| Previous changeset 14:65d76ca44cd2 (2015-04-06) Next changeset 16:e29fef81c126 (2015-05-21) |
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Commit message:
planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/get_orfs_or_cdss commit e8aac97bf20ccd42402cace482c6d93b90cb3608 |
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modified:
tools/get_orfs_or_cdss/README.rst tools/get_orfs_or_cdss/get_orfs_or_cdss.xml |
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removed:
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 test-data/get_orf_input.Suis_ORF.prot.sample_N100.fasta |
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| diff -r 65d76ca44cd2 -r 2eb9e86f5f35 test-data/get_orf_input.Suis_ORF.prot.pair_sample_C10.fasta --- a/test-data/get_orf_input.Suis_ORF.prot.pair_sample_C10.fasta Mon Apr 06 05:21:48 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,119 +0,0 @@ ->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 65d76ca44cd2 -r 2eb9e86f5f35 test-data/get_orf_input.Suis_ORF.prot.pair_sample_N100.fasta --- a/test-data/get_orf_input.Suis_ORF.prot.pair_sample_N100.fasta Mon Apr 06 05:21:48 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,214 +0,0 @@\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 65d76ca44cd2 -r 2eb9e86f5f35 test-data/get_orf_input.Suis_ORF.prot.sample_C10.fasta --- a/test-data/get_orf_input.Suis_ORF.prot.sample_C10.fasta Mon Apr 06 05:21:48 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,50 +0,0 @@ ->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 65d76ca44cd2 -r 2eb9e86f5f35 test-data/get_orf_input.Suis_ORF.prot.sample_N100.fasta --- a/test-data/get_orf_input.Suis_ORF.prot.sample_N100.fasta Mon Apr 06 05:21:48 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,194 +0,0 @@\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|ORF101 length 112 aa, 339 bp, from complement(72006..72344) of Streptococcus_suis\n-LQFNFYVYTTWKIQFHQSVNCFLSWVDDVDQTFVCTHFELLTRIFVLVSRTDDCVEATFC\n-WKWNWTCYLSTCTCCSFNDFCSCCIKCTVFVRFQADANFFVCHLFLLFVYLT\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|ORF301 length 105 aa, 318 bp, from complement(191714..192031) of Streptococcus_suis\n-NQGQTVRFFHIRGNFCQKFIIGNTCGSCQMQFIPNIVLDKLGNLNRRADAQLIFCYIQVS\n-LIDRHGLHQISIAMENFSNLSPNFLIFFIIARNENRLRTTLISLF\n->Streptococcus_suis|ORF401 length 120 aa, 363 bp, from 265643..266005 of Streptococcus_suis\n-TTGTTSPIAPKWKASSKSLRVPTSEPTTLIPSSTVFTILRSMYSDGSPTATTYPPARTLS\n-IAWLKATLETAVTTVECTPPPVISLIYPGTSSTSSPLIVTSAPTSLASSNLSLLMSTAIT\n->Streptococcus_suis|ORF501 length 104 aa, 315 bp, from 336857..337171 of Streptococcus_suis\n-KDLIRKSSLLVYKLFSPSRTMSKSIVAWRMIYSDEDPIRRRSKAFRPVAPSNIRSAPVSF\n-GISIASRVLGLPNSMRICTSVRPALRASCLYSSRRSSASLSKDS\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|ORF701 length 182 aa, 549 bp, from 489284..489832 of Streptococcus_suis\n-LGKSVALSSLSRVTIYRGENLGKLRFFVAYLTSRYIIDIQNEGRMNMNIKEVSDVTGLSA\n-DTIRYYERVGLIPKIARKSSGVRDFVENDVAVLEFVRCFRSAGMSIERLIEYMGLVQAGD\n-STVEARIDLLKEEREVLQSRLSKIQQALERLDYKIENYQTILRGAENQLFTDGSGSCKKD\n-RE\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|ORF901 length 241 aa, 726 bp, from 628396..629121 of Streptococcus_suis\n-NSPMRLDKCLEKAKVGSRKQVKKLFKAQQIKINGQAAQSLSQIVDPELQTIQVSGKKVAL\n-EGSAYYLLHKPAGVVSAVTDQEHQTVIDLISPQDSREGLYPVGRLDRDTEGLVLITNNGP\n-LGYRMLHPSHHVDKVYYVEVNGCLAEDASKFFASGVTFLDGTRCQPADLTVLEASLDHSR\n-ATIKLAEGKFHQVKKMFLAYGVKVTYLKRISFGGFELGDLERGTYRQLTPNEMEHLFTYF\n-D\n->Streptococcus_suis|ORF1001 length 374 aa, 1125 bp, from 694014..695138 of Streptococcus_suis\n-HYLLFQGGILMKVFASPSRYIQGKHVLFQGAEAIGKLGTKPLILCDDLVY'..b'W\n-PSLLALTPKKAQQLLILAPNTELAGQIFEVCKTWSETIGLTAQLFLSGSSQKRQIERLKK\n-GPEILIGTPGRIFELIKLKKIKMMNINTIVLDEFDQLFSDSQYQFVEKIINYVPRDHQLI\n-YMSATAKFDRQKIAEDIESIDLSEQKLDNIQHCYMMVDKRERLETLRKFANIPDFRALAF\n-FNSLSDLGASEDKLLYNGVNAVSLVSDVNVKFRKVIIERFKNHELNLLLATDMVARGIDI\n-DNLECVLNFEVPFDQEAYTHRSGRTGRMGKEGLVITLVSSPSELKQLKKYASVQEVILKN\n-QELYKI\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|ORF2301 length 102 aa, 309 bp, from 1597247..1597555 of Streptococcus_suis\n-IDVIKDASEIFHSIPIEFYIGVKMIENRLVVTRYNLTVINFGYQSCPGIFRLDGIPKVRS\n-CIFQMLYQVIPNCFSRIGILNSFSWSRTDNFIFHQETLLMLR\n->Streptococcus_suis|ORF2401 length 141 aa, 426 bp, from 1658030..1658455 of Streptococcus_suis\n-ASITVPIARTVGSAFSSWISATKRTVSNNSSMFWLNLAEISTNSDSPPQAVEITPCSANS\n-PMTRSGFAPGLSILLIATMIGTLAAFEWLIASIVCGMTPSSAATTRMVKSVTDAPRARIE\n-VKAACPGVSKKVIFLPASSIW\n->Streptococcus_suis|ORF2501 length 630 aa, 1893 bp, from complement(1722511..1724403) of Streptococcus_suis\n-GEMMMLQINHSLRQSEGVLEEICSSLGLDCQLELEVGGKESLRIEGSAGSYRIRAPKEHM\n-IYRGLLVLASQLAQGETDIQILERPAYRQLGFMEDCSRNAVLTVEASKILIRQLALIGYS\n-HFQLYMEDTYQLRDEPYFGYFRGAYTKEELQAIEEECHRYGMEFIPCIQTLAHLIAYLKW\n-NISSIQAIRDVDNILLIGDERTYALIDKMFEALSHLKTRTINIGMDEAHLVGLGQYLNQH\n-GYQKRSLIMCQHLERVLDIADKYGFHCSMWSDMFFQLLTASKDYTGQLEIDSEIQAYLDR\n-LKDRVTLIYWDYYQTSRESYGQKLASHQQLGDQIAFASGAWKWIGFTPDNDFSMRIAPKA\n-HAACQEYGVQEVTVTAWGDNGGECATFSILPSLHAWAELQYRGNLGCLAEHFYQLHQVSL\n-DDFLQLDLPNKTPSHPGPGHHGFNPSRYILYQDILCPLLQEHIDAEKDNAFYQELAPRLA\n-EIGSRAKGYAYLFDTQAKLCQVLATKAAISVGIRQAYQEGNRQVLAEKVDGLQQLRIDLE\n-SFYQALSYQWMVEKKVFGLDTVDIRLGGLDARIRRAIQRLQAYLNNEVPKLDELEVPILP\n-YDDFHQDKGFIATTANQWQIIATASTIYTT\n->Streptococcus_suis|ORF2601 length 100 aa, 303 bp, from 1790150..1790452 of Streptococcus_suis\n-LKDGYQRLVVEGFADIAETFLQTETNLMTTVIFIARHDDDRPIAFPLGSLNQVNMTLVHG\n-SKGPKNNCYCLFHNLPFYCFLYFISYSFLKPKSRVFYIFL\n->Streptococcus_suis|ORF2701 length 215 aa, 648 bp, from 1851361..1852008 of Streptococcus_suis\n-SLHPHEASHDNGKHDLHEVTHKGSKATDCLQVGFQHPGHQVERCKNRHVRDKHHQGLQDS\n-KTIADKEVEVQEFIGYFLELGILIFFLYKRLNHTNPTEVFLSNTVHLVHEGLEFPKTWSH\n-LPHDNCHNSHNQDHHENNHPPEFWHGPHCHDKGSDKQQWNPHQHCKEHHDKVLDLIDIVS\n-HPNNQVPCVKLFDISIREALDLPKGLLTNICRYPL\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|ORF2901 length 306 aa, 921 bp, from 1998013..1998933 of Streptococcus_suis\n-IRDNRNCFYNTNQGEYMKERIKDFISVTLGSVVMAIGFNSFFLENNIVSGGVGGLAIALN\n-ALLRWSPSDFVLYCNIPLLIICWFFLGKSVFIKTVYGAIIYPLCIKLTAGLPNLTENPLL\n-AAIFGGIILGFGLGLVFLGNSSTGGTGILIQFIHKYTPLSLGLTMAIIDGIIVGLGFVAF\n-DTDTVMYSIIALMTITYIVNRMMSGTQSSRNVMIISQKSEEIKDYITKVADRGVTELPII\n-GGFTGVDKRMLMTTISIPEMQKLETAVLEIDETAFMVVMPASQVRGRGFSLQKDHKHYDE\n-DILIPM\n' |
| b |
| diff -r 65d76ca44cd2 -r 2eb9e86f5f35 tools/get_orfs_or_cdss/README.rst --- a/tools/get_orfs_or_cdss/README.rst Mon Apr 06 05:21:48 2015 -0400 +++ b/tools/get_orfs_or_cdss/README.rst Tue May 12 11:27:35 2015 -0400 |
| b |
| @@ -1,7 +1,7 @@ Galaxy tool to find ORFs or simple CDSs ======================================= -This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute +This tool is copyright 2011-2015 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below (MIT licence). @@ -74,6 +74,7 @@ v0.1.0 - Tool now outputs BED formatted calls (by @erasche, Eric Rasche). - Using ``optparse`` for the Python command line API (Eric Rasche). - Added NCBI genetic code table 24, Pterobranchia Mitochondrial. +v0.1.1 - Reorder XML elements (internal change only). ======= ====================================================================== @@ -86,32 +87,41 @@ Development has now moved to a dedicated GitHub repository: https://github.com/peterjc/pico_galaxy/tree/master/tools -For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use -the following command from the Galaxy root folder:: +For pushing a release to the test or main "Galaxy Tool Shed", use the following +Planemo commands (which requires you have set your Tool Shed access details in +``~/.planemo.yml`` and that you have access rights on the Tool Shed):: - $ tar -czf get_orfs_or_cdss.tar.gz tools/get_orfs_or_cdss/README.rst tools/get_orfs_or_cdss/get_orfs_or_cdss.* tools/get_orfs_or_cdss/tool_dependencies.xml test-data/get_orf_input*.fasta test-data/Ssuis.fasta test-data/get_orf_input*.bed + $ planemo shed_upload --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/get_orfs_or_cdss/ + ... -Check this worked:: +or:: - $ tar -tzf get_orfs_or_cdss.tar.gz - tools/get_orfs_or_cdss/README.rst - tools/get_orfs_or_cdss/get_orfs_or_cdss.py - tools/get_orfs_or_cdss/get_orfs_or_cdss.xml - tools/get_orfs_or_cdss/tool_dependencies.xml - test-data/get_orf_input.fasta + $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/get_orfs_or_cdss/ + ... + +To just build and check the tar ball, use:: + + $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/get_orfs_or_cdss/ + ... + $ tar -tzf shed_upload.tar.gz + test-data/Ssuis.fasta + test-data/get_orf_input.Suis_ORF.bed test-data/get_orf_input.Suis_ORF.nuc.fasta test-data/get_orf_input.Suis_ORF.prot.fasta + test-data/get_orf_input.fasta + test-data/get_orf_input.t11_bed_out.bed test-data/get_orf_input.t11_nuc_out.fasta + test-data/get_orf_input.t11_open_bed_out.bed test-data/get_orf_input.t11_open_nuc_out.fasta test-data/get_orf_input.t11_open_prot_out.fasta test-data/get_orf_input.t11_prot_out.fasta + test-data/get_orf_input.t1_bed_out.bed test-data/get_orf_input.t1_nuc_out.fasta test-data/get_orf_input.t1_prot_out.fasta - test-data/Ssuis.fasta - test-data/get_orf_input.Suis_ORF.bed - test-data/get_orf_input.t11_open_bed_out.bed - test-data/get_orf_input.t11_bed_out.bed - test-data/get_orf_input.t1_bed_out.bed + tools/get_orfs_or_cdss/get_orfs_or_cdss.py + tools/get_orfs_or_cdss/get_orfs_or_cdss.xml + tools/get_orfs_or_cdss/README.rst + tools/get_orfs_or_cdss/tool_dependencies.xml Licence (MIT) |
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| diff -r 65d76ca44cd2 -r 2eb9e86f5f35 tools/get_orfs_or_cdss/get_orfs_or_cdss.xml --- a/tools/get_orfs_or_cdss/get_orfs_or_cdss.xml Mon Apr 06 05:21:48 2015 -0400 +++ b/tools/get_orfs_or_cdss/get_orfs_or_cdss.xml Tue May 12 11:27:35 2015 -0400 |
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| @@ -1,18 +1,18 @@ -<tool id="get_orfs_or_cdss" name="Get open reading frames (ORFs) or coding sequences (CDSs)" version="0.1.0"> +<tool id="get_orfs_or_cdss" name="Get open reading frames (ORFs) or coding sequences (CDSs)" version="0.1.1"> <description>e.g. to get peptides from ESTs</description> <requirements> <requirement type="package" version="1.65">biopython</requirement> <requirement type="python-module">Bio</requirement> </requirements> - <version_command interpreter="python">get_orfs_or_cdss.py --version</version_command> - <command interpreter="python"> -get_orfs_or_cdss.py -i $input_file -f $input_file.ext --table $table -t $ftype -e $ends -m $mode --min_len $min_len -s $strand --on $out_nuc_file --op $out_prot_file --ob $out_bed_file - </command> <stdio> <!-- Anything other than zero is an error --> <exit_code range="1:" /> <exit_code range=":-1" /> </stdio> + <version_command interpreter="python">get_orfs_or_cdss.py --version</version_command> + <command interpreter="python"> +get_orfs_or_cdss.py -i $input_file -f $input_file.ext --table $table -t $ftype -e $ends -m $mode --min_len $min_len -s $strand --on $out_nuc_file --op $out_prot_file --ob $out_bed_file + </command> <inputs> <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file (nucleotides)" help="FASTA, FASTQ, or SFF format." /> <param name="table" type="select" label="Genetic code" help="Tables from the NCBI, these determine the start and stop codons"> |