 -ok 744 -ok 745 -ok 746 -ok 747 -ok 748 -ok 749 -ok 750 -ok 751 -ok 752 -ok 753 -ok 754 -ok 755 -ok 756 -ok 757 -ok 758 -ok 759 -ok 760 -ok 761 -ok 762 -ok 763 -ok 764 -ok 765 -ok 766 -ok 767 -ok 768 -ok 769 -ok 770 -ok 771 -ok 772 -ok 773 -ok 774 -ok 775 -ok 776 -ok 777 -ok 778 -ok 779 -ok 780 -ok 781 -ok 782 -ok 783 -ok 784 -ok 785 -ok 786 -ok 787 -ok 788 -ok 789 -ok 790 -ok 791 -ok 792 -ok 793 -ok 794 -ok 795 -ok 796 -ok 797 -ok 798 -ok 799 -ok 800 -ok 801 -ok 802 -ok 803 -ok 804 -ok 805 -ok 806 -ok 807 -ok 808 -ok 809 -ok 810 -ok 811 -ok 812 -ok 813 -ok 814 -ok 815 -ok 816 -ok 817 -ok 818 -ok 819 -ok 820 -ok 821 -ok 822 -ok 823 -ok 824 -ok 825 -ok 826 -ok 827 -ok 828 -ok 829 -ok 830 -ok 831 -ok 832 -ok 833 -ok 834 -ok 835 -ok 836 -ok 837 -ok 838 -ok 839 -ok 840 -ok 841 -ok 842 -ok 843 -ok 844 -ok 845 -ok 846 -ok 847 -ok 848 -ok 849 -ok 850 -ok 851 -ok 852 -ok 853 -ok 854 -ok 855 -ok 856 -ok 857 -ok 858 -ok 859 -ok 860 -ok 861 -ok 862 -ok 863 -ok 864 -ok 865 -ok 866 -ok 867 -ok 868 -ok 869 -ok 870 -ok 871 -ok 872 -ok 873 -ok 874 -ok 875 -ok 876 -ok 877 -ok 878 -ok 879 -ok 880 -ok 881 -ok 882 -ok 883 -ok 884 -ok 885 - An object of class 'Bio::Search::Result::BlastResult' isa 'Bio::Search::Result::ResultI' -ok 886 -ok 887 -ok 888 -ok 889 -ok 890 -ok 891 -ok 892 -ok 893 -ok 894 -ok 895 -ok 896 -ok 897 -ok 898 -ok 899 -ok 900 -ok 901 -ok 902 -ok 903 -ok 904 -ok 905 - An object of class 'Bio::Search::Result::BlastResult' isa 'Bio::Search::Result::ResultI' -ok 906 -ok 907 -ok 908 -ok 909 -ok 910 -ok 911 -ok 912 -ok 913 -ok 914 -ok 915 -ok 916 -ok 917 -ok 918 -ok 919 -ok 920 -ok 921 -ok 922 -ok 923 -ok 924 -ok 925 -ok 926 -ok 927 -ok 928 -ok 929 - An object of class 'Bio::Search::Result::BlastResult' isa 'Bio::Search::Result::ResultI' -ok 930 -ok 931 -ok 932 -ok 933 -ok 934 -ok 935 -ok 936 -ok 937 -ok 938 -ok 939 -ok 940 -ok 941 -ok 942 -ok 943 -ok 944 -ok 945 -ok 946 -ok 947 -ok 948 -ok 949 -ok 950 -ok 951 -ok 952 -ok 953 - An object of class 'Bio::Search::Result::BlastResult' isa 'Bio::Search::Result::ResultI' -ok 954 -ok 955 -ok 956 -ok 957 -ok 958 -ok 959 -ok 960 -ok 961 -ok 962 -ok 963 -ok 964 -ok 965 -ok 966 -ok 967 -ok 968 -ok 969 -ok 970 -ok 971 -ok 972 -ok 973 -ok 974 -ok 975 -ok 976 -ok 977 -ok 978 -ok 979 -ok 980 -ok 981 -ok 982 - An object of class 'Bio::Search::Result::BlastResult' isa 'Bio::Search::Result::ResultI' -ok 983 -ok 984 -ok 985 -ok 986 -ok 987 -ok 988 -ok 989 -ok 990 -ok 991 -ok 992 -ok 993 -ok 994 -ok 995 -ok 996 -ok 997 -ok 998 -ok 999 -ok 1000 -ok 1001 -ok 1002 -ok 1003 -ok 1004 -ok 1005 -ok 1006 -ok 1007 - An object of class 'Bio::Search::Result::BlastResult' isa 'Bio::Search::Result::ResultI' -ok 1008 -ok 1009 -ok 1010 -ok 1011 -ok 1012 -ok 1013 -ok 1014 -ok 1015 -ok 1016 -ok 1017 -ok 1018 -ok 1019 -ok 1020 -ok 1021 -ok 1022 -ok 1023 -ok 1024 -ok 1025 -ok 1026 -ok 1027 -ok 1028 -ok 1029 -ok 1030 -ok 1031 -ok 1032 -ok 1033 -ok 1034 -ok 1035 - An object of class 'Bio::Search::Result::BlastResult' isa 'Bio::Search::Result::ResultI' -ok 1036 -ok 1037 -ok 1038 -ok 1039 -ok 1040 -ok 1041 -ok 1042 -ok 1043 -ok 1044 -ok 1045 -ok 1046 -ok 1047 -ok 1048 -ok 1049 -ok 1050 -ok 1051 -ok 1052 -ok 1053 -ok 1054 -ok 1055 -ok 1056 -ok 1057 -ok 1058 -ok 1059 -ok 1060 -ok 1061 -ok 1062 -ok 1063 -ok 1064 - An object of class 'Bio::Search::Result::BlastResult' isa 'Bio::Search::Result::ResultI' -ok 1065 -ok 1066 -ok 1067 -ok 1068 -ok 1069 -ok 1070 -ok 1071 -ok 1072 -ok 1073 -ok 1074 -ok 1075 -ok 1076 -ok 1077 -ok 1078 -ok 1079 -ok 1080 -ok 1081 -ok 1082 -ok 1083 - blast for f.tblx -ok 1084 - fasta for f.ssearch -ok 1085 - blastxml for f.xml -ok 1086 - exonerate for f.exonerate -ok 1087 - blast for f.blx -ok 1088 - blast for filename.blast -ok 1089 - fasta for f.SSEARCH.m9 -ok 1090 - blastxml for f.blastxml -ok 1091 - fasta for f.m9 -ok 1092 - fasta for f.fasta -ok 1093 - fasta for f.psearch -ok 1094 - exonerate for f.exon -ok 1095 - blast for fast.bls -ok 1096 - fasta for f.fa -ok 1097 - fasta for f.osearch -ok 1098 - fasta for f.fy -ok 1099 - fasta for f.fx -ok 1100 - blast for filename.bls -ok 1101 -ok 1102 -ok 1103 -ok 1104 -ok 1105 -ok 1106 -ok 1107 -ok 1108 -ok 1109 -ok 1110 -ok 1111 -ok 1112 -ok 1113 -ok 1114 -ok 1115 -ok 1116 - full hit name -ok 1117 - hit accession -ok 1118 -ok 1119 -ok 1120 - query start -ok 1121 - query start -ok 1122 -ok 1123 -ok 1124 -ok 1125 -ok 1126 -ok 1127 -ok 1128 -ok 1129 -ok 1130 -ok 1131 -ok 1132 -ok 1133 -ok 1134 -ok 1135 -ok 1136 -ok 1137 -ok 1138 -ok 1139 -ok 1140 -ok 1141 -ok 1142 -ok 1143 -ok 1144 -ok 1145 -ok 1146 -ok 1147 -ok 1148 -ok 1149 -ok 1150 -ok 1151 -ok 1152 -ok 1153 -ok 1154 -ok 1155 -ok 1156 -ok 1157 -ok 1158 -ok 1159 -ok 1160 -ok 1161 -ok 1162 -ok 1163 -ok 1164 -ok 1165 -ok 1166 -ok 1167 -ok 1168 -ok 1169 -ok 1170 -ok 1171 -ok 1172 -ok 1173 -ok 1174 -ok 1175 -ok 1176 -ok 1177 -ok 1178 -ok 1179 -ok 1180 -ok 1181 -ok 1182 -ok 1183 -ok 1184 -ok 1185 -ok 1186 -ok 1187 -ok 1188 -ok 1189 -ok 1190 -ok 1191 -ok 1192 -ok 1193 -ok 1194 -ok 1195 -ok 1196 -ok 1197 -ok 1198 -ok 1199 -ok 1200 -ok 1201 -ok 1202 -ok 1203 -ok 1204 -ok 1205 -ok 1206 -ok 1207 -ok 1208 -ok 1209 -ok 1210 -ok 1211 -ok 1212 -ok 1213 -ok 1214 -ok 1215 -ok 1216 -ok 1217 -ok 1218 -ok 1219 -ok 1220 -ok 1221 -ok 1222 -ok 1223 -ok 1224 -ok 1225 -ok 1226 -ok 1227 -ok 1228 -ok 1229 -ok 1230 -ok 1231 -ok 1232 -ok 1233 -ok 1234 -ok 1235 -ok 1236 -ok 1237 -ok 1238 -ok 1239 -ok 1240 -ok 1241 -ok 1242 -ok 1243 -ok 1244 -ok 1245 -ok 1246 -ok 1247 -ok 1248 -ok 1249 -ok 1250 -ok 1251 -ok 1252 -ok 1253 -ok 1254 -ok 1255 -ok 1256 -ok 1257 -ok 1258 -ok 1259 -ok 1260 -ok 1261 -ok 1262 -ok 1263 -ok 1264 -ok 1265 -ok 1266 -ok 1267 -ok 1268 -ok 1269 -ok 1270 -ok 1271 -ok 1272 -ok 1273 -ok 1274 -ok 1275 -ok 1276 -ok 1277 -ok 1278 -ok 1279 -ok 1280 -ok 1281 -ok 1282 -ok 1283 -ok 1284 -ok 1285 -ok 1286 -ok 1287 -ok 1288 -ok 1289 -ok 1290 -ok 1291 -ok 1292 -ok 1293 -ok 1294 -ok 1295 -ok 1296 -ok 1297 -ok 1298 -ok 1299 -ok 1300 -ok 1301 -ok 1302 -ok 1303 -ok 1304 -ok 1305 -ok 1306 -ok 1307 -ok 1308 -ok 1309 -ok 1310 -ok 1311 -ok 1312 -ok 1313 -ok 1314 -ok 1315 -ok 1316 -ok 1317 -ok 1318 -ok 1319 -ok 1320 -ok 1321 -ok 1322 -ok 1323 -ok 1324 -ok 1325 -ok 1326 -ok 1327 -ok 1328 -ok 1329 -ok 1330 -ok 1331 -ok 1332 -ok 1333 -ok 1334 -ok 1335 -ok 1336 -ok 1337 -ok 1338 -ok 1339 -ok 1340 -ok 1341 -ok 1342 -ok 1343 -ok 1344 -ok 1345 -ok 1346 -ok 1347 -ok 1348 -ok 1349 -ok 1350 -ok 1351 -ok 1352 -ok 1353 -ok 1354 -ok 1355 -ok 1356 -ok 1357 -ok 1358 -ok 1359 -ok 1360 -ok 1361 -ok 1362 -ok 1363 -ok 1364 -ok 1365 -ok 1366 -ok 1367 -ok 1368 -ok 1369 -ok 1370 -ok 1371 -ok 1372 -ok 1373 -ok 1374 -ok 1375 -ok 1376 -ok 1377 -ok 1378 -ok 1379 -ok 1380 -ok 1381 -ok 1382 -ok 1383 -ok 1384 - testing Bug 3298 -ok 1385 - testing Bug 3298 -ok 1386 - testing Bug 3298 -ok 1387 - testing Bug 3251 -ok 1388 - testing Bug 3251 -ok 1389 - testing Bug 3251 -ok -t/SearchIO/blast_pull.t ............. -1..289 -ok 1 - use Bio::SearchIO; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 -ok 43 -ok 44 -ok 45 -ok 46 -ok 47 -ok 48 -ok 49 -ok 50 -ok 51 -ok 52 -ok 53 -ok 54 -ok 55 -ok 56 -ok 57 -ok 58 -ok 59 - database_name() -ok 60 -ok 61 -ok 62 -ok 63 -ok 64 -ok 65 -ok 66 -ok 67 -ok 68 -ok 69 -ok 70 -ok 71 -ok 72 -ok 73 -ok 74 -ok 75 -ok 76 -ok 77 -ok 78 -ok 79 -ok 80 -ok 81 -ok 82 -ok 83 -ok 84 -ok 85 -ok 86 -ok 87 -ok 88 -ok 89 -ok 90 -ok 91 -ok 92 -ok 93 -ok 94 -ok 95 -ok 96 -ok 97 -ok 98 -ok 99 -ok 100 -ok 101 -ok 102 -ok 103 -ok 104 -ok 105 -ok 106 -ok 107 -ok 108 -ok 109 -ok 110 -ok 111 -ok 112 -ok 113 -ok 114 -ok 115 -ok 116 -ok 117 -ok 118 -ok 119 -ok 120 -ok 121 -ok 122 -ok 123 -ok 124 -ok 125 -ok 126 -ok 127 -ok 128 -ok 129 -ok 130 -ok 131 -ok 132 -ok 133 -ok 134 -ok 135 -ok 136 -ok 137 -ok 138 -ok 139 -ok 140 -ok 141 -ok 142 -ok 143 -ok 144 -ok 145 -ok 146 -ok 147 -ok 148 -ok 149 -ok 150 -ok 151 -ok 152 -ok 153 -ok 154 -ok 155 -ok 156 -ok 157 -ok 158 -ok 159 -ok 160 -ok 161 -ok 162 -ok 163 -ok 164 -ok 165 -ok 166 -ok 167 -ok 168 -ok 169 -ok 170 -ok 171 -ok 172 -ok 173 -ok 174 -ok 175 -ok 176 -ok 177 -ok 178 -ok 179 -ok 180 -ok 181 -ok 182 -ok 183 -ok 184 -ok 185 -ok 186 -ok 187 -ok 188 -ok 189 -ok 190 -not ok 191 # TODO frac_identical failing! -# Failed (TODO) test at t/SearchIO/blast_pull.t line 259. -# got: '0.946' -# expected: '0.943' -ok 192 -ok 193 -ok 194 -ok 195 -ok 196 - Multiblast query test -ok 197 - Multiblast query test -ok 198 - Multiblast query test -ok 199 - Multiblast query test -ok 200 -ok 201 -ok 202 -ok 203 - full hit name -ok 204 - hit accession -ok 205 -ok 206 - query start -ok 207 - query start -ok 208 -ok 209 -ok 210 -ok 211 -ok 212 -ok 213 -ok 214 -ok 215 -ok 216 -ok 217 -ok 218 -ok 219 -ok 220 -ok 221 -ok 222 -ok 223 -ok 224 -ok 225 -ok 226 -ok 227 -ok 228 -ok 229 -ok 230 -ok 231 -ok 232 -ok 233 -ok 234 -ok 235 -ok 236 -ok 237 -ok 238 -ok 239 -ok 240 -ok 241 -ok 242 -ok 243 -ok 244 -ok 245 -ok 246 -ok 247 -ok 248 -ok 249 -ok 250 -ok 251 -ok 252 -ok 253 -ok 254 -ok 255 -ok 256 -ok 257 -ok 258 -ok 259 -ok 260 -ok 261 -ok 262 -ok 263 -ok 264 -ok 265 -ok 266 -ok 267 -ok 268 -ok 269 -ok 270 -ok 271 -ok 272 -ok 273 -ok 274 -ok 275 -ok 276 -ok 277 -ok 278 -ok 279 -ok 280 -ok 281 -ok 282 -ok 283 -ok 284 -ok 285 -ok 286 -ok 287 -ok 288 -ok 289 -ok -t/SearchIO/blasttable.t ............. -1..166 -ok 1 - use Bio::SearchIO; -ok 2 - use Bio::Search::SearchUtils; -ok 3 - An object of class 'Bio::Search::Result::BlastResult' isa 'Bio::Search::Result::ResultI' -ok 4 -ok 5 -ok 6 - hit1_bits -ok 7 - hit1_name -ok 8 - hsp1_bits -ok 9 - hsp1_gaps -ok 10 - hsp1_he -ok 11 - hsp1_hs -ok 12 - hsp1_hstr -ok 13 - hsp1_qe -ok 14 - hsp1_qs -ok 15 - hsp1_qstr -ok 16 - hsp2_bits -ok 17 - hsp2_gaps -ok 18 - hsp2_he -ok 19 - hsp2_hs -ok 20 - hsp2_hstr -ok 21 - hsp2_qe -ok 22 - hsp2_qs -ok 23 - hsp2_qstr -ok 24 - hsp3_bits -ok 25 - hsp3_gaps -ok 26 - hsp3_he -ok 27 - hsp3_hs -ok 28 - hsp3_hstr -ok 29 - hsp3_qe -ok 30 - hsp3_qs -ok 31 - hsp3_qstr -ok 32 - hsp4_bits -ok 33 - hsp4_gaps -ok 34 - hsp4_he -ok 35 - hsp4_hs -ok 36 - hsp4_hstr -ok 37 - hsp4_qe -ok 38 - hsp4_qs -ok 39 - hsp4_qstr -ok 40 - hsp5_bits -ok 41 - hsp5_gaps -ok 42 - hsp5_he -ok 43 - hsp5_hs -ok 44 - hsp5_hstr -ok 45 - hsp5_qe -ok 46 - hsp5_qs -ok 47 - hsp5_qstr -ok 48 - hsp6_bits -ok 49 - hsp6_gaps -ok 50 - hsp6_he -ok 51 - hsp6_hs -ok 52 - hsp6_hstr -ok 53 - hsp6_qe -ok 54 - hsp6_qs -ok 55 - hsp6_qstr -ok 56 - hsp7_bits -ok 57 - hsp7_gaps -ok 58 - hsp7_he -ok 59 - hsp7_hs -ok 60 - hsp7_hstr -ok 61 - hsp7_qe -ok 62 - hsp7_qs -ok 63 - hsp7_qstr -ok 64 - hsp8_bits -ok 65 - hsp8_gaps -ok 66 - hsp8_he -ok 67 - hsp8_hs -ok 68 - hsp8_hstr -ok 69 - hsp8_qe -ok 70 - hsp8_qs -ok 71 - hsp8_qstr -ok 72 - query_name -ok 73 - An object of class 'Bio::Search::Result::BlastResult' isa 'Bio::Search::Result::ResultI' -ok 74 -ok 75 -ok 76 - hit1_bits -ok 77 - hit1_name -ok 78 - hsp1_bits -ok 79 - hsp1_gaps -ok 80 - hsp1_he -ok 81 - hsp1_hs -ok 82 - hsp1_hstr -ok 83 - hsp1_qe -ok 84 - hsp1_qs -ok 85 - hsp1_qstr -ok 86 - hsp2_bits -ok 87 - hsp2_gaps -ok 88 - hsp2_he -ok 89 - hsp2_hs -ok 90 - hsp2_hstr -ok 91 - hsp2_qe -ok 92 - hsp2_qs -ok 93 - hsp2_qstr -ok 94 - hsp3_bits -ok 95 - hsp3_gaps -ok 96 - hsp3_he -ok 97 - hsp3_hs -ok 98 - hsp3_hstr -ok 99 - hsp3_qe -ok 100 - hsp3_qs -ok 101 - hsp3_qstr -ok 102 - hsp4_bits -ok 103 - hsp4_gaps -ok 104 - hsp4_he -ok 105 - hsp4_hs -ok 106 - hsp4_hstr -ok 107 - hsp4_qe -ok 108 - hsp4_qs -ok 109 - hsp4_qstr -ok 110 - hsp5_bits -ok 111 - hsp5_gaps -ok 112 - hsp5_he -ok 113 - hsp5_hs -ok 114 - hsp5_hstr -ok 115 - hsp5_qe -ok 116 - hsp5_qs -ok 117 - hsp5_qstr -ok 118 - hsp6_bits -ok 119 - hsp6_gaps -ok 120 - hsp6_he -ok 121 - hsp6_hs -ok 122 - hsp6_hstr -ok 123 - hsp6_qe -ok 124 - hsp6_qs -ok 125 - hsp6_qstr -ok 126 - hsp7_bits -ok 127 - hsp7_gaps -ok 128 - hsp7_he -ok 129 - hsp7_hs -ok 130 - hsp7_hstr -ok 131 - hsp7_qe -ok 132 - hsp7_qs -ok 133 - hsp7_qstr -ok 134 - hsp8_bits -ok 135 - hsp8_gaps -ok 136 - hsp8_he -ok 137 - hsp8_hs -ok 138 - hsp8_hstr -ok 139 - hsp8_qe -ok 140 - hsp8_qs -ok 141 - hsp8_qstr -ok 142 - query_name -ok 143 -ok 144 -ok 145 -ok 146 -ok 147 - hit score -ok 148 - hit raw_score -ok 149 - An object of class 'Bio::Search::HSP::GenericHSP' isa 'Bio::SeqFeatureI' -ok 150 -ok 151 -ok 152 -ok 153 -ok 154 -ok 155 -ok 156 -ok 157 - fixed bug 3343 (percent identity) -ok 158 - side effect of fixing bug 3343 (number of gaps) -ok 159 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeatureI' -ok 160 -ok 161 -ok 162 -ok 163 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeatureI' -ok 164 -ok 165 -ok 166 -ok -t/SearchIO/CigarString.t ............ -1..4 -ok 1 - use Bio::SearchIO; -ok 2 -ok 3 -ok 4 -ok -t/SearchIO/cross_match.t ............ -1..15 -ok 1 - use Bio::SearchIO; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok -t/SearchIO/erpin.t .................. -1..91 -ok 1 - use Bio::SearchIO; -ok 2 - An object of class 'Bio::Search::Result::GenericResult' isa 'Bio::Search::Result::ResultI' -ok 3 - Result ERPIN -ok 4 - Result ERPIN reference -ok 5 - Result ERPIN version -ok 6 - Result parameters -ok 7 - Result statistics -ok 8 - Result entries -ok 9 - Result letters -ok 10 - Result database_name -ok 11 - Result num_hits -ok 12 - Result program_reference -ok 13 - Result query_accession -ok 14 - Result query_description -ok 15 - Result query_name -ok 16 - An object of class 'Bio::Search::Hit::ModelHit' isa 'Bio::Search::Hit::HitI' -ok 17 - Hit accession -ok 18 - Hit GI -ok 19 - Hit algorithm -ok 20 - Hit bits -ok 21 - Hit description -ok 22 - Hit length -ok 23 - Hit locus -ok 24 - Hit n -ok 25 - Hit name -ok 26 - Hit num_hsps -ok 27 - Hit overlap -ok 28 - Hit query_length -ok 29 - Hit rank -ok 30 - Hit raw_score -ok 31 - Hit score -ok 32 -ok 33 - An object of class 'Bio::Search::HSP::ModelHSP' isa 'Bio::Search::HSP::HSPI' -ok 34 - HSP algorithm -ok 35 -ok 36 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity' -ok 37 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity' -ok 38 - HSP frame -ok 39 - HSP gaps -ok 40 - 'HSP hit' isa 'Bio::SeqFeature::Similarity' -ok 41 - HSP hit_string -ok 42 - HSP homology_string -ok 43 - HSP hsp_group -ok 44 - HSP hsp_length -ok 45 - HSP length -ok 46 - HSP links -ok 47 - 'HSP query' isa 'Bio::SeqFeature::Similarity' -ok 48 - HSP query_string -ok 49 - HSP range -ok 50 - HSP rank -ok 51 -ok 52 - HSP expect -ok 53 - An object of class 'Bio::LocatableSeq' isa 'Bio::LocatableSeq' -ok 54 - HSP seq_str -ok 55 - HSP start -ok 56 - HSP custom_score -ok 57 - HSP meta -ok 58 -ok 59 -ok 60 - HSP strand -ok 61 -ok 62 -ok 63 - ERPIN get_aln warning -ok 64 - An object of class 'Bio::Search::HSP::ModelHSP' isa 'Bio::Search::HSP::HSPI' -ok 65 - HSP algorithm -ok 66 -ok 67 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity' -ok 68 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity' -ok 69 - HSP frame -ok 70 - HSP gaps -ok 71 - 'HSP hit' isa 'Bio::SeqFeature::Similarity' -ok 72 - HSP hit_string -ok 73 - HSP homology_string -ok 74 - HSP query_string -ok 75 - HSP hsp_group -ok 76 - HSP hsp_length -ok 77 - HSP length -ok 78 - HSP links -ok 79 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity' -ok 80 - HSP range -ok 81 - HSP rank -ok 82 -ok 83 - HSP end -ok 84 - HSP expect -ok 85 - An object of class 'Bio::LocatableSeq' isa 'Bio::LocatableSeq' -ok 86 - HSP seq_str -ok 87 - HSP start -ok 88 - HSP custom_score -ok 89 -ok 90 -ok 91 - HSP strand -ok -t/SearchIO/exonerate.t .............. -1..52 -ok 1 - use Bio::SearchIO; -ok 2 -ok 3 # skip no query length available in default output -ok 4 -ok 5 # skip no hit length available in default output -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 # skip no query length available in default output -ok 26 -ok 27 # skip no hit length available in default output -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 -ok 43 -ok 44 -ok 45 -ok 46 - query_name -ok 47 -ok 48 - query_name -ok 49 -ok 50 - query_name -ok 51 -ok 52 -ok -t/SearchIO/fasta.t .................. -1..301 -ok 1 - use Bio::SearchIO; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 -ok 43 -ok 44 -ok 45 -ok 46 -ok 47 -ok 48 -ok 49 -ok 50 -ok 51 -ok 52 -ok 53 -ok 54 -ok 55 -ok 56 -ok 57 -ok 58 -ok 59 -ok 60 -ok 61 -ok 62 -ok 63 -ok 64 -ok 65 -ok 66 -ok 67 -ok 68 -ok 69 -ok 70 -ok 71 -ok 72 -ok 73 -ok 74 -ok 75 -ok 76 -ok 77 -ok 78 -ok 79 -ok 80 -ok 81 -ok 82 -ok 83 -ok 84 -ok 85 -ok 86 -ok 87 -ok 88 -ok 89 -ok 90 -ok 91 -ok 92 -ok 93 -ok 94 -ok 95 -ok 96 -ok 97 -ok 98 -ok 99 -ok 100 -ok 101 -ok 102 -ok 103 -ok 104 -ok 105 -ok 106 -ok 107 -ok 108 -ok 109 -ok 110 -ok 111 -ok 112 -ok 113 -ok 114 -ok 115 -ok 116 -ok 117 -ok 118 -ok 119 -ok 120 -ok 121 -ok 122 -ok 123 -ok 124 -ok 125 -ok 126 -ok 127 -ok 128 -ok 129 -ok 130 -ok 131 -ok 132 -ok 133 -ok 134 -ok 135 -ok 136 -ok 137 -ok 138 -ok 139 -ok 140 -ok 141 -ok 142 -ok 143 -ok 144 -ok 145 -ok 146 -ok 147 -ok 148 -ok 149 -ok 150 -ok 151 -ok 152 -ok 153 -ok 154 -ok 155 -ok 156 -ok 157 -ok 158 -ok 159 -ok 160 -ok 161 -ok 162 -ok 163 -ok 164 -ok 165 -ok 166 -ok 167 -ok 168 -ok 169 -ok 170 -ok 171 -ok 172 -ok 173 -ok 174 -ok 175 -ok 176 -ok 177 -ok 178 -ok 179 -ok 180 -ok 181 -ok 182 -ok 183 -ok 184 -ok 185 -ok 186 -ok 187 -ok 188 -ok 189 -ok 190 -ok 191 -ok 192 -ok 193 -ok 194 -ok 195 -ok 196 -ok 197 -ok 198 -ok 199 -ok 200 -ok 201 -ok 202 -ok 203 -ok 204 -ok 205 -ok 206 -ok 207 -ok 208 -ok 209 -ok 210 -ok 211 -ok 212 -ok 213 -ok 214 -ok 215 -ok 216 -ok 217 -ok 218 -ok 219 -ok 220 -ok 221 -ok 222 -ok 223 -ok 224 -ok 225 -ok 226 -ok 227 -ok 228 -ok 229 -ok 230 -ok 231 -ok 232 -ok 233 -ok 234 -ok 235 -ok 236 -ok 237 -ok 238 -ok 239 -ok 240 -ok 241 -ok 242 -ok 243 -ok 244 -ok 245 -ok 246 -ok 247 -ok 248 -ok 249 -ok 250 -ok 251 -ok 252 -ok 253 -ok 254 -ok 255 -ok 256 -ok 257 -ok 258 -ok 259 -ok 260 -ok 261 -ok 262 -ok 263 -ok 264 -ok 265 -ok 266 -ok 267 - TFASTXY -ok 268 -ok 269 -ok 270 -ok 271 -ok 272 -ok 273 -ok 274 -ok 275 -ok 276 -ok 277 -ok 278 -ok 279 -ok 280 -ok 281 -ok 282 -ok 283 -ok 284 -ok 285 -ok 286 - num_identical() -ok 287 - num_conserved() -ok 288 - bug 2937 and FASTA version 3.5 -ok 289 - algorithm version -ok 290 - query name -ok 291 - query description -ok 292 - query length -ok 293 - algorithm -ok 294 - num_identical() -ok 295 - num_conserved() -ok 296 - hsp->strand(hit) -ok 297 - hsp->hit->strand -ok 298 - hsp->strand(query) -ok 299 - hsp->query->strand -ok 300 - issue 255 -ok 301 - issue 255: first hsp score -ok -t/SearchIO/gmap_f9.t ................ -1..54 -ok 1 - use Bio::SearchIO; -ok 2 - 'Did we get a Result?' isa 'Bio::Search::Result::GenericResult' -ok 3 - Did we get the expected number of hits? -ok 4 - Did we get the expected algorithm? -ok 5 - Did we get the expected query_name? -ok 6 - 'Did we get a Hit?' isa 'Bio::Search::Hit::GenericHit' -ok 7 - An object of class 'Bio::Search::Hit::GenericHit' isa 'Bio::Search::Hit::HitI' -ok 8 - Check the name -ok 9 - Check the hit length -ok 10 - Check the number of hsps -ok 11 - Check the query length -ok 12 - An object of class 'Bio::Search::HSP::GenericHSP' isa 'Bio::Search::HSP::HSPI' -ok 13 - Check the algorithm -ok 14 - Count gaps in the query -ok 15 - Count gaps in the hit -ok 16 - Length of the query -ok 17 - Length of the hit -ok 18 - Query sequence -ok 19 - Hit sequence -ok 20 - Check query start -ok 21 - Check query end -ok 22 - Check query end -ok 23 - Check the homology string -ok 24 - Check seq_inds -ok 25 - Check hit start -ok 26 - Check hit end -ok 27 - Check hit end -ok 28 - 'Did we get a Result?' isa 'Bio::Search::Result::GenericResult' -ok 29 - Did we get the expected number of hits? -ok 30 - Did we get the expected algorithm? -ok 31 - Did we get the expected query_name? -ok 32 - An object of class 'Bio::Search::Hit::GenericHit' isa 'Bio::Search::Hit::HitI' -ok 33 - Check the name -ok 34 - Check the hit length -ok 35 - Check the number of hsps -ok 36 - Check the query length -ok 37 - An object of class 'Bio::Search::HSP::GenericHSP' isa 'Bio::Search::HSP::HSPI' -ok 38 - Check the algorithm -ok 39 - Count gaps in the query -ok 40 - Count gaps in the hit -ok 41 - Length of the query -ok 42 - Length of the hit -ok 43 - Query sequence -ok 44 - Hit sequence -ok 45 - Check query start -ok 46 - Check query end -ok 47 - Check query end -ok 48 - Check the homology string -ok 49 - Check seq_inds -ok 50 - Check hit start -ok 51 - Check hit end -ok 52 - Check hit end -ok 53 - Can we loop over multiple results properly (expecting 58)? -ok 54 - simple query_name now caught, bug 3021 -ok -t/SearchIO/infernal.t ............... -1..496 -ok 1 - use Bio::SearchIO; -ok 2 - An object of class 'Bio::Search::Result::INFERNALResult' isa 'Bio::Search::Result::ResultI' -ok 3 - Check for the correct Result reference type -ok 4 - Check algorithm -ok 5 - Check cmsearch algorithm version -ok 6 - Check cm_name -ok 7 - Check database_name -ok 8 - Check database_entries -ok 9 - Check database_letters -ok 10 - Check query_name -ok 11 - Check query_length -ok 12 - Check query_accession -ok 13 - Check query_description -ok 14 - Check num_hits -ok 15 - Check for the correct hit reference type -ok 16 - Hit algorithm -ok 17 - Check hit name -ok 18 - Check hit description -ok 19 - Check hit length -ok 20 - Check hit score -ok 21 - Check hit bits -ok 22 - Check number of HSPs -ok 23 - Check hit significance -ok 24 - Check hit rank -ok 25 - Check for correct hsp reference type -ok 26 - An object of class 'Bio::Search::HSP::ModelHSP' isa 'Bio::Search::HSP::HSPI' -ok 27 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 28 - 'Check for hsp hit isa seqfeature similarity' isa 'Bio::SeqFeature::Similarity' -ok 29 - Check for HSP hit seq_id -ok 30 - Check for HSP query seq_id -ok 31 - Check hsp query start -ok 32 - Check hsp query end -ok 33 - Check hsp hit start -ok 34 - Check hsp hit end -ok 35 - Check hsp score -ok 36 - Check hsp bits -ok 37 - Check hsp evalue -ok 38 - Check for hsp query length -ok 39 - Check for hsp hit length -ok 40 - Check for hsp total length -ok 41 - Check for hsp query gaps -ok 42 - Check for hsp hit gaps -ok 43 - Check for hsp total gaps -ok 44 - Check hsp hit strand -ok 45 - Check hit name -ok 46 - Check hit description -ok 47 - Check hit score -ok 48 - Check hit raw_score -ok 49 - Check hit bits -ok 50 - Check hit significance -ok 51 - Check hit length -ok 52 - Hit rank -ok 53 - Check for hit seq_id -ok 54 - Check for query seq_id -ok 55 - Check hsp query start -ok 56 - Check hsp query end -ok 57 - Check hsp hit start -ok 58 - Check hsp hit end -ok 59 - Check hsp score -ok 60 - Check hsp bits -ok 61 - Check hsp evalue -ok 62 - Check for hsp query gaps -ok 63 - Check for hsp hit gaps -ok 64 - Check for hsp total gaps -ok 65 - Check hsp hit strand -ok 66 - Check for NC string -ok 67 - Check for CS string -ok 68 - Check for query string -ok 69 - Check for homology string -ok 70 - Check for hit string -ok 71 - Check for posterior probability string -ok 72 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity' -ok 73 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity' -ok 74 - Check hsp feature1 get_tag_values -ok 75 - Check hsp feature2 get_tag_values -ok 76 - Check for undefined result -ok 77 - Check result num_hits - multi report -ok 78 - Check result query_name - multi report -ok 79 - Check hit length - multi report -ok 80 - Check result\#2 num_hits - multi report -ok 81 - Check result\#2 query_name - multi report -ok 82 - Check result\#2 hit length - multi report -ok 83 - Check result\#2 hsp hit strand - multi report -ok 84 - Check cm_name -ok 85 - Check for undefined hit -ok 86 - An object of class 'Bio::Search::Result::INFERNALResult' isa 'Bio::Search::Result::ResultI' -ok 87 - Result -ok 88 - Result reference -ok 89 - Result version -ok 90 - Result parameters -ok 91 - Result statistics -ok 92 - Result entries -ok 93 - Result letters -ok 94 - Result database_name -ok 95 - Result num_hits -ok 96 - Result program_reference -ok 97 - Result query_accession -ok 98 - Result query_description -ok 99 - Result query_length -ok 100 - Result query_name -ok 101 - An object of class 'Bio::Search::Hit::ModelHit' isa 'Bio::Search::Hit::HitI' -ok 102 - Hit GI -ok 103 - Hit accession -ok 104 - Hit algorithm -ok 105 - Hit bits -ok 106 - Hit description -ok 107 - Hit locus -ok 108 - Hit n -ok 109 - Hit name -ok 110 - Hit num_hsps -ok 111 - Hit length_aln() not implemented -ok 112 - Hit num_unaligned_hit() not implemented -ok 113 - Hit num_unaligned_query() not implemented -ok 114 - Hit num_unaligned_sbjct() not implemented -ok 115 - Hit start not implemented -ok 116 - Hit end not implemented -ok 117 - Hit strand not implemented -ok 118 - Hit logical_length not implemented -ok 119 - Hit frac_aligned_hit not implemented -ok 120 - Hit frac_aligned_query not implemented -ok 121 - Hit frac_conserved not implemented -ok 122 - Hit frac_identical not implemented -ok 123 - Hit matches not implemented -ok 124 - Hit gaps not implemented -ok 125 - Hit frame not implemented -ok 126 - Hit range not implemented -ok 127 - Hit seq_inds not implemented -ok 128 - Hit length -ok 129 - Hit overlap -ok 130 - Hit query_length -ok 131 - Hit rank -ok 132 - Hit raw_score -ok 133 - Hit score -ok 134 - Hit p -ok 135 -ok 136 - An object of class 'Bio::Search::HSP::ModelHSP' isa 'Bio::Search::HSP::HSPI' -ok 137 - HSP algorithm -ok 138 -ok 139 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity' -ok 140 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity' -ok 141 -ok 142 -ok 143 - HSP frame -ok 144 - HSP gaps -ok 145 - Hit length -ok 146 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 147 - 'HSP hit' isa 'Bio::SeqFeature::Similarity' -ok 148 - HSP hit_string -ok 149 - HSP homology_string -ok 150 - HSP hsp_group -ok 151 - HSP hsp_length -ok 152 - HSP length -ok 153 - HSP links -ok 154 - HSP n -ok 155 - HSP pvalue -ok 156 - 'HSP query' isa 'Bio::SeqFeature::Similarity' -ok 157 - HSP query_string -ok 158 - HSP range -ok 159 - HSP rank -ok 160 -ok 161 - HSP end -ok 162 - HSP expect -ok 163 - HSP seq_inds not implemented -ok 164 - HSP matches not implemented -ok 165 - HSP frac_conserved not implemented -ok 166 - HSP frac_identical not implemented -ok 167 - HSP num_conserved not implemented -ok 168 - HSP num_identical not implemented -ok 169 - HSP percent_identity not implemented -ok 170 - HSP cigar_string not implemented -ok 171 - HSP cigar_string not implemented -ok 172 - An object of class 'Bio::LocatableSeq' isa 'Bio::LocatableSeq' -ok 173 - HSP seq_str -ok 174 - HSP start -ok 175 - HSP custom_score -ok 176 - HSP meta -ok 177 - HSP strand -ok 178 - An object of class 'Bio::Search::HSP::ModelHSP' isa 'Bio::Search::HSP::HSPI' -ok 179 - HSP algorithm -ok 180 -ok 181 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity' -ok 182 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity' -ok 183 - HSP frame -ok 184 - HSP gaps -ok 185 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 186 - 'HSP hit' isa 'Bio::SeqFeature::Similarity' -ok 187 - HSP hit_string -ok 188 - HSP homology_string -ok 189 - HSP hsp_group -ok 190 - HSP hsp_length -ok 191 - HSP length -ok 192 - HSP links -ok 193 - HSP n -ok 194 - HSP pvalue -ok 195 - 'HSP query' isa 'Bio::SeqFeature::Similarity' -ok 196 - HSP query_string -ok 197 - HSP range -ok 198 - HSP rank -ok 199 -ok 200 - HSP end -ok 201 - HSP expect -ok 202 - An object of class 'Bio::LocatableSeq' isa 'Bio::LocatableSeq' -ok 203 - HSP seq_str -ok 204 - HSP start -ok 205 - HSP custom_score -ok 206 - HSP meta -ok 207 - HSP strand -ok 208 - An object of class 'Bio::Search::Result::INFERNALResult' isa 'Bio::Search::Result::ResultI' -ok 209 - Result CMSEARCH -ok 210 - Result CMSEARCH reference -ok 211 - Result CMSEARCH version -ok 212 - Result parameters -ok 213 - Result statistics -ok 214 - Result entries -ok 215 - Result letters -ok 216 - Result database_name -ok 217 - Result num_hits -ok 218 - Result program_reference -ok 219 - Result query_accession -ok 220 - Result query_description -ok 221 - Result query_length -ok 222 - Result query_name -ok 223 - An object of class 'Bio::Search::Hit::ModelHit' isa 'Bio::Search::Hit::HitI' -ok 224 - Hit GI -ok 225 - Hit accession -ok 226 - Hit algorithm -ok 227 - Hit bits -ok 228 - Hit description -ok 229 - Hit locus -ok 230 - Hit n -ok 231 - Hit name -ok 232 - Hit num_hsps -ok 233 - No p values -ok 234 - Hit length -ok 235 - Hit overlap -ok 236 - Hit query_length -ok 237 - Hit rank -ok 238 - Hit raw_score -ok 239 - Hit score -ok 240 -ok 241 - An object of class 'Bio::Search::HSP::ModelHSP' isa 'Bio::Search::HSP::HSPI' -ok 242 - HSP algorithm -ok 243 -ok 244 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity' -ok 245 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity' -ok 246 -ok 247 -ok 248 - HSP frame -ok 249 - HSP gaps -ok 250 - Hit length -ok 251 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 252 - 'HSP hit' isa 'Bio::SeqFeature::Similarity' -ok 253 - HSP hit_string -ok 254 - HSP homology_string -ok 255 - HSP hsp_group -ok 256 - HSP hsp_length -ok 257 - HSP length -ok 258 - HSP links -ok 259 - HSP n -ok 260 - HSP pvalue -ok 261 - 'HSP query' isa 'Bio::SeqFeature::Similarity' -ok 262 - HSP query_string -ok 263 - HSP range -ok 264 - HSP rank -ok 265 -ok 266 - HSP end -ok 267 - HSP expect -ok 268 - An object of class 'Bio::LocatableSeq' isa 'Bio::LocatableSeq' -ok 269 - HSP seq_str -ok 270 - HSP start -ok 271 - HSP custom_score -ok 272 - HSP meta -ok 273 - HSP strand -ok 274 - An object of class 'Bio::Search::HSP::ModelHSP' isa 'Bio::Search::HSP::HSPI' -ok 275 - HSP algorithm -ok 276 -ok 277 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity' -ok 278 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity' -ok 279 - HSP frame -ok 280 - HSP gaps -ok 281 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 282 - 'HSP hit' isa 'Bio::SeqFeature::Similarity' -ok 283 - HSP hit_string -ok 284 - HSP homology_string -ok 285 - HSP hsp_group -ok 286 - HSP hsp_length -ok 287 - HSP length -ok 288 - HSP links -ok 289 - HSP n -ok 290 - HSP pvalue -ok 291 - 'HSP query' isa 'Bio::SeqFeature::Similarity' -ok 292 - HSP query_string -ok 293 - HSP range -ok 294 - HSP rank -ok 295 -ok 296 - HSP end -ok 297 - HSP expect -ok 298 - An object of class 'Bio::LocatableSeq' isa 'Bio::LocatableSeq' -ok 299 - HSP seq_str -ok 300 - HSP start -ok 301 - HSP custom_score -ok 302 - HSP meta -ok 303 - HSP strand -ok 304 - An object of class 'Bio::Search::Hit::ModelHit' isa 'Bio::Search::Hit::HitI' -ok 305 - Hit accession -ok 306 - Hit GI -ok 307 - Hit algorithm -ok 308 - Hit bits -ok 309 - Hit description -ok 310 - Hit length -ok 311 - Hit locus -ok 312 - Hit n -ok 313 - Hit name -ok 314 - Hit num_hsps -ok 315 - Hit overlap -ok 316 - Hit query_length -ok 317 - Hit rank -ok 318 - Hit raw_score -ok 319 - Hit score -ok 320 -ok 321 - An object of class 'Bio::Search::HSP::ModelHSP' isa 'Bio::Search::HSP::HSPI' -ok 322 - HSP algorithm -ok 323 -ok 324 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity' -ok 325 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity' -ok 326 - HSP frame -ok 327 - HSP gaps -ok 328 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 329 - 'HSP hit' isa 'Bio::SeqFeature::Similarity' -ok 330 - HSP hit_string -ok 331 - HSP homology_string -ok 332 - HSP hsp_group -ok 333 - HSP hsp_length -ok 334 - HSP length -ok 335 - HSP links -ok 336 - HSP n -ok 337 - 'HSP query' isa 'Bio::SeqFeature::Similarity' -ok 338 - HSP query_string -ok 339 - HSP range -ok 340 - HSP rank -ok 341 -ok 342 - HSP end -ok 343 - HSP expect -ok 344 - An object of class 'Bio::LocatableSeq' isa 'Bio::LocatableSeq' -ok 345 - HSP seq_str -ok 346 - HSP start -ok 347 - HSP custom_score -ok 348 - HSP meta -ok 349 - HSP strand -ok 350 - HSP meta gap bug -ok 351 - HSP meta -ok 352 - HSP meta -ok 353 -ok 354 -ok 355 - An object of class 'Bio::Search::Result::INFERNALResult' isa 'Bio::Search::Result::ResultI' -ok 356 - Result CMSEARCH -ok 357 - Result CMSEARCH reference -ok 358 - Result CMSEARCH version -ok 359 - Result parameters -ok 360 - Result statistics -ok 361 - Result entries -ok 362 - Result letters -ok 363 - Result database_name -ok 364 - Result num_hits -ok 365 - Result program_reference -ok 366 - Result query_accession -ok 367 - Result query_description -ok 368 - Result query_length -ok 369 - Result query_name -ok 370 - An object of class 'Bio::Search::Hit::ModelHit' isa 'Bio::Search::Hit::HitI' -ok 371 - Hit GI -ok 372 - Hit accession -ok 373 - Hit algorithm -ok 374 - Hit bits -ok 375 - Hit description -ok 376 - Hit locus -ok 377 - Hit n -ok 378 - Hit name -ok 379 - Hit num_hsps -ok 380 - No p values -ok 381 - Hit length -ok 382 - Hit overlap -ok 383 - Hit query_length -ok 384 - Hit rank -ok 385 - Hit raw_score -ok 386 - Hit score -ok 387 -ok 388 - An object of class 'Bio::Search::HSP::ModelHSP' isa 'Bio::Search::HSP::HSPI' -ok 389 - HSP algorithm -ok 390 -ok 391 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity' -ok 392 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity' -ok 393 -ok 394 -ok 395 - HSP frame -ok 396 - HSP gaps -ok 397 - Hit length -ok 398 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 399 - 'HSP hit' isa 'Bio::SeqFeature::Similarity' -ok 400 - HSP hit_string -ok 401 - HSP homology_string -ok 402 - HSP hsp_group -ok 403 - HSP hsp_length -ok 404 - HSP length -ok 405 - HSP links -ok 406 - HSP n -ok 407 - HSP pvalue -ok 408 - 'HSP query' isa 'Bio::SeqFeature::Similarity' -ok 409 - HSP query_string -ok 410 - HSP range -ok 411 - HSP rank -ok 412 -ok 413 - HSP end -ok 414 - HSP expect -ok 415 - An object of class 'Bio::LocatableSeq' isa 'Bio::LocatableSeq' -ok 416 - HSP seq_str -ok 417 - HSP start -ok 418 - HSP custom_score -ok 419 - HSP meta -ok 420 - HSP strand -ok 421 - An object of class 'Bio::Search::HSP::ModelHSP' isa 'Bio::Search::HSP::HSPI' -ok 422 - HSP algorithm -ok 423 -ok 424 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity' -ok 425 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity' -ok 426 - HSP frame -ok 427 - HSP gaps -ok 428 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 429 - 'HSP hit' isa 'Bio::SeqFeature::Similarity' -ok 430 - HSP hit_string -ok 431 - HSP homology_string -ok 432 - HSP hsp_group -ok 433 - HSP hsp_length -ok 434 - HSP length -ok 435 - HSP links -ok 436 - HSP n -ok 437 - HSP pvalue -ok 438 - 'HSP query' isa 'Bio::SeqFeature::Similarity' -ok 439 - HSP query_string -ok 440 - HSP range -ok 441 - HSP rank -ok 442 -ok 443 - HSP end -ok 444 - HSP expect -ok 445 - An object of class 'Bio::LocatableSeq' isa 'Bio::LocatableSeq' -ok 446 - HSP seq_str -ok 447 - HSP start -ok 448 - HSP custom_score -ok 449 - HSP meta -ok 450 - HSP strand -ok 451 - An object of class 'Bio::Search::Hit::ModelHit' isa 'Bio::Search::Hit::HitI' -ok 452 - Hit accession -ok 453 - Hit GI -ok 454 - Hit algorithm -ok 455 - Hit bits -ok 456 - Hit description -ok 457 - Hit length -ok 458 - Hit locus -ok 459 - Hit n -ok 460 - Hit name -ok 461 - Hit num_hsps -ok 462 - Hit overlap -ok 463 - Hit query_length -ok 464 - Hit rank -ok 465 - Hit raw_score -ok 466 - Hit score -ok 467 -ok 468 - An object of class 'Bio::Search::HSP::ModelHSP' isa 'Bio::Search::HSP::HSPI' -ok 469 - HSP algorithm -ok 470 -ok 471 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity' -ok 472 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity' -ok 473 - HSP frame -ok 474 - HSP gaps -ok 475 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 476 - 'HSP hit' isa 'Bio::SeqFeature::Similarity' -ok 477 - HSP hit_string -ok 478 - HSP homology_string -ok 479 - HSP hsp_group -ok 480 - HSP hsp_length -ok 481 - HSP length -ok 482 - HSP links -ok 483 - HSP n -ok 484 - 'HSP query' isa 'Bio::SeqFeature::Similarity' -ok 485 - HSP query_string -ok 486 - HSP range -ok 487 - HSP rank -ok 488 -ok 489 - HSP end -ok 490 - HSP expect -ok 491 - An object of class 'Bio::LocatableSeq' isa 'Bio::LocatableSeq' -ok 492 - HSP seq_str -ok 493 - HSP start -ok 494 - HSP custom_score -ok 495 - HSP meta -ok 496 - HSP strand -ok -t/SearchIO/megablast.t .............. -1..31 -ok 1 - use Bio::SearchIO; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok -t/SearchIO/psl.t .................... -1..53 -ok 1 - use Bio::SearchIO; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 -ok 43 -ok 44 -ok 45 -ok 46 -ok 47 -ok 48 -ok 49 -ok 50 - next_hsp should be undef -ok 51 - next_hit should be undef -not ok 52 - next_result should be undef # TODO next_result should really return undef, not empty string -# Failed (TODO) test 'next_result should be undef' -# at t/SearchIO/psl.t line 96. -# got: '' -# expected: undef -ok 53 -ok -t/SearchIO/rnamotif.t ............... -1..60 -ok 1 - use Bio::SearchIO; -ok 2 - An object of class 'Bio::Search::Result::GenericResult' isa 'Bio::Search::Result::ResultI' -ok 3 - Result RNAMOTIF -ok 4 - Result RNAMOTIF reference -ok 5 - Result RNAMOTIF version -ok 6 - Result entries -ok 7 - Result letters -ok 8 - Result database_name -ok 9 - Result num_hits -ok 10 - Result program_reference -ok 11 - Result query_accession -ok 12 - Result query_description -ok 13 - Result query_length -ok 14 - Result query_name -ok 15 - An object of class 'Bio::Search::Hit::ModelHit' isa 'Bio::Search::Hit::HitI' -ok 16 - Hit accession -ok 17 - Hit GI -ok 18 - Hit algorithm -ok 19 - Hit description -ok 20 - Hit length -ok 21 - Hit locus -ok 22 - Hit n -ok 23 - Hit name -ok 24 - Hit num_hsps -ok 25 - Hit overlap -ok 26 - Hit rank -ok 27 - Hit raw_score -ok 28 - Hit score -ok 29 -ok 30 - An object of class 'Bio::Search::HSP::ModelHSP' isa 'Bio::Search::HSP::HSPI' -ok 31 - HSP algorithm -ok 32 -ok 33 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity' -ok 34 - An object of class 'Bio::SeqFeature::Similarity' isa 'Bio::SeqFeature::Similarity' -ok 35 - HSP frame -ok 36 - HSP gaps -ok 37 - RNAMotif get_aln warning -ok 38 - 'HSP hit' isa 'Bio::SeqFeature::Similarity' -ok 39 - HSP hit_string -ok 40 - HSP homology_string -ok 41 - HSP hsp_group -ok 42 - HSP hsp_length -ok 43 - HSP length -ok 44 - HSP links -ok 45 - HSP n -ok 46 - 'HSP query' isa 'Bio::SeqFeature::Similarity' -ok 47 - HSP query_string -ok 48 - HSP range -ok 49 - HSP rank -ok 50 -ok 51 - HSP end -ok 52 - HSP expect -ok 53 - An object of class 'Bio::LocatableSeq' isa 'Bio::LocatableSeq' -ok 54 - HSP seq_str -ok 55 - HSP start -ok 56 - HSP custom_score -ok 57 - HSP meta -ok 58 - HSP strand -ok 59 -ok 60 -ok -t/SearchIO/SearchIO.t ............... -1..19 -ok 1 - use Bio::SearchIO; -ok 2 - exonerate for f.exon -ok 3 - exonerate for f.exonerate -ok 4 - fasta for f.fasta -ok 5 - blast for fast.bls -ok 6 - fasta for f.psearch -ok 7 - fasta for f.fx -ok 8 - fasta for f.osearch -ok 9 - fasta for f.fa -ok 10 - blast for f.tblx -ok 11 - fasta for f.SSEARCH.m9 -ok 12 - fasta for f.fy -ok 13 - blast for filename.blast -ok 14 - blast for filename.bls -ok 15 - fasta for f.m9 -ok 16 - blastxml for f.xml -ok 17 - blast for f.blx -ok 18 - blastxml for f.blastxml -ok 19 - fasta for f.ssearch -ok -t/SearchIO/sim4.t ................... -1..102 -ok 1 - use Bio::SearchIO; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 -ok 43 -ok 44 -ok 45 -ok 46 -ok 47 -ok 48 -ok 49 -ok 50 -ok 51 -ok 52 -ok 53 -ok 54 -ok 55 -ok 56 -ok 57 -ok 58 -ok 59 -ok 60 -ok 61 -ok 62 -ok 63 -ok 64 -ok 65 -ok 66 -ok 67 -ok 68 -ok 69 -ok 70 -ok 71 -ok 72 -ok 73 -ok 74 -ok 75 -ok 76 -ok 77 -ok 78 -ok 79 -ok 80 -ok 81 -ok 82 -ok 83 -ok 84 -ok 85 -ok 86 -ok 87 -ok 88 -ok 89 -ok 90 -ok 91 -ok 92 -ok 93 -ok 94 -ok 95 -ok 96 -ok 97 -ok 98 -ok 99 -ok 100 -ok 101 -ok 102 -ok -t/SearchIO/SimilarityPair.t ......... -1..12 -ok 1 - use Bio::SearchIO; -ok 2 - use Bio::SeqIO; -ok 3 -ok 4 - An object of class 'Bio::Seq' isa 'Bio::SeqI' -ok 5 -ok 6 - An object of class 'Bio::SearchIO::blast' isa 'Bio::SearchIO' -ok 7 -ok 8 - An object of class 'Bio::Search::Hit::BlastHit' isa 'Bio::Search::Hit::HitI' -ok 9 -ok 10 - An object of class 'Bio::Search::HSP::GenericHSP' isa 'Bio::SeqFeatureI' -ok 11 -ok 12 -ok -t/SearchIO/Tiling.t ................. -1..1141 -ok 1 - use Bio::Search::Tiling::MapTiling; -ok 2 - use Bio::Search::Tiling::MapTileUtils; -ok 3 - use Bio::SearchIO; -ok 4 - use Bio::Search::Hit::BlastHit; -ok 5 - use File::Spec; -ok 6 - parse data file -ok 7 - got test hit -ok 8 - create tiling -ok 9 - An object of class 'Bio::Search::Tiling::MapTiling' isa 'Bio::Search::Tiling::TilingI' -ok 10 - implements 'next_tiling' -ok 11 - implements 'rewind_tilings' -ok 12 - implements 'identities' -ok 13 - implements 'conserved' -ok 14 - implements 'length' -ok 15 - identities regression test -ok 16 - conserved regression test -ok 17 - tiling iterator regression test(1) -ok 18 - tiling iterator regression test(2) -ok 19 - tiling iterator regression test(3, rewind) -ok 20 - ecolitst.wublastp -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 - dnaEbsub_ecoli.wublastx -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 - tricky.wublast -ok 37 - tricky.wublast(1) -ok 38 - tricky.wublast(2) -ok 39 - tricky.wublast(3) -ok 40 - tricky.wublast(4) -ok 41 - ecolitst.bls -ok 42 - tile ecolitst.bls hit 1 \#hsps 1 -ok 43 - q id: est (0.98293) = fast (0.98293) -ok 44 - q cn: est (0.98293) = fast (0.98293) -ok 45 - h id: est (0.98293) = fast (0.98293) -ok 46 - h cn: est (0.98293) = fast (0.98293) -ok 47 - tile ecolitst.bls hit 2 \#hsps 1 -ok 48 - q id: est (0.30074) = fast (0.30074) -ok 49 - q cn: est (0.49876) = fast (0.49876) -ok 50 - h id: est (0.30759) = fast (0.30759) -ok 51 - h cn: est (0.51013) = fast (0.51013) -ok 52 - tile ecolitst.bls hit 3 \#hsps 1 -ok 53 - q id: est (0.31004) = fast (0.31004) -ok 54 - q cn: est (0.49782) = fast (0.49782) -ok 55 - h id: est (0.32054) = fast (0.32054) -ok 56 - h cn: est (0.51467) = fast (0.51467) -ok 57 - tile ecolitst.bls hit 4 \#hsps 1 -ok 58 - q id: est (0.30435) = fast (0.30435) -ok 59 - q cn: est (0.47826) = fast (0.47826) -ok 60 - h id: est (0.29787) = fast (0.29787) -ok 61 - h cn: est (0.46809) = fast (0.46809) -ok 62 - tricky.wublast -ok 63 - tile tricky.wublast hit 1 \#hsps 7 -ok 64 - q id: exact (0.22153) ~ est (0.22153) -ok 65 - q id: exact (0.22153) <= max (0.22153) -ok 66 - q cn: exact (0.42760) ~ est (0.42760) -ok 67 - q cn: exact (0.42760) <= max (0.42760) -ok 68 - h id: exact (0.22704) ~ est (0.22704) -ok 69 - h id: exact (0.22704) <= max (0.22704) -ok 70 - h cn: exact (0.43335) ~ est (0.43335) -ok 71 - h cn: exact (0.43335) <= max (0.43335) -ok 72 - a_thaliana.blastn -ok 73 - tile a_thaliana.blastn hit 1 \#hsps 1 -ok 74 - q id: est (0.96667) = fast (0.96667) -ok 75 - q cn: est (0.96667) = fast (0.96667) -ok 76 - h id: est (0.98305) = fast (0.98305) -ok 77 - h cn: est (0.98305) = fast (0.98305) -ok 78 - tile a_thaliana.blastn hit 2 \#hsps 1 -ok 79 - q id: est (0.96667) = fast (0.96667) -ok 80 - q cn: est (0.96667) = fast (0.96667) -ok 81 - h id: est (0.98305) = fast (0.98305) -ok 82 - h cn: est (0.98305) = fast (0.98305) -ok 83 - tile a_thaliana.blastn hit 3 \#hsps 1 -ok 84 - q id: est (1.00000) = fast (1.00000) -ok 85 - q cn: est (1.00000) = fast (1.00000) -ok 86 - h id: est (1.00000) = fast (1.00000) -ok 87 - h cn: est (1.00000) = fast (1.00000) -ok 88 - tile a_thaliana.blastn hit 4 \#hsps 1 -ok 89 - q id: est (1.00000) = fast (1.00000) -ok 90 - q cn: est (1.00000) = fast (1.00000) -ok 91 - h id: est (1.00000) = fast (1.00000) -ok 92 - h cn: est (1.00000) = fast (1.00000) -ok 93 - tile a_thaliana.blastn hit 5 \#hsps 1 -ok 94 - q id: est (0.92308) = fast (0.92308) -ok 95 - q cn: est (0.92308) = fast (0.92308) -ok 96 - h id: est (0.92308) = fast (0.92308) -ok 97 - h cn: est (0.92308) = fast (0.92308) -ok 98 - tile a_thaliana.blastn hit 6 \#hsps 1 -ok 99 - q id: est (1.00000) = fast (1.00000) -ok 100 - q cn: est (1.00000) = fast (1.00000) -ok 101 - h id: est (1.00000) = fast (1.00000) -ok 102 - h cn: est (1.00000) = fast (1.00000) -ok 103 - tile a_thaliana.blastn hit 7 \#hsps 1 -ok 104 - q id: est (1.00000) = fast (1.00000) -ok 105 - q cn: est (1.00000) = fast (1.00000) -ok 106 - h id: est (1.00000) = fast (1.00000) -ok 107 - h cn: est (1.00000) = fast (1.00000) -ok 108 - tile a_thaliana.blastn hit 8 \#hsps 1 -ok 109 - q id: est (1.00000) = fast (1.00000) -ok 110 - q cn: est (1.00000) = fast (1.00000) -ok 111 - h id: est (1.00000) = fast (1.00000) -ok 112 - h cn: est (1.00000) = fast (1.00000) -ok 113 - tile a_thaliana.blastn hit 9 \#hsps 1 -ok 114 - q id: est (1.00000) = fast (1.00000) -ok 115 - q cn: est (1.00000) = fast (1.00000) -ok 116 - h id: est (1.00000) = fast (1.00000) -ok 117 - h cn: est (1.00000) = fast (1.00000) -ok 118 - tile a_thaliana.blastn hit 10 \#hsps 1 -ok 119 - q id: est (1.00000) = fast (1.00000) -ok 120 - q cn: est (1.00000) = fast (1.00000) -ok 121 - h id: est (1.00000) = fast (1.00000) -ok 122 - h cn: est (1.00000) = fast (1.00000) -ok 123 - tile a_thaliana.blastn hit 11 \#hsps 1 -ok 124 - q id: est (1.00000) = fast (1.00000) -ok 125 - q cn: est (1.00000) = fast (1.00000) -ok 126 - h id: est (1.00000) = fast (1.00000) -ok 127 - h cn: est (1.00000) = fast (1.00000) -ok 128 - tile a_thaliana.blastn hit 12 \#hsps 1 -ok 129 - q id: est (1.00000) = fast (1.00000) -ok 130 - q cn: est (1.00000) = fast (1.00000) -ok 131 - h id: est (1.00000) = fast (1.00000) -ok 132 - h cn: est (1.00000) = fast (1.00000) -ok 133 - tile a_thaliana.blastn hit 13 \#hsps 1 -ok 134 - q id: est (1.00000) = fast (1.00000) -ok 135 - q cn: est (1.00000) = fast (1.00000) -ok 136 - h id: est (1.00000) = fast (1.00000) -ok 137 - h cn: est (1.00000) = fast (1.00000) -ok 138 - tile a_thaliana.blastn hit 14 \#hsps 1 -ok 139 - q id: est (1.00000) = fast (1.00000) -ok 140 - q cn: est (1.00000) = fast (1.00000) -ok 141 - h id: est (1.00000) = fast (1.00000) -ok 142 - h cn: est (1.00000) = fast (1.00000) -ok 143 - tile a_thaliana.blastn hit 15 \#hsps 1 -ok 144 - q id: est (1.00000) = fast (1.00000) -ok 145 - q cn: est (1.00000) = fast (1.00000) -ok 146 - h id: est (1.00000) = fast (1.00000) -ok 147 - h cn: est (1.00000) = fast (1.00000) -ok 148 - tile a_thaliana.blastn hit 16 \#hsps 1 -ok 149 - q id: est (1.00000) = fast (1.00000) -ok 150 - q cn: est (1.00000) = fast (1.00000) -ok 151 - h id: est (1.00000) = fast (1.00000) -ok 152 - h cn: est (1.00000) = fast (1.00000) -ok 153 - tile a_thaliana.blastn hit 17 \#hsps 1 -ok 154 - q id: est (1.00000) = fast (1.00000) -ok 155 - q cn: est (1.00000) = fast (1.00000) -ok 156 - h id: est (1.00000) = fast (1.00000) -ok 157 - h cn: est (1.00000) = fast (1.00000) -ok 158 - tile a_thaliana.blastn hit 18 \#hsps 1 -ok 159 - q id: est (1.00000) = fast (1.00000) -ok 160 - q cn: est (1.00000) = fast (1.00000) -ok 161 - h id: est (1.00000) = fast (1.00000) -ok 162 - h cn: est (1.00000) = fast (1.00000) -ok 163 - tile a_thaliana.blastn hit 19 \#hsps 1 -ok 164 - q id: est (1.00000) = fast (1.00000) -ok 165 - q cn: est (1.00000) = fast (1.00000) -ok 166 - h id: est (1.00000) = fast (1.00000) -ok 167 - h cn: est (1.00000) = fast (1.00000) -ok 168 - tile a_thaliana.blastn hit 20 \#hsps 1 -ok 169 - q id: est (0.95238) = fast (0.95238) -ok 170 - q cn: est (0.95238) = fast (0.95238) -ok 171 - h id: est (0.95238) = fast (0.95238) -ok 172 - h cn: est (0.95238) = fast (0.95238) -ok 173 - tile a_thaliana.blastn hit 21 \#hsps 1 -ok 174 - q id: est (1.00000) = fast (1.00000) -ok 175 - q cn: est (1.00000) = fast (1.00000) -ok 176 - h id: est (1.00000) = fast (1.00000) -ok 177 - h cn: est (1.00000) = fast (1.00000) -ok 178 - tile a_thaliana.blastn hit 22 \#hsps 1 -ok 179 - q id: est (0.95238) = fast (0.95238) -ok 180 - q cn: est (0.95238) = fast (0.95238) -ok 181 - h id: est (0.95238) = fast (0.95238) -ok 182 - h cn: est (0.95238) = fast (0.95238) -ok 183 - tile a_thaliana.blastn hit 23 \#hsps 1 -ok 184 - q id: est (1.00000) = fast (1.00000) -ok 185 - q cn: est (1.00000) = fast (1.00000) -ok 186 - h id: est (1.00000) = fast (1.00000) -ok 187 - h cn: est (1.00000) = fast (1.00000) -ok 188 - tile a_thaliana.blastn hit 24 \#hsps 1 -ok 189 - q id: est (0.95238) = fast (0.95238) -ok 190 - q cn: est (0.95238) = fast (0.95238) -ok 191 - h id: est (0.95238) = fast (0.95238) -ok 192 - h cn: est (0.95238) = fast (0.95238) -ok 193 - tile a_thaliana.blastn hit 25 \#hsps 1 -ok 194 - q id: est (1.00000) = fast (1.00000) -ok 195 - q cn: est (1.00000) = fast (1.00000) -ok 196 - h id: est (1.00000) = fast (1.00000) -ok 197 - h cn: est (1.00000) = fast (1.00000) -ok 198 - tile a_thaliana.blastn hit 26 \#hsps 1 -ok 199 - q id: est (1.00000) = fast (1.00000) -ok 200 - q cn: est (1.00000) = fast (1.00000) -ok 201 - h id: est (1.00000) = fast (1.00000) -ok 202 - h cn: est (1.00000) = fast (1.00000) -ok 203 - tile a_thaliana.blastn hit 27 \#hsps 1 -ok 204 - q id: est (1.00000) = fast (1.00000) -ok 205 - q cn: est (1.00000) = fast (1.00000) -ok 206 - h id: est (1.00000) = fast (1.00000) -ok 207 - h cn: est (1.00000) = fast (1.00000) -ok 208 - tile a_thaliana.blastn hit 28 \#hsps 1 -ok 209 - q id: est (1.00000) = fast (1.00000) -ok 210 - q cn: est (1.00000) = fast (1.00000) -ok 211 - h id: est (1.00000) = fast (1.00000) -ok 212 - h cn: est (1.00000) = fast (1.00000) -ok 213 - tile a_thaliana.blastn hit 29 \#hsps 1 -ok 214 - q id: est (1.00000) = fast (1.00000) -ok 215 - q cn: est (1.00000) = fast (1.00000) -ok 216 - h id: est (1.00000) = fast (1.00000) -ok 217 - h cn: est (1.00000) = fast (1.00000) -ok 218 - tile a_thaliana.blastn hit 30 \#hsps 1 -ok 219 - q id: est (1.00000) = fast (1.00000) -ok 220 - q cn: est (1.00000) = fast (1.00000) -ok 221 - h id: est (1.00000) = fast (1.00000) -ok 222 - h cn: est (1.00000) = fast (1.00000) -ok 223 - tile a_thaliana.blastn hit 31 \#hsps 1 -ok 224 - q id: est (1.00000) = fast (1.00000) -ok 225 - q cn: est (1.00000) = fast (1.00000) -ok 226 - h id: est (1.00000) = fast (1.00000) -ok 227 - h cn: est (1.00000) = fast (1.00000) -ok 228 - brassica_ATH.WUBLASTN -ok 229 - tile brassica_ATH.WUBLASTN hit 1 \#hsps 3 -ok 230 - q id: exact (0.82465) ~ est (0.82343) -ok 231 - q id: exact (0.82465) <= max (0.83333) -ok 232 - q cn: exact (0.85590) ~ est (0.85312) -ok 233 - q cn: exact (0.85590) <= max (0.86458) -ok 234 - h id: exact (0.83920) ~ est (0.83920) -ok 235 - h id: exact (0.83920) <= max (0.83920) -ok 236 - h cn: exact (0.86935) ~ est (0.86935) -ok 237 - h cn: exact (0.86935) <= max (0.86935) -ok 238 - tile brassica_ATH.WUBLASTN hit 2 \#hsps 2 -ok 239 - q id: exact (0.82486) ~ est (0.82486) -ok 240 - q id: exact (0.82486) <= max (0.82486) -ok 241 - q cn: exact (0.85122) ~ est (0.85122) -ok 242 - q cn: exact (0.85122) <= max (0.85122) -ok 243 - h id: exact (0.82955) ~ est (0.82955) -ok 244 - h id: exact (0.82955) <= max (0.82955) -ok 245 - h cn: exact (0.85606) ~ est (0.85606) -ok 246 - h cn: exact (0.85606) <= max (0.85606) -ok 247 - no_hsps.blastp -ok 248 - tile no_hsps.blastp hit 1 \#hsps 0 -ok 249 - tile no_hsps.blastp hit 2 \#hsps 0 -ok 250 - tile no_hsps.blastp hit 3 \#hsps 0 -ok 251 - tile no_hsps.blastp hit 4 \#hsps 0 -ok 252 - tile no_hsps.blastp hit 5 \#hsps 0 -ok 253 - tile no_hsps.blastp hit 6 \#hsps 0 -ok 254 - tile no_hsps.blastp hit 7 \#hsps 0 -ok 255 - tile no_hsps.blastp hit 8 \#hsps 0 -ok 256 - tile no_hsps.blastp hit 9 \#hsps 0 -ok 257 - tile no_hsps.blastp hit 10 \#hsps 0 -ok 258 - tile no_hsps.blastp hit 11 \#hsps 0 -ok 259 - tile no_hsps.blastp hit 12 \#hsps 0 -ok 260 - tile no_hsps.blastp hit 13 \#hsps 0 -ok 261 - tile no_hsps.blastp hit 14 \#hsps 0 -ok 262 - tile no_hsps.blastp hit 15 \#hsps 0 -ok 263 - tile no_hsps.blastp hit 16 \#hsps 0 -ok 264 - tile no_hsps.blastp hit 17 \#hsps 0 -ok 265 - tile no_hsps.blastp hit 18 \#hsps 0 -ok 266 - tile no_hsps.blastp hit 19 \#hsps 0 -ok 267 - tile no_hsps.blastp hit 20 \#hsps 0 -ok 268 - tile no_hsps.blastp hit 21 \#hsps 0 -ok 269 - tile no_hsps.blastp hit 22 \#hsps 0 -ok 270 - tile no_hsps.blastp hit 23 \#hsps 0 -ok 271 - tile no_hsps.blastp hit 24 \#hsps 0 -ok 272 - tile no_hsps.blastp hit 25 \#hsps 0 -ok 273 - tile no_hsps.blastp hit 26 \#hsps 0 -ok 274 - tile no_hsps.blastp hit 27 \#hsps 0 -ok 275 - tile no_hsps.blastp hit 28 \#hsps 0 -ok 276 - tile no_hsps.blastp hit 29 \#hsps 0 -ok 277 - tile no_hsps.blastp hit 30 \#hsps 0 -ok 278 - tile no_hsps.blastp hit 31 \#hsps 0 -ok 279 - tile no_hsps.blastp hit 32 \#hsps 0 -ok 280 - tile no_hsps.blastp hit 33 \#hsps 0 -ok 281 - tile no_hsps.blastp hit 34 \#hsps 0 -ok 282 - tile no_hsps.blastp hit 35 \#hsps 0 -ok 283 - tile no_hsps.blastp hit 36 \#hsps 0 -ok 284 - tile no_hsps.blastp hit 37 \#hsps 0 -ok 285 - tile no_hsps.blastp hit 38 \#hsps 0 -ok 286 - tile no_hsps.blastp hit 39 \#hsps 0 -ok 287 - tile no_hsps.blastp hit 40 \#hsps 0 -ok 288 - tile no_hsps.blastp hit 41 \#hsps 0 -ok 289 - tile no_hsps.blastp hit 42 \#hsps 0 -ok 290 - tile no_hsps.blastp hit 43 \#hsps 0 -ok 291 - tile no_hsps.blastp hit 44 \#hsps 0 -ok 292 - tile no_hsps.blastp hit 45 \#hsps 0 -ok 293 - tile no_hsps.blastp hit 46 \#hsps 0 -ok 294 - tile no_hsps.blastp hit 47 \#hsps 0 -ok 295 - tile no_hsps.blastp hit 48 \#hsps 0 -ok 296 - tile no_hsps.blastp hit 49 \#hsps 0 -ok 297 - tile no_hsps.blastp hit 50 \#hsps 0 -ok 298 - tile no_hsps.blastp hit 51 \#hsps 0 -ok 299 - tile no_hsps.blastp hit 52 \#hsps 0 -ok 300 - tile no_hsps.blastp hit 53 \#hsps 0 -ok 301 - tile no_hsps.blastp hit 54 \#hsps 0 -ok 302 - tile no_hsps.blastp hit 55 \#hsps 0 -ok 303 - tile no_hsps.blastp hit 56 \#hsps 0 -ok 304 - tile no_hsps.blastp hit 57 \#hsps 0 -ok 305 - tile no_hsps.blastp hit 58 \#hsps 0 -ok 306 - tile no_hsps.blastp hit 59 \#hsps 0 -ok 307 - tile no_hsps.blastp hit 60 \#hsps 0 -ok 308 - tile no_hsps.blastp hit 61 \#hsps 0 -ok 309 - tile no_hsps.blastp hit 62 \#hsps 0 -ok 310 - tile no_hsps.blastp hit 63 \#hsps 0 -ok 311 - tile no_hsps.blastp hit 64 \#hsps 0 -ok 312 - tile no_hsps.blastp hit 65 \#hsps 0 -ok 313 - tile no_hsps.blastp hit 66 \#hsps 0 -ok 314 - tile no_hsps.blastp hit 67 \#hsps 0 -ok 315 - tile no_hsps.blastp hit 68 \#hsps 0 -ok 316 - tile no_hsps.blastp hit 69 \#hsps 0 -ok 317 - tile no_hsps.blastp hit 70 \#hsps 0 -ok 318 - tile no_hsps.blastp hit 71 \#hsps 0 -ok 319 - tile no_hsps.blastp hit 72 \#hsps 0 -ok 320 - tile no_hsps.blastp hit 73 \#hsps 0 -ok 321 - tile no_hsps.blastp hit 74 \#hsps 0 -ok 322 - tile no_hsps.blastp hit 75 \#hsps 0 -ok 323 - tile no_hsps.blastp hit 76 \#hsps 0 -ok 324 - tile no_hsps.blastp hit 77 \#hsps 0 -ok 325 - tile no_hsps.blastp hit 78 \#hsps 0 -ok 326 - tile no_hsps.blastp hit 79 \#hsps 0 -ok 327 - tile no_hsps.blastp hit 80 \#hsps 0 -ok 328 - tile no_hsps.blastp hit 81 \#hsps 0 -ok 329 - tile no_hsps.blastp hit 82 \#hsps 0 -ok 330 - tile no_hsps.blastp hit 83 \#hsps 0 -ok 331 - tile no_hsps.blastp hit 84 \#hsps 0 -ok 332 - tile no_hsps.blastp hit 85 \#hsps 0 -ok 333 - tile no_hsps.blastp hit 86 \#hsps 0 -ok 334 - tile no_hsps.blastp hit 87 \#hsps 0 -ok 335 - tile no_hsps.blastp hit 88 \#hsps 0 -ok 336 - tile no_hsps.blastp hit 89 \#hsps 0 -ok 337 - tile no_hsps.blastp hit 90 \#hsps 0 -ok 338 - tile no_hsps.blastp hit 91 \#hsps 0 -ok 339 - tile no_hsps.blastp hit 92 \#hsps 0 -ok 340 - tile no_hsps.blastp hit 93 \#hsps 0 -ok 341 - tile no_hsps.blastp hit 94 \#hsps 0 -ok 342 - tile no_hsps.blastp hit 95 \#hsps 0 -ok 343 - tile no_hsps.blastp hit 96 \#hsps 0 -ok 344 - tile no_hsps.blastp hit 97 \#hsps 0 -ok 345 - tile no_hsps.blastp hit 98 \#hsps 0 -ok 346 - tile no_hsps.blastp hit 99 \#hsps 0 -ok 347 - tile no_hsps.blastp hit 100 \#hsps 0 -ok 348 - tile no_hsps.blastp hit 101 \#hsps 0 -ok 349 - tile no_hsps.blastp hit 102 \#hsps 0 -ok 350 - tile no_hsps.blastp hit 103 \#hsps 0 -ok 351 - tile no_hsps.blastp hit 104 \#hsps 0 -ok 352 - tile no_hsps.blastp hit 105 \#hsps 0 -ok 353 - tile no_hsps.blastp hit 106 \#hsps 0 -ok 354 - tile no_hsps.blastp hit 107 \#hsps 0 -ok 355 - tile no_hsps.blastp hit 108 \#hsps 0 -ok 356 - tile no_hsps.blastp hit 109 \#hsps 0 -ok 357 - tile no_hsps.blastp hit 110 \#hsps 0 -ok 358 - tile no_hsps.blastp hit 111 \#hsps 0 -ok 359 - tile no_hsps.blastp hit 112 \#hsps 0 -ok 360 - tile no_hsps.blastp hit 113 \#hsps 0 -ok 361 - tile no_hsps.blastp hit 114 \#hsps 0 -ok 362 - tile no_hsps.blastp hit 115 \#hsps 0 -ok 363 - tile no_hsps.blastp hit 116 \#hsps 0 -ok 364 - tile no_hsps.blastp hit 117 \#hsps 0 -ok 365 - tile no_hsps.blastp hit 118 \#hsps 0 -ok 366 - tile no_hsps.blastp hit 119 \#hsps 0 -ok 367 - tile no_hsps.blastp hit 120 \#hsps 0 -ok 368 - tile no_hsps.blastp hit 121 \#hsps 0 -ok 369 - tile no_hsps.blastp hit 122 \#hsps 0 -ok 370 - tile no_hsps.blastp hit 123 \#hsps 0 -ok 371 - tile no_hsps.blastp hit 124 \#hsps 0 -ok 372 - tile no_hsps.blastp hit 125 \#hsps 0 -ok 373 - tile no_hsps.blastp hit 126 \#hsps 0 -ok 374 - tile no_hsps.blastp hit 127 \#hsps 0 -ok 375 - tile no_hsps.blastp hit 128 \#hsps 0 -ok 376 - tile no_hsps.blastp hit 129 \#hsps 0 -ok 377 - tile no_hsps.blastp hit 130 \#hsps 0 -ok 378 - tile no_hsps.blastp hit 131 \#hsps 0 -ok 379 - tile no_hsps.blastp hit 132 \#hsps 0 -ok 380 - tile no_hsps.blastp hit 133 \#hsps 0 -ok 381 - tile no_hsps.blastp hit 134 \#hsps 0 -ok 382 - tile no_hsps.blastp hit 135 \#hsps 0 -ok 383 - tile no_hsps.blastp hit 136 \#hsps 0 -ok 384 - tile no_hsps.blastp hit 137 \#hsps 0 -ok 385 - tile no_hsps.blastp hit 138 \#hsps 0 -ok 386 - tile no_hsps.blastp hit 139 \#hsps 0 -ok 387 - tile no_hsps.blastp hit 140 \#hsps 0 -ok 388 - tile no_hsps.blastp hit 141 \#hsps 0 -ok 389 - tile no_hsps.blastp hit 142 \#hsps 0 -ok 390 - tile no_hsps.blastp hit 143 \#hsps 0 -ok 391 - tile no_hsps.blastp hit 144 \#hsps 0 -ok 392 - tile no_hsps.blastp hit 145 \#hsps 0 -ok 393 - tile no_hsps.blastp hit 146 \#hsps 0 -ok 394 - tile no_hsps.blastp hit 147 \#hsps 0 -ok 395 - tile no_hsps.blastp hit 148 \#hsps 0 -ok 396 - tile no_hsps.blastp hit 149 \#hsps 0 -ok 397 - tile no_hsps.blastp hit 150 \#hsps 0 -ok 398 - tile no_hsps.blastp hit 151 \#hsps 0 -ok 399 - tile no_hsps.blastp hit 152 \#hsps 0 -ok 400 - tile no_hsps.blastp hit 153 \#hsps 0 -ok 401 - tile no_hsps.blastp hit 154 \#hsps 0 -ok 402 - tile no_hsps.blastp hit 155 \#hsps 0 -ok 403 - tile no_hsps.blastp hit 156 \#hsps 0 -ok 404 - tile no_hsps.blastp hit 157 \#hsps 0 -ok 405 - tile no_hsps.blastp hit 158 \#hsps 0 -ok 406 - tile no_hsps.blastp hit 159 \#hsps 0 -ok 407 - tile no_hsps.blastp hit 160 \#hsps 0 -ok 408 - tile no_hsps.blastp hit 161 \#hsps 0 -ok 409 - tile no_hsps.blastp hit 162 \#hsps 0 -ok 410 - tile no_hsps.blastp hit 163 \#hsps 0 -ok 411 - tile no_hsps.blastp hit 164 \#hsps 0 -ok 412 - tile no_hsps.blastp hit 165 \#hsps 0 -ok 413 - tile no_hsps.blastp hit 166 \#hsps 0 -ok 414 - tile no_hsps.blastp hit 167 \#hsps 0 -ok 415 - tile no_hsps.blastp hit 168 \#hsps 0 -ok 416 - tile no_hsps.blastp hit 169 \#hsps 0 -ok 417 - tile no_hsps.blastp hit 170 \#hsps 0 -ok 418 - tile no_hsps.blastp hit 171 \#hsps 0 -ok 419 - tile no_hsps.blastp hit 172 \#hsps 0 -ok 420 - tile no_hsps.blastp hit 173 \#hsps 0 -ok 421 - tile no_hsps.blastp hit 174 \#hsps 0 -ok 422 - tile no_hsps.blastp hit 175 \#hsps 0 -ok 423 - tile no_hsps.blastp hit 176 \#hsps 0 -ok 424 - tile no_hsps.blastp hit 177 \#hsps 0 -ok 425 - tile no_hsps.blastp hit 178 \#hsps 0 -ok 426 - tile no_hsps.blastp hit 179 \#hsps 0 -ok 427 - tile no_hsps.blastp hit 180 \#hsps 0 -ok 428 - tile no_hsps.blastp hit 181 \#hsps 0 -ok 429 - tile no_hsps.blastp hit 182 \#hsps 0 -ok 430 - tile no_hsps.blastp hit 183 \#hsps 0 -ok 431 - tile no_hsps.blastp hit 184 \#hsps 0 -ok 432 - tile no_hsps.blastp hit 185 \#hsps 0 -ok 433 - tile no_hsps.blastp hit 186 \#hsps 0 -ok 434 - tile no_hsps.blastp hit 187 \#hsps 0 -ok 435 - tile no_hsps.blastp hit 188 \#hsps 0 -ok 436 - tile no_hsps.blastp hit 189 \#hsps 0 -ok 437 - tile no_hsps.blastp hit 190 \#hsps 0 -ok 438 - tile no_hsps.blastp hit 191 \#hsps 0 -ok 439 - tile no_hsps.blastp hit 192 \#hsps 0 -ok 440 - tile no_hsps.blastp hit 193 \#hsps 0 -ok 441 - tile no_hsps.blastp hit 194 \#hsps 0 -ok 442 - tile no_hsps.blastp hit 195 \#hsps 0 -ok 443 - tile no_hsps.blastp hit 196 \#hsps 0 -ok 444 - tile no_hsps.blastp hit 197 \#hsps 0 -ok 445 - tile no_hsps.blastp hit 198 \#hsps 0 -ok 446 - tile no_hsps.blastp hit 199 \#hsps 0 -ok 447 - tile no_hsps.blastp hit 200 \#hsps 0 -ok 448 - tile no_hsps.blastp hit 201 \#hsps 0 -ok 449 - tile no_hsps.blastp hit 202 \#hsps 0 -ok 450 - tile no_hsps.blastp hit 203 \#hsps 0 -ok 451 - tile no_hsps.blastp hit 204 \#hsps 0 -ok 452 - tile no_hsps.blastp hit 205 \#hsps 0 -ok 453 - tile no_hsps.blastp hit 206 \#hsps 0 -ok 454 - tile no_hsps.blastp hit 207 \#hsps 0 -ok 455 - tile no_hsps.blastp hit 208 \#hsps 0 -ok 456 - tile no_hsps.blastp hit 209 \#hsps 0 -ok 457 - tile no_hsps.blastp hit 210 \#hsps 0 -ok 458 - tile no_hsps.blastp hit 211 \#hsps 0 -ok 459 - tile no_hsps.blastp hit 212 \#hsps 0 -ok 460 - tile no_hsps.blastp hit 213 \#hsps 0 -ok 461 - tile no_hsps.blastp hit 214 \#hsps 0 -ok 462 - tile no_hsps.blastp hit 215 \#hsps 0 -ok 463 - tile no_hsps.blastp hit 216 \#hsps 0 -ok 464 - tile no_hsps.blastp hit 217 \#hsps 0 -ok 465 - tile no_hsps.blastp hit 218 \#hsps 0 -ok 466 - tile no_hsps.blastp hit 219 \#hsps 0 -ok 467 - tile no_hsps.blastp hit 220 \#hsps 0 -ok 468 - tile no_hsps.blastp hit 221 \#hsps 0 -ok 469 - tile no_hsps.blastp hit 222 \#hsps 0 -ok 470 - tile no_hsps.blastp hit 223 \#hsps 0 -ok 471 - tile no_hsps.blastp hit 224 \#hsps 0 -ok 472 - tile no_hsps.blastp hit 225 \#hsps 0 -ok 473 - tile no_hsps.blastp hit 226 \#hsps 0 -ok 474 - tile no_hsps.blastp hit 227 \#hsps 0 -ok 475 - tile no_hsps.blastp hit 228 \#hsps 0 -ok 476 - tile no_hsps.blastp hit 229 \#hsps 0 -ok 477 - tile no_hsps.blastp hit 230 \#hsps 0 -ok 478 - tile no_hsps.blastp hit 231 \#hsps 0 -ok 479 - tile no_hsps.blastp hit 232 \#hsps 0 -ok 480 - tile no_hsps.blastp hit 233 \#hsps 0 -ok 481 - tile no_hsps.blastp hit 234 \#hsps 0 -ok 482 - tile no_hsps.blastp hit 235 \#hsps 0 -ok 483 - tile no_hsps.blastp hit 236 \#hsps 0 -ok 484 - tile no_hsps.blastp hit 237 \#hsps 0 -ok 485 - tile no_hsps.blastp hit 238 \#hsps 0 -ok 486 - tile no_hsps.blastp hit 239 \#hsps 0 -ok 487 - tile no_hsps.blastp hit 240 \#hsps 0 -ok 488 - tile no_hsps.blastp hit 241 \#hsps 0 -ok 489 - tile no_hsps.blastp hit 242 \#hsps 0 -ok 490 - tile no_hsps.blastp hit 243 \#hsps 0 -ok 491 - tile no_hsps.blastp hit 244 \#hsps 0 -ok 492 - tile no_hsps.blastp hit 245 \#hsps 0 -ok 493 - tile no_hsps.blastp hit 246 \#hsps 0 -ok 494 - tile no_hsps.blastp hit 247 \#hsps 0 -ok 495 - tile no_hsps.blastp hit 248 \#hsps 0 -ok 496 - tile no_hsps.blastp hit 249 \#hsps 0 -ok 497 - tile no_hsps.blastp hit 250 \#hsps 0 -ok 498 - tile no_hsps.blastp hit 251 \#hsps 0 -ok 499 - tile no_hsps.blastp hit 252 \#hsps 0 -ok 500 - tile no_hsps.blastp hit 253 \#hsps 0 -ok 501 - tile no_hsps.blastp hit 254 \#hsps 0 -ok 502 - tile no_hsps.blastp hit 255 \#hsps 0 -ok 503 - tile no_hsps.blastp hit 256 \#hsps 0 -ok 504 - tile no_hsps.blastp hit 257 \#hsps 0 -ok 505 - tile no_hsps.blastp hit 258 \#hsps 0 -ok 506 - tile no_hsps.blastp hit 259 \#hsps 0 -ok 507 - tile no_hsps.blastp hit 260 \#hsps 0 -ok 508 - tile no_hsps.blastp hit 261 \#hsps 0 -ok 509 - tile no_hsps.blastp hit 262 \#hsps 0 -ok 510 - tile no_hsps.blastp hit 263 \#hsps 0 -ok 511 - tile no_hsps.blastp hit 264 \#hsps 0 -ok 512 - tile no_hsps.blastp hit 265 \#hsps 0 -ok 513 - tile no_hsps.blastp hit 266 \#hsps 0 -ok 514 - tile no_hsps.blastp hit 267 \#hsps 0 -ok 515 - tile no_hsps.blastp hit 268 \#hsps 0 -ok 516 - tile no_hsps.blastp hit 269 \#hsps 0 -ok 517 - tile no_hsps.blastp hit 270 \#hsps 0 -ok 518 - tile no_hsps.blastp hit 271 \#hsps 0 -ok 519 - tile no_hsps.blastp hit 272 \#hsps 0 -ok 520 - tile no_hsps.blastp hit 273 \#hsps 0 -ok 521 - tile no_hsps.blastp hit 274 \#hsps 0 -ok 522 - tile no_hsps.blastp hit 275 \#hsps 0 -ok 523 - tile no_hsps.blastp hit 276 \#hsps 0 -ok 524 - tile no_hsps.blastp hit 277 \#hsps 0 -ok 525 - tile no_hsps.blastp hit 278 \#hsps 0 -ok 526 - tile no_hsps.blastp hit 279 \#hsps 0 -ok 527 - tile no_hsps.blastp hit 280 \#hsps 0 -ok 528 - tile no_hsps.blastp hit 281 \#hsps 0 -ok 529 - tile no_hsps.blastp hit 282 \#hsps 0 -ok 530 - tile no_hsps.blastp hit 283 \#hsps 0 -ok 531 - tile no_hsps.blastp hit 284 \#hsps 0 -ok 532 - tile no_hsps.blastp hit 285 \#hsps 0 -ok 533 - tile no_hsps.blastp hit 286 \#hsps 0 -ok 534 - tile no_hsps.blastp hit 287 \#hsps 0 -ok 535 - tile no_hsps.blastp hit 288 \#hsps 0 -ok 536 - tile no_hsps.blastp hit 289 \#hsps 0 -ok 537 - tile no_hsps.blastp hit 290 \#hsps 0 -ok 538 - tile no_hsps.blastp hit 291 \#hsps 0 -ok 539 - tile no_hsps.blastp hit 292 \#hsps 0 -ok 540 - tile no_hsps.blastp hit 293 \#hsps 0 -ok 541 - tile no_hsps.blastp hit 294 \#hsps 0 -ok 542 - tile no_hsps.blastp hit 295 \#hsps 0 -ok 543 - tile no_hsps.blastp hit 296 \#hsps 0 -ok 544 - tile no_hsps.blastp hit 297 \#hsps 0 -ok 545 - tile no_hsps.blastp hit 298 \#hsps 0 -ok 546 - tile no_hsps.blastp hit 299 \#hsps 0 -ok 547 - tile no_hsps.blastp hit 300 \#hsps 0 -ok 548 - tile no_hsps.blastp hit 301 \#hsps 0 -ok 549 - tile no_hsps.blastp hit 302 \#hsps 0 -ok 550 - tile no_hsps.blastp hit 303 \#hsps 0 -ok 551 - tile no_hsps.blastp hit 304 \#hsps 0 -ok 552 - tile no_hsps.blastp hit 305 \#hsps 0 -ok 553 - tile no_hsps.blastp hit 306 \#hsps 0 -ok 554 - tile no_hsps.blastp hit 307 \#hsps 0 -ok 555 - tile no_hsps.blastp hit 308 \#hsps 0 -ok 556 - tile no_hsps.blastp hit 309 \#hsps 0 -ok 557 - tile no_hsps.blastp hit 310 \#hsps 0 -ok 558 - tile no_hsps.blastp hit 311 \#hsps 0 -ok 559 - tile no_hsps.blastp hit 312 \#hsps 0 -ok 560 - tile no_hsps.blastp hit 313 \#hsps 0 -ok 561 - tile no_hsps.blastp hit 314 \#hsps 0 -ok 562 - tile no_hsps.blastp hit 315 \#hsps 0 -ok 563 - tile no_hsps.blastp hit 316 \#hsps 0 -ok 564 - tile no_hsps.blastp hit 317 \#hsps 0 -ok 565 - tile no_hsps.blastp hit 318 \#hsps 0 -ok 566 - tile no_hsps.blastp hit 319 \#hsps 0 -ok 567 - tile no_hsps.blastp hit 320 \#hsps 0 -ok 568 - tile no_hsps.blastp hit 321 \#hsps 0 -ok 569 - tile no_hsps.blastp hit 322 \#hsps 0 -ok 570 - tile no_hsps.blastp hit 323 \#hsps 0 -ok 571 - tile no_hsps.blastp hit 324 \#hsps 0 -ok 572 - tile no_hsps.blastp hit 325 \#hsps 0 -ok 573 - tile no_hsps.blastp hit 326 \#hsps 0 -ok 574 - tile no_hsps.blastp hit 327 \#hsps 0 -ok 575 - tile no_hsps.blastp hit 328 \#hsps 0 -ok 576 - tile no_hsps.blastp hit 329 \#hsps 0 -ok 577 - tile no_hsps.blastp hit 330 \#hsps 0 -ok 578 - tile no_hsps.blastp hit 331 \#hsps 0 -ok 579 - tile no_hsps.blastp hit 332 \#hsps 0 -ok 580 - tile no_hsps.blastp hit 333 \#hsps 0 -ok 581 - tile no_hsps.blastp hit 334 \#hsps 0 -ok 582 - tile no_hsps.blastp hit 335 \#hsps 0 -ok 583 - tile no_hsps.blastp hit 336 \#hsps 0 -ok 584 - tile no_hsps.blastp hit 337 \#hsps 0 -ok 585 - tile no_hsps.blastp hit 338 \#hsps 0 -ok 586 - tile no_hsps.blastp hit 339 \#hsps 0 -ok 587 - tile no_hsps.blastp hit 340 \#hsps 0 -ok 588 - tile no_hsps.blastp hit 341 \#hsps 0 -ok 589 - tile no_hsps.blastp hit 342 \#hsps 0 -ok 590 - tile no_hsps.blastp hit 343 \#hsps 0 -ok 591 - tile no_hsps.blastp hit 344 \#hsps 0 -ok 592 - tile no_hsps.blastp hit 345 \#hsps 0 -ok 593 - tile no_hsps.blastp hit 346 \#hsps 0 -ok 594 - tile no_hsps.blastp hit 347 \#hsps 0 -ok 595 - tile no_hsps.blastp hit 348 \#hsps 0 -ok 596 - tile no_hsps.blastp hit 349 \#hsps 0 -ok 597 - tile no_hsps.blastp hit 350 \#hsps 0 -ok 598 - tile no_hsps.blastp hit 351 \#hsps 0 -ok 599 - tile no_hsps.blastp hit 352 \#hsps 0 -ok 600 - tile no_hsps.blastp hit 353 \#hsps 0 -ok 601 - tile no_hsps.blastp hit 354 \#hsps 0 -ok 602 - tile no_hsps.blastp hit 355 \#hsps 0 -ok 603 - tile no_hsps.blastp hit 356 \#hsps 0 -ok 604 - tile no_hsps.blastp hit 357 \#hsps 0 -ok 605 - tile no_hsps.blastp hit 358 \#hsps 0 -ok 606 - tile no_hsps.blastp hit 359 \#hsps 0 -ok 607 - tile no_hsps.blastp hit 360 \#hsps 0 -ok 608 - tile no_hsps.blastp hit 361 \#hsps 0 -ok 609 - tile no_hsps.blastp hit 362 \#hsps 0 -ok 610 - tile no_hsps.blastp hit 363 \#hsps 0 -ok 611 - tile no_hsps.blastp hit 364 \#hsps 0 -ok 612 - tile no_hsps.blastp hit 365 \#hsps 0 -ok 613 - tile no_hsps.blastp hit 366 \#hsps 0 -ok 614 - tile no_hsps.blastp hit 367 \#hsps 0 -ok 615 - tile no_hsps.blastp hit 368 \#hsps 0 -ok 616 - tile no_hsps.blastp hit 369 \#hsps 0 -ok 617 - tile no_hsps.blastp hit 370 \#hsps 0 -ok 618 - tile no_hsps.blastp hit 371 \#hsps 0 -ok 619 - tile no_hsps.blastp hit 372 \#hsps 0 -ok 620 - tile no_hsps.blastp hit 373 \#hsps 0 -ok 621 - tile no_hsps.blastp hit 374 \#hsps 0 -ok 622 - tile no_hsps.blastp hit 375 \#hsps 0 -ok 623 - tile no_hsps.blastp hit 376 \#hsps 0 -ok 624 - tile no_hsps.blastp hit 377 \#hsps 0 -ok 625 - tile no_hsps.blastp hit 378 \#hsps 0 -ok 626 - tile no_hsps.blastp hit 379 \#hsps 0 -ok 627 - tile no_hsps.blastp hit 380 \#hsps 0 -ok 628 - tile no_hsps.blastp hit 381 \#hsps 0 -ok 629 - tile no_hsps.blastp hit 382 \#hsps 0 -ok 630 - tile no_hsps.blastp hit 383 \#hsps 0 -ok 631 - tile no_hsps.blastp hit 384 \#hsps 0 -ok 632 - tile no_hsps.blastp hit 385 \#hsps 0 -ok 633 - tile no_hsps.blastp hit 386 \#hsps 0 -ok 634 - tile no_hsps.blastp hit 387 \#hsps 0 -ok 635 - tile no_hsps.blastp hit 388 \#hsps 0 -ok 636 - tile no_hsps.blastp hit 389 \#hsps 0 -ok 637 - tile no_hsps.blastp hit 390 \#hsps 0 -ok 638 - tile no_hsps.blastp hit 391 \#hsps 0 -ok 639 - tile no_hsps.blastp hit 392 \#hsps 0 -ok 640 - tile no_hsps.blastp hit 393 \#hsps 0 -ok 641 - tile no_hsps.blastp hit 394 \#hsps 0 -ok 642 - tile no_hsps.blastp hit 395 \#hsps 0 -ok 643 - tile no_hsps.blastp hit 396 \#hsps 0 -ok 644 - tile no_hsps.blastp hit 397 \#hsps 0 -ok 645 - tile no_hsps.blastp hit 398 \#hsps 0 -ok 646 - tile no_hsps.blastp hit 399 \#hsps 0 -ok 647 - tile no_hsps.blastp hit 400 \#hsps 0 -ok 648 - tile no_hsps.blastp hit 401 \#hsps 0 -ok 649 - tile no_hsps.blastp hit 402 \#hsps 0 -ok 650 - tile no_hsps.blastp hit 403 \#hsps 0 -ok 651 - tile no_hsps.blastp hit 404 \#hsps 0 -ok 652 - tile no_hsps.blastp hit 405 \#hsps 0 -ok 653 - tile no_hsps.blastp hit 406 \#hsps 0 -ok 654 - tile no_hsps.blastp hit 407 \#hsps 0 -ok 655 - tile no_hsps.blastp hit 408 \#hsps 0 -ok 656 - tile no_hsps.blastp hit 409 \#hsps 0 -ok 657 - tile no_hsps.blastp hit 410 \#hsps 0 -ok 658 - tile no_hsps.blastp hit 411 \#hsps 0 -ok 659 - tile no_hsps.blastp hit 412 \#hsps 0 -ok 660 - tile no_hsps.blastp hit 413 \#hsps 0 -ok 661 - tile no_hsps.blastp hit 414 \#hsps 0 -ok 662 - tile no_hsps.blastp hit 415 \#hsps 0 -ok 663 - catalase-webblast.BLASTP -ok 664 - tile catalase-webblast.BLASTP hit 1 \#hsps 1 -ok 665 - q id: est (1.00000) = fast (1.00000) -ok 666 - q cn: est (1.00000) = fast (1.00000) -ok 667 - h id: est (1.00000) = fast (1.00000) -ok 668 - h cn: est (1.00000) = fast (1.00000) -ok 669 - tile catalase-webblast.BLASTP hit 2 \#hsps 1 -ok 670 - q id: est (0.80973) = fast (0.80973) -ok 671 - q cn: est (0.89006) = fast (0.89006) -ok 672 - h id: est (0.82543) = fast (0.82543) -ok 673 - h cn: est (0.90733) = fast (0.90733) -ok 674 - tile catalase-webblast.BLASTP hit 3 \#hsps 1 -ok 675 - q id: est (0.71670) = fast (0.71670) -ok 676 - q cn: est (0.84144) = fast (0.84144) -ok 677 - h id: est (0.72747) = fast (0.72747) -ok 678 - h cn: est (0.85408) = fast (0.85408) -ok 679 - tile catalase-webblast.BLASTP hit 4 \#hsps 1 -ok 680 - q id: est (0.58910) = fast (0.58910) -ok 681 - q cn: est (0.70860) = fast (0.70860) -ok 682 - h id: est (0.65654) = fast (0.65654) -ok 683 - h cn: est (0.78972) = fast (0.78972) -ok 684 - tile catalase-webblast.BLASTP hit 5 \#hsps 1 -ok 685 - q id: est (0.49245) = fast (0.49245) -ok 686 - q cn: est (0.65257) = fast (0.65257) -ok 687 - h id: est (0.49544) = fast (0.49544) -ok 688 - h cn: est (0.65653) = fast (0.65653) -ok 689 - tile catalase-webblast.BLASTP hit 6 \#hsps 1 -ok 690 - q id: est (0.44366) = fast (0.44366) -ok 691 - q cn: est (0.58920) = fast (0.58920) -ok 692 - h id: est (0.44787) = fast (0.44787) -ok 693 - h cn: est (0.59479) = fast (0.59479) -ok 694 - tile catalase-webblast.BLASTP hit 7 \#hsps 1 -ok 695 - q id: est (0.42564) = fast (0.42564) -ok 696 - q cn: est (0.61282) = fast (0.61282) -ok 697 - h id: est (0.43229) = fast (0.43229) -ok 698 - h cn: est (0.62240) = fast (0.62240) -ok 699 - tile catalase-webblast.BLASTP hit 8 \#hsps 1 -ok 700 - q id: est (0.48358) = fast (0.48358) -ok 701 - q cn: est (0.63881) = fast (0.63881) -ok 702 - h id: est (0.48943) = fast (0.48943) -ok 703 - h cn: est (0.64653) = fast (0.64653) -ok 704 - tile catalase-webblast.BLASTP hit 9 \#hsps 1 -ok 705 - q id: est (0.42308) = fast (0.42308) -ok 706 - q cn: est (0.61282) = fast (0.61282) -ok 707 - h id: est (0.42969) = fast (0.42969) -ok 708 - h cn: est (0.62240) = fast (0.62240) -ok 709 - tile catalase-webblast.BLASTP hit 10 \#hsps 1 -ok 710 - q id: est (0.39675) = fast (0.39675) -ok 711 - q cn: est (0.58933) = fast (0.58933) -ok 712 - h id: est (0.39767) = fast (0.39767) -ok 713 - h cn: est (0.59070) = fast (0.59070) -ok 714 - dcr1_sp.WUBLASTP -ok 715 - tile dcr1_sp.WUBLASTP hit 1 \#hsps 1 -ok 716 - q id: est (1.00000) = fast (1.00000) -ok 717 - q cn: est (1.00000) = fast (1.00000) -ok 718 - h id: est (1.00000) = fast (1.00000) -ok 719 - h cn: est (1.00000) = fast (1.00000) -ok 720 - tile dcr1_sp.WUBLASTP hit 2 \#hsps 4 -ok 721 - q id: exact (0.36876) ~ est (0.36973) -ok 722 - q id: exact (0.36876) <= max (0.37070) -ok 723 - q cn: exact (0.55022) ~ est (0.55041) -ok 724 - q cn: exact (0.55022) <= max (0.55105) -ok 725 - h id: exact (0.35111) ~ est (0.35111) -ok 726 - h id: exact (0.35111) <= max (0.35111) -ok 727 - h cn: exact (0.52305) ~ est (0.52305) -ok 728 - h cn: exact (0.52305) <= max (0.52305) -ok 729 - tile dcr1_sp.WUBLASTP hit 3 \#hsps 1 -ok 730 - q id: est (0.38685) = fast (0.38685) -ok 731 - q cn: est (0.55397) = fast (0.55397) -ok 732 - h id: est (0.37613) = fast (0.37613) -ok 733 - h cn: est (0.53863) = fast (0.53863) -ok 734 - tile dcr1_sp.WUBLASTP hit 4 \#hsps 1 -ok 735 - q id: est (0.38247) = fast (0.38247) -ok 736 - q cn: est (0.55068) = fast (0.55068) -ok 737 - h id: est (0.37306) = fast (0.37306) -ok 738 - h cn: est (0.53715) = fast (0.53715) -ok 739 - tile dcr1_sp.WUBLASTP hit 5 \#hsps 5 -ok 740 - q id: exact (0.35010) ~ est (0.35010) -ok 741 - q id: exact (0.35010) <= max (0.35010) -ok 742 - q cn: exact (0.53183) ~ est (0.53183) -ok 743 - q cn: exact (0.53183) <= max (0.53183) -ok 744 - h id: exact (0.35082) ~ est (0.35082) -ok 745 - h id: exact (0.35082) <= max (0.35082) -ok 746 - h cn: exact (0.53292) ~ est (0.53292) -ok 747 - h cn: exact (0.53292) <= max (0.53292) -ok 748 - tile dcr1_sp.WUBLASTP hit 6 \#hsps 8 -ok 749 - q id: exact (0.30547) ~ est (0.30659) -ok 750 - q id: exact (0.30547) <= max (0.30623) -ok 751 - q cn: exact (0.50076) ~ est (0.50205) -ok 752 - q cn: exact (0.50076) <= max (0.50076) -ok 753 - h id: exact (0.31390) ~ est (0.31179) -ok 754 - h id: exact (0.31390) <= max (0.31795) -ok 755 - h cn: exact (0.50531) ~ est (0.50557) -ok 756 - h cn: exact (0.50531) <= max (0.51091) -ok 757 - tile dcr1_sp.WUBLASTP hit 7 \#hsps 7 -ok 758 - q id: exact (0.30136) ~ est (0.30184) -ok 759 - q id: exact (0.30136) <= max (0.30498) -ok 760 - q cn: exact (0.48688) ~ est (0.48742) -ok 761 - q cn: exact (0.48688) <= max (0.49140) -ok 762 - h id: exact (0.30944) ~ est (0.31034) -ok 763 - h id: exact (0.30944) <= max (0.30988) -ok 764 - h cn: exact (0.50178) ~ est (0.50277) -ok 765 - h cn: exact (0.50178) <= max (0.50223) -ok 766 - tile dcr1_sp.WUBLASTP hit 8 \#hsps 10 -ok 767 - q id: exact (0.28918) ~ est (0.28961) -ok 768 - q id: exact (0.28918) <= max (0.28955) -ok 769 - q cn: exact (0.46418) ~ est (0.46247) -ok 770 - q cn: exact (0.46418) <= max (0.46866) -ok 771 - h id: exact (0.30166) ~ est (0.30299) -ok 772 - h id: exact (0.30166) <= max (0.30800) -ok 773 - h cn: exact (0.48179) ~ est (0.48439) -ok 774 - h cn: exact (0.48179) <= max (0.48535) -ok 775 - tile dcr1_sp.WUBLASTP hit 9 \#hsps 8 -ok 776 - q id: exact (0.30289) ~ est (0.30238) -ok 777 - q id: exact (0.30289) <= max (0.30651) -ok 778 - q cn: exact (0.49955) ~ est (0.49787) -ok 779 - q cn: exact (0.49955) <= max (0.50362) -ok 780 - h id: exact (0.31395) ~ est (0.31347) -ok 781 - h id: exact (0.31395) <= max (0.31721) -ok 782 - h cn: exact (0.51535) ~ est (0.51578) -ok 783 - h cn: exact (0.51535) <= max (0.51814) -ok 784 - tile dcr1_sp.WUBLASTP hit 10 \#hsps 5 -ok 785 - q id: exact (0.29334) ~ est (0.29534) -ok 786 - q id: exact (0.29334) <= max (0.29810) -ok 787 - q cn: exact (0.46617) ~ est (0.46719) -ok 788 - q cn: exact (0.46617) <= max (0.47040) -ok 789 - h id: exact (0.31176) ~ est (0.31176) -ok 790 - h id: exact (0.31176) <= max (0.31176) -ok 791 - h cn: exact (0.49299) ~ est (0.49299) -ok 792 - h cn: exact (0.49299) <= max (0.49299) -ok 793 - tile dcr1_sp.WUBLASTP hit 11 \#hsps 7 -ok 794 - q id: exact (0.30456) ~ est (0.30514) -ok 795 - q id: exact (0.30456) <= max (0.30650) -ok 796 - q cn: exact (0.48739) ~ est (0.48879) -ok 797 - q cn: exact (0.48739) <= max (0.49370) -ok 798 - h id: exact (0.32062) ~ est (0.31987) -ok 799 - h id: exact (0.32062) <= max (0.32932) -ok 800 - h cn: exact (0.51071) ~ est (0.51306) -ok 801 - h cn: exact (0.51071) <= max (0.52410) -ok 802 - tile dcr1_sp.WUBLASTP hit 12 \#hsps 8 -ok 803 - q id: exact (0.29615) ~ est (0.29879) -ok 804 - q id: exact (0.29615) <= max (0.30009) -ok 805 - q cn: exact (0.47419) ~ est (0.47394) -ok 806 - q cn: exact (0.47419) <= max (0.48119) -ok 807 - h id: exact (0.31611) ~ est (0.31482) -ok 808 - h id: exact (0.31611) <= max (0.32227) -ok 809 - h cn: exact (0.49779) ~ est (0.49788) -ok 810 - h cn: exact (0.49779) <= max (0.50616) -ok 811 - tile dcr1_sp.WUBLASTP hit 13 \#hsps 8 -ok 812 - q id: exact (0.30390) ~ est (0.30440) -ok 813 - q id: exact (0.30390) <= max (0.30701) -ok 814 - q cn: exact (0.45874) ~ est (0.45993) -ok 815 - q cn: exact (0.45874) <= max (0.45963) -ok 816 - h id: exact (0.32282) ~ est (0.32324) -ok 817 - h id: exact (0.32282) <= max (0.32560) -ok 818 - h cn: exact (0.48052) ~ est (0.48136) -ok 819 - h cn: exact (0.48052) <= max (0.48330) -ok 820 - tile dcr1_sp.WUBLASTP hit 14 \#hsps 6 -ok 821 - q id: exact (0.29769) ~ est (0.29851) -ok 822 - q id: exact (0.29769) <= max (0.29769) -ok 823 - q cn: exact (0.48480) ~ est (0.48628) -ok 824 - q cn: exact (0.48480) <= max (0.48637) -ok 825 - h id: exact (0.30704) ~ est (0.30810) -ok 826 - h id: exact (0.30704) <= max (0.30917) -ok 827 - h cn: exact (0.50107) ~ est (0.50292) -ok 828 - h cn: exact (0.50107) <= max (0.50320) -ok 829 - tile dcr1_sp.WUBLASTP hit 15 \#hsps 6 -ok 830 - q id: exact (0.27854) ~ est (0.27854) -ok 831 - q id: exact (0.27854) <= max (0.27854) -ok 832 - q cn: exact (0.48174) ~ est (0.48174) -ok 833 - q cn: exact (0.48174) <= max (0.48174) -ok 834 - h id: exact (0.28514) ~ est (0.28623) -ok 835 - h id: exact (0.28514) <= max (0.28594) -ok 836 - h cn: exact (0.49197) ~ est (0.49154) -ok 837 - h cn: exact (0.49197) <= max (0.49237) -ok 838 - tile dcr1_sp.WUBLASTP hit 16 \#hsps 8 -ok 839 - q id: exact (0.30362) ~ est (0.30824) -ok 840 - q id: exact (0.30362) <= max (0.30852) -ok 841 - q cn: exact (0.47111) ~ est (0.47587) -ok 842 - q cn: exact (0.47111) <= max (0.47405) -ok 843 - h id: exact (0.32347) ~ est (0.32392) -ok 844 - h id: exact (0.32347) <= max (0.32643) -ok 845 - h cn: exact (0.49310) ~ est (0.49360) -ok 846 - h cn: exact (0.49310) <= max (0.49606) -ok 847 - tile dcr1_sp.WUBLASTP hit 17 \#hsps 4 -ok 848 - q id: exact (0.29174) ~ est (0.29174) -ok 849 - q id: exact (0.29174) <= max (0.29174) -ok 850 - q cn: exact (0.46230) ~ est (0.46230) -ok 851 - q cn: exact (0.46230) <= max (0.46230) -ok 852 - h id: exact (0.30204) ~ est (0.30204) -ok 853 - h id: exact (0.30204) <= max (0.30204) -ok 854 - h cn: exact (0.47862) ~ est (0.47862) -ok 855 - h cn: exact (0.47862) <= max (0.47862) -ok 856 - tile dcr1_sp.WUBLASTP hit 18 \#hsps 6 -ok 857 - q id: exact (0.29064) ~ est (0.29089) -ok 858 - q id: exact (0.29064) <= max (0.29115) -ok 859 - q cn: exact (0.48765) ~ est (0.48670) -ok 860 - q cn: exact (0.48765) <= max (0.48868) -ok 861 - h id: exact (0.29848) ~ est (0.29887) -ok 862 - h id: exact (0.29848) <= max (0.29902) -ok 863 - h cn: exact (0.50108) ~ est (0.50116) -ok 864 - h cn: exact (0.50108) <= max (0.50163) -ok 865 - tile dcr1_sp.WUBLASTP hit 19 \#hsps 5 -ok 866 - q id: exact (0.29510) ~ est (0.29505) -ok 867 - q id: exact (0.29510) <= max (0.29510) -ok 868 - q cn: exact (0.48982) ~ est (0.49039) -ok 869 - q cn: exact (0.48982) <= max (0.49029) -ok 870 - h id: exact (0.30019) ~ est (0.30019) -ok 871 - h id: exact (0.30019) <= max (0.30019) -ok 872 - h cn: exact (0.49906) ~ est (0.49906) -ok 873 - h cn: exact (0.49906) <= max (0.49906) -ok 874 - 503384.MEGABLAST.2 -ok 875 - tile 503384.MEGABLAST.2 hit 1 \#hsps 5 -ok 876 - q id: exact (0.91435) ~ est (0.91435) -ok 877 - q id: exact (0.91435) <= max (0.91435) -ok 878 - q cn: exact (0.91435) ~ est (0.91435) -ok 879 - q cn: exact (0.91435) <= max (0.91435) -ok 880 - h id: exact (0.91157) ~ est (0.91157) -ok 881 - h id: exact (0.91157) <= max (0.91157) -ok 882 - h cn: exact (0.91157) ~ est (0.91157) -ok 883 - h cn: exact (0.91157) <= max (0.91157) -ok 884 - tile 503384.MEGABLAST.2 hit 2 \#hsps 9 -ok 885 - q id: exact (0.92895) ~ est (0.92895) -ok 886 - q id: exact (0.92895) <= max (0.92895) -ok 887 - q cn: exact (0.92895) ~ est (0.92895) -ok 888 - q cn: exact (0.92895) <= max (0.92895) -ok 889 - h id: exact (0.92854) ~ est (0.92854) -ok 890 - h id: exact (0.92854) <= max (0.92854) -ok 891 - h cn: exact (0.92854) ~ est (0.92854) -ok 892 - h cn: exact (0.92854) <= max (0.92854) -ok 893 - tile 503384.MEGABLAST.2 hit 3 \#hsps 3 -ok 894 - q id: exact (0.93516) ~ est (0.93516) -ok 895 - q id: exact (0.93516) <= max (0.93516) -ok 896 - q cn: exact (0.93516) ~ est (0.93516) -ok 897 - q cn: exact (0.93516) <= max (0.93516) -ok 898 - h id: exact (0.93651) ~ est (0.93651) -ok 899 - h id: exact (0.93651) <= max (0.93651) -ok 900 - h cn: exact (0.93651) ~ est (0.93651) -ok 901 - h cn: exact (0.93651) <= max (0.93651) -ok 902 - tile 503384.MEGABLAST.2 hit 4 \#hsps 3 -ok 903 - q id: exact (0.93064) ~ est (0.93064) -ok 904 - q id: exact (0.93064) <= max (0.93064) -ok 905 - q cn: exact (0.93064) ~ est (0.93064) -ok 906 - q cn: exact (0.93064) <= max (0.93064) -ok 907 - h id: exact (0.92885) ~ est (0.92885) -ok 908 - h id: exact (0.92885) <= max (0.92885) -ok 909 - h cn: exact (0.92885) ~ est (0.92885) -ok 910 - h cn: exact (0.92885) <= max (0.92885) -ok 911 - bl2seq.blastx.out -ok 912 - tile bl2seq.blastx.out hit 1 \#hsps 6 -ok 913 - q id: est (0.35714) = fast (0.35714) -ok 914 - q cn: est (0.57143) = fast (0.57143) -ok 915 - q id: exact (0.70536) ~ est (0.70495) -ok 916 - q id: exact (0.70536) <= max (0.94286) -ok 917 - q cn: exact (0.78810) ~ est (0.78803) -ok 918 - q cn: exact (0.78810) <= max (0.96429) -ok 919 - q id: est (0.71429) = fast (0.71429) -ok 920 - q cn: est (1.00000) = fast (1.00000) -ok 921 - h id: exact (0.61923) ~ est (0.61955) -ok 922 - h id: exact (0.61923) <= max (0.64231) -ok 923 - h cn: exact (0.73077) ~ est (0.73077) -ok 924 - h cn: exact (0.73077) <= max (0.75000) -ok 925 - dnaEbsub_ecoli.wublastx -ok 926 - tile dnaEbsub_ecoli.wublastx hit 1 \#hsps 1 -ok 927 - q id: est (0.36386) = fast (0.36386) -ok 928 - q cn: est (0.53735) = fast (0.53735) -ok 929 - h id: est (0.36562) = fast (0.36562) -ok 930 - h cn: est (0.53995) = fast (0.53995) -ok 931 - tblastn.out -ok 932 - tile tblastn.out hit 1 \#hsps 2 -ok 933 - q id: exact (0.31250) ~ est (0.33325) -ok 934 - q id: exact (0.31250) <= max (0.33333) -ok 935 - q cn: exact (0.44792) ~ est (0.47055) -ok 936 - q cn: exact (0.44792) <= max (0.45833) -ok 937 - h id: exact (0.33333) ~ est (0.33333) -ok 938 - h id: exact (0.33333) <= max (0.33333) -ok 939 - h cn: exact (0.47059) ~ est (0.47059) -ok 940 - h cn: exact (0.47059) <= max (0.47059) -ok 941 - tile tblastn.out hit 2 \#hsps 2 -ok 942 - q id: exact (0.68750) ~ est (0.68750) -ok 943 - q id: exact (0.68750) <= max (0.68750) -ok 944 - q cn: exact (0.81250) ~ est (0.81250) -ok 945 - q cn: exact (0.81250) <= max (0.81250) -ok 946 - h id: est (0.71429) = fast (0.71429) -ok 947 - h cn: est (0.85714) = fast (0.85714) -ok 948 - h id: est (0.66667) = fast (0.66667) -ok 949 - h cn: est (0.77778) = fast (0.77778) -ok 950 - dnaEbsub_ecoli.wutblastn -ok 951 - tile dnaEbsub_ecoli.wutblastn hit 1 \#hsps 1 -ok 952 - q id: est (0.36386) = fast (0.36386) -ok 953 - q cn: est (0.53735) = fast (0.53735) -ok 954 - h id: est (0.36562) = fast (0.36562) -ok 955 - h cn: est (0.53995) = fast (0.53995) -ok 956 - HUMBETGLOA.tblastx -ok 957 - tile HUMBETGLOA.tblastx hit 1 \#hsps 1 -ok 958 - q id: est (0.42308) = fast (0.42308) -ok 959 - q cn: est (0.61538) = fast (0.61538) -ok 960 - h id: est (0.42308) = fast (0.42308) -ok 961 - h cn: est (0.61538) = fast (0.61538) -ok 962 - tile HUMBETGLOA.tblastx hit 2 \#hsps 1 -ok 963 - q id: est (0.47059) = fast (0.47059) -ok 964 - q cn: est (0.76471) = fast (0.76471) -ok 965 - h id: est (0.47059) = fast (0.47059) -ok 966 - h cn: est (0.76471) = fast (0.76471) -ok 967 - tile HUMBETGLOA.tblastx hit 3 \#hsps 1 -ok 968 - q id: est (0.36000) = fast (0.36000) -ok 969 - q cn: est (0.56000) = fast (0.56000) -ok 970 - h id: est (0.36000) = fast (0.36000) -ok 971 - h cn: est (0.56000) = fast (0.56000) -ok 972 - tile HUMBETGLOA.tblastx hit 4 \#hsps 1 -ok 973 - q id: est (0.29268) = fast (0.29268) -ok 974 - q cn: est (0.58537) = fast (0.58537) -ok 975 - h id: est (0.29268) = fast (0.29268) -ok 976 - h cn: est (0.58537) = fast (0.58537) -ok 977 - tile HUMBETGLOA.tblastx hit 5 \#hsps 1 -ok 978 - q id: est (0.38889) = fast (0.38889) -ok 979 - q cn: est (0.55556) = fast (0.55556) -ok 980 - h id: est (0.38889) = fast (0.38889) -ok 981 - h cn: est (0.55556) = fast (0.55556) -ok 982 - tile HUMBETGLOA.tblastx hit 6 \#hsps 1 -ok 983 - q id: est (0.43590) = fast (0.43590) -ok 984 - q cn: est (0.51282) = fast (0.51282) -ok 985 - h id: est (0.43590) = fast (0.43590) -ok 986 - h cn: est (0.51282) = fast (0.51282) -ok 987 - tile HUMBETGLOA.tblastx hit 7 \#hsps 1 -ok 988 - q id: est (0.35714) = fast (0.35714) -ok 989 - q cn: est (0.42857) = fast (0.42857) -ok 990 - h id: est (0.35714) = fast (0.35714) -ok 991 - h cn: est (0.42857) = fast (0.42857) -ok 992 - tile HUMBETGLOA.tblastx hit 8 \#hsps 1 -ok 993 - q id: est (0.33333) = fast (0.33333) -ok 994 - q cn: est (0.66667) = fast (0.66667) -ok 995 - h id: est (0.33333) = fast (0.33333) -ok 996 - h cn: est (0.66667) = fast (0.66667) -ok 997 - tile HUMBETGLOA.tblastx hit 9 \#hsps 2 -ok 998 - q id: exact (0.40541) ~ est (0.40541) -ok 999 - q id: exact (0.40541) <= max (0.40541) -ok 1000 - q cn: exact (0.56757) ~ est (0.56757) -ok 1001 - q cn: exact (0.56757) <= max (0.56757) -ok 1002 - h id: est (0.36364) = fast (0.36364) -ok 1003 - h cn: est (0.63636) = fast (0.63636) -ok 1004 - h id: est (0.42308) = fast (0.42308) -ok 1005 - h cn: est (0.53846) = fast (0.53846) -ok 1006 - tile HUMBETGLOA.tblastx hit 10 \#hsps 1 -ok 1007 - q id: est (0.29167) = fast (0.29167) -ok 1008 - q cn: est (0.39583) = fast (0.39583) -ok 1009 - h id: est (0.29167) = fast (0.29167) -ok 1010 - h cn: est (0.39583) = fast (0.39583) -ok 1011 - tile HUMBETGLOA.tblastx hit 11 \#hsps 1 -ok 1012 - q id: est (0.60000) = fast (0.60000) -ok 1013 - q cn: est (0.65000) = fast (0.65000) -ok 1014 - h id: est (0.60000) = fast (0.60000) -ok 1015 - h cn: est (0.65000) = fast (0.65000) -ok 1016 - tile HUMBETGLOA.tblastx hit 12 \#hsps 1 -ok 1017 - q id: est (0.50000) = fast (0.50000) -ok 1018 - q cn: est (0.68182) = fast (0.68182) -ok 1019 - h id: est (0.50000) = fast (0.50000) -ok 1020 - h cn: est (0.68182) = fast (0.68182) -ok 1021 - tile HUMBETGLOA.tblastx hit 13 \#hsps 1 -ok 1022 - q id: est (0.29630) = fast (0.29630) -ok 1023 - q cn: est (0.48148) = fast (0.48148) -ok 1024 - h id: est (0.29630) = fast (0.29630) -ok 1025 - h cn: est (0.48148) = fast (0.48148) -ok 1026 - tile HUMBETGLOA.tblastx hit 14 \#hsps 1 -ok 1027 - q id: est (0.47826) = fast (0.47826) -ok 1028 - q cn: est (0.52174) = fast (0.52174) -ok 1029 - h id: est (0.47826) = fast (0.47826) -ok 1030 - h cn: est (0.52174) = fast (0.52174) -ok 1031 - tile HUMBETGLOA.tblastx hit 15 \#hsps 1 -ok 1032 - q id: est (0.47368) = fast (0.47368) -ok 1033 - q cn: est (0.63158) = fast (0.63158) -ok 1034 - h id: est (0.47368) = fast (0.47368) -ok 1035 - h cn: est (0.63158) = fast (0.63158) -ok 1036 - tile HUMBETGLOA.tblastx hit 16 \#hsps 1 -ok 1037 - q id: est (0.44444) = fast (0.44444) -ok 1038 - q cn: est (0.55556) = fast (0.55556) -ok 1039 - h id: est (0.44444) = fast (0.44444) -ok 1040 - h cn: est (0.55556) = fast (0.55556) -ok 1041 - tile HUMBETGLOA.tblastx hit 17 \#hsps 1 -ok 1042 - q id: est (0.47059) = fast (0.47059) -ok 1043 - q cn: est (0.70588) = fast (0.70588) -ok 1044 - h id: est (0.47059) = fast (0.47059) -ok 1045 - h cn: est (0.70588) = fast (0.70588) -ok 1046 - tile HUMBETGLOA.tblastx hit 18 \#hsps 1 -ok 1047 - q id: est (0.38889) = fast (0.38889) -ok 1048 - q cn: est (0.66667) = fast (0.66667) -ok 1049 - h id: est (0.38889) = fast (0.38889) -ok 1050 - h cn: est (0.66667) = fast (0.66667) -ok 1051 - tile HUMBETGLOA.tblastx hit 19 \#hsps 1 -ok 1052 - q id: est (0.27660) = fast (0.27660) -ok 1053 - q cn: est (0.48936) = fast (0.48936) -ok 1054 - h id: est (0.27660) = fast (0.27660) -ok 1055 - h cn: est (0.48936) = fast (0.48936) -ok 1056 - tile HUMBETGLOA.tblastx hit 20 \#hsps 1 -ok 1057 - q id: est (0.40000) = fast (0.40000) -ok 1058 - q cn: est (0.60000) = fast (0.60000) -ok 1059 - h id: est (0.40000) = fast (0.40000) -ok 1060 - h cn: est (0.60000) = fast (0.60000) -ok 1061 - dnaEbsub_ecoli.wutblastx -ok 1062 - tile dnaEbsub_ecoli.wutblastx hit 1 \#hsps 12 -ok 1063 - q id: exact (0.44118) ~ est (0.44118) -ok 1064 - q id: exact (0.44118) <= max (0.44118) -ok 1065 - q cn: exact (0.54412) ~ est (0.54412) -ok 1066 - q cn: exact (0.54412) <= max (0.54412) -ok 1067 - q id: est (0.25352) = fast (0.25352) -ok 1068 - q cn: est (0.47887) = fast (0.47887) -ok 1069 - q id: est (0.37500) = fast (0.37500) -ok 1070 - q cn: est (0.62500) = fast (0.62500) -ok 1071 - q id: exact (0.40224) ~ est (0.40912) -ok 1072 - q id: exact (0.40224) <= max (0.42628) -ok 1073 - q cn: exact (0.58494) ~ est (0.58968) -ok 1074 - q cn: exact (0.58494) <= max (0.62179) -ok 1075 - h id: exact (0.39848) ~ est (0.40304) -ok 1076 - h id: exact (0.39848) <= max (0.40355) -ok 1077 - h cn: exact (0.58376) ~ est (0.58889) -ok 1078 - h cn: exact (0.58376) <= max (0.58883) -ok 1079 - h id: est (0.25352) = fast (0.25352) -ok 1080 - h cn: est (0.47887) = fast (0.47887) -ok 1081 - h id: exact (0.44118) ~ est (0.44118) -ok 1082 - h id: exact (0.44118) <= max (0.44118) -ok 1083 - h cn: exact (0.54412) ~ est (0.54412) -ok 1084 - h cn: exact (0.54412) <= max (0.54412) -ok 1085 - tile dnaEbsub_ecoli.wutblastx hit 2 \#hsps 2 -ok 1086 - q id: exact (0.41818) ~ est (0.41818) -ok 1087 - q id: exact (0.41818) <= max (0.41818) -ok 1088 - q cn: exact (0.52727) ~ est (0.52727) -ok 1089 - q cn: exact (0.52727) <= max (0.52727) -ok 1090 - h id: est (0.53333) = fast (0.53333) -ok 1091 - h cn: est (0.66667) = fast (0.66667) -ok 1092 - h id: est (0.37500) = fast (0.37500) -ok 1093 - h cn: est (0.47500) = fast (0.47500) -ok 1094 - bug2942: query m0: range correct -ok 1095 - bug2942: query m1: range correct -ok 1096 - bug2942: query m2: range correct -ok 1097 - bug2942: subject all : range correct -ok 1098 - get_tiled_alns -ok 1099 - got all alns -ok 1100 -ok 1101 - aln and qfeat lengths correspond -ok 1102 - q length correct -ok 1103 -ok 1104 - features on q and s correspond -ok 1105 - aln and hfeat lengths correspond -ok 1106 - s length correct -ok 1107 -ok 1108 - aln and qfeat lengths correspond -ok 1109 - q length correct -ok 1110 -ok 1111 - features on q and s correspond -ok 1112 - aln and hfeat lengths correspond -ok 1113 - s length correct -ok 1114 -ok 1115 - aln and qfeat lengths correspond -ok 1116 - q length correct -ok 1117 -ok 1118 - features on q and s correspond -ok 1119 - aln and hfeat lengths correspond -ok 1120 - s length correct -ok 1121 -ok 1122 - aln and qfeat lengths correspond -ok 1123 - q length correct -ok 1124 -ok 1125 - features on q and s correspond -ok 1126 - aln and hfeat lengths correspond -ok 1127 - s length correct -ok 1128 -ok 1129 - aln and qfeat lengths correspond -ok 1130 - q length correct -ok 1131 -ok 1132 - features on q and s correspond -ok 1133 - aln and hfeat lengths correspond -ok 1134 - s length correct -ok 1135 -ok 1136 - aln and qfeat lengths correspond -ok 1137 - q length correct -ok 1138 -ok 1139 - features on q and s correspond -ok 1140 - aln and hfeat lengths correspond -ok 1141 - s length correct -ok -t/SearchIO/waba.t ................... -1..64 -ok 1 - use Bio::SearchIO; -ok 2 - An object of class 'Bio::SearchIO::waba' isa 'Bio::SearchIO' -ok 3 - query_name -ok 4 - query database -ok 5 - database name -ok 6 - name -ok 7 - hsps -ok 8 - total length -ok 9 - start -ok 10 - end -ok 11 - strand -ok 12 - start -ok 13 - end -ok 14 - strand -ok 15 - query string -ok 16 - hit_string -ok 17 - hmmstate string -ok 18 -ok 19 -ok 20 -ok 21 - total length -ok 22 - start -ok 23 - end -ok 24 - strand -ok 25 - start -ok 26 - end -ok 27 - strand -ok 28 - query string -ok 29 - hit_string -ok 30 - hmmstate string -ok 31 -ok 32 -ok 33 -ok 34 - total length -ok 35 - start -ok 36 - end -ok 37 - strand -ok 38 - start -ok 39 - end -ok 40 - strand -ok 41 - query string -ok 42 - hit_string -ok 43 - hmmstate string -ok 44 -ok 45 -ok 46 -ok 47 - query_name -ok 48 - query database -ok 49 - database name -ok 50 - name -ok 51 - hsps -ok 52 - total length -ok 53 - start -ok 54 - end -ok 55 - strand -ok 56 - start -ok 57 - end -ok 58 - strand -ok 59 - query string -ok 60 - hit_string -ok 61 - hmmstate string -ok 62 -ok 63 -ok 64 -ok -t/SearchIO/wise.t ................... -1..20 -ok 1 - use Bio::SearchIO; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok -t/SearchIO/Writer/GbrowseGFF.t ...... -1..4 -ok 1 - use Bio::SearchIO; -ok 2 -ok 3 -ok 4 -ok -t/SearchIO/Writer/HitTableWriter.t .. -1..8 -ok 1 - use Bio::SearchIO; -ok 2 - use Bio::SearchIO::Writer::HitTableWriter; -ok 3 - An object of class 'Bio::Search::Result::BlastResult' isa 'Bio::Search::Result::ResultI' -ok 4 -ok 5 -ok 6 -ok 7 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 8 -ok -t/SearchIO/Writer/HSPTableWriter.t .. -1..8 -ok 1 - use Bio::SearchIO; -ok 2 - use Bio::SearchIO::Writer::HSPTableWriter; -ok 3 - An object of class 'Bio::Search::Result::BlastResult' isa 'Bio::Search::Result::ResultI' -ok 4 -ok 5 -ok 6 -ok 7 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 8 -ok -t/SearchIO/Writer/HTMLWriter.t ...... -1..8 -ok 1 - use Bio::SearchIO; -ok 2 - use Bio::SearchIO::Writer::HTMLResultWriter; -ok 3 - An object of class 'Bio::Search::Result::BlastResult' isa 'Bio::Search::Result::ResultI' -ok 4 -ok 5 -ok 6 -ok 7 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 8 -ok -t/SearchIO/Writer/TextWriter.t ...... -1..8 -ok 1 - use Bio::SearchIO; -ok 2 - use Bio::SearchIO::Writer::TextResultWriter; -ok 3 - An object of class 'Bio::Search::Result::BlastResult' isa 'Bio::Search::Result::ResultI' -ok 4 -ok 5 -ok 6 -ok 7 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 8 -ok -t/Seq/DBLink.t ...................... -1..131 -ok 1 - use Bio::SeqIO; -ok 2 - "swissprot:K1C9_HUMAN" -ok 3 - no double colon -ok 4 - no trailing colon -ok 5 - no double space -ok 6 - dblink value is splittable -ok 7 - "GenBank:Z29074.1" -ok 8 - no double colon -ok 9 - no trailing colon -ok 10 - no double space -ok 11 - dblink value is splittable -ok 12 - "GenPept:CAA82315.1" -ok 13 - no double colon -ok 14 - no trailing colon -ok 15 - no double space -ok 16 - dblink value is splittable -ok 17 - "GenBank:S69510.1" -ok 18 - no double colon -ok 19 - no trailing colon -ok 20 - no double space -ok 21 - dblink value is splittable -ok 22 - "GenPept:AAC60619.1" -ok 23 - no double colon -ok 24 - no trailing colon -ok 25 - no double space -ok 26 - dblink value is splittable -ok 27 - "GenBank:X75015.1" -ok 28 - no double colon -ok 29 - no trailing colon -ok 30 - no double space -ok 31 - dblink value is splittable -ok 32 - "GenPept:CAA52924.1" -ok 33 - no double colon -ok 34 - no trailing colon -ok 35 - no double space -ok 36 - dblink value is splittable -ok 37 - "GenBank:AB001594.1" -ok 38 - no double colon -ok 39 - no trailing colon -ok 40 - no double space -ok 41 - dblink value is splittable -ok 42 - "GenPept:BAA19418.1" -ok 43 - no double colon -ok 44 - no trailing colon -ok 45 - no double space -ok 46 - dblink value is splittable -ok 47 - "GenBank:I37984" -ok 48 - no double colon -ok 49 - no trailing colon -ok 50 - no double space -ok 51 - dblink value is splittable -ok 52 - "HSSP:P08670" -ok 53 - no double colon -ok 54 - no trailing colon -ok 55 - no double space -ok 56 - dblink value is splittable -ok 57 - "IntAct:P35527" -ok 58 - no double colon -ok 59 - no trailing colon -ok 60 - no double space -ok 61 - dblink value is splittable -ok 62 - "Ensembl:ENSG00000171403" -ok 63 - no double colon -ok 64 - no trailing colon -ok 65 - no double space -ok 66 - dblink value is splittable -ok 67 - "KEGG:hsa:3857" -ok 68 - no double colon -ok 69 - no trailing colon -ok 70 - no double space -ok 71 - dblink value is splittable -ok 72 - "HGNC:6447" -ok 73 - no double colon -ok 74 - no trailing colon -ok 75 - no double space -ok 76 - dblink value is splittable -ok 77 - "MIM:144200" -ok 78 - no double colon -ok 79 - no trailing colon -ok 80 - no double space -ok 81 - dblink value is splittable -ok 82 - "MIM:607606" -ok 83 - no double colon -ok 84 - no trailing colon -ok 85 - no double space -ok 86 - dblink value is splittable -ok 87 - "ArrayExpress:P35527" -ok 88 - no double colon -ok 89 - no trailing colon -ok 90 - no double space -ok 91 - dblink value is splittable -ok 92 - "GO:0005200" -ok 93 - no double colon -ok 94 - no trailing colon -ok 95 - no double space -ok 96 - dblink value is splittable -ok 97 - "GO:0008544" -ok 98 - no double colon -ok 99 - no trailing colon -ok 100 - no double space -ok 101 - dblink value is splittable -ok 102 - "InterPro:IPR011000" -ok 103 - no double colon -ok 104 - no trailing colon -ok 105 - no double space -ok 106 - dblink value is splittable -ok 107 - "InterPro:IPR001664" -ok 108 - no double colon -ok 109 - no trailing colon -ok 110 - no double space -ok 111 - dblink value is splittable -ok 112 - "InterPro:IPR002957" -ok 113 - no double colon -ok 114 - no trailing colon -ok 115 - no double space -ok 116 - dblink value is splittable -ok 117 - "Pfam:PF00038" -ok 118 - no double colon -ok 119 - no trailing colon -ok 120 - no double space -ok 121 - dblink value is splittable -ok 122 - "PRINTS:PR01248" -ok 123 - no double colon -ok 124 - no trailing colon -ok 125 - no double space -ok 126 - dblink value is splittable -ok 127 - "PROSITE:PS00226" -ok 128 - no double colon -ok 129 - no trailing colon -ok 130 - no double space -ok 131 - dblink value is splittable -ok -t/Seq/EncodedSeq.t .................. -1..37 -ok 1 - use Bio::Seq::EncodedSeq; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 - An object of class 'Bio::Location::Simple' isa 'Bio::Location::Simple' -ok 12 -ok 13 -ok 14 - An object of class 'Bio::Location::Simple' isa 'Bio::Location::Simple' -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok -t/Seq/LargeLocatableSeq.t ........... -1..8 -ok 1 - use Bio::Seq::LargeLocatableSeq; -ok 2 -ok 3 - An object of class 'Bio::Seq::LargeLocatableSeq' isa 'Bio::Seq::LargeSeqI' -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok -t/Seq/LargePSeq.t ................... -1..30 -ok 1 - use Bio::Seq::LargePrimarySeq; -ok 2 - use Bio::Seq::LargeSeq; -ok 3 - use Bio::Location::Simple; -ok 4 - use Bio::Location::Fuzzy; -ok 5 - use Bio::Location::Split; -ok 6 - use Bio::SeqIO; -ok 7 -ok 8 -ok 9 - Sequence is ATGGGGTGGGGTGAAACCCTTTGGGGGTGGGGTAAATGTTTGGGGTTAAACCCCTTTGGGGGGT -ok 10 - Subseq is GGGGT -ok 11 -ok 12 -ok 13 -ok 14 - trunc seq was GGGGTGAA -ok 15 -ok 16 -ok 17 -ok 18 - Sequence is ATGGGGTGGGGTGAAACCCTTTGGGGGTGGGGTAAATGTTTGGGGTTAAACCCCTTTGGGGGGT -ok 19 -ok 20 - output via Bio::SeqIO::fasta -ok 21 - Subseq is GGGGT -ok 22 - trunc seq was GGGGTGAA -ok 23 -ok 24 -ok 25 -ok 26 - Sequence is ATGGGGTGGGGT -ok 27 - Subseq is GGGGT -ok 28 - trunc seq was GGGGT -ok 29 -ok 30 -ok -t/Seq/LocatableSeq.t ................ -1..119 -ok 1 - use Bio::LocatableSeq; -ok 2 - use Bio::AlignIO; -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 - An object of class 'Bio::Location::Simple' isa 'Bio::Location::Simple' -ok 13 -ok 14 -ok 15 - An object of class 'Bio::Location::Simple' isa 'Bio::Location::Simple' -ok 16 -ok 17 -ok 18 -ok 19 -not ok 20 # TODO Need to fix columns before start of seq w/ start > 1 -# Failed (TODO) test at t/Seq/LocatableSeq.t line 46. -# got: 'Bio::Location::Simple=HASH(0xaaab03d717c0)' -# expected: undef -ok 21 -ok 22 - An object of class 'Bio::AlignIO::pfam' isa 'Bio::AlignIO' -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 - threw Regexp ((?^:.+)) -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 -ok 43 -ok 44 -ok 45 -ok 46 -ok 47 -ok 48 -ok 49 -ok 50 - An object of class 'Bio::Location::Simple' isa 'Bio::Location::Simple' -ok 51 -ok 52 -ok 53 - An object of class 'Bio::Location::Simple' isa 'Bio::Location::Simple' -ok 54 -ok 55 -ok 56 -ok 57 -ok 58 -ok 59 -ok 60 -ok 61 -ok 62 -ok 63 -ok 64 -ok 65 -ok 66 -ok 67 -ok 68 -ok 69 -ok 70 -ok 71 -ok 72 -ok 73 -ok 74 -ok 75 -ok 76 -ok 77 -ok 78 -ok 79 -ok 80 -ok 81 -ok 82 -ok 83 -ok 84 -ok 85 -ok 86 -ok 87 -ok 88 -ok 89 -ok 90 -ok 91 -ok 92 -ok 93 -ok 94 -ok 95 -ok 96 -ok 97 -ok 98 -ok 99 -ok 100 -ok 101 -ok 102 -ok 103 -ok 104 -ok 105 -ok 106 - * is counted in length -ok 107 - * is counted in length, but end is wrong -ok 108 -ok 109 -ok 110 -ok 111 -ok 112 -ok 113 -ok 114 -ok 115 -ok 116 -ok 117 -not ok 118 # TODO Bio::LocatableSeq global variables have scoping issues -# Failed (TODO) test at t/Seq/LocatableSeq.t line 306. -# got: '\-\.=~' -# expected: '-\?' -not ok 119 # TODO Bio::LocatableSeq global variables have scoping issues -# Failed (TODO) test at t/Seq/LocatableSeq.t line 308. -# got: '19' -# expected: anything else -ok -t/Seq/MetaSeq.t ..................... -1..132 -ok 1 - use Bio::Seq::Meta; -ok 2 - use Bio::Seq::Meta::Array; -ok 3 - use Bio::SeqIO; -ok 4 - use Bio::AlignIO; -ok 5 - use Bio::Seq::Quality; -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 - aa-bb bb -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 -ok 43 -ok 44 -ok 45 -ok 46 -ok 47 -ok 48 -ok 49 -ok 50 -ok 51 -ok 52 -ok 53 -ok 54 -ok 55 -ok 56 -ok 57 -ok 58 -ok 59 -ok 60 -ok 61 -ok 62 -ok 63 -ok 64 -ok 65 -ok 66 -ok 67 -ok 68 -ok 69 -ok 70 -ok 71 -ok 72 -ok 73 -ok 74 -ok 75 -ok 76 -ok 77 -ok 78 -ok 79 -ok 80 -ok 81 -ok 82 -ok 83 -ok 84 -ok 85 -ok 86 -ok 87 -ok 88 -ok 89 -ok 90 -ok 91 -ok 92 -ok 93 -ok 94 -ok 95 -ok 96 -ok 97 -ok 98 -ok 99 -ok 100 -ok 101 -ok 102 -ok 103 -ok 104 -ok 105 -ok 106 -ok 107 -ok 108 -ok 109 -ok 110 -ok 111 -ok 112 -ok 113 -ok 114 -ok 115 -ok 116 -ok 117 -ok 118 -ok 119 -ok 120 -ok 121 -ok 122 -ok 123 -ok 124 -ok 125 -ok 126 -ok 127 -ok 128 -ok 129 -ok 130 -ok 131 -ok 132 -ok -t/Seq/PrimaryQual.t ................. -1..70 -ok 1 - use Bio::SeqIO; -ok 2 - use Bio::Seq::Quality; -ok 3 - use Bio::Seq::PrimaryQual; -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 - A reference of type 'ARRAY' isa 'ARRAY' -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 - threw Regexp ((?^:.+)) -ok 27 - threw Regexp ((?^:.+)) -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 - threw Regexp ((?^:EX)) -ok 34 -ok 35 -ok 36 - threw Regexp ((?^:EX)) -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 -ok 43 -ok 44 -ok 45 -ok 46 -ok 47 -ok 48 -ok 49 -ok 50 -ok 51 -ok 52 -ok 53 -ok 54 -ok 55 -ok 56 -ok 57 -ok 58 -ok 59 -ok 60 -ok 61 -ok 62 -ok 63 -ok 64 -ok 65 -ok 66 -ok 67 -ok 68 -ok 69 -ok 70 -ok -t/Seq/PrimarySeq.t .................. -1..312 -ok 1 - use Bio::PrimarySeq; -ok 2 - use Bio::Location::Simple; -ok 3 - use Bio::Location::Fuzzy; -ok 4 - use Bio::Location::Split; -ok 5 - Bare object -ok 6 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeqI' -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 - An object of class 'Bio::PrimarySeq' isa 'Bio::IdentifiableI' -ok 26 - An object of class 'Bio::PrimarySeq' isa 'Bio::DescribableI' -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 -ok 43 -ok 44 -ok 45 -ok 46 -ok 47 -ok 48 -ok 49 -ok 50 -ok 51 - threw Regexp ((?^:.+)) -ok 52 -ok 53 -ok 54 -ok 55 -ok 56 -ok 57 -ok 58 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeqI' -ok 59 -ok 60 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeqI' -ok 61 -ok 62 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeqI' -ok 63 -ok 64 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeqI' -ok 65 -ok 66 -ok 67 -ok 68 -ok 69 -ok 70 -ok 71 -ok 72 -ok 73 -ok 74 -ok 75 -ok 76 - Translation: LVAST -ok 77 - Translation: MVAST -ok 78 - Translation: MVAST -ok 79 - Translation: MVAST* -ok 80 - Translation: M* -ok 81 - Translation: M -ok 82 -ok 83 - Translation: MWP -ok 84 -ok 85 -ok 86 -ok 87 -ok 88 -ok 89 -ok 90 -ok 91 -ok 92 - frame 0 start, frame 1 stop < frame 0 stop -ok 93 - frame 1 start, frame 2 stop < frame 1 stop -ok 94 -ok 95 -ok 96 -ok 97 - Alphabet -ok 98 -ok 99 -ok 100 -ok 101 -ok 102 -ok 103 -ok 104 -ok 105 -ok 106 -ok 107 -ok 108 -ok 109 -ok 110 -ok 111 -ok 112 -ok 113 -ok 114 -ok 115 -ok 116 -ok 117 -ok 118 -ok 119 -ok 120 -ok 121 -ok 122 -ok 123 -ok 124 -ok 125 -ok 126 -ok 127 -ok 128 -ok 129 -ok 130 -ok 131 - Bug 2438 -ok 132 -ok 133 -ok 134 -ok 135 -ok 136 -ok 137 -ok 138 -ok 139 -ok 140 - Bug \#2864 -ok 141 - Terminator + inside sequence -ok 142 -ok 143 - Length method -ok 144 -ok 145 -ok 146 -ok 147 -ok 148 -ok 149 -ok 150 -ok 151 -ok 152 -ok 153 -ok 154 -ok 155 -ok 156 -ok 157 -ok 158 -ok 159 -ok 160 -ok 161 -ok 162 -ok 163 - threw Regexp ((?^:.+)) -ok 164 -ok 165 -ok 166 -ok 167 -ok 168 -ok 169 -ok 170 -ok 171 -ok 172 -ok 173 -ok 174 -ok 175 - threw Regexp ((?^:.+)) -ok 176 - Validation -ok 177 -ok 178 -ok 179 - threw Regexp ((?^:.+)) -ok 180 -ok 181 -ok 182 - _find_orfs 1 -ok 183 - orfs are sorted by descending length -ok 184 - got correct -orf => "longest" seq -ok 185 - _find_orfs 1 -ok 186 - orfs are sorted by descending length -ok 187 - got correct -orf => "longest" seq -ok 188 -ok 189 -ok 190 -ok 191 -ok 192 -ok 193 -ok 194 -ok 195 -ok 196 -ok 197 -ok 198 -ok 199 -ok 200 -ok 201 -ok 202 -ok 203 -ok 204 -ok 205 -ok 206 -ok 207 -ok 208 -ok 209 -ok 210 -ok 211 -ok 212 -ok 213 -ok 214 -ok 215 -ok 216 -ok 217 -ok 218 -ok 219 -ok 220 -ok 221 -ok 222 -ok 223 -ok 224 -ok 225 -ok 226 -ok 227 -ok 228 -ok 229 -ok 230 -ok 231 -ok 232 -ok 233 -ok 234 -ok 235 -ok 236 -ok 237 -ok 238 -ok 239 -ok 240 -ok 241 -ok 242 -ok 243 -ok 244 -ok 245 -ok 246 -ok 247 -ok 248 -ok 249 -ok 250 -ok 251 -ok 252 -ok 253 -ok 254 -ok 255 -ok 256 -ok 257 -ok 258 -ok 259 -ok 260 -ok 261 -ok 262 -ok 263 -ok 264 -ok 265 -ok 266 -ok 267 -ok 268 -ok 269 -ok 270 -ok 271 -ok 272 -ok 273 -ok 274 -ok 275 -ok 276 -ok 277 -ok 278 -ok 279 -ok 280 -ok 281 -ok 282 -ok 283 -ok 284 -ok 285 -ok 286 -ok 287 -ok 288 -ok 289 -ok 290 -ok 291 -ok 292 -ok 293 -ok 294 -ok 295 -ok 296 -ok 297 -ok 298 -ok 299 -ok 300 -ok 301 -ok 302 -ok 303 -ok 304 -ok 305 -ok 306 -ok 307 -ok 308 -ok 309 -ok 310 -ok 311 -ok 312 -ok -t/Seq/PrimedSeq.t ................... -1..65 -ok 1 - use Bio::SeqIO; -ok 2 - use Bio::Seq::PrimedSeq; -ok 3 - Priming the target with sequence objects -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 - An object of class 'Bio::SeqFeature::Primer' isa 'Bio::SeqFeature::Primer' -ok 13 -ok 14 -ok 15 - An object of class 'Bio::SeqFeature::Primer' isa 'Bio::SeqFeature::Primer' -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 - Priming the target with primer objects -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 -ok 43 -ok 44 -ok 45 -ok 46 - Priming the target with located primer objects -ok 47 -ok 48 -ok 49 -ok 50 -ok 51 -ok 52 -ok 53 -ok 54 -ok 55 -ok 56 -ok 57 -ok 58 -ok 59 -ok 60 -ok 61 -ok 62 -ok 63 -ok 64 -ok 65 -ok -t/Seq/Quality.t ..................... -1..85 -ok 1 - use Bio::Seq::Quality; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 -ok 43 -ok 44 -ok 45 -ok 46 -ok 47 -ok 48 -ok 49 -ok 50 -ok 51 -ok 52 -ok 53 -ok 54 -ok 55 -ok 56 -ok 57 -ok 58 -ok 59 -ok 60 -ok 61 -ok 62 -ok 63 -ok 64 -ok 65 -ok 66 -ok 67 -ok 68 -ok 69 -ok 70 -ok 71 -ok 72 - Bug 2845 -ok 73 -ok 74 - Bug 2845 -ok 75 -ok 76 -ok 77 -ok 78 -ok 79 -ok 80 -ok 81 -ok 82 -ok 83 -ok 84 -ok 85 -ok -t/Seq/Seq.t ......................... -1..76 -ok 1 - use Bio::Seq; -ok 2 - use Bio::Seq::RichSeq; -ok 3 - use Bio::SeqFeature::Generic; -ok 4 - use Bio::Species; -ok 5 - use Bio::Annotation::SimpleValue; -ok 6 -ok 7 - An object of class 'Bio::Seq' isa 'Bio::AnnotatableI' -ok 8 -ok 9 -ok 10 -ok 11 - truncated sequence length -ok 12 - truncated sequence string -ok 13 -ok 14 -ok 15 - alphabet -ok 16 - id -ok 17 - accession number -ok 18 - subseq -ok 19 - An object of class 'Bio::Seq' isa 'Bio::IdentifiableI' -ok 20 - An object of class 'Bio::Seq' isa 'Bio::DescribableI' -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 - translated sequence -ok 35 - translated sequence with explicit unambiguous codons -ok 36 - translated sequence with unknown unambiguous codons -ok 37 - translated sequence with unknown unambiguous codons, completed -ok 38 - translated sequence with unambiguous codons -ok 39 - translated sequence with unambiguous codons -ok 40 - translated sequence with unknown unambiguous codons, completed -ok 41 - translated sequence with unambiguous codons -ok 42 - translated sequence with unknown unambiguous codons, completed -ok 43 - translated sequence with stop -ok 44 - translated sequence -ok 45 -ok 46 -ok 47 -ok 48 -ok 49 -ok 50 -ok 51 -ok 52 -ok 53 -ok 54 -ok 55 -ok 56 -ok 57 -ok 58 -ok 59 -ok 60 -ok 61 -ok 62 - Don't use clone for trunc of Bio::Seq::RichSeq -ok 63 -ok 64 -ok 65 -ok 66 -ok 67 -ok 68 - Bug \#2864 -ok 69 -ok 70 -ok 71 -ok 72 -ok 73 -ok 74 -ok 75 -ok 76 -ok -t/Seq/SimulatedRead.t ............... -1..194 -ok 1 - use Bio::Seq; -ok 2 - use Bio::Seq::Quality; -ok 3 - use Bio::PrimarySeq; -ok 4 - use Bio::LocatableSeq; -ok 5 - use Bio::Seq::SimulatedRead; -ok 6 -ok 7 - An object of class 'Bio::Seq::SimulatedRead' isa 'Bio::Seq::SimulatedRead' -ok 8 - An object of class 'Bio::Seq::SimulatedRead' isa 'Bio::LocatableSeq' -ok 9 - An object of class 'Bio::Seq::SimulatedRead' isa 'Bio::Seq::Quality' -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 -ok 43 -ok 44 -ok 45 -ok 46 -ok 47 -ok 48 -ok 49 -ok 50 -ok 51 -ok 52 -ok 53 -ok 54 -ok 55 -ok 56 -ok 57 -ok 58 -ok 59 -ok 60 -ok 61 -ok 62 -ok 63 -ok 64 -ok 65 -ok 66 -ok 67 -ok 68 -ok 69 -ok 70 -ok 71 -ok 72 -ok 73 -ok 74 -ok 75 -ok 76 -ok 77 -ok 78 -ok 79 -ok 80 -ok 81 -ok 82 -ok 83 -ok 84 -ok 85 -ok 86 -ok 87 -ok 88 -ok 89 -ok 90 -ok 91 -ok 92 -ok 93 -ok 94 -ok 95 -ok 96 -ok 97 -ok 98 -ok 99 -ok 100 -ok 101 -ok 102 - redundant errors -ok 103 -ok 104 -ok 105 -ok 106 -ok 107 -ok 108 -ok 109 -ok 110 -ok 111 -ok 112 -ok 113 -ok 114 - errors() -ok 115 -ok 116 -ok 117 -ok 118 -ok 119 -ok 120 -ok 121 -ok 122 -ok 123 -ok 124 -ok 125 -ok 126 -ok 127 -ok 128 -ok 129 -ok 130 - track() -ok 131 -ok 132 -ok 133 -ok 134 -ok 135 -ok 136 -ok 137 - qual_levels() -ok 138 -ok 139 - reference() -ok 140 -ok 141 - mid() -ok 142 -ok 143 -ok 144 -ok 145 - ACGT -ok 146 -ok 147 -ok 148 -ok 149 -ok 150 - TTTAAA -ok 151 -ok 152 -ok 153 -ok 154 -ok 155 - Bio::Seq::Quality -ok 156 - Bio::Seq -ok 157 - Bio::PrimarySeq -ok 158 - Bio::LocatableSeq -ok 159 -ok 160 -ok 161 -ok 162 -ok 163 -ok 164 -ok 165 -ok 166 -ok 167 -ok 168 -ok 169 -ok 170 -ok 171 -ok 172 -ok 173 -ok 174 -ok 175 -ok 176 -ok 177 -ok 178 -ok 179 -ok 180 -ok 181 -ok 182 -ok 183 -ok 184 -ok 185 -ok 186 -ok 187 -ok 188 -ok 189 -ok 190 -ok 191 -ok 192 -ok 193 -ok 194 -ok -t/SeqFeature/Amplicon.t ............. -1..21 -ok 1 - use Bio::PrimarySeq; -ok 2 - use Bio::SeqFeature::Primer; -ok 3 - use Bio::SeqFeature::Amplicon; -ok 4 - An object of class 'Bio::SeqFeature::Amplicon' isa 'Bio::SeqFeature::Amplicon' -ok 5 - An object of class 'Bio::SeqFeature::Amplicon' isa 'Bio::SeqFeature::SubSeq' -ok 6 -ok 7 -ok 8 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeq' -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeq' -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeq' -ok 21 -ok -t/SeqFeature/Clone.t ................ -1..17 -ok 1 - clone() -ok 2 - start() clone set -ok 3 - start() clone get -ok 4 - start() original unchanged -ok 5 - clone() with arguments -ok 6 - start() orig get -ok 7 - end() orig get -ok 8 - start() clone get -ok 9 - end() clone get -ok 10 - start() clone set -ok 11 - start() clone get -ok 12 - start() original unchanged -ok 13 - location() Bio::Location::Split -ok 14 - clone() -ok 15 - start() clone set -ok 16 - start() clone get -ok 17 - start() original unchanged -ok -t/SeqFeature/Collection.t ........... -1..24 -ok 1 - use Bio::SeqFeature::Collection; -ok 2 - use Bio::Location::Simple; -ok 3 - use Bio::Tools::GFF; -ok 4 - use Bio::SeqIO; -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok -t/SeqFeature/Computation.t .......... -1..12 -ok 1 - use Bio::SeqFeature::Computation; -ok 2 -ok 3 - computation id -ok 4 - score value -ok 5 -ok 6 -ok 7 -ok 8 - sft[0] is exon -ok 9 -ok 10 - computation id -ok 11 -ok 12 - score value -ok -t/SeqFeature/FeaturePair.t .......... -1..19 -ok 1 - use Bio::SeqFeature::Generic; -ok 2 - use Bio::SeqFeature::FeaturePair; -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 - feature1 of pair stored -ok 9 - feature2 of pair stored -ok 10 - feature start -ok 11 - feature end -ok 12 - primary tag -ok 13 - source tag -ok 14 - hstart -ok 15 - hend -ok 16 - hprimary tag -ok 17 - hsource tag -ok 18 -ok 19 - inverted end -ok -t/SeqFeature/Gene.t ................. -1..28 -ok 1 - use Bio::SeqIO; -ok 2 - use Bio::SeqFeature::Gene::Transcript; -ok 3 - use Bio::SeqFeature::Gene::UTR; -ok 4 - use Bio::SeqFeature::Gene::Exon; -ok 5 - use Bio::SeqFeature::Gene::Poly_A_site; -ok 6 - use Bio::SeqFeature::Gene::GeneStructure; -ok 7 - use Bio::Location::Fuzzy; -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 - mRNA spliced length -ok 28 - has 2 UTRs -ok -t/SeqFeature/Generic.t .............. -1..364 -ok 1 - use Bio::Seq; -ok 2 - use Bio::SeqIO; -ok 3 - use Bio::SeqFeature::Generic; -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 - Start of feature location -ok 10 - End of feature location -ok 11 - Primary tag -ok 12 - Source tag -ok 13 - Display name -ok 14 - Undef phase by default -ok 15 - Phase accessor returns -ok 16 - Phase is persistent -ok 17 -ok 18 -ok 19 - Set phase from constructor -ok 20 -ok 21 -ok 22 - Start of first seqfeature -ok 23 - End of first seqfeature -ok 24 - Strand of first seqfeature -ok 25 -ok 26 - Sequence of first seqfeature -ok 27 -ok 28 -ok 29 -ok 30 - Start of second seqfeature -ok 31 - End of second seqfeature -ok 32 - Strand of second seqfeature -ok 33 -ok 34 - Sequence of second seqfeature -ok 35 -ok 36 -ok 37 -ok 38 - sfeat start for EXPAND-ED feature (bug \#947) -ok 39 - sfeat end for EXPAND-ED feature (bug \#947) -ok 40 -ok 41 -ok 42 - Can create feature starting and ending at 0 -ok 43 -ok 44 - Can create feature starting and ending at 0 -ok 45 -ok 46 -ok 47 -ok 48 -ok 49 -ok 50 -ok 51 -ok 52 -ok 53 -ok 54 - An object of class 'Bio::SeqIO::genbank' isa 'Bio::SeqIO' -ok 55 -ok 56 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::Seq' -ok 57 -ok 58 # skip The optional module Bio::DB::GenBank (or dependencies thereof) was not installed -ok 59 # skip The optional module Bio::DB::GenBank (or dependencies thereof) was not installed -ok 60 # skip The optional module Bio::DB::GenBank (or dependencies thereof) was not installed -ok 61 # skip The optional module Bio::DB::GenBank (or dependencies thereof) was not installed -ok 62 # skip The optional module Bio::DB::GenBank (or dependencies thereof) was not installed -ok 63 -ok 64 - An object of class 'Bio::SeqIO::genbank' isa 'Bio::SeqIO' -ok 65 -ok 66 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::Seq' -ok 67 -ok 68 # skip The optional module Bio::DB::GenBank (or dependencies thereof) was not installed -ok 69 # skip The optional module Bio::DB::GenBank (or dependencies thereof) was not installed -ok 70 -ok 71 - An object of class 'Bio::SeqIO::genbank' isa 'Bio::SeqIO' -ok 72 -ok 73 -ok 74 - spliced_seq translation matches expected -ok 75 -ok 76 - spliced_seq translation matches expected -ok 77 -ok 78 - spliced_seq translation matches expected -ok 79 -ok 80 - spliced_seq translation matches expected -ok 81 -ok 82 - spliced_seq translation matches expected -ok 83 -ok 84 - spliced_seq translation matches expected -ok 85 -ok 86 - spliced_seq translation matches expected -ok 87 -ok 88 - spliced_seq translation matches expected -ok 89 -ok 90 - spliced_seq translation matches expected -ok 91 -ok 92 - spliced_seq translation matches expected -ok 93 -ok 94 - spliced_seq translation matches expected -ok 95 -ok 96 - spliced_seq translation matches expected -ok 97 -ok 98 - spliced_seq translation matches expected -ok 99 -ok 100 - spliced_seq translation matches expected -ok 101 -ok 102 - spliced_seq translation matches expected -ok 103 -ok 104 - spliced_seq translation matches expected -ok 105 -ok 106 - spliced_seq translation matches expected -ok 107 -ok 108 - spliced_seq translation matches expected -ok 109 -ok 110 - spliced_seq translation matches expected -ok 111 -ok 112 - spliced_seq translation matches expected -ok 113 -ok 114 - spliced_seq translation matches expected -ok 115 -ok 116 - spliced_seq translation matches expected -ok 117 -ok 118 - spliced_seq translation matches expected -ok 119 -ok 120 - spliced_seq translation matches expected -ok 121 -ok 122 - spliced_seq translation matches expected -ok 123 -ok 124 - spliced_seq translation matches expected -ok 125 -ok 126 - spliced_seq translation matches expected -ok 127 -ok 128 - spliced_seq translation matches expected -ok 129 -ok 130 - spliced_seq translation matches expected -ok 131 -ok 132 - spliced_seq translation matches expected -ok 133 -ok 134 - spliced_seq translation matches expected -ok 135 -ok 136 - spliced_seq translation matches expected -ok 137 -ok 138 - spliced_seq translation matches expected -ok 139 -ok 140 - spliced_seq translation matches expected -ok 141 -ok 142 - spliced_seq translation matches expected -ok 143 -ok 144 - spliced_seq translation matches expected -ok 145 -ok 146 - spliced_seq translation matches expected -ok 147 -ok 148 - spliced_seq translation matches expected -ok 149 -ok 150 - spliced_seq translation matches expected -ok 151 -ok 152 - spliced_seq translation matches expected -ok 153 -ok 154 - spliced_seq translation matches expected -ok 155 -ok 156 - spliced_seq translation matches expected -ok 157 -ok 158 - spliced_seq translation matches expected -ok 159 -ok 160 - spliced_seq translation matches expected -ok 161 -ok 162 - spliced_seq translation matches expected -ok 163 -ok 164 - spliced_seq translation matches expected -ok 165 -ok 166 - spliced_seq translation matches expected -ok 167 -ok 168 - spliced_seq translation matches expected -ok 169 -ok 170 - spliced_seq translation matches expected -ok 171 -ok 172 - spliced_seq translation matches expected -ok 173 -ok 174 - spliced_seq translation matches expected -ok 175 -ok 176 - spliced_seq translation matches expected -ok 177 -ok 178 - spliced_seq translation matches expected -ok 179 -ok 180 - spliced_seq translation matches expected -ok 181 -ok 182 - spliced_seq translation matches expected -ok 183 -ok 184 - spliced_seq translation matches expected -ok 185 -ok 186 - spliced_seq translation matches expected -ok 187 -ok 188 - spliced_seq translation matches expected -ok 189 -ok 190 - spliced_seq translation matches expected -ok 191 -ok 192 - spliced_seq translation matches expected -ok 193 -ok 194 - spliced_seq translation matches expected -ok 195 -ok 196 - spliced_seq translation matches expected -ok 197 -ok 198 - spliced_seq translation matches expected -ok 199 -ok 200 - spliced_seq translation matches expected -ok 201 -ok 202 - spliced_seq translation matches expected -ok 203 -ok 204 - spliced_seq translation matches expected -ok 205 -ok 206 - spliced_seq translation matches expected -ok 207 -ok 208 - spliced_seq translation matches expected -ok 209 -ok 210 - spliced_seq translation matches expected -ok 211 -ok 212 - spliced_seq translation matches expected -ok 213 -ok 214 - spliced_seq translation matches expected -ok 215 -ok 216 - spliced_seq translation matches expected -ok 217 -ok 218 - spliced_seq translation matches expected -ok 219 -ok 220 - spliced_seq translation matches expected -ok 221 -ok 222 - spliced_seq translation matches expected -ok 223 -ok 224 - spliced_seq translation matches expected -ok 225 -ok 226 - spliced_seq translation matches expected -ok 227 -ok 228 - spliced_seq translation matches expected -ok 229 -ok 230 - spliced_seq translation matches expected -ok 231 -ok 232 - spliced_seq translation matches expected -ok 233 -ok 234 - spliced_seq translation matches expected -ok 235 -ok 236 - spliced_seq translation matches expected -ok 237 -ok 238 - spliced_seq translation matches expected -ok 239 -ok 240 - spliced_seq translation matches expected -ok 241 -ok 242 - spliced_seq translation matches expected -ok 243 -ok 244 - spliced_seq translation matches expected -ok 245 -ok 246 - spliced_seq translation matches expected -ok 247 -ok 248 - spliced_seq translation matches expected -ok 249 -ok 250 - spliced_seq translation matches expected -ok 251 -ok 252 - spliced_seq translation matches expected -ok 253 -ok 254 - spliced_seq translation matches expected -ok 255 -ok 256 - spliced_seq translation matches expected -ok 257 -ok 258 - spliced_seq translation matches expected -ok 259 -ok 260 - spliced_seq translation matches expected -ok 261 -ok 262 - spliced_seq translation matches expected -ok 263 -ok 264 - spliced_seq translation matches expected -ok 265 -ok 266 - spliced_seq translation matches expected -ok 267 -ok 268 - spliced_seq translation matches expected -ok 269 -ok 270 - spliced_seq translation matches expected -ok 271 -ok 272 - spliced_seq translation matches expected -ok 273 -ok 274 - spliced_seq translation matches expected -ok 275 -ok 276 - spliced_seq translation matches expected -ok 277 -ok 278 - spliced_seq translation matches expected -ok 279 -ok 280 - spliced_seq translation matches expected -ok 281 -ok 282 - spliced_seq translation matches expected -ok 283 -ok 284 - spliced_seq translation matches expected -ok 285 -ok 286 - spliced_seq translation matches expected -ok 287 -ok 288 - spliced_seq translation matches expected -ok 289 -ok 290 - spliced_seq translation matches expected -ok 291 -ok 292 - spliced_seq translation matches expected -ok 293 -ok 294 - spliced_seq translation matches expected -ok 295 -ok 296 - spliced_seq translation matches expected -ok 297 -ok 298 - spliced_seq translation matches expected -ok 299 -ok 300 - spliced_seq translation matches expected -ok 301 -ok 302 - spliced_seq translation matches expected -ok 303 -ok 304 - spliced_seq translation matches expected -ok 305 -ok 306 - spliced_seq translation matches expected -ok 307 -ok 308 -ok 309 -ok 310 -ok 311 -ok 312 - phase check -ok 313 -ok 314 -ok 315 - phase check -ok 316 -ok 317 -ok 318 - phase check -ok 319 -ok 320 -ok 321 - phase check -ok 322 -ok 323 -ok 324 - phase check -ok 325 -ok 326 -ok 327 -ok 328 - Tags found -ok 329 - get_tagset_values tag values found -ok 330 - get_tagset_values tag values for multiple tags found -ok 331 - get_tag_values tag values found -ok 332 - get_tag_values lives with tag -ok 333 - get_tagset_values no tag values found -ok 334 - get_tagset_values lives with no tag -ok 335 - get_tag_values throws with no tag -ok 336 - Phi-X174 genome is circular -ok 337 -ok 338 - Only 3 split locations -ok 339 - An object of class 'Bio::Location::Split' isa 'Bio::Location::SplitLocationI' -ok 340 -ok 341 - Feature string -ok 342 - First ten nucleotides -ok 343 - Strand -ok 344 - Start -ok 345 - End -ok 346 - Expected length -ok 347 - An object of class 'Bio::Location::Split' isa 'Bio::Location::SplitLocationI' -ok 348 -ok 349 - Feature string -ok 350 - First ten nucleotides -ok 351 - Strand -ok 352 - Start -ok 353 - End -ok 354 - Expected length -ok 355 - An object of class 'Bio::Location::Split' isa 'Bio::Location::SplitLocationI' -ok 356 -ok 357 - Feature string -ok 358 - First ten nucleotides -ok 359 - Strand -ok 360 - Start -ok 361 - End -ok 362 - Expected length -ok 363 - Reverse strand is spliced correctly -ok 364 - Reverse strand is spliced correctly -ok -t/SeqFeature/Location.t ............. -1..109 -ok 1 - use Bio::Location::Simple; -ok 2 - use Bio::Location::Split; -ok 3 - use Bio::Location::Fuzzy; -ok 4 - use Bio::SeqFeature::Generic; -ok 5 - use Bio::SeqFeature::SimilarityPair; -ok 6 - use Bio::SeqFeature::FeaturePair; -ok 7 - use Bio::SeqFeature::Lite; -ok 8 - An object of class 'Bio::Location::Simple' isa 'Bio::LocationI' -ok 9 - An object of class 'Bio::Location::Simple' isa 'Bio::RangeI' -ok 10 - Bio::Location::Simple tests -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 - 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeatureI' -ok 16 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::RangeI' -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 - Bio::SeqFeature::FeaturePair tests -ok 25 -ok 26 -ok 27 -ok 28 - Bio::SeqFeature::Generic tests -ok 29 -ok 30 - Bio::Location::Fuzzy tests -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 -ok 43 -ok 44 - Bio::Location::Split tests -ok 45 -ok 46 -ok 47 -ok 48 -ok 49 -ok 50 -ok 51 -ok 52 -ok 53 -ok 54 -ok 55 -ok 56 -ok 57 -ok 58 -ok 59 -ok 60 -ok 61 - Bugfix 1074 -ok 62 -ok 63 -ok 64 -ok 65 - Positive length -ok 66 -ok 67 - seq_id() on Bio::Location::Split -ok 68 -ok 69 -ok 70 - An object of class 'Bio::Location::Simple' isa 'Bio::LocationI' -ok 71 - An object of class 'Bio::Location::Simple' isa 'Bio::RangeI' -ok 72 - Bio::Location::Simple EXACT -ok 73 -ok 74 -ok 75 -ok 76 -ok 77 -ok 78 - Bio::Location::Simple IN-BETWEEN -ok 79 -ok 80 -ok 81 -ok 82 -ok 83 - Testing error handling -ok 84 -ok 85 -ok 86 -ok 87 - use Bio::Location::WidestCoordPolicy; -ok 88 - use Bio::Location::NarrowestCoordPolicy; -ok 89 - use Bio::Location::AvWithinCoordPolicy; -ok 90 - Default coodinate policy -ok 91 -ok 92 -ok 93 -ok 94 - An object of class 'Bio::Location::WidestCoordPolicy' isa 'Bio::Location::WidestCoordPolicy' -ok 95 - Narrowest coodinate policy -ok 96 -ok 97 -ok 98 -ok 99 - An object of class 'Bio::Location::NarrowestCoordPolicy' isa 'Bio::Location::NarrowestCoordPolicy' -ok 100 - Average coodinate policy -ok 101 -ok 102 -ok 103 -ok 104 - An object of class 'Bio::Location::AvWithinCoordPolicy' isa 'Bio::Location::AvWithinCoordPolicy' -ok 105 - Widest coodinate policy -ok 106 -ok 107 -ok 108 -ok 109 - An object of class 'Bio::Location::WidestCoordPolicy' isa 'Bio::Location::WidestCoordPolicy' -ok -t/SeqFeature/LocationFactory.t ...... -1..325 -ok 1 - use Bio::Factory::FTLocationFactory; -ok 2 - An object of class 'Bio::Factory::FTLocationFactory' isa 'Bio::Factory::LocationFactoryI' -ok 3 - Bio::Location::Fuzzy -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 - Location String: (122.133)..(204.221) -ok 13 -ok 14 - Bio::Location::Fuzzy -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 - Location String: ?..536 -ok 24 -ok 25 - Bio::Location::Fuzzy -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 - Location String: <345..500 -ok 35 -ok 36 - Bio::Location::Split -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 -ok 43 -ok 44 -ok 45 - Location String: join(12..78,134..202) -ok 46 -ok 47 - Bio::Location::Fuzzy -ok 48 -ok 49 -ok 50 -ok 51 -ok 52 -ok 53 -ok 54 -ok 55 -ok 56 - Location String: ?2465..2774 -ok 57 -ok 58 - Bio::Location::Fuzzy -ok 59 -ok 60 -ok 61 -ok 62 -ok 63 -ok 64 -ok 65 -ok 66 -ok 67 - Location String: ?..>393 -ok 68 -ok 69 - Bio::Location::Fuzzy -ok 70 -ok 71 -ok 72 -ok 73 -ok 74 -ok 75 -ok 76 -ok 77 -ok 78 - Location String: 22..?64 -ok 79 -ok 80 - Bio::Location::Fuzzy -ok 81 -ok 82 -ok 83 -ok 84 -ok 85 -ok 86 -ok 87 -ok 88 -ok 89 - Location String: 1..? -ok 90 -ok 91 - Bio::Location::Fuzzy -ok 92 -ok 93 -ok 94 -ok 95 -ok 96 -ok 97 -ok 98 -ok 99 -ok 100 - Location String: ?1..12 -ok 101 -ok 102 - Bio::Location::Simple -ok 103 -ok 104 -ok 105 -ok 106 -ok 107 -ok 108 -ok 109 -ok 110 -ok 111 - Location String: 123^124 -ok 112 -ok 113 - Bio::Location::Fuzzy -ok 114 -ok 115 -ok 116 -ok 117 -ok 118 -ok 119 -ok 120 -ok 121 -ok 122 - Location String: (102.110) -ok 123 -ok 124 - Bio::Location::Simple -ok 125 -ok 126 -ok 127 -ok 128 -ok 129 -ok 130 -ok 131 -ok 132 -ok 133 - Location String: J00194:100..202 -ok 134 -ok 135 - Bio::Location::Split -ok 136 -ok 137 -ok 138 -ok 139 -ok 140 -ok 141 -ok 142 -ok 143 -ok 144 - Location String: join(1..100,J00194.1:100..202) -ok 145 -ok 146 - Bio::Location::Fuzzy -ok 147 -ok 148 -ok 149 -ok 150 -ok 151 -ok 152 -ok 153 -ok 154 -ok 155 - Location String: 1..>888 -ok 156 -ok 157 - Bio::Location::Fuzzy -ok 158 -ok 159 -ok 160 -ok 161 -ok 162 -ok 163 -ok 164 -ok 165 -ok 166 - Location String: <1..888 -ok 167 -ok 168 - Bio::Location::Fuzzy -ok 169 -ok 170 -ok 171 -ok 172 -ok 173 -ok 174 -ok 175 -ok 176 -ok 177 - Location String: (23.45)..600 -ok 178 -ok 179 - Bio::Location::Simple -ok 180 -ok 181 -ok 182 -ok 183 -ok 184 -ok 185 -ok 186 -ok 187 -ok 188 - Location String: 467 -ok 189 -ok 190 - Bio::Location::Fuzzy -ok 191 -ok 192 -ok 193 -ok 194 -ok 195 -ok 196 -ok 197 -ok 198 -ok 199 - Location String: ?22..?64 -ok 200 -ok 201 - Bio::Location::Fuzzy -ok 202 -ok 203 -ok 204 -ok 205 -ok 206 -ok 207 -ok 208 -ok 209 -ok 210 - Location String: complement(34..(122.126)) -ok 211 -ok 212 - Bio::Location::Split -ok 213 -ok 214 -ok 215 -ok 216 -ok 217 -ok 218 -ok 219 -ok 220 -ok 221 - Location String: join(AY016290.1:108..185,AY016291.1:1546..1599) -ok 222 -ok 223 - Bio::Location::Fuzzy -ok 224 -ok 225 -ok 226 -ok 227 -ok 228 -ok 229 -ok 230 -ok 231 -ok 232 - Location String: <1..? -ok 233 -ok 234 - Bio::Location::Fuzzy -ok 235 -ok 236 -ok 237 -ok 238 -ok 239 -ok 240 -ok 241 -ok 242 -ok 243 - Location String: 145^177 -ok 244 -ok 245 - Bio::Location::Simple -ok 246 -ok 247 -ok 248 -ok 249 -ok 250 -ok 251 -ok 252 -ok 253 -ok 254 - Location String: 340..565 -ok 255 -ok 256 - Bio::Location::Simple -ok 257 -ok 258 -ok 259 -ok 260 -ok 261 -ok 262 -ok 263 -ok 264 -ok 265 - Location String: J00194:100..202 -ok 266 -ok 267 - Bio::Location::Split -ok 268 -ok 269 -ok 270 -ok 271 -ok 272 -ok 273 -ok 274 -ok 275 -ok 276 - Location String: complement(join(94468..94578,94578..>94889)) -ok 277 -ok 278 - Bio::Location::Fuzzy -ok 279 -ok 280 -ok 281 -ok 282 -ok 283 -ok 284 -ok 285 -ok 286 -ok 287 - Location String: (122.133)..(204.221) -ok 288 -ok 289 - Bio::Location::Fuzzy -ok 290 -ok 291 -ok 292 -ok 293 -ok 294 -ok 295 -ok 296 -ok 297 -ok 298 - Location String: ?..? -ok 299 -ok 300 - Bio::Location::Split -ok 301 -ok 302 -ok 303 -ok 304 -ok 305 -ok 306 -ok 307 -ok 308 -ok 309 - Location String: complement(join(2691..4571,4918..5163)) -ok 310 -ok 311 - complement(join(2691..4571,4918..5163)) -ok 312 - join(complement(4918..5163),complement(2691..4571)) -ok 313 - equivalent remote location strings -ok 314 - complement(join(TEST0001.1:2691..4571,4918..5163)) -ok 315 - join(complement(4918..5163),complement(TEST0001.1:2691..4571)) -ok 316 - equivalent remote location strings -ok 317 - complement(join(TEST0001.1:2691..4571,TEST0008.1:4918..5163)) -ok 318 - join(complement(TEST0008.1:4918..5163),complement(TEST0001.1:2691..4571)) -ok 319 - equivalent remote location strings -ok 320 - join(11025..11049,join(complement(239890..240081),complement(241499..241580),complement(251354..251412),complement(315036..315294))) -ok 321 - join(11025..11049,complement(join(315036..315294,251354..251412,241499..241580,239890..240081))) -ok 322 - join(20464..20694,21548..22763,complement(join(231520..231669,232596..232990,314652..314672))) -ok 323 - join(20464..20694,21548..22763,join(complement(314652..314672),complement(232596..232990),complement(231520..231669))) -ok 324 - join(1000..2000,join(3000..4000,join(5000..6000,7000..8000)),9000..10000) -ok 325 - order(S67862.1:72..75,join(S67863.1:1..788,1..19)) -ok -t/SeqFeature/Primer.t ............... -1..47 -ok 1 - use Bio::SeqFeature::Primer; -ok 2 - use Bio::PrimarySeq; -ok 3 - Implied primer sequence -ok 4 - An object of class 'Bio::SeqFeature::Primer' isa 'Bio::SeqFeature::Primer' -ok 5 - An object of class 'Bio::SeqFeature::Primer' isa 'Bio::SeqFeature::SubSeq' -ok 6 -ok 7 -ok 8 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeqI' -ok 9 -ok 10 - PrimarySeq primer -ok 11 -ok 12 -ok 13 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeqI' -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 - An object of class 'Bio::Location::Simple' isa 'Bio::LocationI' -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 - An object of class 'Bio::SeqFeature::Primer' isa 'Bio::SeqFeature::Primer' -ok 42 -ok 43 -ok 44 - An object of class 'Bio::SeqFeature::Primer' isa 'Bio::SeqFeature::Primer' -ok 45 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeq' -ok 46 -ok 47 -ok -t/SeqFeature/Range.t ................ -1..49 -ok 1 - use Bio::Range; -ok 2 - 'BioRange object' isa 'Bio::Range' -ok 3 -ok 4 - 'BioRange object' isa 'Bio::Range' -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 - 'BioRange object' isa 'Bio::Range' -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 - 'BioRange object' isa 'Bio::Range' -ok 26 - 'BioRange object' isa 'Bio::Range' -ok 27 - 'BioRange object' isa 'Bio::Range' -ok 28 - 1 & -1 -ok 29 - 1 & 1 true -ok 30 - 1 & 0 true -ok 31 - 1 & -1 false -ok 32 - 1 & 1 true -ok 33 - 1 & 0 false -ok 34 - 1 & -1 false -ok 35 -ok 36 -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 -ok 43 -ok 44 -ok 45 - 'Bio::Range object' isa 'Bio::Range' -ok 46 -ok 47 -ok 48 -ok 49 -ok -t/SeqFeature/RangeI.t ............... -1..45 -ok 1 - use Bio::SeqFeature::Generic; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok 39 - subtract() of split features -ok 40 - 0 start -ok 41 - 0 end -ok 42 - 1 start -ok 43 - 1 end -ok 44 - 2 start -ok 45 - 2 end -ok -t/SeqFeature/SeqAnalysisParser.t .... -1..14 -ok 1 - use Bio::Factory::SeqAnalysisParserFactory; -ok 2 - use Bio::SeqIO; -ok 3 - An object of class 'Bio::SeqIO::fasta' isa 'Bio::SeqIO' -ok 4 - An object of class 'Bio::Seq' isa 'Bio::PrimarySeqI' -ok 5 - An object of class 'Bio::Tools::Genscan' isa 'Bio::SeqAnalysisParserI' -ok 6 -ok 7 -ok 8 -ok 9 - An object of class 'Bio::Seq' isa 'Bio::PrimarySeqI' -ok 10 - An object of class 'Bio::Tools::MZEF' isa 'Bio::SeqAnalysisParserI' -ok 11 -ok 12 -ok 13 - An object of class 'Bio::Tools::EPCR' isa 'Bio::SeqAnalysisParserI' -ok 14 -ok -t/SeqFeature/SubSeq.t ............... -1..37 -ok 1 - use Bio::PrimarySeq; -ok 2 - use Bio::SeqFeature::SubSeq; -ok 3 - An object of class 'Bio::SeqFeature::SubSeq' isa 'Bio::SeqFeature::SubSeq' -ok 4 - An object of class 'Bio::SeqFeature::SubSeq' isa 'Bio::SeqFeature::Generic' -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeq' -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeq' -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeq' -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeq' -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeq' -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeq' -ok 36 -ok 37 -ok -t/SeqFeature/Unflattener.t .......... -1..21 -ok 1 - use Bio::SeqIO; -ok 2 - use Bio::SeqFeature::Tools::Unflattener; -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok -t/SeqIO/ace.t ....................... -1..7 -ok 1 - use Bio::SeqIO; -ok 2 - number of sequence objects -ok 3 - unescaping of characters, Name; 4% strewn with \ various / escaped characters -ok 4 - alphabets detected -ok 5 - alphabets detected -ok 6 - writing sequence -ok 7 - test output -ok -t/SeqIO/asciitree.t ................. -1..2 -ok 1 - use Bio::SeqIO; -not ok 2 # TODO Output doesn't exists on linux -# Failed (TODO) test at t/SeqIO/asciitree.t line 38. -ok -t/SeqIO/bsml.t ...................... -1..16 -ok 1 - use XML::DOM; -ok 2 - use Bio::SeqIO::bsml; -ok 3 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::Seq::RichSeqI' -ok 4 - got correct number of refs -ok 5 - display_id -ok 6 - molecule -ok 7 - is_circular -ok 8 - dates -ok 9 - accession_number -ok 10 - seq_version -ok 11 - got correct number of SeqFeatures -ok 12 - feature start -ok 13 - feature end -ok 14 - get_tag_values db_xref -ok 15 - get_Annotations reference -ok 16 - get_Annotations dblink -ok -t/SeqIO/bsml_sax.t .................. -1..15 -ok 1 - use Bio::SeqIO; -ok 2 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::Seq::RichSeqI' -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok -t/SeqIO/embl.t ...................... -1..100 -ok 1 - use Bio::SeqIO::embl; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 - success reading Embl with ^ location and badly split double quotes -ok 25 -ok 26 - success writing Embl format with ^ < and > locations -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 -ok 43 -ok 44 -ok 45 -ok 46 -ok 47 -ok 48 -ok 49 -ok 50 -ok 51 -ok 52 -ok 53 -ok 54 - genus duplication test -ok 55 -ok 56 -ok 57 -ok 58 -ok 59 - CDS - accession on PA line -ok 60 -ok 61 -ok 62 -ok 63 -ok 64 -ok 65 -ok 66 -ok 67 - CDS - OX tagname -ok 68 - CDS - OX database -ok 69 - CDS - OX primary_id -ok 70 -ok 71 -ok 72 -ok 73 -ok 74 -ok 75 -ok 76 -ok 77 -ok 78 -ok 79 -ok 80 -ok 81 -ok 82 -ok 83 -ok 84 -ok 85 - Check if product was parsed correctly -ok 86 - Parse long qualifier -ok 87 -ok 88 - TaxID set correctly -ok 89 - The read sequence has a species object -ok 90 - NCBI TaxID has roundtripped -ok 91 - Name has roundtripped -ok 92 - TaxID set correctly -ok 93 - The read sequence has a species object -ok 94 - The taxid of the source feature overrides that of the OX line -ok 95 - Name has roundtripped -ok 96 - The ID field was written correctly -ok 97 - EMBL format with space after equal sign parses -ok 98 - CDS read -ok 99 - /product found -ok 100 - Qualifier /product value matches -ok -t/SeqIO/fasta.t ..................... -1..22 -ok 1 - use Bio::SeqIO::fasta; -ok 2 - An object of class 'Bio::SeqIO::fasta' isa 'Bio::SeqIO' -ok 3 - Bio::SeqIO::fasta->can('next_seq') -ok 4 - Bio::SeqIO::fasta->can('write_seq') -ok 5 - An object of class 'Bio::Seq' isa 'Bio::Seq' -ok 6 - sequence -ok 7 - length -ok 8 - primary_id -ok 9 - description -ok 10 - An object of class 'Bio::Seq' isa 'Bio::Seq' -ok 11 - sequence -ok 12 - length -ok 13 - primary_id -ok 14 - description -ok 15 - use Algorithm::Diff; -ok 16 - use IO::ScalarArray; -ok 17 - use IO::String; -ok 18 - fasta format can round-trip -ok 19 - dies with roa1.genbank -ok 20 - dies with test.gcg -ok 21 - dies with test.ace -ok 22 - dies with test.raw -ok -t/SeqIO/fastq.t ..................... -1..149 -ok 1 - use Bio::SeqIO::fastq; -ok 2 - use Bio::Seq::Quality; -ok 3 - RT98876 parses -ok 4 - correct num. seqs in RT98876 -ok 5 - sample sequence obtained -ok 6 - An object of class 'Bio::Seq::Quality' isa 'Bio::Seq::Quality' -ok 7 - seq() matches RT98876 -ok 8 - desc() matches RT98876 -ok 9 - display_id() matches RT98876 -ok 10 - qual() matches RT98876 -ok 11 -ok 12 - bug2335 parses -ok 13 - correct num. seqs in bug2335 -ok 14 - sample sequence obtained -ok 15 - An object of class 'Bio::Seq::Quality' isa 'Bio::Seq::Quality' -ok 16 - seq() matches bug2335 -ok 17 - desc() matches bug2335 -ok 18 - display_id() matches bug2335 -ok 19 - qual() matches bug2335 -ok 20 -ok 21 - evil_wrapping parses -ok 22 - correct num. seqs in evil_wrapping -ok 23 - sample sequence obtained -ok 24 - An object of class 'Bio::Seq::Quality' isa 'Bio::Seq::Quality' -ok 25 - seq() matches evil_wrapping -ok 26 - desc() matches evil_wrapping -ok 27 - display_id() matches evil_wrapping -ok 28 - qual() matches evil_wrapping -ok 29 -ok 30 - example parses -ok 31 - correct num. seqs in example -ok 32 - sample sequence obtained -ok 33 - An object of class 'Bio::Seq::Quality' isa 'Bio::Seq::Quality' -ok 34 - seq() matches example -ok 35 - desc() matches example -ok 36 - display_id() matches example -ok 37 - qual() matches example -ok 38 -ok 39 - illumina_faked parses -ok 40 - correct num. seqs in illumina_faked -ok 41 - sample sequence obtained -ok 42 - An object of class 'Bio::Seq::Quality' isa 'Bio::Seq::Quality' -ok 43 - seq() matches illumina_faked -ok 44 - desc() matches illumina_faked -ok 45 - display_id() matches illumina_faked -ok 46 - qual() matches illumina_faked -ok 47 -ok 48 - sanger_93 parses -ok 49 - correct num. seqs in sanger_93 -ok 50 - sample sequence obtained -ok 51 - An object of class 'Bio::Seq::Quality' isa 'Bio::Seq::Quality' -ok 52 - seq() matches sanger_93 -ok 53 - desc() matches sanger_93 -ok 54 - display_id() matches sanger_93 -ok 55 - qual() matches sanger_93 -ok 56 -ok 57 - sanger_faked parses -ok 58 - correct num. seqs in sanger_faked -ok 59 - sample sequence obtained -ok 60 - An object of class 'Bio::Seq::Quality' isa 'Bio::Seq::Quality' -ok 61 - seq() matches sanger_faked -ok 62 - desc() matches sanger_faked -ok 63 - display_id() matches sanger_faked -ok 64 - qual() matches sanger_faked -ok 65 -ok 66 - solexa_example parses -ok 67 - correct num. seqs in solexa_example -ok 68 - sample sequence obtained -ok 69 - An object of class 'Bio::Seq::Quality' isa 'Bio::Seq::Quality' -ok 70 - seq() matches solexa_example -ok 71 - desc() matches solexa_example -ok 72 - display_id() matches solexa_example -ok 73 - qual() matches solexa_example -ok 74 -ok 75 - solexa_faked parses -ok 76 - correct num. seqs in solexa_faked -ok 77 - sample sequence obtained -ok 78 - An object of class 'Bio::Seq::Quality' isa 'Bio::Seq::Quality' -ok 79 - seq() matches solexa_faked -ok 80 - desc() matches solexa_faked -ok 81 - display_id() matches solexa_faked -ok 82 - qual() matches solexa_faked -ok 83 -ok 84 - test1_sanger parses -ok 85 - correct num. seqs in test1_sanger -ok 86 - sample sequence obtained -ok 87 - An object of class 'Bio::Seq::Quality' isa 'Bio::Seq::Quality' -ok 88 - seq() matches test1_sanger -ok 89 - desc() matches test1_sanger -ok 90 - display_id() matches test1_sanger -ok 91 - qual() matches test1_sanger -ok 92 -ok 93 - test2_solexa parses -ok 94 - correct num. seqs in test2_solexa -ok 95 - sample sequence obtained -ok 96 - An object of class 'Bio::Seq::Quality' isa 'Bio::Seq::Quality' -ok 97 - seq() matches test2_solexa -ok 98 - desc() matches test2_solexa -ok 99 - display_id() matches test2_solexa -ok 100 - qual() matches test2_solexa -ok 101 -ok 102 - test3_illumina parses -ok 103 - correct num. seqs in test3_illumina -ok 104 - sample sequence obtained -ok 105 - An object of class 'Bio::Seq::Quality' isa 'Bio::Seq::Quality' -ok 106 - seq() matches test3_illumina -ok 107 - desc() matches test3_illumina -ok 108 - display_id() matches test3_illumina -ok 109 - qual() matches test3_illumina -ok 110 -ok 111 - tricky parses -ok 112 - correct num. seqs in tricky -ok 113 - sample sequence obtained -ok 114 - An object of class 'Bio::Seq::Quality' isa 'Bio::Seq::Quality' -ok 115 - seq() matches tricky -ok 116 - desc() matches tricky -ok 117 - display_id() matches tricky -ok 118 - qual() matches tricky -ok 119 -ok 120 - Conversion from illumina to sanger -ok 121 - Conversion from illumina to illumina -ok 122 - Conversion from illumina to solexa -ok 123 - Conversion from sanger to sanger -ok 124 - Conversion from sanger to illumina -ok 125 - Conversion from sanger to solexa -ok 126 - Conversion from solexa to sanger -ok 127 - Conversion from solexa to illumina -ok 128 - Conversion from solexa to solexa -ok 129 - Exception caught for error_diff_ids -ok 130 - Exception caught for error_long_qual -ok 131 - Exception caught for error_no_qual -ok 132 - Exception caught for error_qual_del -ok 133 - Exception caught for error_qual_escape -ok 134 - Exception caught for error_qual_null -ok 135 - Exception caught for error_qual_space -ok 136 - Exception caught for error_qual_tab -ok 137 - Exception caught for error_qual_unit_sep -ok 138 - Exception caught for error_qual_vtab -ok 139 - Exception caught for error_short_qual -ok 140 - Exception caught for error_spaces -ok 141 - Exception caught for error_tabs -ok 142 - Exception caught for error_trunc_at_plus -ok 143 - Exception caught for error_trunc_at_qual -ok 144 - Exception caught for error_trunc_at_seq -ok 145 - Exception caught for error_trunc_in_plus -ok 146 - Exception caught for error_trunc_in_qual -ok 147 - Exception caught for error_trunc_in_seq -ok 148 - Exception caught for error_trunc_in_title -ok 149 - edge case; single 0 in quality fails -ok -t/SeqIO/game.t ...................... -1..24 -ok 1 - use Bio::SeqIO::game; -ok 2 - An object of class 'Bio::SeqIO::game' isa 'Bio::SeqIO' -ok 3 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::Seq::RichSeq' -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok -t/SeqIO/gbxml.t ..................... -1..14 -ok 1 - use Bio::SeqIO::gbxml; -ok 2 - An object of class 'Bio::SeqIO::gbxml' isa 'Bio::SeqIO' -ok 3 - molecule -ok 4 - alphabet -ok 5 - primary_id -ok 6 - display_id -ok 7 - version -ok 8 - is_circular -ok 9 - description -ok 10 - sequence -ok 11 - classification -ok 12 - feat - clone_lib -ok 13 - feat - db_xref -ok 14 - feat - lab_host -ok -t/SeqIO/gcg.t ....................... -1..17 -ok 1 - use Bio::SeqIO::gcg; -ok 2 - An object of class 'Bio::SeqIO::gcg' isa 'Bio::SeqIO' -ok 3 - Bio::SeqIO::gcg->can('next_seq') -ok 4 - Bio::SeqIO::gcg->can('write_seq') -ok 5 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::Seq' -ok 6 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::Seq::RichSeq' -ok 7 - sequence -ok 8 - length -not ok 9 - primary_id # TODO possible bug: RichSeq not setting primary_id? -# Failed (TODO) test 'primary_id' -# at t/SeqIO/gcg.t line 53. -# got: 'Bio::PrimarySeq=HASH(0xaaaad883b128)' -# expected: 'roa1_drome' -ok 10 - description -ok 11 -ok 12 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::SeqI' -ok 13 -ok 14 - use Algorithm::Diff; -ok 15 - use IO::ScalarArray; -ok 16 - use IO::String; -ok 17 - gcg format can round-trip -ok -t/SeqIO/genbank.t ................... -1..306 -ok 1 - use Bio::SeqIO::genbank; -ok 2 - An object of class 'Bio::SeqIO::genbank' isa 'Bio::SeqIO' -ok 3 - AI129902 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 - NT_021877 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 - BAB68554 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 - operator overloading in AnnotationI is deprecated -ok 29 - NC_006346 -ok 30 -ok 31 -ok 32 - U71225 -ok 33 -ok 34 - AB077698 -ok 35 -ok 36 - DQ018368 -ok 37 - D10483 -ok 38 -ok 39 -ok 40 -ok 41 - bug 1487 -ok 42 -ok 43 - bug 1647 -ok 44 -ok 45 -ok 46 - bug 1673 -ok 47 -ok 48 -ok 49 -ok 50 -ok 51 -ok 52 - AF165282 -ok 53 -ok 54 -ok 55 -ok 56 -ok 57 -ok 58 -ok 59 -ok 60 -ok 61 - species parsing incorrect for genbank -ok 62 - genus duplicated in genbank parsing -ok 63 -ok 64 -ok 65 - species parsing incorrect for genbank -ok 66 - genus duplicated in genbank parsing -ok 67 -ok 68 -ok 69 - species parsing incorrect for genbank -ok 70 - genus duplicated in genbank parsing -ok 71 -ok 72 - streaming -ok 73 -ok 74 -ok 75 -ok 76 -ok 77 -ok 78 - Total number of sequences in test file -ok 79 -ok 80 - Fuzzy in -ok 81 -ok 82 -ok 83 -ok 84 -ok 85 -ok 86 -ok 87 -ok 88 -ok 89 -ok 90 -ok 91 -ok 92 - Fuzzy out -ok 93 - BK000016 -ok 94 -ok 95 - BK000016 -ok 96 -ok 97 -ok 98 -ok 99 -ok 100 -ok 101 -ok 102 -ok 103 -ok 104 -ok 105 -ok 106 -ok 107 -ok 108 -ok 109 -ok 110 - BK000016 -ok 111 - roundtrip -ok 112 -ok 113 -ok 114 -ok 115 -ok 116 -ok 117 -ok 118 -ok 119 -ok 120 -ok 121 -ok 122 -ok 123 -ok 124 -ok 125 -ok 126 -ok 127 -ok 128 -ok 129 - revcomp split location -ok 130 - Bug 1925 -ok 131 -ok 132 -ok 133 - wgs -ok 134 -ok 135 - wgs_scafld -ok 136 -ok 137 - wgs_scafld -ok 138 -ok 139 -ok 140 - BC000007 -ok 141 - BK000016-tpa.gbk -ok 142 - ay116458.gb -ok 143 - ay149291.gb -ok 144 - NC_006346.gb -ok 145 - ay007676.gb -ok 146 - dq519393.gb -ok 147 -ok 148 - swissprot:K1C9_HUMAN -ok 149 -ok 150 - swissprot -ok 151 -ok 152 - GenBank:Z29074.1 -ok 153 -ok 154 - GenBank -ok 155 -ok 156 - GenPept:CAA82315.1 -ok 157 -ok 158 - GenPept -ok 159 -ok 160 - GenBank:S69510.1 -ok 161 -ok 162 - GenBank -ok 163 -ok 164 - GenPept:AAC60619.1 -ok 165 -ok 166 - GenPept -ok 167 -ok 168 - GenBank:X75015.1 -ok 169 -ok 170 - GenBank -ok 171 -ok 172 - GenPept:CAA52924.1 -ok 173 -ok 174 - GenPept -ok 175 -ok 176 - GenBank:AB001594.1 -ok 177 -ok 178 - GenBank -ok 179 -ok 180 - GenPept:BAA19418.1 -ok 181 -ok 182 - GenPept -ok 183 -ok 184 - GenBank:I37984 -ok 185 -ok 186 - GenBank -ok 187 -ok 188 - HSSP:P08670 -ok 189 -ok 190 - HSSP -ok 191 -ok 192 - IntAct:P35527 -ok 193 -ok 194 - IntAct -ok 195 -ok 196 - Ensembl:ENSG00000171403 -ok 197 -ok 198 - Ensembl -ok 199 -ok 200 - KEGG:hsa:3857 -ok 201 -ok 202 - KEGG -ok 203 -ok 204 - HGNC:6447 -ok 205 -ok 206 - HGNC -ok 207 -ok 208 - MIM:144200 -ok 209 -ok 210 - MIM -ok 211 -ok 212 - MIM:607606 -ok 213 -ok 214 - MIM -ok 215 -ok 216 - ArrayExpress:P35527 -ok 217 -ok 218 - ArrayExpress -ok 219 -ok 220 - GO:0005200 -ok 221 -ok 222 - GO -ok 223 -ok 224 - GO:0008544 -ok 225 -ok 226 - GO -ok 227 -ok 228 - InterPro:IPR011000 -ok 229 -ok 230 - InterPro -ok 231 -ok 232 - InterPro:IPR001664 -ok 233 -ok 234 - InterPro -ok 235 -ok 236 - InterPro:IPR002957 -ok 237 -ok 238 - InterPro -ok 239 -ok 240 - Pfam:PF00038 -ok 241 -ok 242 - Pfam -ok 243 -ok 244 - PRINTS:PR01248 -ok 245 -ok 246 - PRINTS -ok 247 -ok 248 - PROSITE:PS00226 -ok 249 -ok 250 - PROSITE -ok 251 -ok 252 - Bug 2195 -ok 253 - Bug 2195 -ok 254 - An object of class 'Bio::Annotation::SimpleValue' isa 'Bio::Annotation::SimpleValue' -ok 255 -ok 256 - An object of class 'Bio::Annotation::SimpleValue' isa 'Bio::Annotation::SimpleValue' -ok 257 -ok 258 - P39765 -ok 259 - P39765 -ok 260 - P39765 -ok 261 -ok 262 -ok 263 -ok 264 -ok 265 -ok 266 -ok 267 -ok 268 -ok 269 -ok 270 - operator overloading in AnnotationI is deprecated -ok 271 -ok 272 -ok 273 -ok 274 -ok 275 - bug3375 database is BioProject -ok 276 - bug3375 primary_id is PRJNA15288 -ok 277 -ok 278 -ok 279 -ok 280 -ok 281 -ok 282 - Label is the same -ok 283 -ok 284 -ok 285 - An object of class 'Bio::Annotation::SimpleValue' isa 'Bio::Annotation::SimpleValue' -ok 286 -ok 287 -ok 288 -ok 289 -ok 290 - An object of class 'Bio::Annotation::SimpleValue' isa 'Bio::Annotation::SimpleValue' -ok 291 -ok 292 -ok 293 - Got 11 features -ok 294 - Got 1 feature -ok 295 - Correct primary tag for feature -ok 296 - Got 10 features -ok 297 - Got correct Structured Comment -ok 298 - Got correct Structured Comment -ok 299 - Got correct Structured Comment -ok 300 - Got correct Structured Comment -ok 301 - Got correct Structured Comment -ok 302 - Got correct Structured Comment -ok 303 - Got correct Structured Comment -ok 304 - Got correct Structured Comment -ok 305 - unquoted labels wrap at comma -ok 306 - Label is the same -ok -t/SeqIO/Handler.t ................... -1..561 -ok 1 - use Bio::SeqIO; -ok 2 - AI129902 -ok 3 -ok 4 -ok 5 -ok 6 - NT_021877 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 - BAB68554 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 - operator overloading in AnnotationI is deprecated -ok 22 - NC_006346 -ok 23 -ok 24 -ok 25 - U71225 -ok 26 -ok 27 - AB077698 -ok 28 -ok 29 - DQ018368 -ok 30 - D10483 -ok 31 -ok 32 -ok 33 -ok 34 - bug 1487 -ok 35 -ok 36 - bug 1647 -ok 37 -ok 38 -ok 39 - bug 1673 -ok 40 -ok 41 -ok 42 -ok 43 - AF165282 -ok 44 -ok 45 -ok 46 -ok 47 -ok 48 -ok 49 -ok 50 -ok 51 -ok 52 - species parsing incorrect for genbank -ok 53 - genus duplicated in genbank parsing -ok 54 -ok 55 -ok 56 - species parsing incorrect for genbank -ok 57 - genus duplicated in genbank parsing -ok 58 -ok 59 -ok 60 - species parsing incorrect for genbank -ok 61 - genus duplicated in genbank parsing -ok 62 -ok 63 - streaming -ok 64 -ok 65 -ok 66 -ok 67 -ok 68 -ok 69 - Total number of sequences in test file -ok 70 -ok 71 - Fuzzy in -ok 72 -ok 73 -ok 74 -ok 75 -ok 76 -ok 77 -ok 78 -ok 79 -ok 80 -ok 81 -ok 82 -ok 83 - Fuzzy out -ok 84 - BK000016 -ok 85 -ok 86 - BK000016 -ok 87 -ok 88 -ok 89 -ok 90 -ok 91 -ok 92 -ok 93 -ok 94 -ok 95 -ok 96 -ok 97 -ok 98 -ok 99 -ok 100 -ok 101 - BK000016 -ok 102 - roundtrip -ok 103 -ok 104 -ok 105 -ok 106 -ok 107 -ok 108 -ok 109 -ok 110 -ok 111 -ok 112 -ok 113 -ok 114 -ok 115 -ok 116 -ok 117 -ok 118 -ok 119 -ok 120 - revcomp split location -ok 121 - Bug 1925 -ok 122 -ok 123 -ok 124 - wgs -ok 125 -ok 126 - wgs_scafld -ok 127 -ok 128 - wgs_scafld -ok 129 -ok 130 -ok 131 - BC000007 -ok 132 - BK000016-tpa.gbk -ok 133 - ay116458.gb -ok 134 - ay149291.gb -ok 135 - NC_006346.gb -ok 136 - ay007676.gb -ok 137 - dq519393.gb -ok 138 -ok 139 - swissprot:K1C9_HUMAN -ok 140 -ok 141 - swissprot -ok 142 -ok 143 - GenBank:Z29074.1 -ok 144 -ok 145 - GenBank -ok 146 -ok 147 - GenPept:CAA82315.1 -ok 148 -ok 149 - GenPept -ok 150 -ok 151 - GenBank:S69510.1 -ok 152 -ok 153 - GenBank -ok 154 -ok 155 - GenPept:AAC60619.1 -ok 156 -ok 157 - GenPept -ok 158 -ok 159 - GenBank:X75015.1 -ok 160 -ok 161 - GenBank -ok 162 -ok 163 - GenPept:CAA52924.1 -ok 164 -ok 165 - GenPept -ok 166 -ok 167 - GenBank:AB001594.1 -ok 168 -ok 169 - GenBank -ok 170 -ok 171 - GenPept:BAA19418.1 -ok 172 -ok 173 - GenPept -ok 174 -ok 175 - GenBank:I37984 -ok 176 -ok 177 - GenBank -ok 178 -ok 179 - HSSP:P08670 -ok 180 -ok 181 - HSSP -ok 182 -ok 183 - IntAct:P35527 -ok 184 -ok 185 - IntAct -ok 186 -ok 187 - Ensembl:ENSG00000171403 -ok 188 -ok 189 - Ensembl -ok 190 -ok 191 - KEGG:hsa:3857 -ok 192 -ok 193 - KEGG -ok 194 -ok 195 - HGNC:6447 -ok 196 -ok 197 - HGNC -ok 198 -ok 199 - MIM:144200 -ok 200 -ok 201 - MIM -ok 202 -ok 203 - MIM:607606 -ok 204 -ok 205 - MIM -ok 206 -ok 207 - ArrayExpress:P35527 -ok 208 -ok 209 - ArrayExpress -ok 210 -ok 211 - GO:0005200 -ok 212 -ok 213 - GO -ok 214 -ok 215 - GO:0008544 -ok 216 -ok 217 - GO -ok 218 -ok 219 - InterPro:IPR011000 -ok 220 -ok 221 - InterPro -ok 222 -ok 223 - InterPro:IPR001664 -ok 224 -ok 225 - InterPro -ok 226 -ok 227 - InterPro:IPR002957 -ok 228 -ok 229 - InterPro -ok 230 -ok 231 - Pfam:PF00038 -ok 232 -ok 233 - Pfam -ok 234 -ok 235 - PRINTS:PR01248 -ok 236 -ok 237 - PRINTS -ok 238 -ok 239 - PROSITE:PS00226 -ok 240 -ok 241 - PROSITE -ok 242 -ok 243 - Bug 2195 -ok 244 - Bug 2195 -ok 245 - An object of class 'Bio::Annotation::SimpleValue' isa 'Bio::Annotation::SimpleValue' -ok 246 -ok 247 - An object of class 'Bio::Annotation::SimpleValue' isa 'Bio::Annotation::SimpleValue' -ok 248 -ok 249 -ok 250 -ok 251 -ok 252 -ok 253 -ok 254 -ok 255 -ok 256 -ok 257 -ok 258 -ok 259 -ok 260 -ok 261 -ok 262 -ok 263 -ok 264 -ok 265 -ok 266 -ok 267 -ok 268 -ok 269 -ok 270 -ok 271 -ok 272 -ok 273 - success reading Embl with ^ location and badly split double quotes -ok 274 -ok 275 -ok 276 - success writing Embl format with ^ < and > locations -ok 277 -ok 278 -ok 279 -ok 280 -ok 281 -ok 282 -ok 283 -ok 284 -ok 285 -ok 286 -ok 287 -ok 288 -ok 289 -ok 290 -ok 291 -ok 292 -ok 293 -ok 294 -ok 295 -ok 296 -ok 297 -ok 298 -ok 299 -ok 300 -ok 301 -ok 302 -ok 303 -ok 304 -ok 305 -ok 306 -ok 307 -ok 308 -ok 309 - genus duplication test -ok 310 -ok 311 -ok 312 - An object of class 'Bio::SeqIO::swissdriver' isa 'Bio::SeqIO' -ok 313 - An object of class 'Bio::Species' isa 'Bio::Species' -ok 314 -ok 315 -ok 316 - operator overloading in AnnotationI is deprecated -ok 317 -ok 318 - dates -ok 319 - dates -ok 320 - dates -ok 321 -ok 322 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::Seq::RichSeqI' -ok 323 -ok 324 -ok 325 -ok 326 - operator overloading in AnnotationI is deprecated -ok 327 -ok 328 -ok 329 -ok 330 -ok 331 - id is ROA1_HUMAN -ok 332 -ok 333 -ok 334 -ok 335 -ok 336 -ok 337 -ok 338 -ok 339 - operator overloading in AnnotationI is deprecated -ok 340 -ok 341 -ok 342 -ok 343 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::Seq::RichSeqI' -ok 344 -ok 345 -ok 346 -ok 347 -ok 348 -ok 349 -ok 350 -ok 351 -ok 352 -ok 353 - operator overloading in AnnotationI is deprecated -ok 354 -ok 355 -ok 356 -ok 357 - GC1QBP -ok 358 - HABP1 -ok 359 - SF2P32 -ok 360 - C1QBP -ok 361 -ok 362 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::Seq::RichSeqI' -ok 363 -ok 364 -ok 365 -ok 366 -ok 367 -ok 368 -ok 369 - F54H12.1 -ok 370 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::Seq::RichSeqI' -ok 371 -ok 372 -ok 373 -ok 374 -ok 375 -ok 376 -ok 377 -ok 378 -ok 379 -ok 380 -ok 381 -ok 382 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::Seq::RichSeqI' -ok 383 -ok 384 -ok 385 -ok 386 -ok 387 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::Seq::RichSeqI' -ok 388 -ok 389 -ok 390 -ok 391 -ok 392 -ok 393 -ok 394 -ok 395 -ok 396 -ok 397 -ok 398 -ok 399 -ok 400 -ok 401 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::Seq::RichSeqI' -ok 402 -ok 403 -ok 404 -ok 405 -ok 406 -ok 407 -ok 408 -ok 409 -ok 410 -ok 411 -ok 412 -ok 413 -ok 414 -ok 415 -ok 416 -ok 417 -ok 418 -ok 419 -ok 420 -ok 421 -ok 422 -ok 423 -ok 424 -ok 425 -ok 426 -ok 427 -ok 428 -ok 429 -ok 430 -ok 431 -ok 432 -ok 433 -ok 434 -ok 435 -ok 436 -ok 437 -ok 438 -ok 439 -ok 440 -ok 441 -ok 442 -ok 443 -ok 444 -ok 445 -ok 446 -ok 447 -ok 448 -ok 449 -ok 450 -ok 451 -ok 452 -ok 453 -ok 454 -ok 455 -ok 456 -ok 457 -ok 458 -ok 459 -ok 460 -ok 461 -ok 462 -ok 463 -ok 464 -ok 465 -ok 466 -ok 467 -ok 468 -ok 469 -ok 470 -ok 471 -ok 472 -ok 473 -ok 474 -ok 475 -ok 476 -ok 477 -ok 478 -ok 479 -ok 480 -ok 481 -ok 482 -ok 483 -ok 484 -ok 485 - An object of class 'Bio::Species' isa 'Bio::Species' -ok 486 -ok 487 -ok 488 -ok 489 -ok 490 -ok 491 -ok 492 -ok 493 -ok 494 -ok 495 -ok 496 -ok 497 -ok 498 -ok 499 -ok 500 -ok 501 -ok 502 -ok 503 -ok 504 -ok 505 -ok 506 -ok 507 -ok 508 -ok 509 -ok 510 -ok 511 -ok 512 -ok 513 -ok 514 -ok 515 -ok 516 -ok 517 - An object of class 'Bio::Species' isa 'Bio::Species' -ok 518 -ok 519 -ok 520 - operator overloading in AnnotationI is deprecated -ok 521 -ok 522 -ok 523 -ok 524 -ok 525 -ok 526 -ok 527 -ok 528 -ok 529 -ok 530 -ok 531 -ok 532 -ok 533 -ok 534 -ok 535 -ok 536 -ok 537 -ok 538 -ok 539 -ok 540 -ok 541 -ok 542 -ok 543 -ok 544 -ok 545 -ok 546 -ok 547 -ok 548 -ok 549 -ok 550 -ok 551 - P39765 -ok 552 -ok 553 -ok 554 -ok 555 -ok 556 -ok 557 -ok 558 -ok 559 -ok 560 -ok 561 - operator overloading in AnnotationI is deprecated -ok -t/SeqIO/kegg.t ...................... -1..16 -ok 1 - use Bio::SeqIO::kegg; -ok 2 - An object of class 'Bio::SeqIO::kegg' isa 'Bio::SeqIO' -ok 3 -ok 4 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::Seq::RichSeq' -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok -t/SeqIO/largefasta.t ................ -1..16 -ok 1 - use Bio::SeqIO::largefasta; -ok 2 - An object of class 'Bio::SeqIO::largefasta' isa 'Bio::SeqIO' -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok -t/SeqIO/locuslink.t ................. -1..26 -ok 1 - use Bio::SeqIO::locuslink; -ok 2 - use Bio::SeqFeature::Generic; -ok 3 - use Bio::SeqFeature::AnnotationAdaptor; -ok 4 -ok 5 - An object of class 'Bio::SeqIO::locuslink' isa 'Bio::SeqIO' -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok -t/SeqIO/mbsout.t .................... -1..74 -ok 1 - use Bio::SeqIO::mbsout; -ok 2 - Bio::SeqIO::mbsout is at least api version 1.1.3 -ok 3 - An object of class 'Bio::SeqIO::mbsout' isa 'Bio::SeqIO::mbsout' -ok 4 - An object of class 'Bio::SeqIO::mbsout' isa 'Bio::SeqIO::mbsout' -ok 5 - Get SELPOS -ok 6 - Get SEGSITES -ok 7 - Get TOT_RUN_HAPS -ok 8 - Get TRAJ_FILENAME -ok 9 - Get CURRENT_RUN_SEGSITES -ok 10 - Get NREPS -ok 11 - Get NSITES -ok 12 - Get LAST_READ_HAP_NUM -ok 13 - Get POSITIONS -ok 14 - Get RUNS -ok 15 - Get NEXT_RUN_NUM -ok 16 - Get NFILES -ok 17 - Get POP_RECOMB_PARAM_PER_SITE -ok 18 - Get MBS_INFO_LINE -ok 19 - Get POP_MUT_PARAM_PER_SITE -ok 20 - Get next_hap at beginning of run -ok 21 - Get next_hap after beginning of run -ok 22 - Get next_pop after beginning of pop -ok 23 - Get next_hap -ok 24 - Get next_hap -ok 25 - Get next_run after beginning of run -ok 26 - Get next_run at beginning of run -ok 27 - Get next_run at beginning of run -ok 28 - have all lines been read? -ok 29 - An object of class 'Bio::SeqIO::mbsout' isa 'Bio::SeqIO::mbsout' -ok 30 - Get NSITES -ok 31 - Get LAST_READ_HAP_NUM -ok 32 - Get NFILES -ok 33 - Get RUNS -ok 34 - Get POSITIONS -ok 35 - Get NEXT_RUN_NUM -ok 36 - Get POP_MUT_PARAM_PER_SITE -ok 37 - Get POP_RECOMB_PARAM_PER_SITE -ok 38 - Get MBS_INFO_LINE -ok 39 - Get TRAJ_FILENAME -ok 40 - Get SELPOS -ok 41 - Get TOT_RUN_HAPS -ok 42 - Get SEGSITES -ok 43 - Get NREPS -ok 44 - Get CURRENT_RUN_SEGSITES -ok 45 - Get next_hap at beginning of run -ok 46 - Get next_hap after beginning of run -ok 47 - Testing mbsout::outgroup -ok 48 - Get next_run after beginning of run -ok 49 - Get next_run after beginning of run -ok 50 - Get next_run at beginning of run -ok 51 - Get next_hap at beginning of run 2 -ok 52 - Get next_run after hap -ok 53 - next run should be 5. -ok 54 - An object of class 'Bio::SeqIO::mbsout' isa 'Bio::SeqIO::mbsout' -ok 55 - Get LAST_READ_HAP_NUM -ok 56 - Get NSITES -ok 57 - Get POP_MUT_PARAM_PER_SITE -ok 58 - Get MBS_INFO_LINE -ok 59 - Get POP_RECOMB_PARAM_PER_SITE -ok 60 - Get NFILES -ok 61 - Get NEXT_RUN_NUM -ok 62 - Get POSITIONS -ok 63 - Get RUNS -ok 64 - Get TRAJ_FILENAME -ok 65 - Get SEGSITES -ok 66 - Get TOT_RUN_HAPS -ok 67 - Get SELPOS -ok 68 - Get CURRENT_RUN_SEGSITES -ok 69 - Get NREPS -ok 70 - Get next_run at end/beginning of run -ok 71 - have all lines been read? -ok 72 - Get next_run at eof -ok 73 - Get next_hap at eof -ok 74 - Get next_seq at eof -ok -t/SeqIO/metafasta.t ................. -1..6 -ok 1 - use Bio::SeqIO::metafasta; -ok 2 - An object of class 'Bio::SeqIO::metafasta' isa 'Bio::SeqIO' -ok 3 -ok 4 - An object of class 'Bio::Seq::Meta' isa 'Bio::Seq::Meta' -ok 5 -ok 6 -ok -t/SeqIO/msout.t ..................... -1..165 -ok 1 - use Bio::SeqIO::msout; -ok 2 - Bio::SeqIO::msout is at least api version 1.1.5 -ok 3 - An object of class 'Bio::SeqIO::msout' isa 'Bio::SeqIO::msout' -ok 4 - Get RUNS -ok 5 - Get N_SITES -ok 6 - Get SEEDS -ok 7 - Get SEGSITES -ok 8 - Get NEXT_RUN_NUM -ok 9 - Get POPS -ok 10 - Get LAST_READ_HAP_NUM -ok 11 - Get POSITIONS -ok 12 - Get TOT_RUN_HAPS -ok 13 - Get CURRENT_RUN_SEGSITES -ok 14 - Get MS_INFO_LINE -ok 15 - Get next_hap at beginning of run -ok 16 - Get next_hap after beginning of run -ok 17 - Testing msout::outgroup -ok 18 - Get next_pop after beginning of pop -ok 19 - Get next_pop at beginning of pop -ok 20 - Get next_run after beginning of run -ok 21 - Get next_pop at beginning of run -ok 22 - Get next_hap after pop -ok 23 - Get next_run after pop and hap -ok 24 - Get next_run at beginning of run -ok 25 - have all lines been read? -ok 26 - An object of class 'Bio::SeqIO::msout' isa 'Bio::SeqIO::msout' -ok 27 - Get POPS -ok 28 - Get TOT_RUN_HAPS -ok 29 - Get POSITIONS -ok 30 - Get LAST_READ_HAP_NUM -ok 31 - Get MS_INFO_LINE -ok 32 - Get CURRENT_RUN_SEGSITES -ok 33 - Get RUNS -ok 34 - Get SEEDS -ok 35 - Get N_SITES -ok 36 - Get NEXT_RUN_NUM -ok 37 - Get SEGSITES -ok 38 - Get next_hap at beginning of run -ok 39 - Get next_hap after beginning of run -ok 40 - Testing msout::outgroup -ok 41 - Get next_pop after beginning of pop -ok 42 - Get next_pop at beginning of pop/run -ok 43 - Get next_run at beginning of run -ok 44 - Get next_hap at beginning of run 2 -ok 45 - Get next_run after hap -ok 46 - next run should be 5. -ok 47 - Get last hap through next_hap -ok 48 - An object of class 'Bio::SeqIO::msout' isa 'Bio::SeqIO::msout' -ok 49 - Get LAST_READ_HAP_NUM -ok 50 - Get POSITIONS -ok 51 - Get TOT_RUN_HAPS -ok 52 - Get POPS -ok 53 - Get CURRENT_RUN_SEGSITES -ok 54 - Get MS_INFO_LINE -ok 55 - Get SEEDS -ok 56 - Get RUNS -ok 57 - Get NEXT_RUN_NUM -ok 58 - Get SEGSITES -ok 59 - Get next_pop at end of run -ok 60 - have all lines been read? -ok 61 - Get next_pop at eof -ok 62 - Get next_run at eof -ok 63 - Get next_hap at eof -ok 64 - Get next_seq at eof -ok 65 - An object of class 'Bio::SeqIO::msout' isa 'Bio::SeqIO::msout' -ok 66 - Get LAST_READ_HAP_NUM -ok 67 - Get TOT_RUN_HAPS -ok 68 - Get POSITIONS -ok 69 - Get POPS -ok 70 - Get CURRENT_RUN_SEGSITES -ok 71 - Get MS_INFO_LINE -ok 72 - Get N_SITES -ok 73 - Get SEEDS -ok 74 - Get RUNS -ok 75 - Get SEGSITES -ok 76 - Get NEXT_RUN_NUM -ok 77 - Get next_hap at beginning of run -ok 78 - Get next_hap after beginning of run -ok 79 - Testing msout::outgroup -ok 80 - Get next_pop after beginning of pop -ok 81 - Get next_pop at beginning of pop -ok 82 - Get next_run after beginning of run -ok 83 - Get next_pop at beginning of run -ok 84 - Get next_hap after pop -ok 85 - Get next_run after pop and hap -ok 86 - Get next_run at beginning of run -ok 87 - have all lines been read? -ok 88 - An object of class 'Bio::SeqIO::msout' isa 'Bio::SeqIO::msout' -ok 89 - Caught error in bad msout file 1 -ok 90 - An object of class 'Bio::SeqIO::msout' isa 'Bio::SeqIO::msout' -ok 91 - Caught error in bad msout file 2 -ok 92 - An object of class 'Bio::SeqIO::msout' isa 'Bio::SeqIO::msout' -ok 93 - Get LAST_READ_HAP_NUM -ok 94 - Get POSITIONS -ok 95 - Get TOT_RUN_HAPS -ok 96 - Get POPS -ok 97 - Get CURRENT_RUN_SEGSITES -ok 98 - Get MS_INFO_LINE -ok 99 - Get N_SITES -ok 100 - Get SEEDS -ok 101 - Get RUNS -ok 102 - Get NEXT_RUN_NUM -ok 103 - Get SEGSITES -ok 104 - Get next_hap at beginning of run -ok 105 - Get next_hap after beginning of run -ok 106 - Testing msout::outgroup -ok 107 - Get next_pop after beginning of pop -ok 108 - Get next_pop at beginning of pop -ok 109 - Get next_run after beginning of run -ok 110 - Get next_pop at beginning of run -ok 111 - Get next_hap after pop -ok 112 - Get next_run after pop and hap -ok 113 - Get next_run at beginning of run -ok 114 - have all lines been read? -ok 115 - An object of class 'Bio::SeqIO::msout' isa 'Bio::SeqIO::msout' -ok 116 - Get RUNS -ok 117 - Get N_SITES -ok 118 - Get SEEDS -ok 119 - Get NEXT_RUN_NUM -ok 120 - Get SEGSITES -ok 121 - Get POPS -ok 122 - Get LAST_READ_HAP_NUM -ok 123 - Get POSITIONS -ok 124 - Get TOT_RUN_HAPS -ok 125 - Get CURRENT_RUN_SEGSITES -ok 126 - Get MS_INFO_LINE -ok 127 - Get next_hap at beginning of run -ok 128 - Get next_hap after beginning of run -ok 129 - Testing msout::outgroup -ok 130 - Get next_pop after beginning of pop -ok 131 - Get next_pop at beginning of pop/run -ok 132 - Get next_run at beginning of run -ok 133 - Get next_hap at beginning of run 2 -ok 134 - Get next_run after hap -ok 135 - next run should be 5. -ok 136 - Get last hap through next_hap -ok 137 - An object of class 'Bio::SeqIO::msout' isa 'Bio::SeqIO::msout' -ok 138 - Get CURRENT_RUN_SEGSITES -ok 139 - Get MS_INFO_LINE -ok 140 - Get LAST_READ_HAP_NUM -ok 141 - Get TOT_RUN_HAPS -ok 142 - Get POSITIONS -ok 143 - Get POPS -ok 144 - Get NEXT_RUN_NUM -ok 145 - Get SEGSITES -ok 146 - Get N_SITES -ok 147 - Get SEEDS -ok 148 - Get RUNS -ok 149 - Get next_hap at beginning of run -ok 150 - Get next_hap after beginning of run -ok 151 - Testing msout::outgroup -ok 152 - Get next_pop after beginning of pop -ok 153 - Get next_pop at beginning of pop -ok 154 - Get next_run after beginning of run -ok 155 - Get next_pop at beginning of run -ok 156 - Get next_hap after pop -ok 157 - Get next_run after pop and hap -ok 158 - Get next_run at beginning of run -ok 159 - have all lines been read? -ok 160 - An object of class 'Bio::SeqIO::msout' isa 'Bio::SeqIO::msout' -ok 161 - Caught error in bad msout file 1 -ok 162 - An object of class 'Bio::SeqIO::msout' isa 'Bio::SeqIO::msout' -ok 163 - Caught error in bad msout file 2 -ok 164 - threw Regexp ((?^:first argument needs to be a positive integer. argument supplied: -1)) -ok 165 - too few n_sites failed OK -ok -t/SeqIO/MultiFile.t ................. -1..5 -ok 1 - use Bio::SeqIO::MultiFile; -ok 2 -ok 3 -ok 4 -ok 5 -ok -t/SeqIO/Multiple_fasta.t ............ -1..9 -ok 1 - use Bio::SeqIO; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 - all sequences in the file -ok -t/SeqIO/phd.t ....................... -1..21 -ok 1 - use Bio::SeqIO::phd; -ok 2 - An object of class 'Bio::SeqIO::phd' isa 'Bio::SeqIO::phd' -ok 3 - Did you get the 'QUALITY_LEVELS' comment? -ok 4 - An object of class 'Bio::Seq::Quality' isa 'Bio::Seq::Quality' -ok 5 - An object of class 'Bio::SeqIO::phd' isa 'Bio::SeqIO::phd' -ok 6 -ok 7 - $seq->subseq() -ok 8 - $seq->subqual_tex() -ok 9 - $seq->subqual_tex() -ok 10 - $phd->chromat_file() -ok 11 - $phd->chromat_file() -ok 12 -ok 13 - $seq->subseq() -ok 14 - $seq->subqual_tex() -ok 15 - $seq->subqual_tex() -ok 16 -ok 17 - $seq->subseq() -ok 18 - $seq->subqual_tex() -ok 19 - $seq->subqual_tex() -ok 20 - An object of class 'Bio::SeqIO::phd' isa 'Bio::SeqIO::phd' -ok 21 -ok -t/SeqIO/pir.t ....................... -1..12 -ok 1 - use Bio::SeqIO::pir; -ok 2 - new instance is defined -ok 3 - An object of class 'Bio::SeqIO::pir' isa 'Bio::SeqIO' -ok 4 - checked length -ok 5 - checked length -ok 6 - checked length -ok 7 - checked length -ok 8 - checked length -ok 9 - checked length -ok 10 - Correct start -ok 11 - Correct start -ok 12 - Correct start -ok -t/SeqIO/qual.t ...................... -1..18 -ok 1 - use Bio::SeqIO; -ok 2 - use Bio::Seq::PrimaryQual; -ok 3 -ok 4 - An object of class 'Bio::Seq::PrimaryQual' isa 'Bio::Seq::PrimaryQual' -ok 5 -ok 6 - An object of class 'Bio::Seq::PrimaryQual' isa 'Bio::Seq::PrimaryQual' -ok 7 - An object of class 'Bio::Seq::PrimaryQual' isa 'Bio::Seq::PrimaryQual' -ok 8 - An object of class 'Bio::Seq::PrimaryQual' isa 'Bio::Seq::PrimaryQual' -ok 9 - An object of class 'Bio::Seq::PrimaryQual' isa 'Bio::Seq::PrimaryQual' -ok 10 - An object of class 'Bio::Seq::PrimaryQual' isa 'Bio::Seq::PrimaryQual' -ok 11 - An object of class 'Bio::Seq::PrimaryQual' isa 'Bio::Seq::PrimaryQual' -ok 12 - An object of class 'Bio::Seq::PrimaryQual' isa 'Bio::Seq::PrimaryQual' -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok -t/SeqIO/raw.t ....................... -1..25 -ok 1 - use Bio::SeqIO::raw; -ok 2 - An object of class 'Bio::SeqIO::raw' isa 'Bio::SeqIO' -ok 3 -ok 4 - Bio::SeqIO::raw->can('next_seq') -ok 5 - Bio::SeqIO::raw->can('write_seq') -ok 6 - An object of class 'Bio::Seq' isa 'Bio::Seq' -ok 7 - sequence -ok 8 - length -ok 9 - An object of class 'Bio::Seq' isa 'Bio::Seq' -ok 10 - sequence -ok 11 - length -ok 12 - use Algorithm::Diff; -ok 13 - raw format can round-trip -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok -t/SeqIO/scf.t ....................... -1..80 -ok 1 - use Bio::SeqIO::scf; -ok 2 - use Bio::Seq::SequenceTrace; -ok 3 -ok 4 - An object of class 'Bio::Seq::SequenceTrace' isa 'Bio::Seq::SequenceTrace' -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 - An object of class 'Bio::Seq::Quality' isa 'Bio::Seq::Quality' -ok 14 - An object of class 'Bio::Seq::Quality' isa 'Bio::Seq::Quality' -ok 15 - alphabet -ok 16 - display_id -ok 17 - primary_id is the stringified memory position -ok 18 - set primary_id -ok 19 - accession_number -ok 20 - desc -ok 21 - desc -ok 22 - id -ok 23 - id -ok 24 - seq -ok 25 - subseq -ok 26 - baseat -ok 27 - qualat -ok 28 - trace_value_at -not ok 29 - accuracies # TODO documentation and code for accuracies() do not match -# Failed (TODO) test 'accuracies' -# at t/SeqIO/scf.t line 77. -# got: 'ARRAY(0xaaab14ec0238)' -# expected: '482' -ok 30 -ok 31 - sub_peak_index -ok 32 - peak_index_at -ok 33 -ok 34 -ok 35 - An object of class 'Bio::Seq::SequenceTrace' isa 'Bio::Seq::SequenceTrace' -ok 36 - accuracy_at -ok 37 - An object of class 'Bio::Seq::SequenceTrace' isa 'Bio::Seq::SequenceTrace' -ok 38 -ok 39 -ok 40 -ok 41 - An object of class 'Bio::Annotation::Collection' isa 'Bio::Annotation::Collection' -ok 42 -ok 43 - An object of class 'Bio::Annotation::Collection' isa 'Bio::Annotation::Collection' -ok 44 -ok 45 -ok 46 - An object of class 'Bio::Annotation::Collection' isa 'Bio::Annotation::Collection' -ok 47 -ok 48 -ok 49 -ok 50 -ok 51 -ok 52 -ok 53 -ok 54 - An object of class 'Bio::Seq::SequenceTrace' isa 'Bio::Seq::SequenceTrace' -ok 55 - An object of class 'Bio::Annotation::Collection' isa 'Bio::Annotation::Collection' -ok 56 -ok 57 -ok 58 -ok 59 -ok 60 - An object of class 'Bio::Seq::SequenceTrace' isa 'Bio::Seq::SequenceTrace' -ok 61 -ok 62 - An object of class 'Bio::Seq::SequenceTrace' isa 'Bio::Seq::SequenceTrace' -ok 63 - qual scores match -ok 64 - An object of class 'Bio::Seq::SequenceTrace' isa 'Bio::Seq::SequenceTrace' -ok 65 -ok 66 - An object of class 'Bio::Seq::SequenceTrace' isa 'Bio::Seq::SequenceTrace' -not ok 67 - display_id matches # TODO display_id doesn't round trip yet -# Failed (TODO) test 'display_id matches' -# at t/SeqIO/scf.t line 284. -# got: 'ML4942R' -# expected: undef -ok 68 - qual scores match -ok 69 - An object of class 'Bio::Seq::SequenceTrace' isa 'Bio::Seq::SequenceTrace' -ok 70 -ok 71 - An object of class 'Bio::Seq::SequenceTrace' isa 'Bio::Seq::SequenceTrace' -not ok 72 - display_id matches # TODO display_id doesn't round trip yet -# Failed (TODO) test 'display_id matches' -# at t/SeqIO/scf.t line 284. -# got: 'IIABP1D4373' -# expected: undef -ok 73 - qual scores match -ok 74 - An object of class 'Bio::Seq::SequenceTrace' isa 'Bio::Seq::SequenceTrace' -ok 75 -ok 76 - An object of class 'Bio::Seq::SequenceTrace' isa 'Bio::Seq::SequenceTrace' -not ok 77 - display_id matches # TODO display_id doesn't round trip yet -# Failed (TODO) test 'display_id matches' -# at t/SeqIO/scf.t line 284. -# got: 'IIABP1D4373' -# expected: undef -ok 78 - qual scores match -ok 79 - Bio::Sequence::Quality matches -ok 80 - Bio::Sequence::Quality matches -ok -t/SeqIO/SeqBuilder.t ................ -1..137 -ok 1 - use Bio::SeqIO; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 - An object of class 'Bio::Seq::SeqBuilder' isa 'Bio::Factory::ObjectBuilderI' -ok 42 -ok 43 -ok 44 -ok 45 -ok 46 -ok 47 -ok 48 -ok 49 -ok 50 -ok 51 -ok 52 -ok 53 -ok 54 -ok 55 -ok 56 -ok 57 -ok 58 -ok 59 -ok 60 -ok 61 -ok 62 -ok 63 -ok 64 -ok 65 -ok 66 -ok 67 -ok 68 -ok 69 -ok 70 -ok 71 -ok 72 -ok 73 -ok 74 -ok 75 -ok 76 -ok 77 -ok 78 -ok 79 -ok 80 -ok 81 -ok 82 -ok 83 -ok 84 -ok 85 -ok 86 -ok 87 -ok 88 -ok 89 -ok 90 -ok 91 -ok 92 -ok 93 -ok 94 -ok 95 -ok 96 -ok 97 -ok 98 -ok 99 -ok 100 -ok 101 -ok 102 -ok 103 -ok 104 -ok 105 -ok 106 -ok 107 -ok 108 -ok 109 -ok 110 -ok 111 -ok 112 -ok 113 -ok 114 -ok 115 -ok 116 -ok 117 -ok 118 -ok 119 -ok 120 -ok 121 -ok 122 -ok 123 -ok 124 -ok 125 -ok 126 -ok 127 -ok 128 -ok 129 -ok 130 -ok 131 -ok 132 -ok 133 -ok 134 -ok 135 -ok 136 -ok 137 -ok -t/SeqIO/SeqIO.t ..................... -1..58 -ok 1 - use Bio::SeqIO; -ok 2 -ok 3 -ok 4 - ID for format gcg -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 - ID for format fasta -ok 11 -ok 12 -ok 13 -ok 14 - accession.version -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 - ID for format pir -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 - ID for format tab -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 - ID for format ace -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 - use Algorithm::Diff; -ok 43 - use IO::ScalarArray; -ok 44 - use IO::String; -ok 45 -ok 46 -ok 47 -ok 48 -ok 49 -ok 50 -ok 51 -ok 52 -ok 53 -ok 54 -not ok 55 - Must pass a file or file handle # TODO file/fh-based tests should be in Bio::Root::IO, see issue #3204 -# Failed (TODO) test 'Must pass a file or file handle' -# at t/SeqIO/SeqIO.t line 158. -# expecting: Regexp ((?^:No file, fh, or string argument provided)) -# found: Bio::Root::Exception ( -# ------------- EXCEPTION: Bio::Root::Exception ------------- -# MSG: Could not guess format from file, filehandle or string -# STACK: Error::throw -# STACK: Bio::Root::Root::throw /build/reproducible-path/bioperl-1.7.8/blib/lib/Bio/Root/Root.pm:449 -# STACK: Bio::SeqIO::new /build/reproducible-path/bioperl-1.7.8/blib/lib/Bio/SeqIO.pm:420 -# STACK: Test::Exception::throws_ok t/SeqIO/SeqIO.t:157 -# STACK: t/SeqIO/SeqIO.t:158 -# ----------------------------------------------------------- -# ) -ok 56 - Must pass a file or file handle -ok 57 - Must pass a file or file handle -ok 58 - Must pass a real file -ok -t/SeqIO/seqxml.t .................... -1..61 -ok 1 - use Bio::SeqIO; -ok 2 - use Bio::PrimarySeq; -ok 3 - use Bio::SeqIO::seqxml; -ok 4 - stream ok -ok 5 - seqXML version -ok 6 - source -ok 7 - source version -ok 8 - An object of class 'Bio::Seq' isa 'Bio::Seq' -ok 9 - display id -ok 10 - primary id -ok 11 - description -ok 12 - sequence -ok 13 - length -ok 14 - entry source -ok 15 - 'species' isa 'Bio::Species' -ok 16 - species name -ok 17 - NCBI tax id -ok 18 - An object of class 'Bio::Annotation::DBLink' isa 'Bio::Annotation::DBLink' -ok 19 - dblink source -ok 20 - dblink ID -ok 21 - An object of class 'Bio::Annotation::SimpleValue' isa 'Bio::Annotation::SimpleValue' -ok 22 - boolean property -ok 23 - An object of class 'Bio::Annotation::SimpleValue' isa 'Bio::Annotation::SimpleValue' -ok 24 - property with value -ok 25 - writer ok -ok 26 - outfile is created -ok 27 - seqXML version -ok 28 - source -ok 29 - source version -ok 30 - schemaLocation -ok 31 - An object of class 'Bio::Seq' isa 'Bio::Seq' -ok 32 - display id -ok 33 - primary id -ok 34 - description -ok 35 - sequence -ok 36 - length -ok 37 - entry source -ok 38 - 'species' isa 'Bio::Species' -ok 39 - species name -ok 40 - NCBI tax id -ok 41 - An object of class 'Bio::Annotation::DBLink' isa 'Bio::Annotation::DBLink' -ok 42 - dblink source -ok 43 - dblink ID -ok 44 - An object of class 'Bio::Annotation::SimpleValue' isa 'Bio::Annotation::SimpleValue' -ok 45 - property with value -ok 46 - An object of class 'Bio::Annotation::SimpleValue' isa 'Bio::Annotation::SimpleValue' -ok 47 - boolean property -ok 48 - outfile is created -ok 49 - seqXML version -ok 50 - source -ok 51 - source version -ok 52 - display id -ok 53 - primary id -ok 54 - description -ok 55 - sequence -ok 56 - length -ok 57 - display id -ok 58 - primary id -ok 59 - description -ok 60 - sequence -ok 61 - length -ok -t/SeqIO/Splicedseq.t ................ -1..27 -ok 1 - use Bio::Seq; -ok 2 - use Bio::SeqIO; -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 - get_SeqFeatures() -ok 14 - protein sequence -ok 15 - nucleotide sequence - correct CDS range -ok 16 - nucleotide length -ok 17 - appropriate warning if db not provided for remote sequence -ok 18 - correct number of Ns added if remote sequence not provided -ok 19 - cut by origin sequence using $feat->seq -ok 20 - cut by origin sequence using $feat->spliced_seq -ok 21 - cut by origin start using $feat->start -ok 22 - cut by origin end using $feat->end -ok 23 - cut by origin start using $feat->location->start -ok 24 - cut by origin end using $feat->location->end -ok 25 # skip The optional module Bio::DB::GenBank (or dependencies thereof) was not installed -ok 26 # skip The optional module Bio::DB::GenBank (or dependencies thereof) was not installed -ok 27 # skip The optional module Bio::DB::GenBank (or dependencies thereof) was not installed -ok -t/SeqIO/swiss.t ..................... -1..247 -ok 1 - use Bio::SeqIO::swiss; -ok 2 - An object of class 'Bio::SeqIO::swiss' isa 'Bio::SeqIO' -ok 3 - An object of class 'Bio::Species' isa 'Bio::Species' -ok 4 -ok 5 -ok 6 - operator overloading in AnnotationI is deprecated -ok 7 - dates -ok 8 - dates -ok 9 - dates -ok 10 -ok 11 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::Seq::RichSeqI' -ok 12 -ok 13 -ok 14 -ok 15 - operator overloading in AnnotationI is deprecated -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 - id is ROA1_HUMAN -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 - operator overloading in AnnotationI is deprecated -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::Seq::RichSeqI' -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 -ok 43 - operator overloading in AnnotationI is deprecated -ok 44 -ok 45 -ok 46 -ok 47 - GC1QBP -ok 48 - HABP1 -ok 49 - SF2P32 -ok 50 - C1QBP -ok 51 -ok 52 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::Seq::RichSeqI' -ok 53 -ok 54 -ok 55 -ok 56 -ok 57 -ok 58 -ok 59 - F54H12.1 -ok 60 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::Seq::RichSeqI' -ok 61 -ok 62 -ok 63 -ok 64 -ok 65 -ok 66 -ok 67 -ok 68 -ok 69 -ok 70 -ok 71 -ok 72 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::Seq::RichSeqI' -ok 73 -ok 74 -ok 75 -ok 76 -ok 77 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::Seq::RichSeqI' -ok 78 -ok 79 -ok 80 -ok 81 -ok 82 -ok 83 -ok 84 -ok 85 -ok 86 -ok 87 -ok 88 -ok 89 -ok 90 -ok 91 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::Seq::RichSeqI' -ok 92 -ok 93 -ok 94 -ok 95 -ok 96 -ok 97 -ok 98 -ok 99 -ok 100 -ok 101 -ok 102 -ok 103 -ok 104 -ok 105 -ok 106 -ok 107 -ok 108 -ok 109 -ok 110 -ok 111 -ok 112 -ok 113 -ok 114 -ok 115 -ok 116 -ok 117 -ok 118 -ok 119 -ok 120 -ok 121 -ok 122 -ok 123 -ok 124 -ok 125 -ok 126 -ok 127 -ok 128 -ok 129 -ok 130 -ok 131 -ok 132 -ok 133 -ok 134 -ok 135 -ok 136 -ok 137 -ok 138 -ok 139 -ok 140 -ok 141 -ok 142 -ok 143 -ok 144 -ok 145 -ok 146 -ok 147 -ok 148 -ok 149 -ok 150 -ok 151 -ok 152 -ok 153 -ok 154 -ok 155 -ok 156 -ok 157 -ok 158 -ok 159 -ok 160 -ok 161 -ok 162 -ok 163 -ok 164 -ok 165 -ok 166 -ok 167 -ok 168 -ok 169 -ok 170 -ok 171 -ok 172 -ok 173 -ok 174 -ok 175 - An object of class 'Bio::Species' isa 'Bio::Species' -ok 176 -ok 177 -ok 178 - operator overloading in AnnotationI is deprecated -ok 179 -ok 180 -ok 181 -ok 182 -ok 183 -ok 184 -ok 185 -ok 186 -ok 187 -ok 188 -ok 189 -ok 190 -ok 191 -ok 192 -ok 193 -ok 194 -ok 195 -ok 196 -ok 197 -ok 198 -ok 199 -ok 200 -ok 201 -ok 202 -ok 203 -ok 204 -ok 205 -ok 206 -ok 207 - An object of class 'Bio::Species' isa 'Bio::Species' -ok 208 -ok 209 -ok 210 - operator overloading in AnnotationI is deprecated -ok 211 -ok 212 -ok 213 -ok 214 -ok 215 -ok 216 -ok 217 -ok 218 -ok 219 -ok 220 -ok 221 -ok 222 -ok 223 -ok 224 -ok 225 -ok 226 -ok 227 -ok 228 -ok 229 -ok 230 -ok 231 -ok 232 -ok 233 -ok 234 -ok 235 -ok 236 -ok 237 -ok 238 -ok 239 -ok 240 -ok 241 - Converting to fasta seqids match -ok 242 - Converting to fasta sequences match -ok 243 - Can parse generated swiss -ok 244 - Roundtrip, seqids match -ok 245 - Roundtrip, sequences match -ok 246 -ok 247 -ok -t/SeqIO/tab.t ....................... -1..8 -ok 1 - use Bio::SeqIO::tab; -ok 2 - An object of class 'Bio::SeqIO::tab' isa 'Bio::SeqIO' -ok 3 - seq is defined -ok 4 - check seq length -ok 5 - check matching -ok 6 - seq is defined -ok 7 - check seq length -ok 8 - check matching -ok -t/SeqIO/table.t ..................... -1..351 -ok 1 - use Bio::Tools::CodonTable; -ok 2 - use Bio::SeqIO::table; -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 -ok 43 -ok 44 -ok 45 -ok 46 -ok 47 -ok 48 -ok 49 -ok 50 -ok 51 -ok 52 -ok 53 -ok 54 -ok 55 -ok 56 -ok 57 -ok 58 -ok 59 -ok 60 -ok 61 -ok 62 -ok 63 -ok 64 -ok 65 -ok 66 -ok 67 -ok 68 -ok 69 -ok 70 -ok 71 -ok 72 -ok 73 -ok 74 -ok 75 -ok 76 -ok 77 -ok 78 -ok 79 -ok 80 -ok 81 -ok 82 -ok 83 -ok 84 -ok 85 -ok 86 -ok 87 -ok 88 -ok 89 -ok 90 -ok 91 -ok 92 -ok 93 -ok 94 -ok 95 -ok 96 -ok 97 -ok 98 -ok 99 -ok 100 -ok 101 -ok 102 -ok 103 -ok 104 -ok 105 -ok 106 -ok 107 -ok 108 -ok 109 -ok 110 -ok 111 -ok 112 -ok 113 -ok 114 -ok 115 -ok 116 -ok 117 -ok 118 -ok 119 -ok 120 -ok 121 -ok 122 -ok 123 -ok 124 -ok 125 -ok 126 -ok 127 -ok 128 -ok 129 -ok 130 -ok 131 -ok 132 -ok 133 -ok 134 -ok 135 -ok 136 -ok 137 -ok 138 -ok 139 -ok 140 -ok 141 -ok 142 -ok 143 -ok 144 -ok 145 -ok 146 -ok 147 -ok 148 -ok 149 -ok 150 -ok 151 -ok 152 -ok 153 -ok 154 -ok 155 -ok 156 -ok 157 -ok 158 -ok 159 -ok 160 -ok 161 -ok 162 -ok 163 -ok 164 -ok 165 -ok 166 -ok 167 -ok 168 -ok 169 -ok 170 -ok 171 -ok 172 -ok 173 -ok 174 -ok 175 -ok 176 -ok 177 -ok 178 -ok 179 -ok 180 -ok 181 -ok 182 -ok 183 -ok 184 -ok 185 -ok 186 -ok 187 -ok 188 -ok 189 -ok 190 -ok 191 -ok 192 -ok 193 -ok 194 -ok 195 -ok 196 -ok 197 -ok 198 -ok 199 -ok 200 -ok 201 -ok 202 -ok 203 -ok 204 -ok 205 -ok 206 -ok 207 -ok 208 -ok 209 -ok 210 -ok 211 -ok 212 -ok 213 -ok 214 -ok 215 -ok 216 -ok 217 -ok 218 -ok 219 -ok 220 -ok 221 -ok 222 -ok 223 -ok 224 -ok 225 -ok 226 -ok 227 -ok 228 -ok 229 -ok 230 -ok 231 -ok 232 -ok 233 -ok 234 -ok 235 -ok 236 -ok 237 -ok 238 -ok 239 -ok 240 -ok 241 -ok 242 -ok 243 -ok 244 -ok 245 -ok 246 -ok 247 -ok 248 -ok 249 -ok 250 -ok 251 -ok 252 -ok 253 -ok 254 -ok 255 -ok 256 -ok 257 -ok 258 -ok 259 -ok 260 -ok 261 -ok 262 -ok 263 -ok 264 -ok 265 -ok 266 -ok 267 -ok 268 -ok 269 -ok 270 -ok 271 -ok 272 -ok 273 -ok 274 -ok 275 -ok 276 -ok 277 -ok 278 -ok 279 -ok 280 -ok 281 -ok 282 -ok 283 -ok 284 -ok 285 -ok 286 -ok 287 -ok 288 -ok 289 -ok 290 -ok 291 -ok 292 -ok 293 -ok 294 -ok 295 -ok 296 -ok 297 -ok 298 -ok 299 -ok 300 -ok 301 -ok 302 -ok 303 -ok 304 -ok 305 -ok 306 -ok 307 -ok 308 -ok 309 -ok 310 -ok 311 -ok 312 -ok 313 -ok 314 -ok 315 -ok 316 -ok 317 -ok 318 -ok 319 -ok 320 -ok 321 -ok 322 -ok 323 -ok 324 -ok 325 -ok 326 -ok 327 -ok 328 -ok 329 -ok 330 -ok 331 -ok 332 -ok 333 -ok 334 -ok 335 -ok 336 -ok 337 -ok 338 -ok 339 -ok 340 -ok 341 -ok 342 -ok 343 -ok 344 -ok 345 -ok 346 -ok 347 -ok 348 -ok 349 -ok 350 -ok 351 -ok -t/SeqIO/tigr.t ...................... -1..8 -ok 1 - use Bio::SeqIO::tigr; -not ok 2 # TODO & SKIP No tests for tigr format -- no sample file to test against -not ok 3 # TODO & SKIP No tests for tigr format -- no sample file to test against -not ok 4 # TODO & SKIP No tests for tigr format -- no sample file to test against -not ok 5 # TODO & SKIP No tests for tigr format -- no sample file to test against -not ok 6 # TODO & SKIP No tests for tigr format -- no sample file to test against -not ok 7 # TODO & SKIP No tests for tigr format -- no sample file to test against -not ok 8 # TODO & SKIP No tests for tigr format -- no sample file to test against -ok -t/SeqIO/tigrxml.t ................... -1..49 -ok 1 - use Bio::SeqIO::tigrxml; -ok 2 - An object of class 'Bio::SeqIO::tigrxml' isa 'Bio::SeqIO' -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 -ok 43 -ok 44 -ok 45 -ok 46 -ok 47 -ok 48 -ok 49 -ok -t/SeqIO/tinyseq.t ................... -1..16 -ok 1 - use Bio::SeqIO::tinyseq; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok -t/SeqTools/Backtranslate.t .......... -1..8 -ok 1 - use Bio::Tools::SeqPattern::Backtranslate; -ok 2 - Bio::Tools::SeqPattern::Backtranslate->can('_reverse_translate_motif') -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 - threw Regexp ((?^:syntax token)) -ok -t/SeqTools/CodonTable.t ............. -1..84 -ok 1 - use Bio::Tools::CodonTable; -ok 2 - use Bio::CodonUsage::IO; -ok 3 -ok 4 - An object of class 'Bio::Tools::CodonTable' isa 'Bio::Tools::CodonTable' -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 - is_start_codon, ATG -ok 35 - is_start_codon, GGH -ok 36 - is_start_codon, HTG -ok 37 - is_start_codon, CCC -ok 38 - is_ter_codon, U should map to T, UAG -ok 39 - is_ter_codon,TaG -ok 40 - is_ter_codon,TaR -ok 41 - is_ter_codon,tRa -ok 42 - is_ter_codon,ttA -ok 43 - is_ter_codon, ambiguous codons should fail, NNN -ok 44 - is_ter_codon, ambiguous codons should fail, TAN -ok 45 - is_ter_codon, incomplete codons should fail, CC -ok 46 -ok 47 -ok 48 -ok 49 -ok 50 -ok 51 -ok 52 -ok 53 -ok 54 -ok 55 -ok 56 -ok 57 -ok 58 -ok 59 -ok 60 -ok 61 -ok 62 -ok 63 -ok 64 -ok 65 -ok 66 -ok 67 -ok 68 -ok 69 -ok 70 -ok 71 -ok 72 -ok 73 -ok 74 -ok 75 -ok 76 -ok 77 -ok 78 -ok 79 -ok 80 -ok 81 -ok 82 -ok 83 -ok 84 -ok -t/SeqTools/ECnumber.t ............... -1..27 -ok 1 - use Bio::Tools::ECnumber; -ok 2 - An object of class 'Bio::Tools::ECnumber' isa 'Bio::Tools::ECnumber' -ok 3 - An object of class 'Bio::Tools::ECnumber' isa 'Bio::Tools::ECnumber' -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok -t/SeqTools/GuessSeqFormat.t ......... -1..105 -ok 1 - use Bio::Tools::GuessSeqFormat; -ok 2 - use Bio::SeqIO; -ok 3 - use Bio::AlignIO; -ok 4 -ok 5 - An object of class 'Bio::Tools::GuessSeqFormat' isa 'Bio::Tools::GuessSeqFormat' -ok 6 - File input -ok 7 -ok 8 - String input -ok 9 -ok 10 - Filehandle input -ok 11 -ok 12 - Unknown file format -ok 13 - threw Regexp ((?^:Could not guess format)) -ok 14 - ace format -ok 15 -ok 16 -ok 17 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeqI' -ok 18 - embl format -ok 19 -ok 20 -ok 21 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::PrimarySeqI' -ok 22 - fasta format -ok 23 -ok 24 -ok 25 - An object of class 'Bio::Seq' isa 'Bio::PrimarySeqI' -ok 26 - fastq format -ok 27 -ok 28 -ok 29 - An object of class 'Bio::Seq::Quality' isa 'Bio::PrimarySeqI' -ok 30 - game format -ok 31 -ok 32 -ok 33 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::PrimarySeqI' -ok 34 - gcg format -ok 35 -ok 36 -ok 37 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::PrimarySeqI' -ok 38 - genbank format -ok 39 -ok 40 -ok 41 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::PrimarySeqI' -ok 42 - pir format -ok 43 -ok 44 -ok 45 - An object of class 'Bio::Seq' isa 'Bio::PrimarySeqI' -ok 46 - raw format -ok 47 -ok 48 -ok 49 - An object of class 'Bio::Seq' isa 'Bio::PrimarySeqI' -ok 50 - swiss format -ok 51 -ok 52 -ok 53 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::PrimarySeqI' -ok 54 - tab format -ok 55 -ok 56 -ok 57 - An object of class 'Bio::Seq' isa 'Bio::PrimarySeqI' -ok 58 # skip The optional module Bio::AlignIO::stockholm (or dependencies thereof) was not installed -ok 59 # skip The optional module Bio::AlignIO::stockholm (or dependencies thereof) was not installed -ok 60 # skip The optional module Bio::AlignIO::stockholm (or dependencies thereof) was not installed -ok 61 # skip The optional module Bio::AlignIO::stockholm (or dependencies thereof) was not installed -ok 62 - clustalw format -ok 63 -ok 64 -ok 65 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 66 - fasta format -ok 67 -ok 68 -ok 69 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 70 - fastq format -ok 71 - mase format -ok 72 -ok 73 -ok 74 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 75 - mega format -ok 76 -ok 77 -ok 78 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 79 - msf format -ok 80 -ok 81 -ok 82 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 83 - nexus format -ok 84 -ok 85 -ok 86 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 87 - pfam format -ok 88 -ok 89 -ok 90 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 91 - phylip format -ok 92 -ok 93 -ok 94 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 95 - prodom format -ok 96 -ok 97 -ok 98 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 99 - selex format -ok 100 -ok 101 -ok 102 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' -ok 103 - blast format -ok 104 - vcf format -ok 105 - gcgblast format -ok -t/SeqTools/OddCodes.t ............... -1..11 -ok 1 - use Bio::PrimarySeq; -ok 2 - use Bio::Tools::OddCodes; -ok 3 - An object of class 'Bio::Tools::OddCodes' isa 'Bio::Tools::OddCodes' -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok -t/SeqTools/SeqPattern.t ............. -1..28 -ok 1 - use Bio::Tools::SeqPattern; -ok 2 -ok 3 - An object of class 'Bio::Tools::SeqPattern' isa 'Bio::Tools::SeqPattern' -ok 4 -ok 5 -ok 6 -ok 7 - An object of class 'Bio::Tools::SeqPattern' isa 'Bio::Tools::SeqPattern' -ok 8 -ok 9 -ok 10 - An object of class 'Bio::Tools::SeqPattern' isa 'Bio::Tools::SeqPattern' -ok 11 -ok 12 - threw Regexp ((?^:revcom for .+ sequence types)) -ok 13 - threw Regexp ((?^:backtranslate for .+ sequence types)) -ok 14 - An object of class 'Bio::Tools::SeqPattern' isa 'Bio::Tools::SeqPattern' -ok 15 - An object of class 'Bio::Tools::SeqPattern' isa 'Bio::Tools::SeqPattern' -ok 16 -ok 17 - An object of class 'Bio::Tools::SeqPattern' isa 'Bio::Tools::SeqPattern' -ok 18 - An object of class 'Bio::Tools::SeqPattern' isa 'Bio::Tools::SeqPattern' -ok 19 -ok 20 - An object of class 'Bio::Tools::SeqPattern' isa 'Bio::Tools::SeqPattern' -ok 21 - An object of class 'Bio::Tools::SeqPattern' isa 'Bio::Tools::SeqPattern' -ok 22 -ok 23 - An object of class 'Bio::Tools::SeqPattern' isa 'Bio::Tools::SeqPattern' -ok 24 - An object of class 'Bio::Tools::SeqPattern' isa 'Bio::Tools::SeqPattern' -ok 25 -ok 26 - An object of class 'Bio::Tools::SeqPattern' isa 'Bio::Tools::SeqPattern' -ok 27 - An object of class 'Bio::Tools::SeqPattern' isa 'Bio::Tools::SeqPattern' -ok 28 -ok -t/SeqTools/SeqStats.t ............... -1..47 -ok 1 - use Bio::SeqIO; -ok 2 - use Bio::Tools::SeqStats; -ok 3 - new Bio::Root::IO object -ok 4 - new Bio::Tools:SeqStats object -ok 5 - count_monomers() -ok 6 - count_codons() -ok 7 - get_mol_wt() -ok 8 -ok 9 - An object of class 'Bio::Tools::SeqStats' isa 'Bio::Tools::SeqStats' -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 -ok 43 -ok 44 -ok 45 -ok 46 -ok 47 -ok -t/SeqTools/SeqUtils.t ............... -1..133 -ok 1 - use Bio::PrimarySeq; -ok 2 - use Bio::SeqUtils; -ok 3 - use Bio::SeqFeature::Generic; -ok 4 - use Bio::Annotation::SimpleValue; -ok 5 - use Bio::Annotation::Collection; -ok 6 - use Bio::Annotation::Comment; -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 # skip The optional module Bio::LiveSeq::Mutation (or dependencies thereof) was not installed -ok 25 # skip The optional module Bio::LiveSeq::Mutation (or dependencies thereof) was not installed -ok 26 # skip The optional module Bio::LiveSeq::Mutation (or dependencies thereof) was not installed -ok 27 # skip The optional module Bio::LiveSeq::Mutation (or dependencies thereof) was not installed -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 - cat - has expected tags -ok 37 - cat - has expected tag values -ok 38 - cat - note tag transfered (no throw) -ok 39 - cat - note tag values transfered (correct count) -ok 40 - get correct start of feature before 'cat' -ok 41 - get correct start of feature after 'cat' -ok 42 - different alphabets -ok 43 -ok 44 -ok 45 -ok 46 -ok 47 -ok 48 - trunc_with_features - has expected tags -ok 49 - trunc_with_features - has expected tag values -ok 50 -ok 51 - primary_tag matches original feature... -ok 52 - but tagged sf is now revcom -ok 53 - primary_tag matches original feature... -ok 54 - but tagged sf is now revcom -ok 55 - primary_tag matches original feature... -ok 56 - but tagged sf is now revcom -ok 57 - revcom_with_features - has expected tags -ok 58 - revcom_with_features - has expected tag values -ok 59 - still not circular -ok 60 - still circular -ok 61 - No error thrown when deleting a segment of the sequence -ok 62 - annotation of whole sequence has been moved to new molecule -ok 63 - the product has an additional 'misc_feature' and the note specifies the lengths of the deletion' -ok 64 - The composite feature is still present -ok 65 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' -ok 66 - 'a composite feature that spanned the deletion site has been split up, Location' isa 'Bio::Location::Split' -ok 67 - one of the sub-eatures of the composite feature has been deleted completely -ok 68 - sub-feature 1 of the composite feature is still present -ok 69 - the original end of sf1 is 12 -ok 70 - after deletion, the end of sf1 is 1nt before the deletion site -ok 71 - the original end location of sf1 EXACT -ok 72 - annotation of subeature 1 has been moved to new molecule -ok 73 - feature1 is till present -ok 74 - 'feature1 location has now been split by the deletion and location object' isa 'Bio::Location::Split' -ok 75 - feature1 has two locations after the deletion -ok 76 - feature1 start is unaffected by the deletion -ok 77 - feature1 end of first split is 1nt before deletion site -ok 78 - feature1 start of second split is 1nt after deletion site -ok 79 - feature1 end of second split has been adjusted correctly -ok 80 - split feature now has a note -ok 81 - got the expected note about length and position of deletion -ok 82 - feature3 is till present -ok 83 - a feature downstream of the deletion site is shifted entirely by 10nt to the left -ok 84 - feature4 is till present -ok 85 - a feature upstream of the deletion site is not repositioned by the deletion -ok 86 - feature2 is till present -ok 87 - start pos of a feature that started in the deletion site has been altered accordingly -ok 88 - feature 2 now has a note -ok 89 - note added to feature2 about deletion at 3' end -ok 90 - a feature that was completely positioned inside the deletion site is not present on the new molecule -ok 91 - feature6 is till present -ok 92 - start pos of a feature that started in the deletion site has been altered accordingly -ok 93 - end pos of a feature that started in the deletion site has been altered accordingly -ok 94 - No error thrown when inserting a fragment into recipient sequence -ok 95 - annotation of whole sequence has been moved to new molecule -ok 96 - The composite feature is still present -ok 97 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' -ok 98 - 'a composite feature that spanned the insertion site has been split up, Location' isa 'Bio::Location::Split' -ok 99 - all of the parts of the composite feature are still present -ok 100 - sub-feature 1 of the composite feature is still present -ok 101 - the original end of sf1 is 12 -ok 102 - after insertion, the end of sf1 has been shifted by the length of the insertion -ok 103 - 'sub-feature 1 (spans insertion site) is now split up and' isa 'Bio::Location::Split' -ok 104 - the start and end position types of sub-feature1 have not changed -ok 105 - annotation of subeature 1 has been moved to new molecule -ok 106 - split feature now has a note -ok 107 - got the expected note about length and position of insertion -ok 108 - feature3 is till present -ok 109 - a feature downstream of the insertion site is shifted entirely to the left by the length of the insertion -ok 110 - feature4 is till present -ok 111 - a feature upstream of the insertion site is not repositioned -ok 112 - a feature on the inserted fragment is present on the product molecule -ok 113 - position of the feature on the insert has been adjusted to product coordinates -ok 114 - strand of the feature on insert has not changed -ok 115 - desctription of the product contains description of the fragment -ok 116 - desctription of the product contains description of the recipient -ok 117 - the product has an additional 'misc_feature' with note='inserted fragment' -ok 118 - No error thrown using 'ligate' of fragment into recipient -ok 119 - product has the expected length -ok 120 - the sequence of the fragment is inserted into the product -ok 121 - we have a feature annotating the ligated fragment -ok 122 - coordinates of the feature annotating the ligated feature are correct -ok 123 - the fragment feature1 is now a feature of the product -ok 124 - start and end of a feature on the fragment are correct after insertion with "flip" option -ok 125 - Trying to delete from an object of a custom Bio::Seq subclass that doesn't allow calling 'new' throws an error -ok 126 - Deleting from Bio::Seq::Foo does not throw an error when using the 'clone_obj' option to clone instead of calling 'new' -ok 127 - An object of class 'Bio::Seq::Foo' isa 'Bio::Seq::Foo' -ok 128 - the product has an additional 'misc_feature' and the note specifies the lengths of the deletion' -ok 129 - The composite feature is still present -ok 130 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' -ok 131 - 'a composite feature that spanned the deletion site has been split up, Location' isa 'Bio::Location::Split' -ok 132 - 'ligate' without clone_obj option dies with a Bio::Seq::Foo object that can't call new -ok 133 - 'ligate' with clone_obj option works with a Bio::Seq::Foo object that can't call new -ok -t/SeqTools/SeqWords.t ............... -1..22 -ok 1 - use Bio::SeqIO; -ok 2 - use Bio::Tools::SeqWords; -ok 3 - new Bio::Root::IO object -ok 4 - new Bio::Tools::SeqWords object -ok 5 - count_words -ok 6 -ok 7 - An object of class 'Bio::Tools::SeqWords' isa 'Bio::Tools::SeqWords' -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 - An object of class 'Bio::Tools::SeqWords' isa 'Bio::Tools::SeqWords' -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok -t/Species.t ......................... -1..27 -ok 1 - use Bio::Species; -ok 2 - use Bio::DB::Taxonomy; -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 # skip The optional module Bio::DB::Taxonomy::entrez (or dependencies thereof) was not installed -ok 18 # skip The optional module Bio::DB::Taxonomy::entrez (or dependencies thereof) was not installed -ok 19 # skip The optional module Bio::DB::Taxonomy::entrez (or dependencies thereof) was not installed -ok 20 # skip The optional module Bio::DB::Taxonomy::entrez (or dependencies thereof) was not installed -ok 21 # skip The optional module Bio::DB::Taxonomy::entrez (or dependencies thereof) was not installed -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok -t/Tools/Alignment/Consed.t .......... -1..15 -ok 1 - use Bio::Tools::Alignment::Consed; -ok 2 - new CSM::Consed object was created -ok 3 - An object of class 'Bio::Tools::Alignment::Consed' isa 'Bio::Tools::Alignment::Consed' -ok 4 - singlets can be successfully set -ok 5 - singlets can be retrieved -ok 6 - doublets can be set -ok 7 - doublets can be retreived -ok 8 - doublets can be retrieved -ok 9 - pairs can be retrieved -ok 10 - multiplets can be retrieved -ok 11 - singletons can be retrieved -ok 12 - how many sequences there are in the acefile _and_ in the singlets file -ok 13 - statistics from the Bio::Tools::Alignment::Consed object to compare the total number of sequences accounted for there to the number of sequences found via grep -ok 14 -ok 15 -ok -t/Tools/AmpliconSearch.t ............ -1..185 -ok 1 - use Bio::PrimarySeq; -ok 2 - use Bio::SeqFeature::Primer; -ok 3 - use Bio::Tools::AmpliconSearch; -ok 4 - Basic -ok 5 - An object of class 'Bio::Tools::AmpliconSearch' isa 'Bio::Tools::AmpliconSearch' -ok 6 - Forward primer only -ok 7 -ok 8 -ok 9 -ok 10 - An object of class 'Bio::Seq' isa 'Bio::Seq' -ok 11 -ok 12 -ok 13 - An object of class 'Bio::SeqFeature::Amplicon' isa 'Bio::SeqFeature::Amplicon' -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 - Reverse primer only -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 - An object of class 'Bio::SeqFeature::Amplicon' isa 'Bio::SeqFeature::Amplicon' -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 - Two primers, no match -ok 39 -ok 40 -ok 41 -ok 42 -ok 43 - Two degenerate primers from a file -ok 44 -ok 45 -ok 46 -ok 47 -ok 48 - An object of class 'Bio::SeqFeature::Amplicon' isa 'Bio::SeqFeature::Amplicon' -ok 49 -ok 50 -ok 51 -ok 52 -ok 53 -ok 54 - RNA template -ok 55 -ok 56 -ok 57 -ok 58 -ok 59 - An object of class 'Bio::SeqFeature::Amplicon' isa 'Bio::SeqFeature::Amplicon' -ok 60 -ok 61 -ok 62 -ok 63 -ok 64 -ok 65 - Forward primer from file -ok 66 -ok 67 -ok 68 -ok 69 -ok 70 - An object of class 'Bio::Seq' isa 'Bio::Seq' -ok 71 -ok 72 -ok 73 - An object of class 'Bio::SeqFeature::Amplicon' isa 'Bio::SeqFeature::Amplicon' -ok 74 -ok 75 -ok 76 -ok 77 -ok 78 -ok 79 - Multiple amplicons -ok 80 -ok 81 - An object of class 'Bio::SeqFeature::Amplicon' isa 'Bio::SeqFeature::Amplicon' -ok 82 -ok 83 -ok 84 -ok 85 -ok 86 -ok 87 - An object of class 'Bio::SeqFeature::Amplicon' isa 'Bio::SeqFeature::Amplicon' -ok 88 -ok 89 -ok 90 -ok 91 -ok 92 -ok 93 - Amplicon on reverse strand -ok 94 -ok 95 - An object of class 'Bio::SeqFeature::Amplicon' isa 'Bio::SeqFeature::Amplicon' -ok 96 -ok 97 -ok 98 -ok 99 -ok 100 -ok 101 - An object of class 'Bio::SeqFeature::Amplicon' isa 'Bio::SeqFeature::Amplicon' -ok 102 -ok 103 -ok 104 -ok 105 -ok 106 -ok 107 - Overlapping amplicons (1) -ok 108 -ok 109 - An object of class 'Bio::SeqFeature::Amplicon' isa 'Bio::SeqFeature::Amplicon' -ok 110 -ok 111 -ok 112 -ok 113 -ok 114 -ok 115 - Overlapping amplicons (2) -ok 116 -ok 117 - An object of class 'Bio::SeqFeature::Amplicon' isa 'Bio::SeqFeature::Amplicon' -ok 118 -ok 119 -ok 120 -ok 121 -ok 122 -ok 123 - Overlapping amplicons (3) -ok 124 -ok 125 - An object of class 'Bio::SeqFeature::Amplicon' isa 'Bio::SeqFeature::Amplicon' -ok 126 -ok 127 -ok 128 -ok 129 -ok 130 -ok 131 - Amplicons on both strands -ok 132 -ok 133 - An object of class 'Bio::SeqFeature::Amplicon' isa 'Bio::SeqFeature::Amplicon' -ok 134 -ok 135 -ok 136 -ok 137 -ok 138 -ok 139 - An object of class 'Bio::SeqFeature::Amplicon' isa 'Bio::SeqFeature::Amplicon' -ok 140 -ok 141 -ok 142 -ok 143 -ok 144 -ok 145 - Overlapping amplicons on both strands -ok 146 -ok 147 - An object of class 'Bio::SeqFeature::Amplicon' isa 'Bio::SeqFeature::Amplicon' -ok 148 -ok 149 -ok 150 -ok 151 -ok 152 -ok 153 - Annotated template -ok 154 -ok 155 - An object of class 'Bio::Seq' isa 'Bio::Seq' -ok 156 - An object of class 'Bio::SeqFeature::Amplicon' isa 'Bio::SeqFeature::Amplicon' -ok 157 - An object of class 'Bio::SeqFeature::Amplicon' isa 'Bio::SeqFeature::Amplicon' -ok 158 -ok 159 -ok 160 - Update primers -ok 161 -ok 162 -ok 163 -ok 164 -ok 165 -ok 166 -ok 167 -ok 168 -ok 169 -ok 170 -ok 171 -ok 172 -ok 173 -ok 174 -ok 175 - Update template -ok 176 -ok 177 -ok 178 -ok 179 -ok 180 -ok 181 -ok 182 -ok 183 -ok 184 -ok 185 -ok -t/Tools/EMBOSS/Palindrome.t ......... -1..13 -ok 1 - use Bio::Tools::EMBOSS::Palindrome; -ok 2 - use Bio::Tools::GFF; -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok -t/Tools/ePCR.t ...................... -1..27 -ok 1 - use Bio::Tools::EPCR; -ok 2 - use Bio::SeqIO; -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 - got 3 forward strand ePCR hits -ok 27 - got 3 reverse strand ePCR hits -ok -t/Tools/Est2Genome.t ................ -1..61 -ok 1 - use Bio::Tools::Est2Genome; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 -ok 43 -ok 44 -ok 45 -ok 46 -ok 47 -ok 48 -ok 49 -ok 50 -ok 51 -ok 52 -ok 53 -ok 54 -ok 55 -ok 56 -ok 57 -ok 58 -ok 59 -ok 60 -ok 61 -ok -t/Tools/FootPrinter.t ............... -1..27 -ok 1 - use Bio::Tools::FootPrinter; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok -t/Tools/Geneid.t .................... -1..26 -ok 1 - use Bio::Tools::Geneid; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok -t/Tools/Genewise.t .................. -1..33 -ok 1 - use Bio::Tools::Genewise; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok -t/Tools/Genomewise.t ................ -1..21 -ok 1 - use Bio::Tools::Genomewise; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok -t/Tools/Genpred.t ................... -1..185 -ok 1 - use Bio::Tools::Fgenesh; -ok 2 - use Bio::Tools::Genscan; -ok 3 - use Bio::Tools::Genemark; -ok 4 - use Bio::Tools::Glimmer; -ok 5 - use Bio::Tools::MZEF; -ok 6 - use Bio::SeqIO; -ok 7 -ok 8 -ok 9 -ok 10 - strand match (-1 and -1) -ok 11 - score match (1.05 and 1.05) -ok 12 -ok 13 - predicted and extracted protein seqs match -ok 14 - strand match (1 and 1) -ok 15 - score match (4.46 and 4.46) -ok 16 -ok 17 - predicted and extracted protein seqs match -ok 18 - initial exons 0 -ok 19 - score match 1.74 -ok 20 -ok 21 - predicted and extracted protein seqs match -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 - Genemark tests -ok 43 -ok 44 -ok 45 -ok 46 - An object of class 'Bio::Location::Fuzzy' isa 'Bio::Location::Fuzzy' -ok 47 -ok 48 -ok 49 -ok 50 -ok 51 -ok 52 -ok 53 -ok 54 -ok 55 - An object of class 'Bio::Location::Fuzzy' isa 'Bio::Location::Fuzzy' -ok 56 -ok 57 -ok 58 -ok 59 -ok 60 -ok 61 -ok 62 -ok 63 -ok 64 -ok 65 -ok 66 -ok 67 -ok 68 -ok 69 -ok 70 -ok 71 -ok 72 -ok 73 -ok 74 -ok 75 -ok 76 -ok 77 -ok 78 -ok 79 -ok 80 -ok 81 -ok 82 -ok 83 -ok 84 -ok 85 -ok 86 -ok 87 -ok 88 -ok 89 -ok 90 -ok 91 -ok 92 -ok 93 -ok 94 -ok 95 -ok 96 -ok 97 -ok 98 -ok 99 -ok 100 -ok 101 -ok 102 -ok 103 -ok 104 -ok 105 -ok 106 -ok 107 -ok 108 -ok 109 -ok 110 -ok 111 -ok 112 -ok 113 -ok 114 -ok 115 -ok 116 -ok 117 -ok 118 -ok 119 -ok 120 -ok 121 -ok 122 -ok 123 -ok 124 -ok 125 -ok 126 - An object of class 'Bio::Location::Split' isa 'Bio::Location::SplitLocationI' -ok 127 -ok 128 -ok 129 -ok 130 -ok 131 -ok 132 -ok 133 -ok 134 -ok 135 -ok 136 -ok 137 -ok 138 -ok 139 -ok 140 - An object of class 'Bio::Location::Split' isa 'Bio::Location::SplitLocationI' -ok 141 -ok 142 -ok 143 -ok 144 -ok 145 -ok 146 -ok 147 -ok 148 -ok 149 -ok 150 -ok 151 -ok 152 -ok 153 -ok 154 -ok 155 - An object of class 'Bio::Location::Fuzzy' isa 'Bio::Location::Fuzzy' -ok 156 -ok 157 -ok 158 -ok 159 -ok 160 -ok 161 - An object of class 'Bio::Location::Fuzzy' isa 'Bio::Location::Fuzzy' -ok 162 -ok 163 -ok 164 -ok 165 -ok 166 -ok 167 -ok 168 -ok 169 -ok 170 -ok 171 -ok 172 -ok 173 -ok 174 -ok 175 -ok 176 -ok 177 -ok 178 -ok 179 -ok 180 -ok 181 -ok 182 -ok 183 -ok 184 -ok 185 -ok -t/Tools/GFF.t ....................... -1..34 -ok 1 - use Bio::Tools::GFF; -ok 2 - use Bio::SeqFeature::Generic; -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok -t/Tools/IUPAC.t ..................... -1..46 -ok 1 - use Bio::Tools::IUPAC; -ok 2 - use Bio::Seq; -ok 3 - use Bio::PrimarySeq; -ok 4 -ok 5 -ok 6 - Regexp -ok 7 -ok 8 - Regexp -ok 9 - Count -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 - Regexp matches ambiguous sequences -ok 28 -ok 29 - Nucleic IUPAC -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 - Proteic IUPAC -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 -ok 43 -ok 44 -ok 45 -ok 46 -ok -t/Tools/Lucy.t ...................... -1..22 -ok 1 - use Bio::Tools::Lucy; -ok 2 - An object of class 'Bio::Tools::Lucy' isa 'Bio::Tools::Lucy' -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok -t/Tools/Match.t ..................... -1..38 -ok 1 - use Bio::Tools::Match; -ok 2 -ok 3 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' -ok 4 - correct source -ok 5 - feature start correct -ok 6 - feature end correct -ok 7 - feature core score correct -ok 8 - feature matrix score correct -ok 9 - feature matrix id correct -ok 10 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' -ok 11 - correct source -ok 12 - feature start correct -ok 13 - feature end correct -ok 14 - feature core score correct -ok 15 - feature matrix score correct -ok 16 - feature matrix id correct -ok 17 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' -ok 18 - correct source -ok 19 - feature start correct -ok 20 - feature end correct -ok 21 - feature core score correct -ok 22 - feature matrix score correct -ok 23 - feature matrix id correct -ok 24 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' -ok 25 - correct source -ok 26 - feature start correct -ok 27 - feature end correct -ok 28 - feature core score correct -ok 29 - feature matrix score correct -ok 30 - feature matrix id correct -ok 31 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' -ok 32 - correct source -ok 33 - feature start correct -ok 34 - feature end correct -ok 35 - feature core score correct -ok 36 - feature matrix score correct -ok 37 - feature matrix id correct -ok 38 - correct number of results managed to get tested -ok -t/Tools/Phylo/Gerp.t ................ -1..33 -ok 1 - use Bio::Tools::Phylo::Gerp; -ok 2 -ok 3 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' -ok 4 - correct source -ok 5 - feature start correct -ok 6 - feature end correct -ok 7 - feature score correct -ok 8 - feature pvalue correct -ok 9 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' -ok 10 - correct source -ok 11 - feature start correct -ok 12 - feature end correct -ok 13 - feature score correct -ok 14 - feature pvalue correct -ok 15 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' -ok 16 - correct source -ok 17 - feature start correct -ok 18 - feature end correct -ok 19 - feature score correct -ok 20 - feature pvalue correct -ok 21 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' -ok 22 - correct source -ok 23 - feature start correct -ok 24 - feature end correct -ok 25 - feature score correct -ok 26 - feature pvalue correct -ok 27 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' -ok 28 - correct source -ok 29 - feature start correct -ok 30 - feature end correct -ok 31 - feature score correct -ok 32 - feature pvalue correct -ok 33 - correct number of results parsed out -ok -t/Tools/Phylo/Molphy.t .............. -1..18 -ok 1 - use Bio::Tools::Phylo::Molphy; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok -t/Tools/Phylo/Phylip/ProtDist.t ..... -1..47 -ok 1 - use Bio::Tools::Phylo::Phylip::ProtDist; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 -ok 43 -ok 44 -ok 45 -ok 46 -ok 47 -ok -t/Tools/pICalculator.t .............. -1..38 -ok 1 - use Bio::Seq; -ok 2 - use Bio::Tools::pICalculator; -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok -t/Tools/Primer3.t ................... -1..14 -ok 1 - use Bio::Tools::Primer3; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 - An object of class 'Bio::Seq::PrimedSeq' isa 'Bio::Seq::PrimedSeq' -ok 11 -ok 12 -ok 13 -ok 14 - bug 2862 -ok -t/Tools/Promoterwise.t .............. -1..7 -ok 1 - use Bio::Tools::Promoterwise; -ok 2 - An object of class 'Bio::Tools::Promoterwise' isa 'Bio::Tools::Promoterwise' -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok -t/Tools/PrositeScan.t ............... -1..3 -ok 1 - use Bio::Tools::PrositeScan; -ok 2 - use Bio::SeqFeature::FeaturePair; -# Subtest: Predictions - ok 1 - Comparing parsed prediction input - 1..1 -ok 3 - Predictions -ok -t/Tools/Pseudowise.t ................ -1..21 -ok 1 - use Bio::Tools::Pseudowise; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok -t/Tools/QRNA.t ...................... -1..30 -ok 1 - use Bio::Tools::QRNA; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok -t/Tools/RandDistFunctions.t ......... -1..5 -ok 1 - use Bio::Tools::RandomDistFunctions; -ok 2 -ok 3 -ok 4 -ok 5 -ok -t/Tools/RepeatMasker.t .............. -1..28 -ok 1 - use Bio::Tools::RepeatMasker; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok -t/Tools/Seg.t ....................... -1..15 -ok 1 - use Bio::Tools::Seg; -ok 2 - parser defined -ok 3 -ok 4 - seq id for seq 0 identified -ok 5 - start for seq 0 identified -ok 6 - end for seq 0 identified -ok 7 - score for seq 0 identified -ok 8 - seq id for seq 1 identified -ok 9 - start for seq 1 identified -ok 10 - end for seq 1 identified -ok 11 - score for seq 1 identified -ok 12 - seq id for seq 2 identified -ok 13 - start for seq 2 identified -ok 14 - end for seq 2 identified -ok 15 - score for seq 2 identified -ok -t/Tools/Sigcleave.t ................. -1..18 -ok 1 - use Bio::PrimarySeq; -ok 2 - use Bio::Tools::Sigcleave; -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 - unable to get raw sigcleave results -ok 16 -ok 17 - unable to get raw sigcleave results -ok 18 -ok -t/Tools/Signalp.t ................... -1..11 -ok 1 - use Bio::Tools::Signalp; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok -t/Tools/Signalp/ExtendedSignalp.t ... -1..185 -ok 1 - use Bio::Tools::Signalp::ExtendedSignalp; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok 39 -ok 40 -ok 41 -ok 42 -ok 43 -ok 44 -ok 45 -ok 46 -ok 47 -ok 48 -ok 49 -ok 50 -ok 51 -ok 52 -ok 53 -ok 54 -ok 55 -ok 56 -ok 57 -ok 58 -ok 59 -ok 60 -ok 61 -ok 62 -ok 63 -ok 64 -ok 65 -ok 66 -ok 67 -ok 68 -ok 69 -ok 70 -ok 71 -ok 72 -ok 73 -ok 74 -ok 75 -ok 76 -ok 77 -ok 78 -ok 79 -ok 80 -ok 81 -ok 82 -ok 83 -ok 84 -ok 85 -ok 86 -ok 87 -ok 88 -ok 89 -ok 90 -ok 91 -ok 92 -ok 93 -ok 94 -ok 95 -ok 96 -ok 97 -ok 98 -ok 99 -ok 100 -ok 101 -ok 102 -ok 103 -ok 104 -ok 105 -ok 106 -ok 107 -ok 108 -ok 109 -ok 110 -ok 111 -ok 112 -ok 113 -ok 114 -ok 115 -ok 116 -ok 117 -ok 118 -ok 119 -ok 120 -ok 121 -ok 122 -ok 123 -ok 124 -ok 125 -ok 126 -ok 127 -ok 128 -ok 129 -ok 130 -ok 131 -ok 132 -ok 133 -ok 134 -ok 135 -ok 136 -ok 137 -ok 138 -ok 139 -ok 140 -ok 141 -ok 142 -ok 143 -ok 144 -ok 145 -ok 146 -ok 147 -ok 148 -ok 149 -ok 150 -ok 151 -ok 152 -ok 153 -ok 154 -ok 155 -ok 156 -ok 157 -ok 158 -ok 159 -ok 160 -ok 161 -ok 162 -ok 163 -ok 164 -ok 165 -ok 166 -ok 167 -ok 168 -ok 169 -ok 170 -ok 171 -ok 172 -ok 173 -ok 174 -ok 175 -ok 176 -ok 177 -ok 178 -ok 179 -ok 180 -ok 181 -ok 182 -ok 183 -ok 184 -ok 185 -ok -t/Tools/Sim4.t ...................... -1..27 -ok 1 - use Bio::Tools::Sim4::Results; -ok 2 - new Sim4 results instance -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 - new Sim4 results instance -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok -t/Tools/Spidey/Spidey.t ............. -1..26 -ok 1 - use Bio::Tools::Spidey::Results; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok -t/Tools/TandemRepeatsFinder.t ....... -1..66 -ok 1 - use Bio::Tools::TandemRepeatsFinder; -ok 2 - Parser created successfully -ok 3 - empty results file correctly returns no results -ok 4 - Second parser created successfully -ok 5 - seq_id for first result correctly parsed -ok 6 - start for first result correctly parsed -ok 7 - end for first result correctly parsed -ok 8 - source tag for first result correctly parsed -ok 9 - primary tag for first result correctly parsed -ok 10 - score for first result correctly parsed -ok 11 - sequence description correctly parsed. -ok 12 - correctly parsed all run parameters -ok 13 - correctly parsed period_size for first result -ok 14 - correctly parsed copy_number for first result -ok 15 - correctly parsed consensus_size for first result -ok 16 - correctly parsed percent_matches for first result -ok 17 - correctly parsed percent_indels for first result -ok 18 - correctly parsed percent_a for first result -ok 19 - correctly parsed percent_c for first result -ok 20 - correctly parsed percent_g for first result -ok 21 - correctly parsed percent_t for first result -ok 22 - correctly parsed entropy for first result -ok 23 - correctly parsed repeat_sequence for first result -ok 24 - correctly parsed consensus_sequence for first result -ok 25 - seq_id for second result correctly parsed -ok 26 - start for second result correctly parsed -ok 27 - end for second result correctly parsed -ok 28 - source tag for first result correctly parsed -ok 29 - primary tag for first result correctly parsed -ok 30 - score for first result correctly parsed -ok 31 - sequence description correctly parsed. -ok 32 - correctly reatained all run parameters for second feature -ok 33 - correctly parsed period_size for second result -ok 34 - correctly parsed copy_number for second result -ok 35 - correctly parsed consensus_size for second result -ok 36 - correctly parsed percent_matches for second result -ok 37 - correctly parsed percent_indels for second result -ok 38 - correctly parsed percent_a for second result -ok 39 - correctly parsed percent_c for second result -ok 40 - correctly parsed percent_g for second result -ok 41 - correctly parsed percent_t for second result -ok 42 - correctly parsed entropy for second result -ok 43 - correctly parsed repeat_sequence for second result -ok 44 - correctly parsed consensus_sequence for second result -ok 45 - seq_id for first result correctly parsed -ok 46 - start for first result correctly parsed -ok 47 - end for first result correctly parsed -ok 48 - source tag for first result correctly parsed -ok 49 - primary tag for first result correctly parsed -ok 50 - score for first result correctly parsed -ok 51 - sequence description correctly parsed. -ok 52 - correctly reatained all run parameters for third feature -ok 53 - correctly parsed period_size for third result -ok 54 - correctly parsed copy_number for third result -ok 55 - correctly parsed consensus_size for third result -ok 56 - correctly parsed percent_matches for third result -ok 57 - correctly parsed percent_indels for third result -ok 58 - correctly parsed percent_a for third result -ok 59 - correctly parsed percent_c for third result -ok 60 - correctly parsed percent_g for third result -ok 61 - correctly parsed percent_t for third result -ok 62 - correctly parsed entropy for third result -ok 63 - correctly parsed repeat_sequence for third result -ok 64 - correctly parsed consensus_sequence for third result -ok 65 - correctly return undef when no features are left -ok 66 - Correctly parsed seq_id even if description does not exist -ok -t/Tools/TargetP.t ................... -1..124 -ok 1 - use Bio::Tools::TargetP; -ok 2 -ok 3 -ok 4 -ok 5 - good SeqID -ok 6 - good Seqlength -ok 7 - correct Mitochondrion cutoff -ok 8 - correct signalpPeptide cutoff -ok 9 - correct other cutoff -ok 10 - correct location -ok 11 - correct Reliability class score -ok 12 - No peptide signal length reported -ok 13 - good SeqID -ok 14 - good Seqlength -ok 15 - correct Mitochondrion cutoff -ok 16 - correct signalpPeptide cutoff -ok 17 - correct other cutoff -ok 18 - correct location -ok 19 - correct Reliability class score -ok 20 - correct peptide signal length -ok 21 - good SeqID -ok 22 - good Seqlength -ok 23 - correct Mitochondrion cutoff -ok 24 - correct signalpPeptide cutoff -ok 25 - correct other cutoff -ok 26 - correct location -ok 27 - correct Reliability class score -ok 28 - correct peptide signal length -ok 29 - good SeqID -ok 30 - good Seqlength -ok 31 - correct Mitochondrion cutoff -ok 32 - correct signalpPeptide cutoff -ok 33 - correct other cutoff -ok 34 - correct location -ok 35 - correct Reliability class score -ok 36 - No peptide signal length reported -ok 37 - good SeqID -ok 38 - good Seqlength -ok 39 - correct Mitochondrion cutoff -ok 40 - correct signalpPeptide cutoff -ok 41 - correct other cutoff -ok 42 - correct location -ok 43 - correct Reliability class score -ok 44 - No peptide signal length reported -ok 45 - good SeqID -ok 46 - good Seqlength -ok 47 - correct Mitochondrion cutoff -ok 48 - correct signalpPeptide cutoff -ok 49 - correct other cutoff -ok 50 - correct location -ok 51 - correct Reliability class score -ok 52 - No peptide signal length reported -ok 53 - good SeqID -ok 54 - good Seqlength -ok 55 - correct Mitochondrion cutoff -ok 56 - correct signalpPeptide cutoff -ok 57 - correct other cutoff -ok 58 - correct location -ok 59 - correct Reliability class score -ok 60 - No peptide signal length reported -ok 61 - good SeqID -ok 62 - good Seqlength -ok 63 - correct Mitochondrion cutoff -ok 64 - correct signalpPeptide cutoff -ok 65 - correct other cutoff -ok 66 - correct location -ok 67 - correct Reliability class score -ok 68 - correct peptide signal length -ok 69 - good SeqID -ok 70 - good Seqlength -ok 71 - correct Mitochondrion cutoff -ok 72 - correct signalpPeptide cutoff -ok 73 - correct other cutoff -ok 74 - correct location -ok 75 - correct Reliability class score -ok 76 - No peptide signal length reported -ok 77 - good SeqID -ok 78 - good Seqlength -ok 79 - correct Mitochondrion cutoff -ok 80 - correct signalpPeptide cutoff -ok 81 - correct other cutoff -ok 82 - correct location -ok 83 - correct Reliability class score -ok 84 - No peptide signal length reported -ok 85 - good SeqID -ok 86 - good Seqlength -ok 87 - correct Mitochondrion cutoff -ok 88 - correct signalpPeptide cutoff -ok 89 - correct other cutoff -ok 90 - correct location -ok 91 - correct Reliability class score -ok 92 - No peptide signal length reported -ok 93 - good SeqID -ok 94 - good Seqlength -ok 95 - correct Mitochondrion cutoff -ok 96 - correct signalpPeptide cutoff -ok 97 - correct other cutoff -ok 98 - correct location -ok 99 - correct Reliability class score -ok 100 - No peptide signal length reported -ok 101 - good SeqID -ok 102 - good Seqlength -ok 103 - correct Mitochondrion cutoff -ok 104 - correct signalpPeptide cutoff -ok 105 - correct other cutoff -ok 106 - correct location -ok 107 - correct Reliability class score -ok 108 - correct peptide signal length -ok 109 - good SeqID -ok 110 - good Seqlength -ok 111 - correct Mitochondrion cutoff -ok 112 - correct signalpPeptide cutoff -ok 113 - correct other cutoff -ok 114 - correct location -ok 115 - correct Reliability class score -ok 116 - No peptide signal length reported -ok 117 - good SeqID -ok 118 - good Seqlength -ok 119 - correct Mitochondrion cutoff -ok 120 - correct signalpPeptide cutoff -ok 121 - correct other cutoff -ok 122 - correct location -ok 123 - correct Reliability class score -ok 124 - No peptide signal length reported -ok -t/Tools/Tmhmm.t ..................... -1..12 -ok 1 - use Bio::Tools::Tmhmm; -ok 2 - new() -ok 3 - got 3 feat -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok -t/Tools/tRNAscanSE.t ................ -1..14 -ok 1 - use Bio::Tools::tRNAscanSE; -ok 2 - An object of class 'Bio::Tools::tRNAscanSE' isa 'Bio::Tools::tRNAscanSE' -ok 3 -ok 4 - seq_id -ok 5 - codon -ok 6 - start -ok 7 - end -ok 8 - strand -ok 9 - exons -ok 10 - end -ok 11 - start -ok 12 - start -ok 13 - end -ok 14 - seq_id -ok -t/Tree/Compatible.t ................. -1..5 -ok 1 - use Bio::Tree::Compatible; -ok 2 - use Bio::TreeIO; -ok 3 -ok 4 -ok 5 -ok -t/Tree/Node.t ....................... -1..33 -ok 1 - use Bio::Tree::Node; -ok 2 - use Bio::TreeIO; -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 - retrieve the first value -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 -ok 29 - with fake node -ok 30 - after reroot on fake node -ok 31 - reroot on B -ok 32 - remove fake node, reroot on former B anc -ok 33 - roundtrip -ok -t/Tree/RandomTreeFactory.t .......... -1..5 -ok 1 - use Bio::Tree::RandomFactory; -ok 2 - use Bio::TreeIO; -ok 3 - use Bio::Tree::Statistics; -ok 4 -ok 5 -ok -t/Tree/Tree.t ....................... -1..66 -ok 1 - use Bio::TreeIO; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 - retrieve the first value -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 - Number of nodes that have ADH2 as name -ok 15 - Test Monophyly -ok 16 - Height -ok 17 - Depth -ok 18 - non-monophyletic group -ok 19 - not a binary tree -ok 20 - 12 nodes -ok 21 - after force_binary() it is -ok 22 - and there are more nodes (17) -ok 23 - B,C are Monophyletic -ok 24 - A,B are Monophyletic -ok 25 - B,F are not Monophyletic -ok 26 - A,B are Monophyletic -ok 27 - A,B,C are not Monophyletic w D as outgroup -ok 28 - A,F,E are monophyletic with I as outgroup -ok 29 - subtree_length() without attributes is an alias to total_branch_lenght() -ok 30 - Length of the tree is larger that lenght of a subtree -ok 31 - Can re-root with A as outgroup -ok 32 - Count the number of nodes -ok 33 - same length -ok 34 - Root node is A -ok 35 - Root node is A's ancestor -ok 36 - Can reroot with C's ancsestor -ok 37 - Node count correct -ok 38 - Total original branch length is what it is supposed to be -ok 39 - Updated total branch length after the reroot -ok 40 - Make sure root is really what we asked for -ok 41 - Testing for failed re-rerooting -ok 42 - Test that rooting succeeded -ok 43 - Test that re-rooted tree has proper number of nodes after re-rooting -ok 44 - Branch length before rerooting -ok 45 - Branch length after rerooting -ok 46 - Root is really the ancestor we asked for -ok 47 - BFS traversal order -ok 48 - DFS travfersal order -ok 49 - DFS traversal after removing H -ok 50 - DFS traversal after removing G -ok 51 - DFS traversal after removing E -ok 52 - DFS after removing all but 0,1,2,A,B,C,D -ok 53 - Testing bootstrap copy -ok 54 - Testing bootstrap copy -ok 55 - Testing bootstrap copy -ok 56 - Testing bootstrap copy -ok 57 - Testing bootstrap copy -ok 58 - Testing bootstrap copy -ok 59 - Testing bootstrap copy -ok 60 - Testing bootstrap copy -ok 61 - Testing auto-boostrap copy during parse -ok 62 - Testing auto-boostrap copy during parse -ok 63 - Testing auto-boostrap copy during parse -ok 64 - Testing auto-boostrap copy during parse -ok 65 -ok 66 -ok -t/Tree/TreeIO.t ..................... -1..76 -ok 1 - use Bio::TreeIO; -ok 2 -ok 3 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 - Saw SINFRUP0000006110 as expected -ok 19 -ok 20 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' -ok 21 - Total Nodes -ok 22 -ok 23 -ok 24 -ok 25 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' -ok 26 -ok 27 -ok 28 -ok 29 -ok 30 -ok 31 -ok 32 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' -ok 33 -ok 34 -ok 35 -ok 36 -ok 37 -ok 38 -ok 39 -ok 40 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' -ok 41 - Leaf nodes -ok 42 - All nodes -ok 43 -ok 44 -ok 45 -ok 46 -ok 47 -ok 48 -ok 49 -ok 50 -ok 51 -ok 52 -ok 53 -ok 54 -ok 55 -ok 56 - bug 2356 -ok 57 -ok 58 -ok 59 -ok 60 -ok 61 -ok 62 -ok 63 -ok 64 -ok 65 -ok 66 -ok 67 -ok 68 -ok 69 -ok 70 -ok 71 -ok 72 -ok 73 - An object of class 'Bio::Tree::Node' isa 'Bio::Tree::NodeI' -ok 74 -ok 75 - An object of class 'Bio::Tree::Node' isa 'Bio::Tree::NodeI' -not ok 76 # TODO The nodes are garbage-collected away b/c Tree isn't retained in memory -# Failed (TODO) test at t/Tree/TreeIO.t line 332. -# got: '0' -# expected: '198' -ok -t/Tree/TreeIO/lintree.t ............. -1..24 -ok 1 - use Bio::TreeIO; -ok 2 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' -ok 18 - Leaf nodes -ok 19 - All nodes -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok -t/Tree/TreeIO/newick.t .............. -1..51 -ok 1 - use Bio::TreeIO; -ok 2 -ok 3 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 - Saw SINFRUP0000006110 as expected -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok 25 -ok 26 -ok 27 - Round trip: simple newick -ok 28 - Round trip: Root node branch length -ok 29 - Round trip: Root node branch length -ok 30 - Round trip: from Wikipedia -ok 31 - Branch length on root -ok 32 - Tiny branch length on root -ok 33 - Zero branch lenghts -ok 34 - wkp blank tree -ok 35 - wkp only leaves labeled -ok 36 - wkp all nodes labeled -ok 37 - wkp branch lengths, no labels -ok 38 - wkp branch lengths, including root -ok 39 - wkp distances and leaf names -ok 40 - wkp distances and all names -ok 41 - wkp rooted on leaf node -ok 42 - phylip simple tree -ok 43 - phylip no labels -ok 44 - phylip w/ branch lengths -ok 45 - phylip w/ internal label -ok 46 - phylip raccoon tree -ok 47 - phylip mammal tree -ok 48 - phylip mammal tree w/ underbars -ok 49 - phylip single node -ok 50 - phylip_quartet -ok 51 - phylip greek -ok -t/Tree/TreeIO/nexus.t ............... -1..24 -ok 1 - use Bio::TreeIO; -ok 2 -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 - bug 2356 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok -t/Tree/TreeIO/nhx.t ................. -1..19 -ok 1 - use Bio::TreeIO; -ok 2 -ok 3 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' -ok 4 - Total Nodes -ok 5 -ok 6 -ok 7 -ok 8 - Roundtrip: simple newick -ok 9 - Roundtrip: bug 1471 test -ok 10 - Roundtrip: different combinations of label, NHX, and branch length -ok 11 - Roundtrip: doot node branch length -ok 12 - Roundtrip: Example from Wikipedia -ok 13 - Roundtrip: ADH NHX tree -ok 14 - Roundtrip: notung nhx example http://www.cs.cmu.edu/~aiton/split/Manual-2.6.master014.html -ok 15 - Roundtrip: notung nhx bootstrap http://www.cs.cmu.edu/~aiton/split/Manual-2.6.master014.html -ok 16 - Roundtrip: r-sig-phylo mailing list http://www.mail-archive.com/r-sig-phylo@r-project.org/msg00516.html -ok 17 - Roundtrip: treebest example nhx -ok 18 - Roundtrip: Wellcome Trust ToL (from http://iphylo.blogspot.com/2009/02/thoughts-on-wellcome-interactive-tree.html) -ok 19 - Roundtrip: Biorecipes NHX file (http://www.biorecipes.com/Orthologues/StatusPage/pics/TreeEukaryota.nt) -ok -t/Tree/TreeIO/phyloxml.t ............ -1..98 -ok 1 - use Bio::TreeIO; -ok 2 - use Bio::TreeIO::phyloxml; -ok 3 -ok 4 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' -ok 16 -ok 17 -ok 18 -ok 19 -ok 20 -ok 21 -ok 22 -ok 23 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' -ok 24 -ok 25 -ok 26 -ok 27 -ok 28 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' -ok 29 - An object of class 'Bio::Annotation::Collection' isa 'Bio::Annotation::Collection' -ok 30 - An object of class 'Bio::Annotation::Collection' isa 'Bio::Annotation::Collection' -ok 31 -ok 32 - An object of class 'Bio::Annotation::Collection' isa 'Bio::Annotation::Collection' -ok 33 -ok 34 - An object of class 'Bio::Seq' isa 'Bio::SeqI' -ok 35 - An object of class 'Bio::Annotation::Collection' isa 'Bio::Annotation::Collection' -ok 36 -ok 37 -ok 38 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' -ok 39 -ok 40 - An object of class 'Bio::Seq' isa 'Bio::SeqI' -ok 41 - An object of class 'Bio::Annotation::Relation' isa 'Bio::Annotation::Relation' -ok 42 -ok 43 - An object of class 'Bio::Seq' isa 'Bio::SeqI' -ok 44 - An object of class 'Bio::Annotation::Relation' isa 'Bio::Annotation::Relation' -ok 45 -ok 46 - An object of class 'Bio::Seq' isa 'Bio::SeqI' -ok 47 -ok 48 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' -ok 49 - An object of class 'Bio::Seq' isa 'Bio::SeqI' -ok 50 -ok 51 -ok 52 -ok 53 - An object of class 'Bio::Seq' isa 'Bio::SeqI' -ok 54 -ok 55 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' -ok 56 - An object of class 'Bio::Annotation::Relation' isa 'Bio::Annotation::Relation' -ok 57 -ok 58 - An object of class 'Bio::Tree::AnnotatableNode' isa 'Bio::Tree::AnnotatableNode' -ok 59 -ok 60 -ok 61 -ok 62 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' -ok 63 - An object of class 'Bio::Tree::AnnotatableNode' isa 'Bio::Tree::AnnotatableNode' -ok 64 - An object of class 'Bio::Annotation::Collection' isa 'Bio::AnnotationCollectionI' -ok 65 - An object of class 'Bio::Annotation::Collection' isa 'Bio::Annotation::Collection' -ok 66 -ok 67 -ok 68 -ok 69 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' -ok 70 - An object of class 'Bio::Tree::AnnotatableNode' isa 'Bio::Tree::AnnotatableNode' -ok 71 - An object of class 'Bio::Annotation::Collection' isa 'Bio::AnnotationCollectionI' -ok 72 - An object of class 'Bio::Annotation::Collection' isa 'Bio::Annotation::Collection' -ok 73 -ok 74 -ok 75 -ok 76 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' -ok 77 -ok 78 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' -ok 79 -ok 80 -ok 81 -ok 82 -ok 83 -ok 84 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' -ok 85 -ok 86 -ok 87 -ok 88 -ok 89 -ok 90 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' -ok 91 -ok 92 - An object of class 'Bio::Tree::AnnotatableNode' isa 'Bio::Tree::AnnotatableNode' -ok 93 -ok 94 -ok 95 -ok 96 -ok 97 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' -ok 98 -ok -t/Tree/TreeIO/tabtree.t ............. -1..24 -ok 1 - use Bio::TreeIO; -ok 2 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' -ok 3 -ok 4 -ok 5 -ok 6 -ok 7 -ok 8 -ok 9 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' -ok 10 -ok 11 -ok 12 -ok 13 -ok 14 -ok 15 -ok 16 -ok 17 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::TreeI' -ok 18 - Leaf nodes -ok 19 - All nodes -ok 20 -ok 21 -ok 22 -ok 23 -ok 24 -ok -t/Tree/TreeStatistics.t ............. -1..44 -ok 1 - use Bio::TreeIO; -ok 2 - use Bio::Tree::Statistics; -ok 3 - cherries -ok 4 - cherries -# Subtest: transfer-bootstrap-expectation (experimental) - 1..15 - ok 1 - Testing TBE for node - ok 2 - Testing TBE for node N7 - ok 3 - Testing TBE for node N3 - ok 4 - Testing TBE for node N1 - ok 5 - Testing TBE for node N2 - ok 6 - Testing TBE for node N6 - ok 7 - Testing TBE for node N4 - ok 8 - Testing TBE for node N5 - ok 9 - Testing TBE for node N14 - ok 10 - Testing TBE for node N10 - ok 11 - Testing TBE for node N8 - ok 12 - Testing TBE for node N9 - ok 13 - Testing TBE for node N13 - ok 14 - Testing TBE for node N11 - ok 15 - Testing TBE for node N12 -ok 5 - transfer-bootstrap-expectation (experimental) -# Subtest: assess_bootstrap - 1..15 - ok 1 - Testing bootstrap for node - ok 2 - Testing bootstrap for node N7 - ok 3 - Testing bootstrap for node N3 - ok 4 - Testing bootstrap for node N1 - ok 5 - Testing bootstrap for node N2 - ok 6 - Testing bootstrap for node N6 - ok 7 - Testing bootstrap for node N4 - ok 8 - Testing bootstrap for node N5 - ok 9 - Testing bootstrap for node N14 - ok 10 - Testing bootstrap for node N10 - ok 11 - Testing bootstrap for node N8 - ok 12 - Testing bootstrap for node N9 - ok 13 - Testing bootstrap for node N13 - ok 14 - Testing bootstrap for node N11 - ok 15 - Testing bootstrap for node N12 -ok 6 - assess_bootstrap -ok 7 - read traits -ok 8 - Add traits in second column and ignore missing -ok 9 - Add traits in third column -ok 10 - parsimony score -ok 11 - subtree parsimony score -ok 12 - ps value -ok 13 - fitch_down -ok 14 - ps value after fitch_down -ok 15 - persistence of a leaf -ok 16 - persistence of an internal node value -ok 17 - persistence of an internal node value -ok 18 - persistence of an internal node value -ok 19 - leaf node: number of clusters = 0 -ok 20 - number of clusters -ok 21 - number of clusters -ok 22 - number of clusters -ok 23 - number of leaves in phylotype -ok 24 - number of leaves in phylotype -ok 25 - number of leaves in phylotype -ok 26 - number of leaves in phylotype -ok 27 - phylotype length -ok 28 - phylotype length -ok 29 - phylotype length -ok 30 - phylotype length -ok 31 - phylotype length -ok 32 - sum of leaf distances -ok 33 - sum of leaf distances -ok 34 - sum of leaf distances -ok 35 - sum of leaf distances -ok 36 - sum of leaf distances -ok 37 - genetic diversity -ok 38 - separation -ok 39 - association index -ok 40 - subtree association index -ok 41 - monophyletic clade size -ok 42 - monophyletic clade size -ok 43 - monophyletic clade size -ok 44 - monophyletic clade size -ok -All tests successful. - -Test Summary Report -------------------- -t/Root/IO.t (Wstat: 0 Tests: 154 Failed: 0) - TODO passed: 109, 112, 115, 118 -Files=211, Tests=14791, 98 wallclock secs ( 1.89 usr 0.55 sys + 70.69 cusr 11.57 csys = 84.70 CPU) -Result: PASS -make[1]: Leaving directory '/build/reproducible-path/bioperl-1.7.8' +dh: command-omitted: The call to "dh_auto_test" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install @@ -17723,475 +2178,475 @@ Manifying 33 pod documents Manifying 15 pod documents Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/BioPerl.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/WebAgent.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/UpdateableSeqI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/WebAgent.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SimpleAlign.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Taxon.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SimpleAnalysisI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Species.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SimpleAlign.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqUtils.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Species.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeatureI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqAnalysisParserI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqAnalysisParserI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/PrimarySeqI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/PullParserI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/ParameterBaseI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Range.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/PrimarySeq.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/ParameterBaseI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/RangeI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/PrimarySeqI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Range.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/LocationI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DasI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/LocatableSeq.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/HandlerBaseI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/IdentifiableI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DBLinkContainerI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/IdCollectionI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DescribableI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/IdCollectionI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/LocatableSeq.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/FeatureHolderI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DBLinkContainerI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/IdentifiableI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/HandlerBaseI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AnnotationCollectionI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AnnotationI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AnnotatableI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AnalysisResultI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AnalysisI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AnalysisParserI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/tabtree.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/NewickParser.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/newick.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/pag.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/TreeEventBuilder.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/lintree.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/cluster.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/NewickParser.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/pag.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/phyloxml.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/TreeEventBuilder.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/nexus.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/nhx.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/cluster.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/tabtree.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO/nexus.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/TreeFunctionsI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/TreeI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/NodeI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/Statistics.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/DistanceFactory.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/Compatible.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/Tree.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/AnnotatableNode.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/NodeNHX.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/Node.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/Tree.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/NodeI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/RandomFactory.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/NodeNHX.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tree/DistanceFactory.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/tRNAscanSE.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Tmhmm.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Sigcleave.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Signalp.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/pICalculator.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/isPcr.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/SeqWords.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/TargetP.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/RepeatMasker.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/TandemRepeatsFinder.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/RandomDistFunctions.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Seg.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/pICalculator.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Sigcleave.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Tmhmm.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/TargetP.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/QRNA.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/SeqPattern.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/ipcress.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/RepeatMasker.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/isPcr.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Seg.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Signalp.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/SeqStats.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Genewise.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Geneid.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Grail.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Promoterwise.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/GFF.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/ESTScan.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/MZEF.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/IUPAC.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Genomewise.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Lucy.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Genscan.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/OddCodes.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/RandomDistFunctions.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/ipcress.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/SeqPattern.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/FootPrinter.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Match.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Prints.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/PrositeScan.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Genemark.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Est2Genome.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Profile.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Grail.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/GuessSeqFormat.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Fgenesh.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Genomewise.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Pseudowise.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Coil.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/CodonTable.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Primer3.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/MZEF.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Lucy.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Eponine.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Genemark.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Pseudowise.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/CodonTable.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/IUPAC.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Genewise.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Geneid.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/OddCodes.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Glimmer.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Prints.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Fgenesh.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/GuessSeqFormat.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/FootPrinter.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/PrositeScan.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Promoterwise.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/ESTScan.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/ECnumber.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/GFF.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Profile.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Primer3.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/EPCR.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/AmpliconSearch.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Genscan.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/AnalysisResult.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Blat.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Sim4/Exon.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/AmpliconSearch.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/SeqPattern/Backtranslate.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Signalp/ExtendedSignalp.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Sim4/Results.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Spidey/Exon.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Sim4/Exon.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Spidey/Results.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Signalp/ExtendedSignalp.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/SeqPattern/Backtranslate.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Run/GenericParameters.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Spidey/Exon.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Run/Analysis.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Run/ParametersI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Run/AnalysisFactory.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Run/ParametersI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Run/WrapperBase.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Run/GenericParameters.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Run/WrapperBase/CommandExts.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/PhyloBase.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/EMBOSS/Palindrome.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Prediction/Exon.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Prediction/Gene.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Phylo/Molphy.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Phylo/Gerp.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Phylo/Molphy/Result.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Phylo/Phylip/ProtDist.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/EMBOSS/Palindrome.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Primer/AssessorI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Primer/Feature.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Primer/Pair.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Primer/Assessor/Base.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Phylo/Gerp.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Phylo/Molphy.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Phylo/Molphy/Result.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Phylo/Phylip/ProtDist.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Alignment/Consed.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Alignment/Trim.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Analysis/SimpleAnalysisBase.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Alignment/Trim.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Tools/Alignment/Consed.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/metafasta.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/pir.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/swissdriver.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/kegg.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/scf.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/gcg.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/mbsout.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/game.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/tinyseq.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/scf.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/msout.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/table.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/locuslink.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/game.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/gbdriver.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/genbank.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/seqxml.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/raw.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/qual.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/metafasta.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/tab.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/phd.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/locuslink.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/kegg.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/swiss.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/tigr.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/qual.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/raw.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/gbxml.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/gcg.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/msout.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/swiss.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/pir.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/tab.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/swissdriver.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/table.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/tigrxml.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/gbdriver.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/largefasta.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/embldriver.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/ace.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/bsml.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/fasta.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/asciitree.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/tigrxml.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/MultiFile.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/FTHelper.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/asciitree.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/fasta.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/embl.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/bsml_sax.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/embldriver.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/fastq.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/MultiFile.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/embl.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/bsml.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/ace.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/tinyseq/tinyseqHandler.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/game/gameSubs.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/game/gameHandler.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/game/gameSubs.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/game/seqHandler.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/game/gameWriter.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/game/featHandler.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/game/seqHandler.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO/Handler/GenericRichSeqHandler.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Similarity.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/SubSeq.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/TypedSeqFeatureI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/PositionProxy.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/SimilarityPair.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Primer.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/PositionProxy.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/SubSeq.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Lite.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Generic.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/FeaturePair.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Similarity.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/SimilarityPair.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Collection.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/FeaturePair.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Amplicon.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/CollectionI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/AnnotationAdaptor.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Computation.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Tools/Unflattener.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/CollectionI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Tools/FeatureNamer.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Tools/TypeMapper.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Tools/IDHandler.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/Poly_A_site.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/UTR.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Tools/Unflattener.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Tools/TypeMapper.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/Intron.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/Promoter.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/TranscriptI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/GeneStructureI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/ExonI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/Poly_A_site.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/GeneStructure.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/GeneStructureI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/Transcript.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/NC_Feature.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/Intron.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/UTR.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/TranscriptI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeature/Gene/Exon.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/SeqFactory.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/EncodedSeq.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/LargePrimarySeq.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/MetaI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/PrimedSeq.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/LargeSeq.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/SeqFactory.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/QualI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/PrimaryQual.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/Meta.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/SequenceTrace.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/SeqFastaSpeedFactory.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/RichSeqI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/RichSeq.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/Quality.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/Meta.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/LargeLocatableSeq.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/RichSeq.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/LargeSeq.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/BaseSeqProcessor.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/LargePrimarySeq.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/RichSeqI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/SeqBuilder.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/TraceI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/PrimedSeq.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/PrimaryQual.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/QualI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/EncodedSeq.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/SimulatedRead.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/LargeSeqI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/TraceI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/SeqFastaSpeedFactory.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/BaseSeqProcessor.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq/Meta/Array.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/psl.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/gmap_f9.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/rnamotif.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/sim4.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/exonerate.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/gmap_f9.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/infernal.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/fasta.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/wise.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/rnamotif.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/megablast.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/waba.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/wise.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/infernal.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/exonerate.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/EventHandlerI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/erpin.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/blast_pull.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/SearchWriterI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/blast_pull.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/blast.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/blasttable.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/SearchResultEventBuilder.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/cross_match.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/blasttable.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/IteratedSearchResultEventBuilder.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/EventHandlerI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/axt.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/blast.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/FastHitEventBuilder.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/Writer/HSPTableWriter.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/Writer/HitTableWriter.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/Writer/TextResultWriter.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/axt.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/Writer/ResultTableWriter.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/Writer/HTMLResultWriter.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/Writer/TextResultWriter.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/Writer/GbrowseGFF.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/SearchUtils.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/Writer/HitTableWriter.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/Writer/HTMLResultWriter.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO/Writer/HSPTableWriter.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/StatisticsI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/SearchUtils.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/GenericDatabase.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/DatabaseI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/BlastStatistics.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/GenericStatistics.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/BlastUtils.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Processor.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/BlastStatistics.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Tiling/TilingI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Tiling/MapTiling.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Tiling/MapTileUtils.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Tiling/TilingI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/WABAResult.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/BlastPullResult.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/PullResultI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/ResultI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/CrossMatchResult.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/BlastResult.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/INFERNALResult.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/PullResultI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/GenericResult.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/BlastPullResult.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/BlastResult.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/ResultI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/ResultFactory.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Iteration/GenericIteration.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/WABAResult.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Result/CrossMatchResult.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Iteration/IterationI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/PullHitI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/GenericHit.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/ModelHit.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/HitI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/PsiBlastHit.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/HitFactory.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/Fasta.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/BlastPullHit.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/BlastHit.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/PsiBlastHSP.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Iteration/GenericIteration.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/ModelHSP.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/PSLHSP.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/PullHSPI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/WABAHSP.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/BlastPullHSP.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/HSPI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/BlastHSP.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/PullHSPI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/HSPFactory.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/FastaHSP.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/ModelHSP.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/HSPI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/PsiBlastHSP.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/WABAHSP.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/HSP/GenericHSP.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/PsiBlastHit.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/HitI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/BlastHit.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/ModelHit.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/BlastPullHit.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/HitFactory.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/GenericHit.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/Fasta.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Search/Hit/PullHitI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/RootI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/IO.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/HTTPget.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/TestObject.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/Storable.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/Test.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/Utilities.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/Root.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/RootI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/Version.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/Root.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/Storable.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/HTTPget.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/Test.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Root/Exception.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/simplehierarchy.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/goflat.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/obo.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/InterProParser.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/dagflat.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/simplehierarchy.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/soflat.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/goflat.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/dagflat.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/Handlers/BaseSAXHandler.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/Handlers/InterProHandler.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/Ontology.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/OBOEngine.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/SimpleOntologyEngine.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/Relationship.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/OBOterm.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/WidestCoordPolicy.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/CoordinatePolicyI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/AvWithinCoordPolicy.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/Split.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/Fuzzy.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/FuzzyLocationI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/SplitLocationI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/Simple.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/Atomic.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/NarrowestCoordPolicy.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/RelationshipI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/RelationshipType.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/OntologyStore.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/Path.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/SimpleOntologyEngine.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/RelationshipFactory.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/OntologyEngineI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/OBOterm.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/Ontology.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/Relationship.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/PathI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/InterProTerm.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/OBOEngine.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/TermFactory.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/RelationshipFactory.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/GOterm.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/TermI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/OntologyStore.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/Term.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/GOterm.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/OntologyI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/InterProTerm.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/RelationshipType.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/DocumentRegistry.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/Split.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/Atomic.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/SplitLocationI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/FuzzyLocationI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/CoordinatePolicyI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/Simple.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/NarrowestCoordPolicy.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/Fuzzy.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/AvWithinCoordPolicy.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Location/WidestCoordPolicy.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/IO.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/Scoring.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/Mlagan.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PhylipDist.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/MatrixI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/Generic.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PhylipDist.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/Mlagan.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/IO.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/IO/mlagan.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/IO/scoring.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/IO/phylip.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/SiteMatrixI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/SiteMatrix.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/PsmHeader.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/PsmHeaderI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/ProtMatrix.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/ProtPsm.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/PsmI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/SiteMatrixI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/IO.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/ProtPsm.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/InstanceSiteI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/Psm.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/PsmHeader.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/IO.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/InstanceSite.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/PsmHeaderI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/Psm.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/IO/masta.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/IO/meme.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/IO/psiblast.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/IO/transfac.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/IO/mast.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/IO/phylip.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/IO/scoring.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/IO/mlagan.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/AbstractSeq.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/IO/transfac.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/IO/psiblast.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Matrix/PSM/IO/meme.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Das/FeatureTypeI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Das/SegmentI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Event/EventGeneratorI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Event/EventHandlerI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/GenBank.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/BlastTable.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/Qual.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/Abstract.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/Fastq.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/Swissprot.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/Qual.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/AbstractSeq.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/Fasta.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/SwissPfam.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/Blast.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/GenBank.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/Abstract.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/EMBL.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/Fasta.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Event/EventGeneratorI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Event/EventHandlerI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Das/SegmentI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Das/FeatureTypeI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/ObjectBuilderI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/AnalysisI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/LocationFactoryI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/AnalysisI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/SequenceStreamI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/ObjectFactory.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/DriverFactory.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/SeqAnalysisParserFactory.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/TreeFactoryI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/SequenceFactoryI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/SeqAnalysisParserFactoryI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/SequenceProcessorI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/SeqAnalysisParserFactory.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/ApplicationFactoryI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/FTLocationFactory.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/ObjectFactory.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/SequenceStreamI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/SequenceFactoryI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/ObjectFactoryI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/SequenceProcessorI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/ObjectBuilderI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/FTLocationFactory.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Factory/TreeFactoryI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/CodonUsage/IO.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/CodonUsage/Table.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/WebDBSeqI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/DBFetch.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Failover.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Qual.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/UpdateableSeqI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Fasta.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/QueryI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/InMemoryCache.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/SeqI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/GenericWebAgent.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/RandomAccessI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/LocationI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/ReferenceI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Registry.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Fasta.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Taxonomy.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/FileCache.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Failover.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/IndexedBase.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Flat.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/InMemoryCache.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/ReferenceI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/QueryI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/GenericWebAgent.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/UpdateableSeqI.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/FileCache.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/SeqI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Qual.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Taxonomy/greengenes.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Taxonomy/flatfile.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Taxonomy/silva.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Taxonomy/list.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/GFF/Util/Rearrange.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/GFF/Util/Binning.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Query/WebQuery.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Flat/BDB.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Flat/BinarySearch.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Flat/BDB/genbank.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Flat/BDB/embl.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Flat/BDB/fasta.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Flat/BDB/swiss.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Flat/BDB/genbank.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Taxonomy/list.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Taxonomy/flatfile.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Taxonomy/greengenes.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Taxonomy/silva.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/GFF/Util/Rearrange.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/GFF/Util/Binning.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Align/Utilities.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Align/DNAStatistics.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Align/AlignI.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Align/StatisticsI.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Align/Utilities.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Align/ProteinStatistics.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Align/PairwiseStatistics.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Align/DNAStatistics.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/SimpleValue.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/Target.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/StructuredValue.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/TypeManager.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/TagTree.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/Tree.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/AnnotationFactory.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/Comment.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/Relation.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/Reference.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/SimpleValue.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/TypeManager.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/Collection.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/Comment.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/OntologyTerm.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/Relation.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/DBLink.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/bl2seq.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/metafasta.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/msf.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/Reference.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/AnnotationFactory.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/psi.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/mega.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/emboss.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/pfam.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/meme.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/po.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/selex.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/metafasta.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/phylip.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/xmfa.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/po.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/maf.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/proda.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/emboss.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/mase.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/clustalw.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/psi.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/pfam.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/arp.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/selex.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/largemultifasta.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/clustalw.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/bl2seq.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/prodom.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/fasta.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/maf.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/nexus.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/largemultifasta.pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/meme.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/msf.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/mase.pm +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/fasta.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/Handler/GenericAlignHandler.pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_unflatten_seq.1p Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/man/man1/bp_tree2pag.1p @@ -18704,46 +3159,46 @@ Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Align::PairwiseStatistics.3pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Align::DNAStatistics.3pm Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::Align::AlignI.3pm -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_tree2pag Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_unflatten_seq -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_sreformat -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_taxid4species +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_tree2pag Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_translate_seq -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_seqret Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_taxonomy2tree +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_taxid4species Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_seqretsplit +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_sreformat Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_split_seq -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_seqcut +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_seqret Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_seqpart +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_seqcut Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_seqconvert -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_search2tribe Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_seq_length -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_search2table Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_search2gff +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_search2table Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_search2alnblocks Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_process_gadfly -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_oligo_count Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_revtrans-motif -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_nexus2nh -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_mutate -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_make_mrna_protein +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_search2tribe +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_oligo_count Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_process_sgd Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_nrdb +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_mutate +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_nexus2nh Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_mrtrans Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_mask_by_search -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_gccalc -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_index +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_make_mrna_protein Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_local_taxonomydb_query +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_index Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_find-blast-matches -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_filter_search -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_extract_feature_seq -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_dbsplit Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_genbank2gff3 -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_fastam9_to_table Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_fetch -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_aacomp -Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_biogetseq Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_bioflat_index +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_gccalc +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_extract_feature_seq +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_biogetseq +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_fastam9_to_table +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_aacomp +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_filter_search +Installing /build/reproducible-path/bioperl-1.7.8/debian/tmp/usr/bin/bp_dbsplit make[1]: Leaving directory '/build/reproducible-path/bioperl-1.7.8' dh_install dh_installdocs @@ -18778,12 +3233,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/265301/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/265301/tmp/hooks/B01_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/3047937 and its subdirectories -I: Current time: Fri Nov 7 09:06:15 -12 2025 -I: pbuilder-time-stamp: 1762549575 +I: removing directory /srv/workspace/pbuilder/265301 and its subdirectories +I: Current time: Fri Dec 11 17:30:15 +14 2026 +I: pbuilder-time-stamp: 1796959815