# HG changeset patch # User peterjc # Date 1425660489 18000 # Node ID da64f6a9e32b55c30db378b694dc3fedc03eb6e8 # Parent 16ecf25d521f225f3fbc6115b3813d3ea3372004 Uploaded v0.2.0, adds desired count mode diff -r 16ecf25d521f -r da64f6a9e32b test-data/MID4_GLZRM4E04_rnd30_frclip.pair_sample_N5.sff Binary file test-data/MID4_GLZRM4E04_rnd30_frclip.pair_sample_N5.sff has changed diff -r 16ecf25d521f -r da64f6a9e32b test-data/MID4_GLZRM4E04_rnd30_frclip.sample_C1.sff Binary file test-data/MID4_GLZRM4E04_rnd30_frclip.sample_C1.sff has changed 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 @@ -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 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 @@ -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 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 @@ -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 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 @@ -0,0 +1,214 @@ +>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|ORF201 length 360 aa, 1083 bp, from complement(128035..129117) of Streptococcus_suis +SCHGGRRMTLFGKIKEVTELQSLPGFEGQVRNHIRQKITPHVDRIETDGLGGIFGIKDTA +VENAPRILVVAHMDEVGFMISQIKPDGTFRVVELGGWNPLVVSSQAFTLQLQDGRTIPAI +SGSVPPHLSRGANAPGMPAIADIIFDAGFANYDEAWAFGVRPGDVLVPKNETILTANGKN +VISKAWDNRFGVLMVTELLESLSGHALPNQLIAGANVQEEVGLRGAHASTTKFNPDIFLA +VDCSPAGDIYGDQGKIGDGTLLRFYDPGHIMLKNMKDFLLTTAEEAGVKFQYYCGKGGTD +AGAAHLKNHGVPSTTIGVCARYIHSHQTLYSMDDFLEAQAFLQTIVKKLDRSTVDLIKNY +>Streptococcus_suis|ORF202 length 106 aa, 321 bp, from 128792..129112 of Streptococcus_suis +RVKAWLETTRGFQPPSSTTRKVPSGLIWLIIKPTSSMWATTRIRGAFSTAVSLIPKIPPS +PSVSMRSTCGVIFWRMWLRTCPSNPGKLCNSVTSLIFPKRVILLPP +>Streptococcus_suis|ORF401 length 120 aa, 363 bp, from 265643..266005 of Streptococcus_suis +TTGTTSPIAPKWKASSKSLRVPTSEPTTLIPSSTVFTILRSMYSDGSPTATTYPPARTLS +IAWLKATLETAVTTVECTPPPVISLIYPGTSSTSSPLIVTSAPTSLASSNLSLLMSTAIT +>Streptococcus_suis|ORF402 length 201 aa, 606 bp, from 265741..266346 of Streptococcus_suis +HSLHDTEVHVFRWKSDSYYISTSTNTVNSLVEGYFGNSCYNSRVYTATSNFFNISRNIFY +FKSVDRHICTNFFGEFQFIIIDVYGDNMSVEDFFSVLYSKVSKSTSTIDSNPLTWFQVSF +FNRFVASNASTSDRTCLSWIKTFWNFYCIVRCYNTLLSHTTVNRVACIFYGTAESFATGC +TIFTHTTALEEPSNADTVTNF +>Streptococcus_suis|ORF601 length 665 aa, 1998 bp, from 409896..411893 of Streptococcus_suis +VMIQIGKIFAGRYRIVRQIGRGGMADVYLARDLILDGEEVAVKVLRTNYQTDQIAIQRFQ +REARAMAELDHPNIVRISDIGEEDGQQYLAMEYVNGLDLKRYIKENAPLSNDVAVRIMGQ +ILLAMRMAHTRGIVHRDLKPQNVLLTSNGVAKVTDFGIAVAFAETSLTQTNSMLGSVHYL +SPEQARGSKATIQSDIYAMGIILFEMLTGRIPYDGDSAVTIALQHFQKPLPSVREENANV +PQALENVVLKATAKKLNERYKSVAEMYADLASALSMDRQNEPRVELEGNKVDTKTLPKLS +QANVETKVPHTNSSAQVSATDKGSGKKEVAKSGNKPVSKPRPGIRTRYKVLIGAILLTVI +AAGLMFFNTPRTVTVPDVSGQTVEKATEMIEVAGLEVGNITEEATATVDEGLVIRTSPAA +KTTRRQGSKIDIVVATAALASIPDVVDKESDTARQELEALGFQVTIKEEYSEKVAQGLVI +KTDPGANSSAEKGAKITLYVSKGVAPQVVPNVVGKSQENATQILQTAGFSIGTITQEYSS +SVTAGQVISTDPVANTELAKGSIINLVISKGKELIMPDLTSGNYTYSQARSQLQALGVNA +ESIEKQEDRSYYSTTSDIVIGQYPAAGATIDGTVTLYVSVASTRTSSDSSAGSSTSTSTS +TGSGQ +>Streptococcus_suis|ORF602 length 120 aa, 363 bp, from complement(410593..410955) of Streptococcus_suis +LLSRLCSVYVCLALVLKQAYFPTSPLLSYQTPYPSQKLEQNCLYAVLSFQHWLGRVSARF +LYQPCSLLVQPWVHSDDPWIEPKLNLHTFLQPTYSARLIFLPLLLVQHFLRPEVRWHSLL +>Streptococcus_suis|ORF801 length 428 aa, 1287 bp, from 561960..563246 of Streptococcus_suis +KSSRDCESCLLLFVILKVMQADRRKTFGKMRIRINNLFFVAIAFMGIIISNSQVVLAIGK +ASVIQYLSYLVLILCIVNDLLKNNKHIVVYKLGYLFLIIFLFTIGICQQILPITTKIYLS +ISMMIISVLATLPISLIKDIDDFRRISNHLLFALFITSILGIMMGATMFTGAVEGIGFSQ +GFNGGLTHKNFFGITILMGFVLTYLAYKYGSYKRTDRFILGLELFLILISNTRSVYLILL +LFLFLVNLDKIKIEQRQWSTLKYISMLFCAIFLYYFFGFLITHSDSYAHRVNGLINFFEY +YRNDWFHLMFGAADLAYGDLTLDYAIRVRRVLGWNGTLEMPLLSIMLKNGFIGLVGYGIV +LYKLYRNVRILKTDNIKTIGKSVFIIVVLSATVENYIVNLSFVFMPICFCLLNSISTMES +TINKQLQT +>Streptococcus_suis|ORF802 length 333 aa, 1002 bp, from 563382..564383 of Streptococcus_suis +RMEKVSIIVPIFNTEKYLRECLDSIISQSYTNLEILLIDDGSSDSSTDICLEYAEQDGRI +KLFRLPNGGVSNARNYGIKNSTANYIMFVDSDDIVDGNIVESLYTCLKENDSDLSGGLLA +TFDGNYQESELQKCQIDLEEIKEVRDLGNENFPNHYMSGIFNSPCCKLYKNIYINKGFDT +EQWLGEDLLFNLNYLKNIKKVSYVNRNLYFARRGIQSTTNTFKKDVFIQLENLEEKTFDL +FVKIFGGQYEFSVFKETLQWHIIYYSLLMFKNGDESLPKKLHIFKYLYNRHSLDTLSIKR +TSSVFKRICKLIVANNLFKIFLNTLIREEKNND +>Streptococcus_suis|ORF1001 length 374 aa, 1125 bp, from 694014..695138 of Streptococcus_suis +HYLLFQGGILMKVFASPSRYIQGKHVLFQGAEAIGKLGTKPLILCDDLVYGIIGEKFLSY +LVEEGMQVHRVAFNGEASDKEIQRVVEIGKEQASDVVIGLGGGKTIDSAKAIADLLGVPV +VIAPTIASTDAPTSALSVIYSEEGAFERYIFYKKNPDLVLVDTAIICQAPPRLLASGIAD +GLATWVEARAILQSNGTTMAGGGQTLAGIAIAQTCEQTLFEYGLQAMASCEAKVVTAALE +NIVEANTLLSGLGFESAGLAAAHAIHNGFTALEGDIHHLTHGEKVAYGTLTQLFLENRPK +EELEKYIRFYQALNLPTTLEELHLADASYEELLKVGQQATIEGETIHGMPFAISAEDVAE +ALMAVDYYVRSLDK +>Streptococcus_suis|ORF1002 length 366 aa, 1101 bp, from 695283..696383 of Streptococcus_suis +RIDLKEISMAYVVAVVGATGAVGAQMIKMLEESTLPIEKVRFLASARSAGKTLQFKGQDI +VIEETTETAFEGVDIALFSAGGSTSAKYAPYAVKAGAVVVDNTSYFRQNPDVPLVVPEVN +AHALDAHNGIIACPNCSTIQMMVALEPVRQKWGLERIIVSTYQAVSGAGMGAILETQAQL +RSVLNDGVEPKAVEANILPSGGDKKHYPIGFNAIPQIDLFTENDYTYEEMKMTKETKKIM +EDDSIAVSATCVRIPVLSAHSESVYIETKEIAPIDEVKAAIASFPGAVLEDDVANQIYPQ +AINAVGSRDTFVGRIRKDLDKENGIHMWVVSDNLLKGAAWNSVQIAETLHERGLVRPTAE +LKFELK +>Streptococcus_suis|ORF1201 length 144 aa, 435 bp, from 842957..843391 of Streptococcus_suis +FQTIKEKSRLMNIKKLILTLLTLTLTIVPCACGNQSNSNDSQLSGTYSYEKGGIDGSEMG +FEDEELTLHYELKVSGDENILNINLLSERGNNVKYLYSEKVTIDTDKQIISDSNGTELEY +SVSGDSVTIPDLAGDSGETVTLKR +>Streptococcus_suis|ORF1202 length 343 aa, 1032 bp, from 843537..844568 of Streptococcus_suis +VKVMYIFETTEQNNSKANDFETKSLLYLMSFKSDSTDIDTFFVDCFNDITGASSDLLKLW +DVQAKNISSLRPKTIGKSLITLFQNFISSVDFYEYILFIPKLKENYLMDISLTEFKIDNF +KDIAKIQEGLEEEYKRRKKLGALNLKQLSQLNTFLEQIHFVTGDSSKAIYIKNIIQFKSN +IRDDNFFESVFNEVRSKQTELKNINIHNISINSIEEVLKLNKHLTKRQLETLVVNRIIGV +ELFKQRIPNDFFDVINDKSSSDRKDIIQDCNANLSRLLFDKNSNKKKFWSLLEQILILVE +EKDDIYQILNRIKQYQIPKIINDDYTLLYLISMVKEGMEENAC +>Streptococcus_suis|ORF1401 length 409 aa, 1230 bp, from 991071..992300 of Streptococcus_suis +GDNMKYPTLLDRFLVYVKENTRSDENSTTTPSTQNQVEFAQNILLPEMERIGLQNVHYLP +NGFAVGTLPANDPSLTRKIGFIAHMDTADFNAEGVNPQIIENYDGNPIALGTSGYELHPK +DFPQLANYHGQILITTDGTTLLGSDDKSGIAEIMTAIEFLIQNPDIKHCEIRVGFGPDEE +IGVGADKFDVKDFDVDFAYTMDGGPLGELQYETFSAAGAKIDFLGRNVHPGSAKDQMINA +FQMAIDFHNALPETDRPEKTEGYEGFFHLMNMEGSVDTASTTYIIRDFEEEDFQARKQLM +LDIAEKMNANFDTPRVIVNLHDQYYNMKKIIEKDMTPINIAKDVMENLGIKPLIEPVRGG +TDGSKISFMGIPTPNIFAGGENMHGRFEFVSLETMEKAVDVILGIVAYK +>Streptococcus_suis|ORF1402 length 144 aa, 435 bp, from 992392..992826 of Streptococcus_suis +YNRTIKKKWSFIMTEETLAQGILIGIWGTTLLFSFIWYILVAISNYILFKKAGYAGWKSL +IPIYNLYIQQCITFGYEKRWFILFLLIPLAGPLYGIYLVYNFGRSFGLSAVQAIFYVLLT +PIFNLYIAFNDGSRYQGPQEFFID +>Streptococcus_suis|ORF1601 length 141 aa, 426 bp, from complement(1127307..1127732) of Streptococcus_suis +VHPLHGRSLLIYFDCFAYEGGGIMTIQALAMFLASLGFLYFIFRNINKNKILFEHAFMWI +VIGFGLIVFALFDVIPIKLAYLFGFGLTSNFLLSVAIFVLLVIGFLHSMALSQQKQQIKN +LIQEVSMAKKRISELEEHHAE +>Streptococcus_suis|ORF1602 length 241 aa, 726 bp, from complement(1127663..1128388) of Streptococcus_suis +REKMKVLMIIPAYNEEESILQTVQGIIDYKNSVNFQLDYVVINDGSTDSTKEILIQNKLN +AVHLVQNLGIGGAVQTGYKYALDNDYDVAVQFDGDGQHDIRSLNGLIQPILVGQADMVIG +SRFVGDTLSEFQTSFMRRFGIGVISNMIKLTTGNRIWDTTSGYRLGNRKVIAQFAKRYPI +KYPEPESTVHLLKQNFQVVEAPANMFERAGGVSSITPFKSIRYMVEVCSSILIASLMKEG +E +>Streptococcus_suis|ORF1801 length 128 aa, 387 bp, from 1263312..1263698 of Streptococcus_suis +RLHDSCSICFLFIHGNIAGNRPCKEIGILQNNPHVTAQAFTRIITDVFPINQYTSLLWII +ETIEEIHNRRLTRPSMPNQSNCFSFFCSNGNIFQNWSVFFIAKVHVFKHDLPLFNFQNTI +TVVLQLFF +>Streptococcus_suis|ORF1802 length 578 aa, 1737 bp, from complement(1264661..1266397) of Streptococcus_suis +RRYMFRLIFDYIKRHKWLYLLVAVTLIIYDATLLLPTQIIQRMVDILTKNELTQAILVQE +MTLLLLVTVLNYATAFIWHLKLFQASVNFKFDMQQRAFKKLVTMRTPFYEKFRSGDVMTR +FSTDVDGLMEMVGYGLMIVVYAGGMLAFIIPTMFFIDWKISLVALLPMLFMTLCIFFIGR +KQDKAIDANREAVAQLNNEVLEVIEGIRVTRAYSKKANQKAQFQARTKQLAQGGDRITSL +QSLYNPLATVCLGLSTIFVLLMGAQAVKAGQLTLGQVIALQLYVGSLLEPFWTLADFILV +YQTGKTSFEKLQELIETGDDLEADGSKEIAELSSISFKNYSFSYPQAERASLQDINWTLK +AGQTVGIVGKTGSGKTTLVRQFLRQYPIGQGNFFINHQSILDFKRSSIEEKIGYVPQEHI +LFSRSVGENIALGKVASSSEEIEQAIATAAFSQDLKRMSDGLDTMIGERGVSISGGQKQR +ISIARAFLREPDLLILDDSLSAVDARTERQIIQNIQKERAGKTNVIVTHRLSAVNHADWV +LVLDEGRIVEEGRPADLLAQRGWYYEQYQRQQSQEGGE +>Streptococcus_suis|ORF2001 length 415 aa, 1248 bp, from complement(1398025..1399272) of Streptococcus_suis +EDFIMKMKTFLKCASVCAFASFLVACGNASSSDKVEIEYFSQKPEMQATLQEIIDDFEKE +NPTIDVKFSNVPDAGTVLKTRMANNEAPDVINIYPQNADFKAYAADGRFLEIGDDAGLNH +LKDGAVTPYLVNEKNYTLPLTANAYGIYYNKDKFKELGLEVPTTYAEFVALVDKIKADGS +AAPFALSLNDAWSLNGYHQLAWVTVAGGFDGAEDILIRSAKGAIQDDATTKAVLERLQLL +KDNGQKGATGALYADAVAAFAAGDALMLPQGTWAATAVNQQEPEFEYGMFTFPGDKEGGD +YTIGAADLALSISADTEHPEESKKFLEYLSRPEVIQKYYDVDGSPTSVEGVDTEGKFEET +AGVTQYAFTDKHVVWLQSEWESEEEFWNITVEMVKNPNSAELVKKLNAFFDPMKK +>Streptococcus_suis|ORF2002 length 732 aa, 2199 bp, from complement(1399273..1401471) of Streptococcus_suis +DHKEEIGEMNVIEIYNEKQIFHLKTREFSYIIQVLETGDLVHRYFGKKIEKFSDGNKITY +LDRSFSPSPITGDRTYSLDVLPLEYSSNGLGDFRTSALDVRNEFGVTLDLKYKEYRLYKG +KKELRGLPASFGNQEEVESLEIDLYDQLTDITVTLQYSVFEEASYLARSATIQTGKYPCK +LEKVLSATLDFPHQDFIVHSLAGRYAYEKEWTQTPLTKGQYSIGSIRGASSHSRTPFLAL +VSPDASEDKGDVYAAHLVYSGNFTAFVETTAMETSRLGLGLESHYFSWQLDKDDRFQTPE +VLLSYTDKGFTGMTQNSHHFITKHLIRSSFVNKPRPILINNWEATYFEFTEEKILQLAQV +ASRAGIELFVLDDGWFGKRNNDESSLGDWKVNLDKLPNGLNGLAERINELGMKFGLWFEP +EMISIDSDLYREHPDWAIRTEGRLPIYSREQLVLDLTKQEVCDYIIDSVSSILESANISY +VKWDMNRNITNIPEGLANDQRFEFHHRYMLGLYRVLDHLTKRFPDILFESCAGGGGRNDL +GIMYYMPQAWASDDTDAIERLSIQEGTSLIYPPSSIGAHVSAVPNHQVGRITPLATRGNV +AMMGGAFGYELDLTKLSEKELDEISQQIETYHSIRETIQFGQLYRLKKTSNTWAANYVSQ +DKNQVVFTFVKILAKPEAPLLHVRLKGLDPDALYECPQLGETFYGDELMNIGLTMPHVQK +DYFSVQYIFNKI +>Streptococcus_suis|ORF2201 length 272 aa, 819 bp, from complement(1531599..1532417) of Streptococcus_suis +DCSKIKIIDLAVGKLKLLSSKRKGAFMEIIRSKANHLVKQVKKLQQKKYRTSSYLIEGWH +LLEEAMEAGANIEHIFVVEEYFEKVAGLANVTVVSPEIMQELADSKTPQGVVAQLALPSQ +RLPETLDGKFLVLEDVQDPGNVGTMIRTADAAGFDGVFLSDKSADIYNMKVLRSMQGSHF +HLPVYRMPISSILTALKSNQIQILATTLSSQSVDYKEITPHSSFALVMGNEGQGISDLVA +DEADQLVHITMPGQAESLNVAIAAGILLFSFI +>Streptococcus_suis|ORF2202 length 101 aa, 306 bp, from 1532445..1532750 of Streptococcus_suis +MSCQKEKLMRKVKMIASGRVQGVGFRWSVQFLAVEIGDIYGRVWNNDDGTVTILAQSDNA +EKLSHFIHEIRKGPSRMAKVIYLDVTLANFEDYKDFQVSYR +>Streptococcus_suis|ORF2401 length 141 aa, 426 bp, from 1658030..1658455 of Streptococcus_suis +ASITVPIARTVGSAFSSWISATKRTVSNNSSMFWLNLAEISTNSDSPPQAVEITPCSANS +PMTRSGFAPGLSILLIATMIGTLAAFEWLIASIVCGMTPSSAATTRMVKSVTDAPRARIE +VKAACPGVSKKVIFLPASSIW +>Streptococcus_suis|ORF2402 length 266 aa, 801 bp, from 1658515..1659315 of Streptococcus_suis +GVQQGCFTMVNVSHDSHNRWAFCHLFFIEVALFYEETLNICVIDLYLFFRFNTIINHEEF +DSISIQRLVLSRHNSHKEEFFHNFSRFTFDSFCNFCDGHASSIFKFSWQFVELAFCDRFG +RLVSLAFFIFLVVIPVTCSLISHLILTISISLLFPWTIFFVTIKVTFFIWSSLFLTTGIY +SSFCNLLWYRCNKCRFHKWFAFHNRFFKLNFFWLLRLLFSFLSLTKTFFTGTSILRILFC +FQSSSTRFEVNFRSCWFCSLSLFKAS +>Streptococcus_suis|ORF2601 length 100 aa, 303 bp, from 1790150..1790452 of Streptococcus_suis +LKDGYQRLVVEGFADIAETFLQTETNLMTTVIFIARHDDDRPIAFPLGSLNQVNMTLVHG +SKGPKNNCYCLFHNLPFYCFLYFISYSFLKPKSRVFYIFL +>Streptococcus_suis|ORF2602 length 823 aa, 2472 bp, from complement(1790482..1792953) of Streptococcus_suis +ERGVVRMKISRGLQGVYEDAQLIAQRYSSDYLETWHLLLAFVINPDTVAGAILAEYPADV +LDYERAVYMVMGRRYHEELESFFFLPSSKRVKELQVFAEKIAEIVKSKGLGTEHIFMGML +LDKRSTASQILDQVGFHFEDSDDKVRFLDLRKNLEAKAGFTKEHLKAIRTMTKGGKPKQA +TVGNMMGMTQSQSGGLEDYTRDLTALARSGQLEPVIGRDEEISRMLQILSRKTKNNPVLV +GDAGVGKTALALGLAQRIANGEVPASLVNMRILELDLMNVIAGTRFRGDFEERMNNIIND +IEEDGRVILFIDELHTIMGSGSGIDSILDAANILKPALSRGTLRTVGATTQDEYQKHIEK +DAALVRRFAKVTIEEPSVADSVAILQGLKPAYEAHHKVTISDQAVVTAVAYAKRYLTSKN +LPDSAIDLLDEASATVQNRAKGQVEEGGLTALDQALMAGKYKTVTQLLLKAQEAENQATS +YSLEVTEEDILATLSRLSGIPVTKLSQTDAKKYLNLEQELHKRVIGQEEAISAVSRAIRR +NQSGIRTGHRPIGSFMFLGPTGVGKTELAKALAEILFDDESALIRFDMSEYMEKFAASRL +NGAPPGYVGYEEGGELTEKVRNKPYSVLLFDEVEKAHPDIFNVLLQVLDDGVLTDRKGRK +VDFSNTVIIMTSNLGATALRDDKTVGFGALDLSKSQEHVEKRIFEALKKAYRPEFINRID +EKVVFHSLTEADMQDVVKVMVKPLIAVAASKGITLKLQASALKLLAKEGYDPEMGARPLR +RLLQTKLEDPLAEMLLRGELPAGVTLKVGVKAEQLKFDSVKAG +>Streptococcus_suis|ORF2801 length 1006 aa, 3021 bp, from complement(1921434..1924454) of Streptococcus_suis +TQTKEYEMIEFRKKAVQLASLMSVFFLCTYSFTDAMYIMAESLSTDGASTIRRTYIEDKK +EDKDRLNIELVESLSSPKTIGQKITIDKQSLATQNFNEKGIVVITQKGLELKKDDLEKGW +KLDESYNEKDLAITKSETEKRSLSNELDVLSKTVEELPVYGENYHSYRLLPTTELDYSAD +NVSLTLSFTKVSEVIKGELVAVVDAEHIAYFKAEPSVFKEYSQVNEKPSSTEDVNVVSPS +QDPPVSETKENVPDNPESQGSSTVPESEQAVDALVEQRGVICIKLTKSSSEQEEGIEDTE +NEAIEGATFEVRNVESENLVYTGQTDKDGLLTISNLPLGNYAVIQKSTIDGYEISATKEV +VELTVAQSRQTVSISNSPKNPLEGLMLNSILDSSLIPRSARVARSLLDTSLLDNPTVTGN +ANATTTTTVFGNKTTTITREESNIKYIFKPITISIPGVYQSYSQDGVLKKKEVVVDSNTN +TTKIIWEYTTTVGGVNSNITSIRNAFSTTTDSGLGEPKITSIMKDGVAITPNTTYYGNFD +NFKSATDNLPVGNGTYVYTIETPVVIPSDNYSLDYRSEVTVDAPKGSKLTYNGTSVTLTQ +KETRTLSTADTITLPAKNDGGPLGDLKVDTVNTSNTNRTIGKYRDNDDKVIEWTSSQLND +TSTTQSFTFDVALDSSQAAHEYKVYIYEPSNGTYTETKAEKVATPGNQITVDNVPAGAVA +LVKTVTNVKDEKVNHTISGAQLEALKGDIKIQKNWEADSDKVDVTFTVNGGSLTNRKETL +SANNTQITIANVDKFSGMRSTATKKRIYYDVTEAVPSGYILSSAQTDWENLYYVFTNKKD +NTTTPVFPPDTCGNYGVSSIDLVSINYVMYKSGSKIWGGFDGSMKMNLKIPAFARAGDSF +TLELPPELKLSHVANPNVAWSTVSANGKVIAKVYHEKDNLIRFVLTTEAYSVQEYNGWFE +IGVPTSNVIKINNRETTELYKTGVLPNLPEWYTTTTRNQTLIKRSR +>Streptococcus_suis|ORF2802 length 252 aa, 759 bp, from complement(1925855..1926613) of Streptococcus_suis +LEARMQQYFVNGRAPQGMFQISDKDTAKHMFSVMRLQAGDQIVLVFDDGIKRLARVVDSQ +SQSVEIIEELTDNVELPISVTIAMGFPKGDKLEFVAQKATELGMSALWAFPADWSVVKWD +GKKLAKKAEKLEKIAQGAAEQSKRNRIPAVRLFEKKSDFLAQLAGFDQIILAYEEAAKEG +EQANLVKILSGLEIGQSVLVIVGPEGGVSPEEVAAFEGAGAVKTGLGPRILRAETAPLYA +LSTISYATELLR 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 @@ -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 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 @@ -39,11 +39,12 @@ -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) 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 @@ -2,46 +2,136 @@ """Sub-sample sequence from a FASTA, FASTQ or SFF file. This tool is a short Python script which requires Biopython 1.62 or later -for SFF file support. If you use this tool in scientific work leading to a +for sequence parsing. If you use this tool in scientific work leading to a publication, please cite the Biopython application note: Cock et al 2009. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. -This script is copyright 2010-2013 by Peter Cock, The James Hutton Institute +This script is copyright 2014-2015 by Peter Cock, The James Hutton Institute (formerly the Scottish Crop Research Institute, SCRI), UK. All rights reserved. See accompanying text file for licence details (MIT license). -This is version 0.1.0 of the script, use -v or --version to get the version. +Use -v or --version to get the version, -h or --help for help. """ import os import sys +from optparse import OptionParser -def stop_err(msg, err=1): + +def sys_exit(msg, err=1): sys.stderr.write(msg.rstrip() + "\n") sys.exit(err) -if "-v" in sys.argv or "--version" in sys.argv: - print("v0.1.0") +#Parse Command Line +usage = """Use as follows: + +$ python sample_seqs.py [options] + +e.g. Sample 20% of the reads: + +$ python sample_seqs.py -i my_seq.fastq -f fastq -p 20.0 -o sample.fastq + +This samples uniformly though the file, rather than at random, and therefore +should be reproducible. +""" +parser = OptionParser(usage=usage) +parser.add_option('-i', '--input', dest='input', + default=None, help='Input sequences filename', + metavar="FILE") +parser.add_option('-f', '--format', dest='format', + default=None, + help='Input sequence format (e.g. fasta, fastq, sff)') +parser.add_option('-o', '--output', dest='output', + default=None, help='Output sampled sequenced filename', + metavar="FILE") +parser.add_option('-p', '--percent', dest='percent', + default=None, + help='Take this percent of the reads') +parser.add_option('-n', '--everyn', dest='everyn', + default=None, + help='Take every N-th read') +parser.add_option('-c', '--count', dest='count', + default=None, + help='Take exactly N reads') +parser.add_option("--interleaved", dest="interleaved", + default=False, action="store_true", + help="Input is interleaved reads, preserve the pairings") +parser.add_option("-v", "--version", dest="version", + default=False, action="store_true", + help="Show version and quit") +options, args = parser.parse_args() + +if options.version: + print("v0.2.0") sys.exit(0) -#Parse Command Line -if len(sys.argv) < 5: - stop_err("Requires at least four arguments: seq_format, in_file, out_file, mode, ...") -seq_format, in_file, out_file, mode = sys.argv[1:5] +in_file = options.input +out_file = options.output +interleaved = options.interleaved + +if not in_file: + sys_exit("Require an input filename") if in_file != "/dev/stdin" and not os.path.isfile(in_file): - stop_err("Missing input file %r" % in_file) + sys_exit("Missing input file %r" % in_file) +if not out_file: + sys_exit("Require an output filename") +if not options.format: + sys_exit("Require the sequence format") +seq_format = options.format.lower() + + +def count_fasta(filename): + from Bio.SeqIO.FastaIO import SimpleFastaParser + count = 0 + with open(filename) as handle: + for title, seq in SimpleFastaParser(handle): + count += 1 + return count + + +def count_fastq(filename): + from Bio.SeqIO.QualityIO import FastqGeneralIterator + count = 0 + with open(filename) as handle: + for title, seq, qual in FastqGeneralIterator(handle): + count += 1 + return count + -if mode == "everyNth": - if len(sys.argv) != 6: - stop_err("If using everyNth, just need argument N (integer, at least 2)") +def count_sff(filename): + from Bio import SeqIO + # If the SFF file has a built in index (which is normal), + # this will be parsed and is the quicker than scanning + # the whole file. + return len(SeqIO.index(filename, "sff")) + + +def count_sequences(filename, format): + if seq_format == "sff": + return count_sff(filename) + elif seq_format == "fasta": + return count_fasta(filename) + elif seq_format.startswith("fastq"): + return count_fastq(filename) + else: + sys_exit("Unsupported file type %r" % seq_format) + + +if options.percent and options.everyn: + sys_exit("Cannot combine -p and -n options") +elif options.everyn and options.count: + sys_exit("Cannot combine -p and -c options") +elif options.percent and options.count: + sys_exit("Cannot combine -n and -c options") +elif options.everyn: try: - N = int(sys.argv[5]) + N = int(options.everyn) except: - stop_err("Bad N argument %r" % sys.argv[5]) + sys_exit("Bad -n argument %r" % options.everyn) if N < 2: - stop_err("Bad N argument %r" % sys.argv[5]) + sys_exit("Bad -n argument %r" % options.everyn) if (N % 10) == 1: sys.stderr.write("Sampling every %ist sequence\n" % N) elif (N % 10) == 2: @@ -57,15 +147,13 @@ count += 1 if count % N == 1: yield record -elif mode == "percentage": - if len(sys.argv) != 6: - stop_err("If using percentage, just need percentage argument (float, range 0 to 100)") +elif options.percent: try: - percent = float(sys.argv[5]) / 100.0 + percent = float(options.percent) / 100.0 except: - stop_err("Bad percent argument %r" % sys.argv[5]) + sys_exit("Bad -p percent argument %r" % options.percent) if percent <= 0.0 or 1.0 <= percent: - stop_err("Bad percent argument %r" % sys.argv[5]) + sys_exit("Bad -p percent argument %r" % options.percent) sys.stderr.write("Sampling %0.3f%% of sequences\n" % (100.0 * percent)) def sampler(iterator): global percent @@ -76,8 +164,88 @@ if percent * count > taken: taken += 1 yield record +elif options.count: + try: + N = int(options.count) + except: + sys_exit("Bad -c count argument %r" % options.count) + if N < 1: + sys_exit("Bad -c count argument %r" % options.count) + total = count_sequences(in_file, seq_format) + print("Input file has %i sequences" % total) + if interleaved: + # Paired + if total % 2: + sys_exit("Paired mode, but input file has an odd number of sequences: %i" + % total) + elif N > total // 2: + sys_exit("Requested %i sequence pairs, but file only has %i pairs (%i sequences)." + % (N, total // 2, total)) + total = total // 2 + if N == 1: + sys.stderr.write("Sampling just first sequence pair!\n") + elif N == total: + sys.stderr.write("Taking all the sequence pairs\n") + else: + sys.stderr.write("Sampling %i sequence pairs\n" % N) + else: + # Not paired + if total < N: + sys_exit("Requested %i sequences, but file only has %i." % (N, total)) + if N == 1: + sys.stderr.write("Sampling just first sequence!\n") + elif N == total: + sys.stderr.write("Taking all the sequences\n") + else: + sys.stderr.write("Sampling %i sequences\n" % N) + if N == total: + def sampler(iterator): + """Dummy filter to filter nothing, taking everything.""" + global N + taken = 0 + for record in iterator: + taken += 1 + yield record + assert taken == N, "Picked %i, wanted %i" % (taken, N) + else: + def sampler(iterator): + # Mimic the percentage sampler, with double check on final count + global N, total + # Do we need a floating point fudge factor epsilon? + # i.e. What if percentage comes out slighty too low, and + # we could end up missing last few desired sequences? + percentage = float(N) / float(total) + #print("DEBUG: Want %i out of %i sequences/pairs, as a percentage %0.2f" + # % (N, total, percentage * 100.0)) + count = 0 + taken = 0 + for record in iterator: + count += 1 + # Do we need the extra upper bound? + if percentage * count > taken and taken < N: + taken += 1 + yield record + elif total - count + 1 <= N - taken: + # remaining records (incuding this one) <= what we still need. + # This is a safey check for floating point edge cases where + # we need to take all remaining sequences to meet target + taken += 1 + yield record + assert taken == N, "Picked %i, wanted %i" % (taken, N) else: - stop_err("Unsupported mode %r" % mode) + sys_exit("Must use either -n, -p or -c") + + +def pair(iterator): + """Quick and dirty pair batched iterator.""" + while True: + a = next(iterator) + b = next(iterator) + if not b: + assert not a, "Odd number of records?" + break + yield (a, b) + def raw_fasta_iterator(handle): """Yields raw FASTA records as multi-line strings.""" @@ -113,46 +281,46 @@ if not line: return # StopIteration -def fasta_filter(in_file, out_file, iterator_filter): +def fasta_filter(in_file, out_file, iterator_filter, inter): count = 0 #Galaxy now requires Python 2.5+ so can use with statements, with open(in_file) as in_handle: with open(out_file, "w") as pos_handle: - for record in iterator_filter(raw_fasta_iterator(in_handle)): - count += 1 - pos_handle.write(record) + if inter: + for r1, r2 in iterator_filter(pair(raw_fasta_iterator(in_handle))): + count += 1 + pos_handle.write(r1) + pos_handle.write(r2) + else: + for record in iterator_filter(raw_fasta_iterator(in_handle)): + count += 1 + pos_handle.write(record) return count -try: - from galaxy_utils.sequence.fastq import fastqReader, fastqWriter - def fastq_filter(in_file, out_file, iterator_filter): - count = 0 - #from galaxy_utils.sequence.fastq import fastqReader, fastqWriter - reader = fastqReader(open(in_file, "rU")) - writer = fastqWriter(open(out_file, "w")) - for record in iterator_filter(reader): - count += 1 - writer.write(record) - writer.close() - reader.close() - return count -except ImportError: - from Bio.SeqIO.QualityIO import FastqGeneralIterator - def fastq_filter(in_file, out_file, iterator_filter): - count = 0 - with open(in_file) as in_handle: - with open(out_file, "w") as pos_handle: + +from Bio.SeqIO.QualityIO import FastqGeneralIterator +def fastq_filter(in_file, out_file, iterator_filter, inter): + count = 0 + with open(in_file) as in_handle: + with open(out_file, "w") as pos_handle: + if inter: + for r1, r2 in iterator_filter(pair(FastqGeneralIterator(in_handle))): + count += 1 + pos_handle.write("@%s\n%s\n+\n%s\n" % r1) + pos_handle.write("@%s\n%s\n+\n%s\n" % r2) + else: for title, seq, qual in iterator_filter(FastqGeneralIterator(in_handle)): count += 1 pos_handle.write("@%s\n%s\n+\n%s\n" % (title, seq, qual)) - return count + return count -def sff_filter(in_file, out_file, iterator_filter): + +def sff_filter(in_file, out_file, iterator_filter, inter): count = 0 try: from Bio.SeqIO.SffIO import SffIterator, SffWriter except ImportError: - stop_err("SFF filtering requires Biopython 1.54 or later") + sys_exit("SFF filtering requires Biopython 1.54 or later") try: from Bio.SeqIO.SffIO import ReadRocheXmlManifest except ImportError: @@ -167,17 +335,26 @@ with open(out_file, "wb") as out_handle: writer = SffWriter(out_handle, xml=manifest) in_handle.seek(0) #start again after getting manifest - count = writer.write_file(iterator_filter(SffIterator(in_handle))) - #count = writer.write_file(SffIterator(in_handle)) + if inter: + from itertools import chain + count = writer.write_file(chain.from_iterable(iterator_filter(pair(SffIterator(in_handle))))) + assert count % 2 == 0, "Odd number of records? %i" % count + count /= 2 + else: + count = writer.write_file(iterator_filter(SffIterator(in_handle))) + #count = writer.write_file(SffIterator(in_handle)) return count -if seq_format.lower()=="sff": - count = sff_filter(in_file, out_file, sampler) -elif seq_format.lower()=="fasta": - count = fasta_filter(in_file, out_file, sampler) -elif seq_format.lower().startswith("fastq"): - count = fastq_filter(in_file, out_file, sampler) +if seq_format == "sff": + count = sff_filter(in_file, out_file, sampler, interleaved) +elif seq_format == "fasta": + count = fasta_filter(in_file, out_file, sampler, interleaved) +elif seq_format.startswith("fastq"): + count = fastq_filter(in_file, out_file, sampler, interleaved) else: - stop_err("Unsupported file type %r" % seq_format) + sys_exit("Unsupported file type %r" % seq_format) -sys.stderr.write("Sampled %i records\n" % count) +if interleaved: + sys.stderr.write("Selected %i pairs\n" % count) +else: + sys.stderr.write("Selected %i records\n" % count) 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 @@ -1,18 +1,21 @@ - + e.g. to reduce coverage - biopython + biopython Bio sample_seqs.py --version +sample_seqs.py -f "$input_file.ext" -i "$input_file" -o "$output_file" #if str($sampling.type) == "everyNth": -sample_seqs.py "$input_file.ext" "$input_file" "$output_file" "${sampling.type}" "${sampling.every_n}" +-n "${sampling.every_n}" #elif str($sampling.type) == "percentage": -sample_seqs.py "$input_file.ext" "$input_file" "$output_file" "${sampling.type}" "${sampling.percent}" -#else: -##Should give an error about invalid sampling type: -sample_seqs.py "$input_file.ext" "$input_file" "$output_file" "${sampling.type}" +-p "${sampling.percent}" +#else +-c "${sampling.count}" +#end if +#if $interleaved +--interleaved #end if @@ -24,8 +27,9 @@ - - + + + @@ -34,7 +38,11 @@ + + + + @@ -53,6 +61,13 @@ + + + + + + + @@ -65,35 +80,108 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + **What it does** Takes an input file of sequences (typically FASTA or FASTQ, but also Standard Flowgram Format (SFF) is supported), and returns a new sequence -file sub-sampling from this (in the same format). +file sub-sampling uniformly from this (in the same format, preserving the +input order and selecting sequencing evenly though the input file). -Several sampling modes are supported, all designed to be non-random. This -allows reproducibility, and also works on paired sequence files. Also -note that by sampling uniformly through the file, this avoids any bias -should reads in any part of the file are of lesser quality (e.g. one part -of the slide). +Several sampling modes are supported, all designed to do non-random +uniform sampling (i.e. evenly through the input file). This allows +reproducibility, and also works on paired sequence files (run the tool +twice, once on each file using the same settings). -The simplest mode is to take every N-th sequence, for example taking +By sampling uniformly (evenly) through the file, this avoids any bias +should reads in any part of the file be of lesser quality (e.g. for +high throughput sequencing the reads at the start and end of the file +can be of lower quality). + +The simplest mode is to take every *N*-th sequence, for example taking every 2nd sequence would sample half the file - while taking every 5th sequence would take 20% of the file. +The target count method picks *N* sequences from the input file, which +again will be distributed uniformly (evenly) though the file. This works +by first counting the number of records, then calculating the desired +percentage of sequences to take. Note if your input file has exactly +*N* sequences this selects them all (effectively copying the input file). +If your input file has less than *N* sequences, this is treated as an +error. + +If you tick the interleaved option, the file is processed as pairs of +records to ensure your read pairs are not separated by sampling. +For example using 20% would take every 5th pair of records, or you +could request 1000 read pairs. + +.. class:: warningmark + +Note interleaves/pair mode does *not* actually check your read names +match a known pair naming scheme! **Example Usage** @@ -103,6 +191,14 @@ Taking every 3rd read would reduce the estimated coverage to about x66, and would preserve the pairing as well. +Similarly, if you had some Illumina paired end data interleaved into one +file with an estimated x200 coverage, you would run this tool in +interleaved mode, taking every 3rd read pair. This would again reduce +the estimated coverage to about x66, while preserving the read pairing. + +Suppose you have a transcriptome assembly, and wish to look at the +species distribution of the top BLAST hits for an initial quality check. +Rather than using all your sequences, you could pick 1000 only for this. **Citation** @@ -116,4 +212,7 @@ This tool is available to install into other Galaxy Instances via the Galaxy Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/sample_seqs + + 10.1093/bioinformatics/btp163 + 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 @@ -1,6 +1,6 @@ - - + +