| Previous changeset 1:16ecf25d521f (2014-03-27) Next changeset 3:02c13ef1a669 (2015-03-27) |
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Commit message:
Uploaded v0.2.0, adds desired count mode |
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modified:
tools/sample_seqs/README.rst tools/sample_seqs/sample_seqs.py tools/sample_seqs/sample_seqs.xml tools/sample_seqs/tool_dependencies.xml |
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added:
test-data/MID4_GLZRM4E04_rnd30_frclip.pair_sample_N5.sff test-data/MID4_GLZRM4E04_rnd30_frclip.sample_C1.sff test-data/ecoli.pair_sample_N100.fastq test-data/ecoli.sample_C10.fastq test-data/get_orf_input.Suis_ORF.prot.pair_sample_C10.fasta test-data/get_orf_input.Suis_ORF.prot.pair_sample_N100.fasta test-data/get_orf_input.Suis_ORF.prot.sample_C10.fasta |
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| diff -r 16ecf25d521f -r da64f6a9e32b test-data/MID4_GLZRM4E04_rnd30_frclip.pair_sample_N5.sff |
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| Binary file test-data/MID4_GLZRM4E04_rnd30_frclip.pair_sample_N5.sff has changed |
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| diff -r 16ecf25d521f -r da64f6a9e32b test-data/MID4_GLZRM4E04_rnd30_frclip.sample_C1.sff |
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| Binary file test-data/MID4_GLZRM4E04_rnd30_frclip.sample_C1.sff has changed |
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| diff -r 16ecf25d521f -r da64f6a9e32b test-data/ecoli.pair_sample_N100.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ecoli.pair_sample_N100.fastq Fri Mar 06 11:48:09 2015 -0500 |
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| @@ -0,0 +1,208 @@ +@frag_1 +AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTC ++ +##%')+.024JMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_1_a +GAGACATATTGCCCGTTGCAGTCAGAATGAAAAGCT ++ +MMMMMMMMMMMMMMMMMMMMMMMMMJ420.+)'%## +@frag_200 +TGGTAATGGTGATGGTGGTGGTAATGGTGGTGCTAA ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_201 +TAGCACCACCATTACCACCACCATCACCATTACCAC ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_400 +TGGCCACCTGCCCCTGCCTGGCATTGCTTTCCAGAA ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_401 +TCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCAC ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_600 +TTGGGCAAATTCCTGATCGACGAAAGTTTTCAATTG ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_601 +AATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAA ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_800 +ATATCGACGGTAGATTCGAGGTAATGCCCCACTGCC ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_801 +GCAGTGGGGCATTACCTCGAATCTACCGTCGATATT ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_1000 +TATAGACCCCGTCAACGTCCGTCCAAATCTCGCAAC ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_1001 +TTGCGAGATTTGGACGGACGTTGACGGGGTCTATAC ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_1200 +ATCACGGCTGGCACCAATGAGCGTACCTGGTGCTTG ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_1201 +AAGCACCAGGTACGCTCATTGGTGCCAGCCGTGATG ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_1400 +CAGTCGCTTTGTGGAACGCAGAAACTGATGCTGTAT ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_1401 +TACAGCATCAGTTTCTGCGTTCCACAAAGCGACTGT ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_1600 +ATCCCTGAGCAATGGCGACAATGTTGATATTGGCGC ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_1601 +CGCCAATATCAACATTGTCGCCATTGCTCAGGGATC ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_1800 +GACACGTAAGTCGATATGTTTATTCTTCAGCCAGCT ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_1801 +GCTGGCTGAAGAATAAACATATCGACTTACGTGTCT ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_2000 +AAGTCGGCATATTGATCCGCCACTGCCTGGCTGGAA ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_2001 +TCCAGCCAGGCAGTGGCGGATCAATATGCCGACTTC ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_2200 +CGGAGAACTTCATCAATTCATCACCTGCATTGAGCA ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_2201 +GCTCAATGCAGGTGATGAATTGATGAAGTTCTCCGG ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_2400 +TTCAATATCCGCCAGCTCCAGTTCACGTCCCGTTTC ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_2401 +AAACGGGACGTGAACTGGAGCTGGCGGATATTGAAA ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_2600 +GGATCATTACCATCCACTTCGGCAATCTTCACGCGG ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_2601 +CGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCG ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_2800 +ATTGGCACTGGAAGCCGGGGCATAAACTTTAACCAT ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_2801 +TGGTTAAAGTTTATGCCCCGGCTTCCAGTGCCAATA ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_3000 +TGCTTACCCAGTTCCTGGCAAAAACGCTCCCAGCAC ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_3001 +TGCTGGGAGCGTTTTTGCCAGGAACTGGGTAAGCAA ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_3200 +ACGGTGCCACGTTGTCGTAATGAATGCTGCCGGAGA ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_3201 +CTCCGGCAGCATTCATTACGACAACGTGGCACCGTG ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_3400 +GTGAATGAAGCCTGCCAGATGTCGCCCGTGCGCAAT ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_3401 +TTGCGCACGGGCGACATCTGGCAGGCTTCATTCACG ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_3600 +ACGCGCTGGGCGGTTTCCGGCTTGTCACACAGAGCG ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_3601 +GCTCTGTGTGACAAGCCGGAAACCGCCCAGCGCGTT ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_3800 +GGTCGTGCGGAAAAAACAGCCCCTGATTTTTGCCCA ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_3801 +GGGCAAAAATCAGGGGCTGTTTTTTCCGCACGACCT ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_4000 +CCCGTGGAACAATTCCAGACAACCGACATCGCTTTC ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_4001 +AAAGCGATGTCGGTTGTCTGGAATTGTTCCACGGGC ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_4200 +TTTTCTTGCAGTGGACTGATTTTGCCTCGTGGATAG ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_4201 +TATCCACGAGGCAAAATCAGTCCACTGCAAGAAAAA ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_4400 +GCGGCAGCTGCGCAACAGCTTCAAAGTAGTAGCAAA ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_4401 +TTGCTACTACTTTGAAGCTGTTGCGCAGCTGCCGCA ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_4600 +CATCGCGTTGGATAACGTCGCCTGAGTCGCTTTGGG ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_4601 +CCAAAGCGACTCAGGCGACGTTATCCAACGCGATGG ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_4800 +CCTGGATTCAACTGATCACGCAGCGCACGATAAGCT ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_4801 +GCTTATCGTGCGCTGCGTGATCAGTTGAATCCAGGC ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_5000 +AGATAATGAATAGATTTTACTGATGATTCATCATCA ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_5001 +GATGATGAATCATCAGTAAAATCTATTCATTATCTC ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMK |
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| diff -r 16ecf25d521f -r da64f6a9e32b test-data/ecoli.sample_C10.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ecoli.sample_C10.fastq Fri Mar 06 11:48:09 2015 -0500 |
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| @@ -0,0 +1,40 @@ +@frag_1 +AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTC ++ +##%')+.024JMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_504 +TACGTTCGGCATCGCTGATATTGGGTAAAGCATCCT ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_1008 +GTCGCAGGTATAGACCCCGTCAACGTCCGTCCAAAT ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_1512 +ATCACCTACCACCGAGATAATGGCCAGCCGTTCCGT ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_2016 +GAAACCTTCGCGCAGGAAGTCGGCATATTGATCCGC ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_2520 +TCCTTCATCACGGGCCTTCGCCACGCGCGCGGCAAA ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_3024 +TCCAGGGTCATCGCCACTGGAATTTGCTTACCCAGT ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_3528 +ACCGCGCCGATTTCCGCGACCGCCTGCCGCGCCTGC ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_4032 +CGACCGCCGAAATCTTTAAATGCCAGCGTTGGCCCG ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +@frag_4536 +GGCACGGTATCGTTCACGTTGGTCGCAGCAATAAAA ++ +MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM |
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| diff -r 16ecf25d521f -r da64f6a9e32b test-data/get_orf_input.Suis_ORF.prot.pair_sample_C10.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/get_orf_input.Suis_ORF.prot.pair_sample_C10.fasta Fri Mar 06 11:48:09 2015 -0500 |
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| @@ -0,0 +1,119 @@ +>Streptococcus_suis|ORF1 length 457 aa, 1374 bp, from 1..1374 of Streptococcus_suis +MNQEQLFWQRFIELAKVNFKPSIYDFYVADAKLLGINQQVANIFLNRPFKKDFWEKNFEE +LMIAASFESYGEPLTIQYQFTEDEQEIRNTTNTRSSIVHQVQTLEPATPQETFKPVHSDI +KSQYTFANFVQGDNNHWAKAAALAVSDNLGELYNPLFIFGGPGLGKTHILNAIGNKVLAD +NPQARIKYVSSETFINEFLEHLRLNDMESFKKTYRNLDLLLIDDIQSLRNKATTQEEFFH +TFNALHEKNKQIVLTSDRNPDHLDNLEERLVTRFKWGLTSEITPPDFETRIAILRNKCEN +LPYNFTNETLSYLAGQFDSNVRDLEGALKDIHLIATMRQLSEISVEVAAEAIRSRKQTNP +QNMVIPIEKIQTEVGNFYGVSLKELKGSKRVQHIVHARQVAMFLAREMTDNSLPKIGKEF +GNRDHTTVMHAYNKIKTLLLDDENLEIEITSIKNKLR +>Streptococcus_suis|ORF2 length 385 aa, 1158 bp, from 1507..2664 of Streptococcus_suis +IINKGESMIQFSINKNIFLQALSITKRAISTKNAIPILSTVKITVTSEGITLTGSNGQIS +IEHFISIQDENAGLLISSPGSILLEAGFFINVVSSMPDLVLDFNEIEQKQIVLTSGKSEI +TLKGKEAEQYPRLQEVPTSKPLVLETKVLKQTINETAFAASTQESRPILTGVHFVLTENK +NLKTVATDSHRMSQRKLVLDTSGDDFNVVIPSRSLREFTAVFTDDIETVEVFFSNNQILF +RSEHISFYTRLLEGTYPDTDRLIPTEFKTTAIFDTANLRHSMERARLLSNATQNGTVKLE +IANNVVSAHVNSPEVGRVNEELDTVEVSGEDLVISFNPTYLIEALKATTSEQVKISFISS +VRPFTLIPNNEGEDFIQLVTPVRTN +>Streptococcus_suis|ORF291 length 760 aa, 2283 bp, from complement(184307..186589) of Streptococcus_suis +KRGEFMRFNQFSFIKKETSVYLQELDTLGFQLIPDASSKTNLETFVRKCHFLTANTDFAL +SNMIAEWDTDLLTFFQSDRELTDQIFYQVAFQLLGFVPGMDYTDVMDFVEKSNFPIVYGD +IIDNLYQLLNTRTKSGNTLIDQLVSDDLIPEDNHYHFFNGKSMATFSTKNLIREVVYVET +PVDTAGTGQTDIVKLSILRPHFDGKIPAVITNSPYHQGVNDVASDKALHKMEGELAEKQV +GTIQVKQASITKLDLDQRNLPVSPATEKLGHITSYSLNDYFLARGFASLHVSGVGTLGST +GYMTSGDYQQVEGYKAVIDWLNGRTKAYTDHTRSLEVKADWANGKVATTGLSYLGTMSNA +LATTGVDGLEVIIAEAGISSWYDYYRENGLVTSPGGYPGEDLDSLTALTYSKSLQAGDFL +RNKAAYEKGLAAERAALDRTSGDYNQYWHDRNYLLHADRVKCEVVFTHGSQDWNVKPIHV +WNMFHALPSHIKKHLFFHNGAHVYMNNWQSIDFRESMNALLSQKLLGYENNYQLPTVIWQ +DNSGEQTWTTLDTFGGENETVLPLGTGSQTVANQYTQEDFERYGKSYSAFHQDLYAGKAN +QISIELPVTEGLLLNGQVTLKLRVASSVAKGLLSAQLLDKGNKKRLAPIPAPKARLSLDN +GRYHAQENLVELPYVEMPQRLVTKGFMNLQNRTDLMTVEEVVPGQWMNLTWKLQPTIYQL +KKGDVLELILYTTDFECTVRDNSQWQIHLDLSQSQLILPH +>Streptococcus_suis|ORF292 length 216 aa, 651 bp, from 185183..185833 of Streptococcus_suis +AVGKDHLTLDPISVEQIIAVMPVLIVVTAGAVQGSTLGSQSFFVGCFIAEEVTCLQTLGV +GQGGQAVQIFAWIATRAGHQPVFTVVVIPRGNPCFCDDDFQSVHASCCQGIGHGTEIRQS +RRRYLTIGPIGLDLKRASVVCVGLGATVQPVNHRFIALHLLVVARCHVARRAQRANTRHM +EAGKAASEEVVIEGVRSNVPQFFSSRADRQVPLVQV +>Streptococcus_suis|ORF583 length 391 aa, 1176 bp, from 397805..398980 of Streptococcus_suis +RKKMKKQFELIATAAAGLEAVVGREIRNLGYECQVENGRVRFQGDVKSIIETNIWLRSAD +RIKIIVGQFPAKTFEELFQGVFNLDWENYLPLGCKFPISKAKCVKSKLHNEPSVQAISKK +AVVKKLQKHFSRPEGVPLQEMGAEFKIEVSILKDVATVMIDTTGSSLFKRGYRVEKGGAP +IKENMAAAILQLSNWYPDKPLIDPTCGSGTFCIEAAMLAKNIAPGLKRSFAFEEWPWVED +QLVVALRKEAQASIKTDLVLDITGSDIDARMIEIAKKNAFAAGVEQDIVFKQMRVQDLRT +DKINGVIISNPPYGERLLDDEAIVTLYREMGETFEPLKTWSKFILTSDELFETRFGQQAD +KKRKLYNGTLKVDLYQFFGQRVKRQVQEVQG +>Streptococcus_suis|ORF584 length 487 aa, 1464 bp, from 398981..400444 of Streptococcus_suis +EDIVGEKNSHHLPLDEEKVLDFEVAKDLTIEEAVKKHKEIEAGVTEDDGLLDRYIKQHRA +EIESQKFETKINHLPLVEVADEEKNQGHESAEEVEANESSLTEVSEEIAPIVEELSVTPM +ETLEETVIASTVAMEGLSSVADDSSLELEEDETEDLDHSEGADRDQKKKFYFWSAVGLSM +IGVMATALVWMNSVNKSNTATSSSSTSTSQTSSTASSSTDANVTAFEQLYNSFFTDSSLT +KLKNSEFGKLAELKVLLEKLDKNSDSYTKAKEQYDHLEKAIAAIQAINGQFDKEVVVNGE +IDTTATVKSGESLSATTTGISAVDSLLASVVNFGRSQQEVASATVASEAAVTRNQGADET +VSTGVPATTEVASTTVSGSTTDFGIAVPAGVVLQRDRSRVPYNQAMIDDVNNEAWNFNPG +ILENIVTISQQRGYITGNQYILEKVNIINGNGYYNMFKPDGTYLFSINCKTGYFVGNGAG +HSDALDY +>Streptococcus_suis|ORF873 length 343 aa, 1032 bp, from 605439..606470 of Streptococcus_suis +TLGEETMTNVFKGRHFLAEKDFTRAELEWLIDFSAHLKDLKKRNIPHRYLEGKNIALLFE +KTSTRTRAAFTVASIDLGAHPEYLGANDIQLGKKESTEDTAKVLGRMFDGIEFRGFSQKM +VEELAEFSGVPVWNGLTDAWHPTQMLADYLTVKENFGKLEGLTLVYCGDGRNNVANSLLV +TGAILGVNVHIFSPKELFPEEEVVALAEGFAKESGARVLITDNADEAVKGADVLYTDVWV +SMGEEDKFAERVALLKPYQVNMELVKKAENENLIFLHCLPAFHDTNTVYGKDVAEKFGVE +EMEVTDEVFRSKYARHFDQAENRMHTIKAVMAATLGDPFVPRV +>Streptococcus_suis|ORF874 length 113 aa, 342 bp, from complement(605625..605966) of Streptococcus_suis +VSNIVTAITTVNQSQAFQLAKVFFDSQVVRQHLSWVPCICQTIPYWHTGEFCQFFHHFLT +ETTEFNTVEHTSQNFSSIFCRFFLTKLDVICTKIFWMGTKVNRCYCEGSTSTC +>Streptococcus_suis|ORF1165 length 105 aa, 318 bp, from 811613..811930 of Streptococcus_suis +AYNESVKRKECHLMKQVNMSKIINYLTILGLLILLSAFFLDNWIRDWFFPSSWGNVATML +ILPLLGALILILSIYYKKLWTGLISIFLIISFPLIFGIGYFIFGP +>Streptococcus_suis|ORF1166 length 125 aa, 378 bp, from 811867..812244 of Streptococcus_suis +YLLNNLISSDIRYWLLYIWPLEGVVMNLTLLKRLNLVLYGIAIFLFVMLFLPIGQWFDIV +NVNFKLTFFIIPFFGLASLPTAIYTKNVRQILLSVLLVALYFILFSLITALSGLFHLNFY +SFFFK +>Streptococcus_suis|ORF1455 length 114 aa, 345 bp, from 1026973..1027317 of Streptococcus_suis +SCKLSLHIRWESWMGQGFYCYRFKLIHLRTNSNPFSFFRHLNSHFQHLRNEWTVMLPDSV +LDQDISTSHCRCHHKGTRFDTILHHLMFCASQFFYTSNRNRLCTCPLNFCPHFV +>Streptococcus_suis|ORF1456 length 116 aa, 351 bp, from complement(1027944..1028294) of Streptococcus_suis +YGNACNSRPPTCDKSYSCWETLIYMGLNLVQFHFLISWYNGNMVISILQFFSHILFIYLA +HHLLVTTVDWSRWLKVTGDNQRKINLLILFLAIALGYLVSTFFLELLMMGRSFANM +>Streptococcus_suis|ORF1747 length 335 aa, 1008 bp, from complement(1225218..1226225) of Streptococcus_suis +RMLNTDDTVTIYDVAREAGVSMATVSRVVNGNKNVKENTRKKVLEVIDRLDYRPNAVARG +LASKKTTTVGVVIPNIANAYFATLAKGIDDIADMYKYNIVLANSDENDEKEINVVNTLFS +KQVDGIIFMGYHLTDKIRAEFSRSRTPIVLAGTVDLEHQLPSVNIDYAAASVDAVNLLAK +NNKKIAFVSGPLVDDINGKVRFAGYKQGLKDNGIEFNEGLVFESKYKYEEGYALAERILN +AGATAAYVAEDEIAAGLLNGVSDMGIKVPEDFEIITSDDSLVTKFTRPNLTSINQPLYDI +GAIAMRMLTKIMHKEELENREVVLNHGIKVRKSTK +>Streptococcus_suis|ORF1748 length 377 aa, 1134 bp, from 1226384..1227517 of Streptococcus_suis +TKISLFLPLHARKVSTMSKLHHVKSYLEANKMDLAIFSDPVSIYYLTGYHSDPHERHMML +FVMPDHDSLLFLPALDVERAVATVDFPVAGYMDSENPWQIIKSKLPQKSFSAICAEFDNL +NLTRYHGLQSIFSQPFSDITPLINTMKLIKSRDEIEKMLVAGEFADKAMQVGFNNISLDV +TETDIIAQIEFEMKKQGISKMSFETMVLTGDNAANPHGIPSTNKIENNALLLFDLGVEAL +GYTSDMTRTVAVGKPDQFKKDIYNLTLEAHMAAVNMIKPGVTAGEIDYAARSVIEKAGYG +EYFNHRLGHGLGMSVHEFPSIMEGNDLVIEEGMCFSVEPGIYIPGKVGVRIEDCGYVTKN +GFEVFTKTPKELLYFEG +>Streptococcus_suis|ORF2037 length 234 aa, 705 bp, from complement(1422380..1423084) of Streptococcus_suis +KSMTKTALITGVSSGIGLAQAGIFLENGWRVFGIDLASKPDLAGDFHFLQLDLTGDLSPV +FSWCQSVDVLCNTAGILDDYRPHLDISEDELAQIFAVNFFAVTRLTRPYLQQMVDRQSGI +IINMCSIASSLAGGGGSAYTASKHALAGFTKQLALDYAKDKVQIFGIAPGAVQTGMTQKD +FEPGGLADWVADQTPIGRWTQPSEIAELTFMLATGKLASMQGQIITIDGGWSLK +>Streptococcus_suis|ORF2038 length 112 aa, 339 bp, from 1422849..1423187 of Streptococcus_suis +SSKMPAVLQRTSTDWHQEKTGDKSPVRSSCRKWKSPAKSGLLARSIPKTRQPFSKKIPAC +ARPMPLETPVMRAVLVMDFYPVGRKDIARGRAPHGEAFTLAGHVDEEIGRRL +>Streptococcus_suis|ORF2329 length 160 aa, 483 bp, from 1612284..1612766 of Streptococcus_suis +LIETNWFHHLTGQEGLDVLFFHNLGFRITDQLYLEVRKFHLLQGLSQLLRRWSQESRVKG +ARYIERNHPLDTCFLQQFNRLIHCSHLASDDDLGWCVVVGWGNNPRGNSRTDFFNQVDIC +VENSNHLTSPCWRSQFHIFTTLSNQGNRIFKGQSSRCHQS +>Streptococcus_suis|ORF2330 length 329 aa, 990 bp, from complement(1613050..1614039) of Streptococcus_suis +ARKKDEGIMKTKITELLDIKYPIFQGGMAWVADGDLAGAVSNAGGLGIIGGGNAPKEVVK +ANIDKVKSITDKPFGVNIMLLSPFADDIVDLVIEEGVKVVTTGAGNPGKYMERLHAAGIT +VIPVVPSVALAKRMEKLGVDAVIAEGMEAGGHIGKLTTMTLVRQVVEAVSIPVIAAGGIA +DGAGAAAAFMLGAEAVQVGTRFVVATESNAHQAYKEKVLKAKDIDTTVSASIVGHPVRAI +KNKLSSAYAAAEKDFLAGKISADAIEELGAGALRNAVVDGDVTNGSVMAGQIAGLVSKEE +SCEDILKDIYYGAAKVIREEASRWASVGE +>Streptococcus_suis|ORF2619 length 107 aa, 324 bp, from 1802386..1802709 of Streptococcus_suis +QLCVGSNPINSLFRRNFFVCCISSQSSCYVHTMWFVGIIVEIIVARYIIIAMGNFQCVCP +CRRWSNVLNFRNDTIIQPHVFVLNIQTGVNDCNHHSATICLIFRTCF +>Streptococcus_suis|ORF2620 length 192 aa, 579 bp, from complement(1803558..1804136) of Streptococcus_suis +RLKIPCFQRKEVTMYDSFDKGWFVLQTYSGYENKVKENLLQRAHTYNMLENILRVEIPTQ +TVQVEKNGEVKEVEENRFPGYVLVEMVMTDEAWFVVRNTPNVTGFVGSHGNRSKPTPLLE +EEIRQILVSMGQTVQEFDIDVKVGDTVRIIDGAFTDYTGKITEIDNNKVKMVISMFGNDT +IAEVNLSQIAEL |
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| diff -r 16ecf25d521f -r da64f6a9e32b test-data/get_orf_input.Suis_ORF.prot.pair_sample_N100.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/get_orf_input.Suis_ORF.prot.pair_sample_N100.fasta Fri Mar 06 11:48:09 2015 -0500 |
| b |
| b'@@ -0,0 +1,214 @@\n+>Streptococcus_suis|ORF1 length 457 aa, 1374 bp, from 1..1374 of Streptococcus_suis\n+MNQEQLFWQRFIELAKVNFKPSIYDFYVADAKLLGINQQVANIFLNRPFKKDFWEKNFEE\n+LMIAASFESYGEPLTIQYQFTEDEQEIRNTTNTRSSIVHQVQTLEPATPQETFKPVHSDI\n+KSQYTFANFVQGDNNHWAKAAALAVSDNLGELYNPLFIFGGPGLGKTHILNAIGNKVLAD\n+NPQARIKYVSSETFINEFLEHLRLNDMESFKKTYRNLDLLLIDDIQSLRNKATTQEEFFH\n+TFNALHEKNKQIVLTSDRNPDHLDNLEERLVTRFKWGLTSEITPPDFETRIAILRNKCEN\n+LPYNFTNETLSYLAGQFDSNVRDLEGALKDIHLIATMRQLSEISVEVAAEAIRSRKQTNP\n+QNMVIPIEKIQTEVGNFYGVSLKELKGSKRVQHIVHARQVAMFLAREMTDNSLPKIGKEF\n+GNRDHTTVMHAYNKIKTLLLDDENLEIEITSIKNKLR\n+>Streptococcus_suis|ORF2 length 385 aa, 1158 bp, from 1507..2664 of Streptococcus_suis\n+IINKGESMIQFSINKNIFLQALSITKRAISTKNAIPILSTVKITVTSEGITLTGSNGQIS\n+IEHFISIQDENAGLLISSPGSILLEAGFFINVVSSMPDLVLDFNEIEQKQIVLTSGKSEI\n+TLKGKEAEQYPRLQEVPTSKPLVLETKVLKQTINETAFAASTQESRPILTGVHFVLTENK\n+NLKTVATDSHRMSQRKLVLDTSGDDFNVVIPSRSLREFTAVFTDDIETVEVFFSNNQILF\n+RSEHISFYTRLLEGTYPDTDRLIPTEFKTTAIFDTANLRHSMERARLLSNATQNGTVKLE\n+IANNVVSAHVNSPEVGRVNEELDTVEVSGEDLVISFNPTYLIEALKATTSEQVKISFISS\n+VRPFTLIPNNEGEDFIQLVTPVRTN\n+>Streptococcus_suis|ORF201 length 360 aa, 1083 bp, from complement(128035..129117) of Streptococcus_suis\n+SCHGGRRMTLFGKIKEVTELQSLPGFEGQVRNHIRQKITPHVDRIETDGLGGIFGIKDTA\n+VENAPRILVVAHMDEVGFMISQIKPDGTFRVVELGGWNPLVVSSQAFTLQLQDGRTIPAI\n+SGSVPPHLSRGANAPGMPAIADIIFDAGFANYDEAWAFGVRPGDVLVPKNETILTANGKN\n+VISKAWDNRFGVLMVTELLESLSGHALPNQLIAGANVQEEVGLRGAHASTTKFNPDIFLA\n+VDCSPAGDIYGDQGKIGDGTLLRFYDPGHIMLKNMKDFLLTTAEEAGVKFQYYCGKGGTD\n+AGAAHLKNHGVPSTTIGVCARYIHSHQTLYSMDDFLEAQAFLQTIVKKLDRSTVDLIKNY\n+>Streptococcus_suis|ORF202 length 106 aa, 321 bp, from 128792..129112 of Streptococcus_suis\n+RVKAWLETTRGFQPPSSTTRKVPSGLIWLIIKPTSSMWATTRIRGAFSTAVSLIPKIPPS\n+PSVSMRSTCGVIFWRMWLRTCPSNPGKLCNSVTSLIFPKRVILLPP\n+>Streptococcus_suis|ORF401 length 120 aa, 363 bp, from 265643..266005 of Streptococcus_suis\n+TTGTTSPIAPKWKASSKSLRVPTSEPTTLIPSSTVFTILRSMYSDGSPTATTYPPARTLS\n+IAWLKATLETAVTTVECTPPPVISLIYPGTSSTSSPLIVTSAPTSLASSNLSLLMSTAIT\n+>Streptococcus_suis|ORF402 length 201 aa, 606 bp, from 265741..266346 of Streptococcus_suis\n+HSLHDTEVHVFRWKSDSYYISTSTNTVNSLVEGYFGNSCYNSRVYTATSNFFNISRNIFY\n+FKSVDRHICTNFFGEFQFIIIDVYGDNMSVEDFFSVLYSKVSKSTSTIDSNPLTWFQVSF\n+FNRFVASNASTSDRTCLSWIKTFWNFYCIVRCYNTLLSHTTVNRVACIFYGTAESFATGC\n+TIFTHTTALEEPSNADTVTNF\n+>Streptococcus_suis|ORF601 length 665 aa, 1998 bp, from 409896..411893 of Streptococcus_suis\n+VMIQIGKIFAGRYRIVRQIGRGGMADVYLARDLILDGEEVAVKVLRTNYQTDQIAIQRFQ\n+REARAMAELDHPNIVRISDIGEEDGQQYLAMEYVNGLDLKRYIKENAPLSNDVAVRIMGQ\n+ILLAMRMAHTRGIVHRDLKPQNVLLTSNGVAKVTDFGIAVAFAETSLTQTNSMLGSVHYL\n+SPEQARGSKATIQSDIYAMGIILFEMLTGRIPYDGDSAVTIALQHFQKPLPSVREENANV\n+PQALENVVLKATAKKLNERYKSVAEMYADLASALSMDRQNEPRVELEGNKVDTKTLPKLS\n+QANVETKVPHTNSSAQVSATDKGSGKKEVAKSGNKPVSKPRPGIRTRYKVLIGAILLTVI\n+AAGLMFFNTPRTVTVPDVSGQTVEKATEMIEVAGLEVGNITEEATATVDEGLVIRTSPAA\n+KTTRRQGSKIDIVVATAALASIPDVVDKESDTARQELEALGFQVTIKEEYSEKVAQGLVI\n+KTDPGANSSAEKGAKITLYVSKGVAPQVVPNVVGKSQENATQILQTAGFSIGTITQEYSS\n+SVTAGQVISTDPVANTELAKGSIINLVISKGKELIMPDLTSGNYTYSQARSQLQALGVNA\n+ESIEKQEDRSYYSTTSDIVIGQYPAAGATIDGTVTLYVSVASTRTSSDSSAGSSTSTSTS\n+TGSGQ\n+>Streptococcus_suis|ORF602 length 120 aa, 363 bp, from complement(410593..410955) of Streptococcus_suis\n+LLSRLCSVYVCLALVLKQAYFPTSPLLSYQTPYPSQKLEQNCLYAVLSFQHWLGRVSARF\n+LYQPCSLLVQPWVHSDDPWIEPKLNLHTFLQPTYSARLIFLPLLLVQHFLRPEVRWHSLL\n+>Streptococcus_suis|ORF801 length 428 aa, 1287 bp, from 561960..563246 of Streptococcus_suis\n+KSSRDCESCLLLFVILKVMQADRRKTFGKMRIRINNLFFVAIAFMGIIISNSQVVLAIGK\n+ASVIQYLSYLVLILCIVNDLLKNNKHIVVYKLGYLFLIIFLFTIGICQQILPITTKIYLS\n+ISMMIISVLATLPISLIKDIDDFRRISNHLLFALFITSILGIMMGATMFTGAVEGIGFSQ\n+GFNGGLTHKNFFGITILMGFVLTYLAYKYGSYKRTDRFILGLELFLILISNTRSVYLILL\n+LFLFLVNLDKIKIEQRQWSTLKYISMLFCAIFLYYFFGFLITHSDSYAHRVNGLINFFEY\n+YRNDWFHLMFGAADLAYGDLTLDYAIRVRRVLGWNGTLEMPLLSIMLKNGFIGLVGYGIV\n+LYKLYRNVRILKTDNIKTIGKSVFIIVVLSATVENYIVNLSFVFMPICFCLLNSISTMES\n+TINKQLQT\n+>Streptococcus_suis|ORF802 length 333 aa, 1002 bp, from 563382..564383 of Streptococcus_suis\n+RMEKVSIIVPIFNTEKYLRECLDSIISQSYTNLEILLIDDGSSDSSTDICLEYAEQDGRI\n+KLFRLPNGGVSNARNYGIKNSTANYIMFV'..b'SQQIETYHSIRETIQFGQLYRLKKTSNTWAANYVSQ\n+DKNQVVFTFVKILAKPEAPLLHVRLKGLDPDALYECPQLGETFYGDELMNIGLTMPHVQK\n+DYFSVQYIFNKI\n+>Streptococcus_suis|ORF2201 length 272 aa, 819 bp, from complement(1531599..1532417) of Streptococcus_suis\n+DCSKIKIIDLAVGKLKLLSSKRKGAFMEIIRSKANHLVKQVKKLQQKKYRTSSYLIEGWH\n+LLEEAMEAGANIEHIFVVEEYFEKVAGLANVTVVSPEIMQELADSKTPQGVVAQLALPSQ\n+RLPETLDGKFLVLEDVQDPGNVGTMIRTADAAGFDGVFLSDKSADIYNMKVLRSMQGSHF\n+HLPVYRMPISSILTALKSNQIQILATTLSSQSVDYKEITPHSSFALVMGNEGQGISDLVA\n+DEADQLVHITMPGQAESLNVAIAAGILLFSFI\n+>Streptococcus_suis|ORF2202 length 101 aa, 306 bp, from 1532445..1532750 of Streptococcus_suis\n+MSCQKEKLMRKVKMIASGRVQGVGFRWSVQFLAVEIGDIYGRVWNNDDGTVTILAQSDNA\n+EKLSHFIHEIRKGPSRMAKVIYLDVTLANFEDYKDFQVSYR\n+>Streptococcus_suis|ORF2401 length 141 aa, 426 bp, from 1658030..1658455 of Streptococcus_suis\n+ASITVPIARTVGSAFSSWISATKRTVSNNSSMFWLNLAEISTNSDSPPQAVEITPCSANS\n+PMTRSGFAPGLSILLIATMIGTLAAFEWLIASIVCGMTPSSAATTRMVKSVTDAPRARIE\n+VKAACPGVSKKVIFLPASSIW\n+>Streptococcus_suis|ORF2402 length 266 aa, 801 bp, from 1658515..1659315 of Streptococcus_suis\n+GVQQGCFTMVNVSHDSHNRWAFCHLFFIEVALFYEETLNICVIDLYLFFRFNTIINHEEF\n+DSISIQRLVLSRHNSHKEEFFHNFSRFTFDSFCNFCDGHASSIFKFSWQFVELAFCDRFG\n+RLVSLAFFIFLVVIPVTCSLISHLILTISISLLFPWTIFFVTIKVTFFIWSSLFLTTGIY\n+SSFCNLLWYRCNKCRFHKWFAFHNRFFKLNFFWLLRLLFSFLSLTKTFFTGTSILRILFC\n+FQSSSTRFEVNFRSCWFCSLSLFKAS\n+>Streptococcus_suis|ORF2601 length 100 aa, 303 bp, from 1790150..1790452 of Streptococcus_suis\n+LKDGYQRLVVEGFADIAETFLQTETNLMTTVIFIARHDDDRPIAFPLGSLNQVNMTLVHG\n+SKGPKNNCYCLFHNLPFYCFLYFISYSFLKPKSRVFYIFL\n+>Streptococcus_suis|ORF2602 length 823 aa, 2472 bp, from complement(1790482..1792953) of Streptococcus_suis\n+ERGVVRMKISRGLQGVYEDAQLIAQRYSSDYLETWHLLLAFVINPDTVAGAILAEYPADV\n+LDYERAVYMVMGRRYHEELESFFFLPSSKRVKELQVFAEKIAEIVKSKGLGTEHIFMGML\n+LDKRSTASQILDQVGFHFEDSDDKVRFLDLRKNLEAKAGFTKEHLKAIRTMTKGGKPKQA\n+TVGNMMGMTQSQSGGLEDYTRDLTALARSGQLEPVIGRDEEISRMLQILSRKTKNNPVLV\n+GDAGVGKTALALGLAQRIANGEVPASLVNMRILELDLMNVIAGTRFRGDFEERMNNIIND\n+IEEDGRVILFIDELHTIMGSGSGIDSILDAANILKPALSRGTLRTVGATTQDEYQKHIEK\n+DAALVRRFAKVTIEEPSVADSVAILQGLKPAYEAHHKVTISDQAVVTAVAYAKRYLTSKN\n+LPDSAIDLLDEASATVQNRAKGQVEEGGLTALDQALMAGKYKTVTQLLLKAQEAENQATS\n+YSLEVTEEDILATLSRLSGIPVTKLSQTDAKKYLNLEQELHKRVIGQEEAISAVSRAIRR\n+NQSGIRTGHRPIGSFMFLGPTGVGKTELAKALAEILFDDESALIRFDMSEYMEKFAASRL\n+NGAPPGYVGYEEGGELTEKVRNKPYSVLLFDEVEKAHPDIFNVLLQVLDDGVLTDRKGRK\n+VDFSNTVIIMTSNLGATALRDDKTVGFGALDLSKSQEHVEKRIFEALKKAYRPEFINRID\n+EKVVFHSLTEADMQDVVKVMVKPLIAVAASKGITLKLQASALKLLAKEGYDPEMGARPLR\n+RLLQTKLEDPLAEMLLRGELPAGVTLKVGVKAEQLKFDSVKAG\n+>Streptococcus_suis|ORF2801 length 1006 aa, 3021 bp, from complement(1921434..1924454) of Streptococcus_suis\n+TQTKEYEMIEFRKKAVQLASLMSVFFLCTYSFTDAMYIMAESLSTDGASTIRRTYIEDKK\n+EDKDRLNIELVESLSSPKTIGQKITIDKQSLATQNFNEKGIVVITQKGLELKKDDLEKGW\n+KLDESYNEKDLAITKSETEKRSLSNELDVLSKTVEELPVYGENYHSYRLLPTTELDYSAD\n+NVSLTLSFTKVSEVIKGELVAVVDAEHIAYFKAEPSVFKEYSQVNEKPSSTEDVNVVSPS\n+QDPPVSETKENVPDNPESQGSSTVPESEQAVDALVEQRGVICIKLTKSSSEQEEGIEDTE\n+NEAIEGATFEVRNVESENLVYTGQTDKDGLLTISNLPLGNYAVIQKSTIDGYEISATKEV\n+VELTVAQSRQTVSISNSPKNPLEGLMLNSILDSSLIPRSARVARSLLDTSLLDNPTVTGN\n+ANATTTTTVFGNKTTTITREESNIKYIFKPITISIPGVYQSYSQDGVLKKKEVVVDSNTN\n+TTKIIWEYTTTVGGVNSNITSIRNAFSTTTDSGLGEPKITSIMKDGVAITPNTTYYGNFD\n+NFKSATDNLPVGNGTYVYTIETPVVIPSDNYSLDYRSEVTVDAPKGSKLTYNGTSVTLTQ\n+KETRTLSTADTITLPAKNDGGPLGDLKVDTVNTSNTNRTIGKYRDNDDKVIEWTSSQLND\n+TSTTQSFTFDVALDSSQAAHEYKVYIYEPSNGTYTETKAEKVATPGNQITVDNVPAGAVA\n+LVKTVTNVKDEKVNHTISGAQLEALKGDIKIQKNWEADSDKVDVTFTVNGGSLTNRKETL\n+SANNTQITIANVDKFSGMRSTATKKRIYYDVTEAVPSGYILSSAQTDWENLYYVFTNKKD\n+NTTTPVFPPDTCGNYGVSSIDLVSINYVMYKSGSKIWGGFDGSMKMNLKIPAFARAGDSF\n+TLELPPELKLSHVANPNVAWSTVSANGKVIAKVYHEKDNLIRFVLTTEAYSVQEYNGWFE\n+IGVPTSNVIKINNRETTELYKTGVLPNLPEWYTTTTRNQTLIKRSR\n+>Streptococcus_suis|ORF2802 length 252 aa, 759 bp, from complement(1925855..1926613) of Streptococcus_suis\n+LEARMQQYFVNGRAPQGMFQISDKDTAKHMFSVMRLQAGDQIVLVFDDGIKRLARVVDSQ\n+SQSVEIIEELTDNVELPISVTIAMGFPKGDKLEFVAQKATELGMSALWAFPADWSVVKWD\n+GKKLAKKAEKLEKIAQGAAEQSKRNRIPAVRLFEKKSDFLAQLAGFDQIILAYEEAAKEG\n+EQANLVKILSGLEIGQSVLVIVGPEGGVSPEEVAAFEGAGAVKTGLGPRILRAETAPLYA\n+LSTISYATELLR\n' |
| b |
| diff -r 16ecf25d521f -r da64f6a9e32b test-data/get_orf_input.Suis_ORF.prot.sample_C10.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/get_orf_input.Suis_ORF.prot.sample_C10.fasta Fri Mar 06 11:48:09 2015 -0500 |
| b |
| @@ -0,0 +1,50 @@ +>Streptococcus_suis|ORF1 length 457 aa, 1374 bp, from 1..1374 of Streptococcus_suis +MNQEQLFWQRFIELAKVNFKPSIYDFYVADAKLLGINQQVANIFLNRPFKKDFWEKNFEE +LMIAASFESYGEPLTIQYQFTEDEQEIRNTTNTRSSIVHQVQTLEPATPQETFKPVHSDI +KSQYTFANFVQGDNNHWAKAAALAVSDNLGELYNPLFIFGGPGLGKTHILNAIGNKVLAD +NPQARIKYVSSETFINEFLEHLRLNDMESFKKTYRNLDLLLIDDIQSLRNKATTQEEFFH +TFNALHEKNKQIVLTSDRNPDHLDNLEERLVTRFKWGLTSEITPPDFETRIAILRNKCEN +LPYNFTNETLSYLAGQFDSNVRDLEGALKDIHLIATMRQLSEISVEVAAEAIRSRKQTNP +QNMVIPIEKIQTEVGNFYGVSLKELKGSKRVQHIVHARQVAMFLAREMTDNSLPKIGKEF +GNRDHTTVMHAYNKIKTLLLDDENLEIEITSIKNKLR +>Streptococcus_suis|ORF292 length 216 aa, 651 bp, from 185183..185833 of Streptococcus_suis +AVGKDHLTLDPISVEQIIAVMPVLIVVTAGAVQGSTLGSQSFFVGCFIAEEVTCLQTLGV +GQGGQAVQIFAWIATRAGHQPVFTVVVIPRGNPCFCDDDFQSVHASCCQGIGHGTEIRQS +RRRYLTIGPIGLDLKRASVVCVGLGATVQPVNHRFIALHLLVVARCHVARRAQRANTRHM +EAGKAASEEVVIEGVRSNVPQFFSSRADRQVPLVQV +>Streptococcus_suis|ORF583 length 391 aa, 1176 bp, from 397805..398980 of Streptococcus_suis +RKKMKKQFELIATAAAGLEAVVGREIRNLGYECQVENGRVRFQGDVKSIIETNIWLRSAD +RIKIIVGQFPAKTFEELFQGVFNLDWENYLPLGCKFPISKAKCVKSKLHNEPSVQAISKK +AVVKKLQKHFSRPEGVPLQEMGAEFKIEVSILKDVATVMIDTTGSSLFKRGYRVEKGGAP +IKENMAAAILQLSNWYPDKPLIDPTCGSGTFCIEAAMLAKNIAPGLKRSFAFEEWPWVED +QLVVALRKEAQASIKTDLVLDITGSDIDARMIEIAKKNAFAAGVEQDIVFKQMRVQDLRT +DKINGVIISNPPYGERLLDDEAIVTLYREMGETFEPLKTWSKFILTSDELFETRFGQQAD +KKRKLYNGTLKVDLYQFFGQRVKRQVQEVQG +>Streptococcus_suis|ORF874 length 113 aa, 342 bp, from complement(605625..605966) of Streptococcus_suis +VSNIVTAITTVNQSQAFQLAKVFFDSQVVRQHLSWVPCICQTIPYWHTGEFCQFFHHFLT +ETTEFNTVEHTSQNFSSIFCRFFLTKLDVICTKIFWMGTKVNRCYCEGSTSTC +>Streptococcus_suis|ORF1165 length 105 aa, 318 bp, from 811613..811930 of Streptococcus_suis +AYNESVKRKECHLMKQVNMSKIINYLTILGLLILLSAFFLDNWIRDWFFPSSWGNVATML +ILPLLGALILILSIYYKKLWTGLISIFLIISFPLIFGIGYFIFGP +>Streptococcus_suis|ORF1456 length 116 aa, 351 bp, from complement(1027944..1028294) of Streptococcus_suis +YGNACNSRPPTCDKSYSCWETLIYMGLNLVQFHFLISWYNGNMVISILQFFSHILFIYLA +HHLLVTTVDWSRWLKVTGDNQRKINLLILFLAIALGYLVSTFFLELLMMGRSFANM +>Streptococcus_suis|ORF1747 length 335 aa, 1008 bp, from complement(1225218..1226225) of Streptococcus_suis +RMLNTDDTVTIYDVAREAGVSMATVSRVVNGNKNVKENTRKKVLEVIDRLDYRPNAVARG +LASKKTTTVGVVIPNIANAYFATLAKGIDDIADMYKYNIVLANSDENDEKEINVVNTLFS +KQVDGIIFMGYHLTDKIRAEFSRSRTPIVLAGTVDLEHQLPSVNIDYAAASVDAVNLLAK +NNKKIAFVSGPLVDDINGKVRFAGYKQGLKDNGIEFNEGLVFESKYKYEEGYALAERILN +AGATAAYVAEDEIAAGLLNGVSDMGIKVPEDFEIITSDDSLVTKFTRPNLTSINQPLYDI +GAIAMRMLTKIMHKEELENREVVLNHGIKVRKSTK +>Streptococcus_suis|ORF2038 length 112 aa, 339 bp, from 1422849..1423187 of Streptococcus_suis +SSKMPAVLQRTSTDWHQEKTGDKSPVRSSCRKWKSPAKSGLLARSIPKTRQPFSKKIPAC +ARPMPLETPVMRAVLVMDFYPVGRKDIARGRAPHGEAFTLAGHVDEEIGRRL +>Streptococcus_suis|ORF2329 length 160 aa, 483 bp, from 1612284..1612766 of Streptococcus_suis +LIETNWFHHLTGQEGLDVLFFHNLGFRITDQLYLEVRKFHLLQGLSQLLRRWSQESRVKG +ARYIERNHPLDTCFLQQFNRLIHCSHLASDDDLGWCVVVGWGNNPRGNSRTDFFNQVDIC +VENSNHLTSPCWRSQFHIFTTLSNQGNRIFKGQSSRCHQS +>Streptococcus_suis|ORF2620 length 192 aa, 579 bp, from complement(1803558..1804136) of Streptococcus_suis +RLKIPCFQRKEVTMYDSFDKGWFVLQTYSGYENKVKENLLQRAHTYNMLENILRVEIPTQ +TVQVEKNGEVKEVEENRFPGYVLVEMVMTDEAWFVVRNTPNVTGFVGSHGNRSKPTPLLE +EEIRQILVSMGQTVQEFDIDVKVGDTVRIIDGAFTDYTGKITEIDNNKVKMVISMFGNDT +IAEVNLSQIAEL |
| b |
| diff -r 16ecf25d521f -r da64f6a9e32b tools/sample_seqs/README.rst --- a/tools/sample_seqs/README.rst Thu Mar 27 12:13:22 2014 -0400 +++ b/tools/sample_seqs/README.rst Fri Mar 06 11:48:09 2015 -0500 |
| b |
| @@ -39,11 +39,12 @@ <tool file="sample_seqs/sample_seqs.xml" /> -You will also need to install Biopython 1.62 or later. If you want to run -the unit tests, include this line in ``tools_conf.xml.sample`` and the sample -FASTA files under the ``test-data`` directory. Then:: +You will also need to install Biopython 1.62 or later. - ./run_functional_tests.sh -id sample_seqs +If you wish to run the unit tests, also move/copy the ``test-data/`` files +under Galaxy's ``test-data/`` folder. Then:: + + ./run_tests.sh -id sample_seqs That's it. @@ -55,6 +56,13 @@ Version Changes ------- ---------------------------------------------------------------------- v0.0.1 - Initial version. +v0.1.1 - Using optparse to provide a proper command line API. +v0.1.2 - Interleaved mode for working with paired records. + - Tool definition now embeds citation information. +v0.2.0 - Option to give number of sequences (or pairs) desired. + This works by first counting all your sequences, then calculates + the percentage required in order to sample them uniformly (evenly). + This makes two passes through the input and is therefore slower. ======= ====================================================================== @@ -67,7 +75,7 @@ For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use the following command from the Galaxy root folder:: - $ tar -czf sample_seqs.tar.gz tools/sample_seqs/README.rst tools/sample_seqs/sample_seqs.py tools/sample_seqs/sample_seqs.xml tools/sample_seqs/tool_dependencies.xml test-data/ecoli.fastq test-data/ecoli.sample_N100.fastq test-data/get_orf_input.Suis_ORF.prot.fasta test-data/get_orf_input.Suis_ORF.prot.sample_N100.fasta test-data/MID4_GLZRM4E04_rnd30_frclip.sff test-data/MID4_GLZRM4E04_rnd30_frclip.sample_N5.sff + $ tar -czf sample_seqs.tar.gz tools/sample_seqs/README.rst tools/sample_seqs/sample_seqs.py tools/sample_seqs/sample_seqs.xml tools/sample_seqs/tool_dependencies.xml test-data/ecoli.fastq test-data/ecoli.sample_N100.fastq test-data/ecoli.pair_sample_N100.fastq test-data/ecoli.sample_C10.fastq test-data/get_orf_input.Suis_ORF.prot.fasta test-data/get_orf_input.Suis_ORF.prot.sample_N100.fasta test-data/get_orf_input.Suis_ORF.prot.pair_sample_N100.fasta test-data/get_orf_input.Suis_ORF.prot.sample_C10.fasta test-data/get_orf_input.Suis_ORF.prot.pair_sample_C10.fasta test-data/MID4_GLZRM4E04_rnd30_frclip.sff test-data/MID4_GLZRM4E04_rnd30_frclip.sample_N5.sff test-data/MID4_GLZRM4E04_rnd30_frclip.pair_sample_N5.sff test-data/MID4_GLZRM4E04_rnd30_frclip.sample_C1.sff Check this worked:: @@ -78,10 +86,18 @@ tools/sample_seqs/tool_dependencies.xml test-data/ecoli.fastq test-data/ecoli.sample_N100.fastq + test-data/ecoli.pair_sample_N100.fastq + test-data/ecoli.sample_C10.fastq test-data/get_orf_input.Suis_ORF.prot.fasta test-data/get_orf_input.Suis_ORF.prot.sample_N100.fasta + test-data/get_orf_input.Suis_ORF.prot.pair_sample_N100.fasta + test-data/get_orf_input.Suis_ORF.prot.sample_C10.fasta + test-data/get_orf_input.Suis_ORF.prot.pair_sample_C10.fasta test-data/MID4_GLZRM4E04_rnd30_frclip.sff test-data/MID4_GLZRM4E04_rnd30_frclip.sample_N5.sff + test-data/MID4_GLZRM4E04_rnd30_pair_sample.sff + test-data/MID4_GLZRM4E04_rnd30_frclip.pair_sample_N5.sff + test-data/MID4_GLZRM4E04_rnd30_frclip.sample_C1.sff Licence (MIT) |
| b |
| diff -r 16ecf25d521f -r da64f6a9e32b tools/sample_seqs/sample_seqs.py --- a/tools/sample_seqs/sample_seqs.py Thu Mar 27 12:13:22 2014 -0400 +++ b/tools/sample_seqs/sample_seqs.py Fri Mar 06 11:48:09 2015 -0500 |
| [ |
| b'@@ -2,46 +2,136 @@\n """Sub-sample sequence from a FASTA, FASTQ or SFF file.\n \n This tool is a short Python script which requires Biopython 1.62 or later\n-for SFF file support. If you use this tool in scientific work leading to a\n+for sequence parsing. If you use this tool in scientific work leading to a\n publication, please cite the Biopython application note:\n \n Cock et al 2009. Biopython: freely available Python tools for computational\n molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.\n http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.\n \n-This script is copyright 2010-2013 by Peter Cock, The James Hutton Institute\n+This script is copyright 2014-2015 by Peter Cock, The James Hutton Institute\n (formerly the Scottish Crop Research Institute, SCRI), UK. All rights reserved.\n See accompanying text file for licence details (MIT license).\n \n-This is version 0.1.0 of the script, use -v or --version to get the version.\n+Use -v or --version to get the version, -h or --help for help.\n """\n import os\n import sys\n+from optparse import OptionParser\n \n-def stop_err(msg, err=1):\n+\n+def sys_exit(msg, err=1):\n sys.stderr.write(msg.rstrip() + "\\n")\n sys.exit(err)\n \n-if "-v" in sys.argv or "--version" in sys.argv:\n- print("v0.1.0")\n+#Parse Command Line\n+usage = """Use as follows:\n+\n+$ python sample_seqs.py [options]\n+\n+e.g. Sample 20% of the reads:\n+\n+$ python sample_seqs.py -i my_seq.fastq -f fastq -p 20.0 -o sample.fastq\n+\n+This samples uniformly though the file, rather than at random, and therefore\n+should be reproducible.\n+"""\n+parser = OptionParser(usage=usage)\n+parser.add_option(\'-i\', \'--input\', dest=\'input\',\n+ default=None, help=\'Input sequences filename\',\n+ metavar="FILE")\n+parser.add_option(\'-f\', \'--format\', dest=\'format\',\n+ default=None,\n+ help=\'Input sequence format (e.g. fasta, fastq, sff)\')\n+parser.add_option(\'-o\', \'--output\', dest=\'output\',\n+ default=None, help=\'Output sampled sequenced filename\',\n+ metavar="FILE")\n+parser.add_option(\'-p\', \'--percent\', dest=\'percent\',\n+ default=None,\n+ help=\'Take this percent of the reads\')\n+parser.add_option(\'-n\', \'--everyn\', dest=\'everyn\',\n+ default=None,\n+ help=\'Take every N-th read\')\n+parser.add_option(\'-c\', \'--count\', dest=\'count\',\n+ default=None,\n+ help=\'Take exactly N reads\')\n+parser.add_option("--interleaved", dest="interleaved",\n+ default=False, action="store_true",\n+ help="Input is interleaved reads, preserve the pairings")\n+parser.add_option("-v", "--version", dest="version",\n+ default=False, action="store_true",\n+ help="Show version and quit")\n+options, args = parser.parse_args()\n+\n+if options.version:\n+ print("v0.2.0")\n sys.exit(0)\n \n-#Parse Command Line\n-if len(sys.argv) < 5:\n- stop_err("Requires at least four arguments: seq_format, in_file, out_file, mode, ...")\n-seq_format, in_file, out_file, mode = sys.argv[1:5]\n+in_file = options.input\n+out_file = options.output\n+interleaved = options.interleaved\n+\n+if not in_file:\n+ sys_exit("Require an input filename")\n if in_file != "/dev/stdin" and not os.path.isfile(in_file):\n- stop_err("Missing input file %r" % in_file)\n+ sys_exit("Missing input file %r" % in_file)\n+if not out_file:\n+ sys_exit("Require an output filename")\n+if not options.format:\n+ sys_exit("Require the sequence format")\n+seq_format = options.format.lower()\n+\n+\n+def count_fasta(filename):\n+ from Bio.SeqIO.FastaIO import SimpleFastaParser\n+ count = 0\n+ with open(filename) as handle:\n+ for title, seq in SimpleFastaParser(handle):\n+ count += 1\n+ return count\n+\n+\n+def count_fastq(filename):\n+ from Bio.SeqIO.QualityIO import FastqGeneralIterator\n+ count = 0\n+ with open(filename) as handle:\n+ for titl'..b'ilter(pair(raw_fasta_iterator(in_handle))):\n+ count += 1\n+ pos_handle.write(r1)\n+ pos_handle.write(r2)\n+ else:\n+ for record in iterator_filter(raw_fasta_iterator(in_handle)):\n+ count += 1\n+ pos_handle.write(record)\n return count\n \n-try:\n- from galaxy_utils.sequence.fastq import fastqReader, fastqWriter\n- def fastq_filter(in_file, out_file, iterator_filter):\n- count = 0\n- #from galaxy_utils.sequence.fastq import fastqReader, fastqWriter\n- reader = fastqReader(open(in_file, "rU"))\n- writer = fastqWriter(open(out_file, "w"))\n- for record in iterator_filter(reader):\n- count += 1\n- writer.write(record)\n- writer.close()\n- reader.close()\n- return count\n-except ImportError:\n- from Bio.SeqIO.QualityIO import FastqGeneralIterator\n- def fastq_filter(in_file, out_file, iterator_filter):\n- count = 0\n- with open(in_file) as in_handle:\n- with open(out_file, "w") as pos_handle:\n+\n+from Bio.SeqIO.QualityIO import FastqGeneralIterator\n+def fastq_filter(in_file, out_file, iterator_filter, inter):\n+ count = 0\n+ with open(in_file) as in_handle:\n+ with open(out_file, "w") as pos_handle:\n+ if inter:\n+ for r1, r2 in iterator_filter(pair(FastqGeneralIterator(in_handle))):\n+ count += 1\n+ pos_handle.write("@%s\\n%s\\n+\\n%s\\n" % r1)\n+ pos_handle.write("@%s\\n%s\\n+\\n%s\\n" % r2)\n+ else:\n for title, seq, qual in iterator_filter(FastqGeneralIterator(in_handle)):\n count += 1\n pos_handle.write("@%s\\n%s\\n+\\n%s\\n" % (title, seq, qual))\n- return count\n+ return count\n \n-def sff_filter(in_file, out_file, iterator_filter):\n+\n+def sff_filter(in_file, out_file, iterator_filter, inter):\n count = 0\n try:\n from Bio.SeqIO.SffIO import SffIterator, SffWriter\n except ImportError:\n- stop_err("SFF filtering requires Biopython 1.54 or later")\n+ sys_exit("SFF filtering requires Biopython 1.54 or later")\n try:\n from Bio.SeqIO.SffIO import ReadRocheXmlManifest\n except ImportError:\n@@ -167,17 +335,26 @@\n with open(out_file, "wb") as out_handle:\n writer = SffWriter(out_handle, xml=manifest)\n in_handle.seek(0) #start again after getting manifest\n- count = writer.write_file(iterator_filter(SffIterator(in_handle)))\n- #count = writer.write_file(SffIterator(in_handle))\n+ if inter:\n+ from itertools import chain\n+ count = writer.write_file(chain.from_iterable(iterator_filter(pair(SffIterator(in_handle)))))\n+ assert count % 2 == 0, "Odd number of records? %i" % count\n+ count /= 2\n+ else:\n+ count = writer.write_file(iterator_filter(SffIterator(in_handle)))\n+ #count = writer.write_file(SffIterator(in_handle))\n return count\n \n-if seq_format.lower()=="sff":\n- count = sff_filter(in_file, out_file, sampler)\n-elif seq_format.lower()=="fasta":\n- count = fasta_filter(in_file, out_file, sampler)\n-elif seq_format.lower().startswith("fastq"):\n- count = fastq_filter(in_file, out_file, sampler)\n+if seq_format == "sff":\n+ count = sff_filter(in_file, out_file, sampler, interleaved)\n+elif seq_format == "fasta":\n+ count = fasta_filter(in_file, out_file, sampler, interleaved)\n+elif seq_format.startswith("fastq"):\n+ count = fastq_filter(in_file, out_file, sampler, interleaved)\n else:\n- stop_err("Unsupported file type %r" % seq_format)\n+ sys_exit("Unsupported file type %r" % seq_format)\n \n-sys.stderr.write("Sampled %i records\\n" % count)\n+if interleaved:\n+ sys.stderr.write("Selected %i pairs\\n" % count)\n+else:\n+ sys.stderr.write("Selected %i records\\n" % count)\n' |
| b |
| diff -r 16ecf25d521f -r da64f6a9e32b tools/sample_seqs/sample_seqs.xml --- a/tools/sample_seqs/sample_seqs.xml Thu Mar 27 12:13:22 2014 -0400 +++ b/tools/sample_seqs/sample_seqs.xml Fri Mar 06 11:48:09 2015 -0500 |
| b |
| b'@@ -1,18 +1,21 @@\n-<tool id="sample_seqs" name="Sub-sample sequences files" version="0.0.1">\n+<tool id="sample_seqs" name="Sub-sample sequences files" version="0.2.0">\n <description>e.g. to reduce coverage</description>\n <requirements>\n- <requirement type="package" version="1.63">biopython</requirement>\n+ <requirement type="package" version="1.65">biopython</requirement>\n <requirement type="python-module">Bio</requirement>\n </requirements>\n <version_command interpreter="python">sample_seqs.py --version</version_command>\n <command interpreter="python">\n+sample_seqs.py -f "$input_file.ext" -i "$input_file" -o "$output_file"\n #if str($sampling.type) == "everyNth":\n-sample_seqs.py "$input_file.ext" "$input_file" "$output_file" "${sampling.type}" "${sampling.every_n}"\n+-n "${sampling.every_n}"\n #elif str($sampling.type) == "percentage":\n-sample_seqs.py "$input_file.ext" "$input_file" "$output_file" "${sampling.type}" "${sampling.percent}"\n-#else:\n-##Should give an error about invalid sampling type:\n-sample_seqs.py "$input_file.ext" "$input_file" "$output_file" "${sampling.type}"\n+-p "${sampling.percent}"\n+#else\n+-c "${sampling.count}"\n+#end if\n+#if $interleaved\n+--interleaved\n #end if\n </command>\n <stdio>\n@@ -24,8 +27,9 @@\n <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file" help="FASTA, FASTQ, or SFF format." />\n <conditional name="sampling">\n <param name="type" type="select" label="Sub-sampling approach">\n- <option value="everyNth">Take every N-th sequence (e.g. every fifth sequence)</option>\n- <option value="percentage">Take some percentage of the sequences (e.g. 20% will take every fifth sequence)</option>\n+ <option value="everyNth">Take every N-th sequence (or pair, e.g. every fifth sequence)</option>\n+ <option value="percentage">Take some percentage of the sequences (or pairs, e.g. 20% will take every fifth sequence)</option>\n+ <option value="desired_count">Take exactly N sequences (or pairs, e.g. 1000 sequences)</option>\n <!-- TODO - target coverage etc -->\n </param>\n <when value="everyNth">\n@@ -34,7 +38,11 @@\n <when value="percentage">\n <param name="percent" value="20.0" type="float" min="0" max="100" label="Percentage" help="Between 0 and 100, e.g. 20% will take every 5th sequence" />\n </when>\n+ <when value="desired_count">\n+ <param name="count" value="1000" type="integer" min="1" label="N" help="Number of unique sequences to pick (between 1 and number itotal n input file)" />\n+ </when>\n </conditional>\n+ <param name="interleaved" type="boolean" label="Interleaved paired reads" help="This mode keeps paired reads together (e.g. take every 5th read pair)" />\n </inputs>\n <outputs>\n <data name="output_file" format="input" metadata_source="input_file" label="${input_file.name} (sub-sampled)"/>\n@@ -53,6 +61,13 @@\n <output name="output_file" file="ecoli.sample_N100.fastq" />\n </test>\n <test>\n+ <param name="input_file" value="ecoli.fastq" />\n+ <param name="type" value="everyNth" />\n+ <param name="every_n" value="100" />\n+ <param name="interleaved" value="true" />\n+ <output name="output_file" file="ecoli.pair_sample_N100.fastq" />\n+ </test>\n+ <test>\n <param name="input_file" value="MID4_GLZRM4E04_rnd30_frclip.sff" ftype="sff" />\n <param name="type" value="everyNth" />\n <param name="every_n" value="5" />\n@@ -65,35 +80,108 @@\n <output name="output_file" file="get_orf_input.Suis_ORF.prot.sample_N100.fasta" />\n </test>\n <test>\n+ <param name="input_file" value="get_orf_input.Suis_ORF.prot.fasta" />\n+ <param name="type" value="ever'..b' <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.pair_sample_N5.sff" ftype="sff"/>\n+ </test>\n+ <test>\n+ <param name="input_file" value="MID4_GLZRM4E04_rnd30.sff" ftype="sff" />\n+ <param name="type" value="desired_count" />\n+ <param name="count" value="30" />\n+ <output name="output_file" file="MID4_GLZRM4E04_rnd30.sff" ftype="sff"/>\n+ </test>\n+ <test>\n+ <param name="input_file" value="MID4_GLZRM4E04_rnd30_frclip.sff" ftype="sff" />\n+ <param name="type" value="desired_count" />\n+ <param name="count" value="1" />\n+ <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.sample_C1.sff" ftype="sff"/>\n+ </test>\n </tests>\n <help>\n **What it does**\n \n Takes an input file of sequences (typically FASTA or FASTQ, but also\n Standard Flowgram Format (SFF) is supported), and returns a new sequence\n-file sub-sampling from this (in the same format).\n+file sub-sampling uniformly from this (in the same format, preserving the\n+input order and selecting sequencing evenly though the input file).\n \n-Several sampling modes are supported, all designed to be non-random. This\n-allows reproducibility, and also works on paired sequence files. Also\n-note that by sampling uniformly through the file, this avoids any bias\n-should reads in any part of the file are of lesser quality (e.g. one part\n-of the slide).\n+Several sampling modes are supported, all designed to do non-random\n+uniform sampling (i.e. evenly through the input file). This allows\n+reproducibility, and also works on paired sequence files (run the tool\n+twice, once on each file using the same settings).\n \n-The simplest mode is to take every N-th sequence, for example taking\n+By sampling uniformly (evenly) through the file, this avoids any bias\n+should reads in any part of the file be of lesser quality (e.g. for\n+high throughput sequencing the reads at the start and end of the file\n+can be of lower quality).\n+\n+The simplest mode is to take every *N*-th sequence, for example taking\n every 2nd sequence would sample half the file - while taking every 5th\n sequence would take 20% of the file.\n \n+The target count method picks *N* sequences from the input file, which\n+again will be distributed uniformly (evenly) though the file. This works\n+by first counting the number of records, then calculating the desired\n+percentage of sequences to take. Note if your input file has exactly\n+*N* sequences this selects them all (effectively copying the input file).\n+If your input file has less than *N* sequences, this is treated as an\n+error.\n+\n+If you tick the interleaved option, the file is processed as pairs of\n+records to ensure your read pairs are not separated by sampling.\n+For example using 20% would take every 5th pair of records, or you\n+could request 1000 read pairs.\n+\n+.. class:: warningmark\n+\n+Note interleaves/pair mode does *not* actually check your read names\n+match a known pair naming scheme!\n \n **Example Usage**\n \n@@ -103,6 +191,14 @@\n Taking every 3rd read would reduce the estimated coverage to about x66,\n and would preserve the pairing as well.\n \n+Similarly, if you had some Illumina paired end data interleaved into one\n+file with an estimated x200 coverage, you would run this tool in\n+interleaved mode, taking every 3rd read pair. This would again reduce\n+the estimated coverage to about x66, while preserving the read pairing.\n+\n+Suppose you have a transcriptome assembly, and wish to look at the\n+species distribution of the top BLAST hits for an initial quality check.\n+Rather than using all your sequences, you could pick 1000 only for this.\n \n **Citation**\n \n@@ -116,4 +212,7 @@\n This tool is available to install into other Galaxy Instances via the Galaxy\n Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/sample_seqs\n </help>\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/btp163</citation>\n+ </citations>\n </tool>\n' |
| b |
| diff -r 16ecf25d521f -r da64f6a9e32b tools/sample_seqs/tool_dependencies.xml --- a/tools/sample_seqs/tool_dependencies.xml Thu Mar 27 12:13:22 2014 -0400 +++ b/tools/sample_seqs/tool_dependencies.xml Fri Mar 06 11:48:09 2015 -0500 |
| b |
| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="biopython" version="1.63"> - <repository changeset_revision="a5c49b83e983" name="package_biopython_1_63" owner="biopython" toolshed="http://toolshed.g2.bx.psu.edu" /> + <package name="biopython" version="1.65"> + <repository changeset_revision="dc595937617c" name="package_biopython_1_65" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |