bio-gff3 0.8.7 → 0.9.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/.travis.yml +12 -0
- data/Gemfile +4 -4
- data/Gemfile.lock +34 -20
- data/README.rdoc +22 -13
- data/Rakefile +24 -23
- data/VERSION +1 -1
- data/bin/gff3-fetch +15 -11
- data/bio-gff3.gemspec +30 -39
- data/lib/bio/db/gff/block/gffblockparser.rb +3 -4
- data/lib/bio/db/gff/digest/gfflrucache.rb +2 -1
- data/lib/bio/db/gff/digest/gffnocache.rb +2 -1
- data/lib/bio/db/gff/digest/gffparser.rb +5 -3
- data/lib/bio/db/gff/gffcomponent.rb +6 -5
- data/lib/bio/db/gff/gffsequence.rb +1 -1
- data/lib/bio/db/gff/gffvalidate.rb +2 -1
- data/spec/gff3_fileiterator_spec.rb +3 -4
- data/test/data/gff/m_hapla.WS232.annotations.part.gff3 +3725 -0
- data/test/data/gff/m_hapla.WS232.genomic.part.fa +3187 -0
- data/test/data/regression/test_ext_gff3.rtest +1 -5
- data/test/data/regression/test_gff3.rtest +1 -5
- data/test/data/regression/test_latest_wormbase_ext_gff3.ref +7885 -0
- data/test/data/regression/test_latest_wormbase_ext_gff3.rtest +280 -0
- data/test/data/regression/test_lrucache_ext_gff3.rtest +1 -3
- data/test/data/regression/test_lrucache_gff3.rtest +1 -3
- data/test/data/regression/test_nocache_ext_gff3.rtest +1 -3
- data/test/data/regression/test_nocache_gff3.rtest +1 -3
- data/test/helper.rb +1 -0
- data/test/{regressiontest.rb → regressiontest2.rb} +5 -5
- data/test/test_bio-gff3.rb +35 -10
- metadata +35 -36
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INFO bio-gff3: ---- Digest DB and store data in mRNA Hash (LruCache) <>
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INFO bio-gff3: Adding mRNA <MhA1_Contig0.frz3.fgene1> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 4027 4090> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 4141 4251> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 4311 4390> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 4471 4576> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 4635 4678> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 4760 4959> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 5070 5193> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 5243 5274> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 5348 5631> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 5747 5841> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 5881 5970> <>
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INFO bio-gff3: Adding mRNA <MhA1_Contig0.frz3.fgene2> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 28712 28876> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 28918 29022> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 29230 29583> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 29626 29910> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 29987 30067> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 30928 30968> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 31014 31121> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 31815 31900> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 31943 32141> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 32186 32403> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 32453 32476> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 32517 32705> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 32741 32976> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 33022 33211> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 33255 33346> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 33389 33535> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 33578 33772> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 33818 33936> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 33989 34132> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 34177 34273> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 34353 34395> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 34806 34966> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 35014 35316> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 35359 35649> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 35697 35857> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 35901 36060> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 36103 36216> <>
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INFO bio-gff3: Adding mRNA <MhA1_Contig0.frz3.fgene3> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 6259 6360> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 6396 6564> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 6611 6789> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 6952 7028> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 7090 7246> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 7294 7407> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 7465 7563> <>
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INFO bio-gff3: Adding mRNA <MhA1_Contig0.frz3.fgene4> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 48426 48702> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 48745 48842> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 48941 49079> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 49154 49239> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 49416 49514> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 49687 49874> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 49918 50002> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 50379 50524> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 50570 50663> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 50706 50837> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 50889 50945> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 51018 51146> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 51186 51388> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 51434 51551> <>
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INFO bio-gff3: Adding mRNA <MhA1_Contig0.frz3.fgene5> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 70770 71039> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 71091 71262> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 71334 71722> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 71766 72038> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 72093 72326> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 72387 72500> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 72542 72698> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 72745 72938> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 72984 73162> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 73209 73455> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 73599 73716> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 73767 73855> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 73900 74294> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 74345 74438> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 74484 74660> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 74710 74729> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 74773 74938> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 75082 75207> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 75259 75299> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 75342 75405> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 75461 75491> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 75545 75639> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 75690 75803> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 75852 75926> <>
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INFO bio-gff3: Adding mRNA <MhA1_Contig0.frz3.fgene6> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 99137 99339> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 99402 99529> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 99573 99718> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 100159 100348> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 100488 100531> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 100655 100714> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 100770 100868> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 100934 101021> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 101065 101165> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 101294 101419> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 101587 101736> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 101831 102034> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 102076 102150> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 102198 102414> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 102503 102636> <>
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INFO bio-gff3: Adding mRNA <MhA1_Contig0.frz3.fgene7> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 113735 113854> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 113898 113965> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 114012 114105> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 114148 114275> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 114504 114633> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 114678 114742> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 114784 114861> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 114907 115141> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 115187 115252> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 115302 115434> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 115477 115596> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 115640 115697> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 115742 115803> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 115843 115940> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 115989 116150> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 116198 116299> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 116445 116616> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 116662 116729> <>
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INFO bio-gff3: Adding mRNA <MhA1_Contig0.frz3.fgene8> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 44151 44252> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 44288 44456> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 44503 44681> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 44728 44903> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 45032 45128> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 45175 45285> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 45417 45569> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 45887 46020> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 47085 47165> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 47370 47387> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 47706 47769> <>
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INFO bio-gff3: Adding mRNA <MhA1_Contig0.frz3.fgene9> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 180784 180984> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 181219 181361> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 181425 181624> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 181793 181946> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 182296 182561> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 182881 183133> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 183291 183633> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 183889 184080> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 184122 184262> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 184446 184560> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 184607 184737> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 184784 184857> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 185319 185622> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 185693 185745> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 185886 186126> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 186176 186300> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 186778 186843> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 187036 187410> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 187610 187785> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 187984 188526> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 188567 188673> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 188733 188795> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 188859 189164> <>
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INFO bio-gff3: Adding mRNA <MhA1_Contig0.frz3.fgene10> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 223510 223611> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 224103 224341> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 224713 224870> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 224917 225057> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 225522 225763> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 226177 226291> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 226342 226473> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 226664 226758> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 226961 227137> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 227179 227259> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 227558 227602> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 227654 227836> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 228151 228220> <>
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INFO bio-gff3: Adding CDS <MhA1_Contig0 228273 228596> <>
|
|
176
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 228790 228932> <>
|
|
177
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 229166 229309> <>
|
|
178
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 229354 229407> <>
|
|
179
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 229533 229760> <>
|
|
180
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 229876 229998> <>
|
|
181
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 230106 230153> <>
|
|
182
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 230202 230314> <>
|
|
183
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 230671 230825> <>
|
|
184
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 231052 231134> <>
|
|
185
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 231181 231246> <>
|
|
186
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 231357 231470> <>
|
|
187
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 231511 231677> <>
|
|
188
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 231757 231826> <>
|
|
189
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 231877 231975> <>
|
|
190
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 232359 232634> <>
|
|
191
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 232930 233188> <>
|
|
192
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 233542 233714> <>
|
|
193
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 233761 233929> <>
|
|
194
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 234240 234425> <>
|
|
195
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 234482 234675> <>
|
|
196
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 235064 235171> <>
|
|
197
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 235218 235311> <>
|
|
198
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 235821 235995> <>
|
|
199
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 236262 236424> <>
|
|
200
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 236558 236572> <>
|
|
201
|
+
INFO bio-gff3: Adding mRNA <MhA1_Contig1.frz3.fgene1> <>
|
|
202
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig1 881 961> <>
|
|
203
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig1 1169 1355> <>
|
|
204
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig1 1417 1520> <>
|
|
205
|
+
INFO bio-gff3: Adding mRNA <MhA1_Contig0.frz3.fgene11> <>
|
|
206
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig0 237099 237531> <>
|
|
207
|
+
INFO bio-gff3: Adding mRNA <MhA1_Contig4.frz3.fgene1> <>
|
|
208
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig4 24120 24176> <>
|
|
209
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig4 24219 24442> <>
|
|
210
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig4 24710 24786> <>
|
|
211
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig4 24833 24933> <>
|
|
212
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig4 24980 25195> <>
|
|
213
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig4 25300 25501> <>
|
|
214
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig4 25714 25871> <>
|
|
215
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig4 25916 26188> <>
|
|
216
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig4 26422 26523> <>
|
|
217
|
+
INFO bio-gff3: Adding mRNA <MhA1_Contig5.frz3.fgene1> <>
|
|
218
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig5 483 539> <>
|
|
219
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig5 583 806> <>
|
|
220
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig5 1074 1150> <>
|
|
221
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig5 1198 1298> <>
|
|
222
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig5 1345 1616> <>
|
|
223
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig5 1745 1866> <>
|
|
224
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig5 2079 2236> <>
|
|
225
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig5 2288 2554> <>
|
|
226
|
+
INFO bio-gff3: Adding mRNA <MhA1_Contig1.frz3.fgene2> <>
|
|
227
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig1 10506 10616> <>
|
|
228
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig1 10664 10726> <>
|
|
229
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig1 11173 11278> <>
|
|
230
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig1 11326 11440> <>
|
|
231
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig1 11639 11918> <>
|
|
232
|
+
INFO bio-gff3: Adding mRNA <MhA1_Contig7.frz3.fgene1> <>
|
|
233
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig7 73081 73141> <>
|
|
234
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig7 73270 73419> <>
|
|
235
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig7 73528 73656> <>
|
|
236
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig7 74057 74202> <>
|
|
237
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig7 74683 74723> <>
|
|
238
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig7 75096 75202> <>
|
|
239
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig7 75472 75548> <>
|
|
240
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig7 75593 75694> <>
|
|
241
|
+
INFO bio-gff3: Adding mRNA <MhA1_Contig7.frz3.fgene2> <>
|
|
242
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig7 25361 25669> <>
|
|
243
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig7 26231 26407> <>
|
|
244
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig7 26786 26877> <>
|
|
245
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig7 26920 27242> <>
|
|
246
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig7 27467 27749> <>
|
|
247
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig7 27802 27957> <>
|
|
248
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig7 28200 28272> <>
|
|
249
|
+
INFO bio-gff3: Adding mRNA <MhA1_Contig13.frz3.fgene1> <>
|
|
250
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig13 70665 70800> <>
|
|
251
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig13 71061 71274> <>
|
|
252
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig13 71358 71599> <>
|
|
253
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig13 71651 71893> <>
|
|
254
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig13 72228 72364> <>
|
|
255
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig13 72409 72426> <>
|
|
256
|
+
INFO bio-gff3: Adding mRNA <MhA1_Contig18.frz3.fgene1> <>
|
|
257
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig18 80034 80112> <>
|
|
258
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig18 81258 81434> <>
|
|
259
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig18 81483 81700> <>
|
|
260
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig18 82037 82188> <>
|
|
261
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig18 82242 82536> <>
|
|
262
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig18 82592 82854> <>
|
|
263
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig18 83128 83210> <>
|
|
264
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig18 83269 83375> <>
|
|
265
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig18 83450 83570> <>
|
|
266
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig18 83796 83872> <>
|
|
267
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig18 83923 84129> <>
|
|
268
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig18 84200 84265> <>
|
|
269
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig18 84641 84792> <>
|
|
270
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig18 84836 85080> <>
|
|
271
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig18 85168 85330> <>
|
|
272
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig18 85912 86113> <>
|
|
273
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig18 86152 86382> <>
|
|
274
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig18 86669 86825> <>
|
|
275
|
+
INFO bio-gff3: Adding CDS <MhA1_Contig18 87441 87496> <>
|
|
276
|
+
WARN bio-gff3: Unknown feature is ignored <Contig>
|
|
277
|
+
INFO bio-gff3: Cache calls After reading files = 0 <>
|
|
278
|
+
INFO bio-gff3: Cache hits After reading files = 0 <>
|
|
279
|
+
INFO bio-gff3: Cache misses After reading files = 0 <>
|
|
280
|
+
WARN bio-gff3: Could not find container/component for <MhA1_Contig0.frz3.fgene1>
|
|
@@ -1,4 +1,3 @@
|
|
|
1
|
-
INFO bio-gff3: Memory used BaseLine RAM 10M, VMEM 14M
|
|
2
1
|
INFO bio-gff3: ---- Digest DB and store data in mRNA Hash (LruCache) <>
|
|
3
2
|
INFO bio-gff3: Added transcript with component ID Transcript:trans-1 <>
|
|
4
3
|
INFO bio-gff3: Adding exon <Transcript:trans-1> <>
|
|
@@ -60,5 +59,4 @@ TATTTGCCACCTAGAAGCGCAACATGCCCAGCTTCACACACCATAGCGAACACGCCGCCCCGGTGGCGACTATCGGTCGA
|
|
|
60
59
|
TATTTGCCACCTAGAAGCGCAACATGCCCAGCTTCACACACCATAGCGAACACGCCGCCCCGGTGGCGACTATCGGTCGAAGTTAAGACAATTCATGGGCGAAACGAGATAATGGGTACTGCACCCCTCGTCCTGTAGAGACGTCACAGCCAACGTGCCTTCTTATCTTGATACATTAGT
|
|
61
60
|
INFO bio-gff3: Cache calls After iterating = 54 <>
|
|
62
61
|
INFO bio-gff3: Cache hits After iterating = 37 <>
|
|
63
|
-
INFO bio-gff3: Cache misses After iterating = 17 <>
|
|
64
|
-
INFO bio-gff3: Memory used Done RAM 10M, VMEM 14M
|
|
62
|
+
INFO bio-gff3: Cache misses After iterating = 17 <>
|
|
@@ -1,4 +1,3 @@
|
|
|
1
|
-
INFO bio-gff3: Memory used BaseLine RAM 10M, VMEM 14M
|
|
2
1
|
INFO bio-gff3: ---- Digest DB and store data in mRNA Hash (LruCache) <>
|
|
3
2
|
INFO bio-gff3: Added transcript with component ID Transcript:trans-1 <>
|
|
4
3
|
INFO bio-gff3: Adding exon <Transcript:trans-1> <>
|
|
@@ -64,5 +63,4 @@ TGGCGACTATCGGTCGAAGTTAAGACATTCATGGGC
|
|
|
64
63
|
TTCATGGGC
|
|
65
64
|
INFO bio-gff3: Cache calls After iterating = 76 <>
|
|
66
65
|
INFO bio-gff3: Cache hits After iterating = 52 <>
|
|
67
|
-
INFO bio-gff3: Cache misses After iterating = 24 <>
|
|
68
|
-
INFO bio-gff3: Memory used Done RAM 10M, VMEM 14M
|
|
66
|
+
INFO bio-gff3: Cache misses After iterating = 24 <>
|
|
@@ -1,4 +1,3 @@
|
|
|
1
|
-
INFO bio-gff3: Memory used BaseLine RAM 10M, VMEM 14M
|
|
2
1
|
INFO bio-gff3: ---- Digest DB and store data in mRNA Hash (NoCache) <>
|
|
3
2
|
INFO bio-gff3: Added transcript with component ID Transcript:trans-1 <>
|
|
4
3
|
INFO bio-gff3: Adding exon <Transcript:trans-1> <>
|
|
@@ -54,5 +53,4 @@ GAAGATTTGTAT
|
|
|
54
53
|
TATTTGCCACCTAGAAGCGCAACATGCCCAGCTTCACACACCATAGCGAACACGCCGCCCCGGTGGCGACTATCGGTCGAAGTTAAGACAATTCATGGGCGAAACGAGATAATGGGTACTGCACCCCTC
|
|
55
54
|
INFO bio-gff3: find_component: Matched seqname <test01>
|
|
56
55
|
>mrna01a Sequence:test01_1:400 (101:280)
|
|
57
|
-
TATTTGCCACCTAGAAGCGCAACATGCCCAGCTTCACACACCATAGCGAACACGCCGCCCCGGTGGCGACTATCGGTCGAAGTTAAGACAATTCATGGGCGAAACGAGATAATGGGTACTGCACCCCTCGTCCTGTAGAGACGTCACAGCCAACGTGCCTTCTTATCTTGATACATTAGT
|
|
58
|
-
INFO bio-gff3: Memory used Done RAM 10M, VMEM 14M
|
|
56
|
+
TATTTGCCACCTAGAAGCGCAACATGCCCAGCTTCACACACCATAGCGAACACGCCGCCCCGGTGGCGACTATCGGTCGAAGTTAAGACAATTCATGGGCGAAACGAGATAATGGGTACTGCACCCCTCGTCCTGTAGAGACGTCACAGCCAACGTGCCTTCTTATCTTGATACATTAGT
|
|
@@ -1,4 +1,3 @@
|
|
|
1
|
-
INFO bio-gff3: Memory used BaseLine RAM 10M, VMEM 14M
|
|
2
1
|
INFO bio-gff3: ---- Digest DB and store data in mRNA Hash (NoCache) <>
|
|
3
2
|
INFO bio-gff3: Added transcript with component ID Transcript:trans-1 <>
|
|
4
3
|
INFO bio-gff3: Adding exon <Transcript:trans-1> <>
|
|
@@ -58,5 +57,4 @@ GAAGATTTGTAT
|
|
|
58
57
|
TGGCGACTATCGGTCGAAGTTAAGACATTCATGGGC
|
|
59
58
|
INFO bio-gff3: find_component: Matched seqname <test01>
|
|
60
59
|
>cds2 Sequence:test01_1:400 (192:200)
|
|
61
|
-
TTCATGGGC
|
|
62
|
-
INFO bio-gff3: Memory used Done RAM 10M, VMEM 14M
|
|
60
|
+
TTCATGGGC
|
data/test/helper.rb
CHANGED
|
@@ -6,9 +6,9 @@
|
|
|
6
6
|
# Copyright:: July 2007
|
|
7
7
|
# License:: Ruby License
|
|
8
8
|
|
|
9
|
-
module
|
|
9
|
+
module RegressionTest2
|
|
10
10
|
|
|
11
|
-
def
|
|
11
|
+
def RegressionTest2.create b
|
|
12
12
|
@@test_create = b
|
|
13
13
|
end
|
|
14
14
|
|
|
@@ -16,12 +16,12 @@ module RegressionTest
|
|
|
16
16
|
# in test/regression with +filename+. When +create+ is +true+ the file
|
|
17
17
|
# will be created/overwritten. Otherwise it is tested against returning
|
|
18
18
|
# whether it has equal or not. When a test fails both test file and new
|
|
19
|
-
# file exist in the
|
|
19
|
+
# file exist in the regression directory - so you can execute a diff.
|
|
20
20
|
#
|
|
21
21
|
# Example:
|
|
22
|
-
#
|
|
22
|
+
# RegressionTest2.test `#{cfrubybin} --help`,'cfruby_helptext',$test_create
|
|
23
23
|
|
|
24
|
-
def
|
|
24
|
+
def RegressionTest2.test text, filename, testdir, create = @@test_create
|
|
25
25
|
fn = testdir+'/'+filename+'.rtest'
|
|
26
26
|
fntest = fn+'.new'
|
|
27
27
|
|
data/test/test_bio-gff3.rb
CHANGED
|
@@ -1,18 +1,26 @@
|
|
|
1
|
+
# To recreate the regression files:
|
|
2
|
+
#
|
|
3
|
+
# ruby -Itest test/test_bio-gff3.rb --create
|
|
4
|
+
|
|
1
5
|
$: << '.'
|
|
2
6
|
do_create = if ARGV[0] == '-c' or ARGV[0] == '--create'
|
|
3
7
|
ARGV.shift
|
|
4
8
|
end
|
|
9
|
+
|
|
10
|
+
$:.unshift "../regressiontest/lib" # override gem location, when available
|
|
5
11
|
|
|
6
12
|
require 'test/unit'
|
|
7
13
|
require 'regressiontest'
|
|
14
|
+
require 'regressiontest2'
|
|
15
|
+
|
|
16
|
+
RegressionTest2.create(do_create)
|
|
8
17
|
|
|
9
|
-
|
|
18
|
+
rootpath = File.join(File.dirname(__FILE__),'..')
|
|
19
|
+
DAT = rootpath + '/test/data'
|
|
20
|
+
BIN = rootpath + '/bin/gff3-fetch'
|
|
10
21
|
|
|
11
22
|
class Gff3Test < Test::Unit::TestCase
|
|
12
23
|
|
|
13
|
-
rootpath = File.join(File.dirname(__FILE__),'..')
|
|
14
|
-
BIN = rootpath + '/bin/gff3-fetch'
|
|
15
|
-
DAT = rootpath + '/test/data'
|
|
16
24
|
def test_cache
|
|
17
25
|
assert_equal(true,single_run("mRNA #{DAT}/gff/test-ext-fasta.fa #{DAT}/gff/test-ext-fasta.gff3",'test_ext_gff3'))
|
|
18
26
|
assert_equal(true,single_run("CDS #{DAT}/gff/test.gff3",'test_gff3'))
|
|
@@ -28,15 +36,32 @@ class Gff3Test < Test::Unit::TestCase
|
|
|
28
36
|
assert_equal(true,single_run("CDS --cache lru #{DAT}/gff/test.gff3",this_method+'_gff3'))
|
|
29
37
|
end
|
|
30
38
|
|
|
39
|
+
def test_latest_wormbase
|
|
40
|
+
opts = "CDS #{DAT}/gff/m_hapla.WS232.genomic.part.fa #{DAT}/gff/m_hapla.WS232.annotations.part.gff3"
|
|
41
|
+
arg1 = this_method + '_ext_gff3'
|
|
42
|
+
|
|
43
|
+
bin = File.expand_path(BIN)
|
|
44
|
+
cmd = "#{bin} --logger stdout #{opts}"
|
|
45
|
+
assert_equal(true,RegressionTest::CliExec::exec(cmd,arg1,:ignore => 'Memory used'))
|
|
46
|
+
end
|
|
47
|
+
|
|
31
48
|
private
|
|
32
|
-
|
|
33
|
-
|
|
34
|
-
|
|
49
|
+
|
|
50
|
+
def this_method
|
|
51
|
+
caller[0] =~ /`([^']*)'/ and $1
|
|
52
|
+
end
|
|
35
53
|
|
|
36
54
|
end
|
|
37
55
|
|
|
38
56
|
def single_run opts, name
|
|
39
|
-
|
|
40
|
-
#
|
|
41
|
-
|
|
57
|
+
bin = File.expand_path(BIN)
|
|
58
|
+
cmd = "#{bin} --logger stdout #{opts}"
|
|
59
|
+
if false
|
|
60
|
+
print "Skipping ", cmd, "!\n"
|
|
61
|
+
else
|
|
62
|
+
text = `#{cmd}`.split(/\n/).delete_if { | s | s =~ /Memory/ }.join("\n")
|
|
63
|
+
|
|
64
|
+
RegressionTest2.test text,name,"#{DAT}/regression"
|
|
65
|
+
end
|
|
66
|
+
true
|
|
42
67
|
end
|
metadata
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: bio-gff3
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 0.
|
|
4
|
+
version: 0.9.0
|
|
5
5
|
prerelease:
|
|
6
6
|
platform: ruby
|
|
7
7
|
authors:
|
|
@@ -9,11 +9,11 @@ authors:
|
|
|
9
9
|
autorequire:
|
|
10
10
|
bindir: bin
|
|
11
11
|
cert_chain: []
|
|
12
|
-
date:
|
|
12
|
+
date: 2012-08-20 00:00:00.000000000Z
|
|
13
13
|
dependencies:
|
|
14
14
|
- !ruby/object:Gem::Dependency
|
|
15
15
|
name: bio
|
|
16
|
-
requirement: &
|
|
16
|
+
requirement: &26586340 !ruby/object:Gem::Requirement
|
|
17
17
|
none: false
|
|
18
18
|
requirements:
|
|
19
19
|
- - ! '>='
|
|
@@ -21,10 +21,10 @@ dependencies:
|
|
|
21
21
|
version: 1.3.1
|
|
22
22
|
type: :runtime
|
|
23
23
|
prerelease: false
|
|
24
|
-
version_requirements: *
|
|
24
|
+
version_requirements: *26586340
|
|
25
25
|
- !ruby/object:Gem::Dependency
|
|
26
26
|
name: log4r
|
|
27
|
-
requirement: &
|
|
27
|
+
requirement: &26584780 !ruby/object:Gem::Requirement
|
|
28
28
|
none: false
|
|
29
29
|
requirements:
|
|
30
30
|
- - ! '>'
|
|
@@ -32,10 +32,10 @@ dependencies:
|
|
|
32
32
|
version: 1.1.6
|
|
33
33
|
type: :runtime
|
|
34
34
|
prerelease: false
|
|
35
|
-
version_requirements: *
|
|
35
|
+
version_requirements: *26584780
|
|
36
36
|
- !ruby/object:Gem::Dependency
|
|
37
37
|
name: bio-logger
|
|
38
|
-
requirement: &
|
|
38
|
+
requirement: &26583820 !ruby/object:Gem::Requirement
|
|
39
39
|
none: false
|
|
40
40
|
requirements:
|
|
41
41
|
- - ! '>'
|
|
@@ -43,10 +43,10 @@ dependencies:
|
|
|
43
43
|
version: 0.8.0
|
|
44
44
|
type: :runtime
|
|
45
45
|
prerelease: false
|
|
46
|
-
version_requirements: *
|
|
46
|
+
version_requirements: *26583820
|
|
47
47
|
- !ruby/object:Gem::Dependency
|
|
48
48
|
name: shoulda
|
|
49
|
-
requirement: &
|
|
49
|
+
requirement: &26581520 !ruby/object:Gem::Requirement
|
|
50
50
|
none: false
|
|
51
51
|
requirements:
|
|
52
52
|
- - ! '>='
|
|
@@ -54,51 +54,51 @@ dependencies:
|
|
|
54
54
|
version: '0'
|
|
55
55
|
type: :development
|
|
56
56
|
prerelease: false
|
|
57
|
-
version_requirements: *
|
|
57
|
+
version_requirements: *26581520
|
|
58
58
|
- !ruby/object:Gem::Dependency
|
|
59
59
|
name: bundler
|
|
60
|
-
requirement: &
|
|
60
|
+
requirement: &26579580 !ruby/object:Gem::Requirement
|
|
61
61
|
none: false
|
|
62
62
|
requirements:
|
|
63
63
|
- - ~>
|
|
64
64
|
- !ruby/object:Gem::Version
|
|
65
|
-
version: 1.
|
|
65
|
+
version: 1.1.5
|
|
66
66
|
type: :development
|
|
67
67
|
prerelease: false
|
|
68
|
-
version_requirements: *
|
|
68
|
+
version_requirements: *26579580
|
|
69
69
|
- !ruby/object:Gem::Dependency
|
|
70
70
|
name: jeweler
|
|
71
|
-
requirement: &
|
|
71
|
+
requirement: &26578680 !ruby/object:Gem::Requirement
|
|
72
72
|
none: false
|
|
73
73
|
requirements:
|
|
74
74
|
- - ~>
|
|
75
75
|
- !ruby/object:Gem::Version
|
|
76
|
-
version: 1.
|
|
76
|
+
version: 1.8.3
|
|
77
77
|
type: :development
|
|
78
78
|
prerelease: false
|
|
79
|
-
version_requirements: *
|
|
79
|
+
version_requirements: *26578680
|
|
80
80
|
- !ruby/object:Gem::Dependency
|
|
81
|
-
name:
|
|
82
|
-
requirement: &
|
|
81
|
+
name: rspec
|
|
82
|
+
requirement: &26578060 !ruby/object:Gem::Requirement
|
|
83
83
|
none: false
|
|
84
84
|
requirements:
|
|
85
85
|
- - ! '>='
|
|
86
86
|
- !ruby/object:Gem::Version
|
|
87
|
-
version:
|
|
87
|
+
version: 2.10.0
|
|
88
88
|
type: :development
|
|
89
89
|
prerelease: false
|
|
90
|
-
version_requirements: *
|
|
90
|
+
version_requirements: *26578060
|
|
91
91
|
- !ruby/object:Gem::Dependency
|
|
92
|
-
name:
|
|
93
|
-
requirement: &
|
|
92
|
+
name: regressiontest
|
|
93
|
+
requirement: &26577240 !ruby/object:Gem::Requirement
|
|
94
94
|
none: false
|
|
95
95
|
requirements:
|
|
96
96
|
- - ! '>='
|
|
97
97
|
- !ruby/object:Gem::Version
|
|
98
|
-
version:
|
|
98
|
+
version: '0'
|
|
99
99
|
type: :development
|
|
100
100
|
prerelease: false
|
|
101
|
-
version_requirements: *
|
|
101
|
+
version_requirements: *26577240
|
|
102
102
|
description: ! 'GFF3 (genome browser) information and digest mRNA and CDS sequences.
|
|
103
103
|
|
|
104
104
|
Options for low memory use and caching of records.
|
|
@@ -114,6 +114,7 @@ extra_rdoc_files:
|
|
|
114
114
|
- LICENSE.txt
|
|
115
115
|
- README.rdoc
|
|
116
116
|
files:
|
|
117
|
+
- .travis.yml
|
|
117
118
|
- Gemfile
|
|
118
119
|
- Gemfile.lock
|
|
119
120
|
- LICENSE.txt
|
|
@@ -152,6 +153,8 @@ files:
|
|
|
152
153
|
- test/data/gff/MhA1_Contig1133.gff3
|
|
153
154
|
- test/data/gff/MhA1_Contig125.fa
|
|
154
155
|
- test/data/gff/MhA1_Contig125.gff3
|
|
156
|
+
- test/data/gff/m_hapla.WS232.annotations.part.gff3
|
|
157
|
+
- test/data/gff/m_hapla.WS232.genomic.part.fa
|
|
155
158
|
- test/data/gff/standard.gff3
|
|
156
159
|
- test/data/gff/test-cds.gff3
|
|
157
160
|
- test/data/gff/test-ext-fasta.fa
|
|
@@ -159,12 +162,14 @@ files:
|
|
|
159
162
|
- test/data/gff/test.gff3
|
|
160
163
|
- test/data/regression/test_ext_gff3.rtest
|
|
161
164
|
- test/data/regression/test_gff3.rtest
|
|
165
|
+
- test/data/regression/test_latest_wormbase_ext_gff3.ref
|
|
166
|
+
- test/data/regression/test_latest_wormbase_ext_gff3.rtest
|
|
162
167
|
- test/data/regression/test_lrucache_ext_gff3.rtest
|
|
163
168
|
- test/data/regression/test_lrucache_gff3.rtest
|
|
164
169
|
- test/data/regression/test_nocache_ext_gff3.rtest
|
|
165
170
|
- test/data/regression/test_nocache_gff3.rtest
|
|
166
171
|
- test/helper.rb
|
|
167
|
-
- test/
|
|
172
|
+
- test/regressiontest2.rb
|
|
168
173
|
- test/test_bio-gff3.rb
|
|
169
174
|
homepage: https://github.com/pjotrp/bioruby-gff3-plugin
|
|
170
175
|
licenses:
|
|
@@ -179,6 +184,9 @@ required_ruby_version: !ruby/object:Gem::Requirement
|
|
|
179
184
|
- - ! '>='
|
|
180
185
|
- !ruby/object:Gem::Version
|
|
181
186
|
version: '0'
|
|
187
|
+
segments:
|
|
188
|
+
- 0
|
|
189
|
+
hash: -3577199160742117809
|
|
182
190
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
|
183
191
|
none: false
|
|
184
192
|
requirements:
|
|
@@ -187,17 +195,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
|
187
195
|
version: '0'
|
|
188
196
|
requirements: []
|
|
189
197
|
rubyforge_project:
|
|
190
|
-
rubygems_version: 1.8.
|
|
198
|
+
rubygems_version: 1.8.10
|
|
191
199
|
signing_key:
|
|
192
200
|
specification_version: 3
|
|
193
201
|
summary: GFF3 parser for big data
|
|
194
|
-
test_files:
|
|
195
|
-
- spec/gff3_assemble2_spec.rb
|
|
196
|
-
- spec/gff3_assemble3_spec.rb
|
|
197
|
-
- spec/gff3_assemble_spec.rb
|
|
198
|
-
- spec/gff3_fileiterator_spec.rb
|
|
199
|
-
- spec/gffdb_spec.rb
|
|
200
|
-
- spec/gffparserec.rb
|
|
201
|
-
- test/helper.rb
|
|
202
|
-
- test/regressiontest.rb
|
|
203
|
-
- test/test_bio-gff3.rb
|
|
202
|
+
test_files: []
|