| Previous changeset 0:9cff9a1176ea (2012-01-19) Next changeset 2:324775a016ce (2013-04-23) |
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Commit message:
Uploaded v0.0.2, fixes labelling issue on reverse strand. |
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modified:
tools/filters/get_orfs_or_cdss.py tools/filters/get_orfs_or_cdss.txt tools/filters/get_orfs_or_cdss.xml |
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added:
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_nuc_out.fasta 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_nuc_out.fasta test-data/get_orf_input.t1_prot_out.fasta |
| b |
| diff -r 9cff9a1176ea -r 922d69bd5258 test-data/get_orf_input.Suis_ORF.nuc.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/get_orf_input.Suis_ORF.nuc.fasta Tue Jan 29 10:19:01 2013 -0500 |
| b |
| b'@@ -0,0 +1,41831 @@\n+>Streptococcus_suis|ORF1 length 457 aa, 1374 bp, from 1..1374 of Streptococcus_suis\n+ATGAACCAAGAACAACTTTTTTGGCAACGATTTATTGAATTGGCAAAGGTAAATTTTAAG\n+CCATCTATTTATGATTTTTATGTCGCTGATGCAAAATTACTCGGAATCAACCAGCAAGTT\n+GCCAATATTTTCTTAAATCGTCCATTTAAAAAAGATTTCTGGGAAAAAAACTTCGAAGAG\n+TTAATGATTGCCGCTAGTTTTGAAAGCTACGGAGAGCCTCTTACCATCCAATATCAATTT\n+ACAGAGGATGAACAGGAGATTAGGAATACTACAAACACAAGAAGTTCAATAGTTCACCAG\n+GTACAGACACTTGAGCCGGCTACTCCTCAAGAAACTTTTAAACCGGTTCATTCTGATATA\n+AAATCCCAGTACACCTTTGCTAATTTTGTACAAGGAGACAATAATCACTGGGCAAAGGCT\n+GCAGCTTTAGCTGTATCTGATAACCTAGGTGAGCTCTACAATCCATTATTCATTTTTGGT\n+GGTCCTGGTCTTGGAAAAACTCATATTTTAAATGCGATTGGAAATAAGGTTCTAGCCGAT\n+AATCCCCAGGCAAGGATAAAATATGTCTCATCGGAAACATTCATCAATGAATTTTTAGAA\n+CACCTCCGTCTCAATGATATGGAAAGTTTCAAAAAAACCTATCGCAATCTGGACTTACTT\n+CTAATTGATGACATTCAGTCTCTCCGTAATAAAGCAACAACACAGGAAGAATTTTTCCAT\n+ACTTTTAATGCGCTTCATGAAAAAAATAAGCAGATTGTACTCACAAGCGACCGTAATCCC\n+GATCACTTAGACAATTTGGAAGAAAGACTAGTAACACGTTTCAAATGGGGGTTAACCAGT\n+GAAATCACTCCACCTGATTTTGAAACACGTATCGCAATTTTACGTAACAAGTGCGAGAAC\n+CTGCCTTACAACTTTACAAATGAGACGCTATCCTATCTAGCTGGGCAATTTGATTCGAAC\n+GTACGTGACCTTGAAGGTGCCTTAAAAGATATCCATTTGATAGCCACTATGCGTCAACTG\n+TCTGAGATAAGTGTCGAGGTTGCTGCTGAGGCTATTCGATCAAGAAAACAAACAAATCCA\n+CAAAACATGGTTATTCCTATTGAGAAAATCCAAACCGAAGTGGGAAATTTCTACGGTGTC\n+AGCTTGAAAGAATTAAAAGGTTCTAAGCGTGTTCAACATATCGTTCACGCGCGACAAGTT\n+GCTATGTTTTTAGCACGTGAAATGACAGACAATTCCCTTCCAAAAATTGGGAAAGAATTT\n+GGTAATCGAGACCATACAACCGTTATGCATGCATACAATAAAATAAAAACTCTCCTCTTG\n+GATGATGAGAATTTAGAAATAGAGATTACCAGTATAAAAAATAAACTTCGTTAA\n+>Streptococcus_suis|ORF2 length 385 aa, 1158 bp, from 1507..2664 of Streptococcus_suis\n+ATAATAAATAAAGGAGAATCCATGATTCAATTTTCTATTAATAAAAATATATTTCTACAA\n+GCACTTAGTATTACTAAACGGGCAATCAGTACAAAAAATGCTATTCCAATTCTTTCAACA\n+GTAAAAATTACAGTAACTAGTGAAGGAATCACTTTAACTGGTTCAAATGGACAAATCTCG\n+ATAGAACATTTTATTTCTATTCAAGATGAAAATGCAGGGCTTTTGATCAGTTCTCCAGGT\n+TCCATTCTCTTAGAAGCTGGTTTCTTTATTAATGTCGTATCCAGTATGCCGGATTTGGTC\n+CTTGACTTCAATGAAATTGAACAAAAGCAAATCGTTTTGACAAGTGGTAAGTCTGAAATC\n+ACATTAAAGGGAAAAGAAGCAGAACAGTATCCTCGTTTACAGGAAGTTCCAACTTCAAAA\n+CCATTGGTGTTAGAAACCAAAGTATTAAAACAAACAATTAATGAAACAGCATTTGCAGCT\n+TCTACACAAGAAAGTCGTCCTATTCTTACGGGTGTTCATTTTGTTTTAACAGAAAATAAA\n+AATCTAAAAACTGTTGCAACAGATTCACACCGTATGAGCCAACGGAAATTGGTCCTTGAT\n+ACCTCTGGTGATGATTTTAATGTTGTCATTCCAAGTCGTTCTCTCCGTGAATTTACTGCA\n+GTTTTTACAGATGATATTGAAACAGTAGAAGTCTTCTTTTCAAATAATCAAATCCTTTTT\n+AGAAGCGAGCATATTAGCTTCTATACACGCTTATTAGAAGGTACCTACCCTGATACCGAC\n+CGCTTAATTCCAACTGAGTTTAAAACAACTGCAATTTTTGATACTGCAAATCTTCGTCAC\n+TCGATGGAGCGTGCTCGTCTTCTTTCAAATGCAACCCAAAATGGTACAGTAAAACTAGAA\n+ATTGCTAATAATGTTGTATCGGCTCATGTAAATTCTCCAGAAGTTGGACGTGTGAATGAG\n+GAATTAGATACTGTAGAAGTATCAGGTGAAGATTTAGTAATCAGCTTTAACCCAACTTAC\n+TTGATAGAAGCATTGAAAGCCACAACTAGTGAACAAGTGAAAATTAGCTTTATCTCTTCT\n+GTCCGTCCATTTACATTGATTCCAAATAATGAAGGGGAAGATTTTATTCAATTGGTTACA\n+CCAGTTCGTACCAACTAA\n+>Streptococcus_suis|ORF3 length 104 aa, 315 bp, from complement(1707..2021) of Streptococcus_suis\n+ACACCCGTAAGAATAGGACGACTTTCTTGTGTAGAAGCTGCAAATGCTGTTTCATTAATT\n+GTTTGTTTTAATACTTTGGTTTCTAACACCAATGGTTTTGAAGTTGGAACTTCCTGTAAA\n+CGAGGATACTGTTCTGCTTCTTTTCCCTTTAATGTGATTTCAGACTTACCACTTGTCAAA\n+ACGATTTGCTTTTGTTCAATTTCATTGAAGTCAAGGACCAAATCCGGCATACTGGATACG\n+ACATTAATAAAGAAACCAGCTTCTAAGAGAATGGAACCTGGAGAACTGATCAAAAGCCCT\n+GCATTTTCATCTTGA\n+>Streptococcus_suis|ORF4 length 293 aa, 882 bp, from 2756..3637 of Streptococcus_suis\n+ATGACGTTATATATATTAGCTAATCCTAATGCTGGTAGCCATACTGCTGAACATATCATA\n+TTCAAAATAAAAGAAAGTTATCCACAGCTTGCAGTTAACATTTTTATGACAGTTGGTCCT\n+GAGGATGAAAAAAGTCAAATAGAGGCTATTTTAAAGGAGTTTGTCAGTAGTGAAGATCAA\n+TTAATGATTTTAGGCGGAGACGGCACACTATCTAAAGCTTTGCGTTTTTGGCCAGCTAGT\n+CTACCGTTTGCTTATTATCCAACAGGATCTGGAAATGATTTTGCTAAGGCAATGAATATA\n+ACATCGCTATATAGAAGTGTAGATGCCATTTTAGAGAGAAAAACAAGTCGGATATATGTT\n+TTAAACAGTTCATACGGAACGGTTGTAAACAGTATGGATTTTGGCTTTGCAGCTCAAGTT\n+ATCAATGGTTCAACGAATTCAATTTTGAAAAAAATTCTGAACAAGGTAAAACTTGGGAAG\n+TTAACTTATCTATTCTTTGGTATTAAAACATTATTTTCAAAACAAGCTATAAACTTAGAA\n+TTAACTCTTGATGAAAAATCTTATCAGTTAGATAATCTCTTTTTTATTTCTGTAGCAAAT\n+AGTCTTTATTTTGGTGGAGGAATCATGATATGGCCAACAGCAAGTGCTAAAAAG'..b'GCAACCATTGATGGTAAACCTATCAAAATCCAAAAAGCGCAAGATGGT\n+TTTATGAAAGTGGATGTAAGTCCAGGTCAAACTAAACTAGTTTTAACCTTTGTACCAAAT\n+GGTTTCTATCTAGGTTTACTGATTTCTTTTGGTGCAGTTTTTGTATTTTTCTCCTATCAA\n+TTCATTGGATACTATTATTCTAAGAACCGAGAATACTAA\n+>Streptococcus_suis|ORF2907 length 235 aa, 708 bp, from complement(2003907..2004614) of Streptococcus_suis\n+TTTCACGTGAAACAAGGAGTGAAAATGAATCAAAAAGAGTATCGTGTTTTTGAGGGATTG\n+AGAATTGCTTGTTCATTAACGTTTATCAGTGGTTATTTAAATGCCTTTACTTTTGTGACT\n+CAGGGTGGTCGCTTTGCTGGCGTACAATCTGGAAATGTTATTTCCCTAGCTTATTTTTTA\n+GCTAAAGGTGATTTTGCGCAGGTAGTTAATTTTTCCATTCCCATTTTATTTTTTGTATTC\n+GGACAATTTTTTACCTACTTAGCAAGAAGGTATTTTGAAAAACAAACATGGTCTTGGCAC\n+TTTGGTAGTAGTGTAATGATGTTAGTTCTTATTTTACTAACTATCATTCTCTCACCTATA\n+ATGCCTGCGTCTTTTACAATTGCTAGTCTAGCCTTCGTAGCCTCTATTCAAGTAGAAACA\n+TTTAGAAGGTTACGAGGTGCTCCGTATGCCAATGTGATGATGACAGGGAATGTCAAAAAT\n+GCTGCTTATCTCTGGTTTAAAGGAGTTATTGAAAAAGATTCAGAACTTAGAAAAACAGGT\n+AGAAACATCTTATTGACCATTATAGGGTTTATGCTAGGTGTCATCATATCTACTCACCTA\n+TCCTTCCAATTTGAAGAATATGCCCTTATTGGTCTGATTTTGCCAGTGTTATATATTAAT\n+TATGAATTATGGCAAGAAAAAAGACCTACTCGAGGTAGGTCTAAATGA\n+>Streptococcus_suis|ORF2908 length 180 aa, 543 bp, from complement(2004615..2005157) of Streptococcus_suis\n+CCATATCCTGATTTTCTAAAAATATTTTCTGTCGTATGCTTGTGGATATGTTACAATTAT\n+TTTATGAAAATAAAATTGATTACCGTTGGAAAATTGAAAGAAAAGTACCTCAAAGAAGGT\n+ATTGCAGAATATAGTAAACGATTGGGACGATTTACTAAGTTGGATATGATTGAGCTTCCT\n+GATGAAAAAACACCAGATAAAGCCAGTCAGGCAGAGAATGAACAAATATTAAAAAAAGAA\n+GCCGATAGAATTATGTCTAAAATTGGAGAGCGAGATTTTGTCATTGCCTTAGCGATAGAA\n+GGGAAACAATTTCCATCGGAAGAATTTAGTCAAAGGATATCTGACATTGCAGTAAATGGG\n+TATTCAGATATAACTTTTATCATCGGTGGTAGTTTGGGTCTCGATTCTTGTATTAAAAAA\n+AGAGCTAATTTGTTGATGAGTTTTGGACAGTTGACACTTCCCCATCAACTAATGAAATTA\n+GTTCTCATCGAGCAGATTTATCGTGCATTTATGATTCAGCAGGGAAGCCCATATCATAAG\n+TAG\n+>Streptococcus_suis|ORF2909 length 413 aa, 1242 bp, from 2005223..2006464 of Streptococcus_suis\n+GTTATAATTAAGAAAGAAATAGTACTCTTAAGGAAAATTAAAGAAATGGAAAGGATTCCT\n+TATATGAAAAAATATTTGAAATTTGCGATTTTATTTGTAATTGGATTTTTTGGGGGTCTT\n+ATCGGGGCCTTGTCAGCCTCTTTCTTCCAGCCACAGGTGCAACAAGCAAATTCTGCTATC\n+ACTAGTGTCAGCAATGTTCAATATAATAATGAAACTTCCACCACAAAAGCTGTAGAGAAA\n+GTACAAAATGCTGTTGTGTCTGTTATTAATTACCAAAAATCAGCCAACAATAGTCTTGGT\n+GTTATCTTTGGAAATATTGAATCATCTGACGAACTAGCTGTTGCTGGAGAGGGGTCTGGG\n+GTTATCTATAAAAAATATGGTCAATATGCCTATATTGTGACAAATACGCATGTTATTAAT\n+AACGCAGAAAAGATTGATATCCTTTTAGCATCTGGAGAAAAAATTAGCGGTGAACTTGTT\n+GGTTCCGATACATATTCTGATATAGCTGTTATAAAAATATCAGCAGATAAAGTCACTGCT\n+GTTGCTGAATTTGCTGATTCCGATACAATTAAAGTTGGAGAAACTGCTATCGCAATTGGT\n+AGTCCTCTAGGTAGCGTCTACGCCAATACAGTTACCCAGGGTATTATTTCTAGCTTAAGT\n+CGGACAGTTACTTCACAATCAAAAGATGGACAAACAATCTCAACTAACGCTATTCAAACT\n+GATACAGCTATCAACCCTGGAAACTCTGGCGGACCGTTAATCAATACCCAAGGACAAGTG\n+ATAGGCATTACCTCTAGCAAAATTACCTCAAGTTCTGCAAATAGCTCAGGCGTGGCTGTA\n+GAAGGGTTGGGATTTGCTATTCCTGCAAATGATGCCGTAGCTATTATCAATCAGCTTGAA\n+AAAACTGGACAAGTTAGCCGACCTGCTCTTGGAGTTCATATGGTTAACTTGACGACCTTG\n+TCAACTAGTCAATTAGAAAAAGCTGGATTATCAAATACGGAATTAACATCCGGTGTAGTA\n+ATTGTCTCTACACAAAGTGGGCTACCTGCAGATGGAAAATTAGAAACTTTTGATGTTATT\n+ACTGAGATTGACGGAGAAGCTATTCAAAATAAGAGTGACCTCCAGAGCGCTCTCTACAAA\n+CATCAAATTGGAGATACAATCACTGTAACTTATTACCGCAATAATCAGAAACAAACTGTT\n+GACATTAAGTTGACACATTCTACAGAAGAACTTAGCGAATAA\n+>Streptococcus_suis|ORF2910 length 256 aa, 771 bp, from 2006519..2007289 of Streptococcus_suis\n+GGATATATGGAAGAATTACGTACACTAAATATTTCAGAAATCCATCCCAATCCCTATCAG\n+CCAAGAATTCATTTTGATGAAAAGGAGCTACTTGAGCTCGCTCAATCTATTAAGGAAAAT\n+GGCTTAATTCAACCGATTATTGTAAGAAAATCTTCTATTATCGGATACGAATTATTAGCT\n+GGAGAAAGAAGGTTGCGAGCCAGTCAATTAGCTGGACTGACTACAATACCAGCAGTGGTA\n+AAAGAACTGACTGATGATGATTTACTCTATCAGGCTATCATAGAGAATCTGCAGCGTTCT\n+AACTTAAATCCGATAGAAGAAGCAGCCTCTTATCAAAAATTGATTAGTAGAGGGTTAACA\n+CATGATGAAGTTGCTCAAATCATGGGAAAATCAAGACCATATATCAGTAATTTATTGCGC\n+CTACTAAATCTATCATCTCAGACTAAACAAGCTGTAGAAGAAGGAAAAATTTCACAAGGG\n+CACGCGCGACAATTGGTGTCATTTTCAGAAGAAAAGCAAGCCGAATGGGTTCAACTCATT\n+TTATCAAAGGATTTAAGTGTGCGTACGCTTGAAAAATTAATAGCTGCAAATAAGAAAAAA\n+CACACTAAGCTTAAACAACGCGACCAATTTTTAAAAGAACAGGAAGATTCACTCAGTAAA\n+ACTCTTGGAACAGCTACAAAAATTATCAAGAAGAAAAACGGGAGCGGAGAAATTCGGATT\n+AGCTTTAATGACCTCGATGAATTCGAAAGAATTATCAACAATTTTAAATAG\n' |
| b |
| diff -r 9cff9a1176ea -r 922d69bd5258 test-data/get_orf_input.Suis_ORF.prot.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/get_orf_input.Suis_ORF.prot.fasta Tue Jan 29 10:19:01 2013 -0500 |
| b |
| b'@@ -0,0 +1,16670 @@\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|ORF3 length 104 aa, 315 bp, from complement(1707..2021) of Streptococcus_suis\n+TPVRIGRLSCVEAANAVSLIVCFNTLVSNTNGFEVGTSCKRGYCSASFPFNVISDLPLVK\n+TICFCSISLKSRTKSGILDTTLIKKPASKRMEPGELIKSPAFSS\n+>Streptococcus_suis|ORF4 length 293 aa, 882 bp, from 2756..3637 of Streptococcus_suis\n+MTLYILANPNAGSHTAEHIIFKIKESYPQLAVNIFMTVGPEDEKSQIEAILKEFVSSEDQ\n+LMILGGDGTLSKALRFWPASLPFAYYPTGSGNDFAKAMNITSLYRSVDAILERKTSRIYV\n+LNSSYGTVVNSMDFGFAAQVINGSTNSILKKILNKVKLGKLTYLFFGIKTLFSKQAINLE\n+LTLDEKSYQLDNLFFISVANSLYFGGGIMIWPTASAKKKEVDIVYFKNGNFYQRLQSLLA\n+LLTKRHESSHTIQHLTGVDVVLKSKEKLLLQIDGETCTANEVTLTYQERSMYL\n+>Streptococcus_suis|ORF5 length 126 aa, 381 bp, from 3933..4313 of Streptococcus_suis\n+KKEEEMIMKQLAQQIRVLRTAKNLSQDELAEKLYISRQAVSKWENGEATPDIDKLVQLAE\n+IFGVSLDYLVLGKEPEKEIVVEQRGKMNGWEFLNEESKRPLTRGDVVLLIFLAVMLLGGL\n+FIKHYF\n+>Streptococcus_suis|ORF6 length 377 aa, 1134 bp, from 4381..5514 of Streptococcus_suis\n+LESKKNMSLTAGIVGLPNVGKSTLFNAITKAGAEAANYPFATIDPNVGMVEVPDERLQKL\n+TELIIPKKTVPTTFEFTDIAGIVKGASKGEGLGNKFLANIREVDAIVHVVRAFDDENVMR\n+EQGREDAFVDPIADIDTINLELILADLESINKRYARVEKMARTQKDKDSVAEFAVLEKIK\n+PVLEDGKSARTVEFTDEEQKIVKQLFLLTTKPVLYVANVDEDKVADPEAISYVQQIRDFA\n+ATENAEVVVISARAEEEISELDDEDKGEFLEALGLTESGVDKLTRAAYHLLGLGTYFTAG\n+EKEVRAWTFKRGMKAPQCAGIIHSDFEKGFIRAVTMSYDDLMTYGSEKAVKEAGRLREEG\n+KEYVVQDGDIMEFRFNV\n+>Streptococcus_suis|ORF7 length 115 aa, 348 bp, from complement(4450..4797) of Streptococcus_suis\n+VNGINISDWIHKGIFTALFTHDIFIVKGTHNVDNRINFADIGQEFISKSFTFRSTFYDTS\n+NISKFKSRWHCLFRDDEFGQLLQTLIGHFYHADVWINSCERVVCSFCSCLGNCVK\n+>Streptococcus_suis|ORF8 length 115 aa, 348 bp, from complement(4491..4838) of Streptococcus_suis\n+RLLMLSRSAKINSRLMVSISAIGSTKASSRPCSRMTFSSSKARTTWTIASTSRILAKNLF\n+PSPSPLEAPFTIPAISVNSKVVGTVFLGMMSSVNFCRRSSGTSTMPTFGSIVAKG\n+>Streptococcus_suis|ORF9 length 192 aa, 579 bp, from 5663..6241 of Streptococcus_suis\n+GEKMTRLIIGLGNPGDRYFETKHNVGFMLLDKIAKRENVTFNHDKIFQADIATTFIDGEK\n+IYLVKPTTFMNESGKAVHALMTYYGLDATDILVAYDDLDMAVGKIRFRQKGSAGGHNGIK\n+SIVKHIGTQEFDRIKIGIGRPKGKMSVVNHVLSGFDIEDRIEIDLALDKLDKAVNVYLEE\n+DDFDTVMRKFNG\n+>Streptococcus_suis|ORF10 length 1166 aa, 3501 bp, from 6235..9735 of Streptococcus_suis\n+RIMNILDLLHKNKQINQWQSGLNQSTRQLLLGLSGTSKSLIMATAYDCLAEKIMIVTATQ\n+NDAEKLVADLTAIIGSENVYNFFTDDSPIAEFVFASKERTQSRIDSLNFLTDSTSSGILV\n+ASIVACRVLLPSPETYKGSKIQLEVGQEIEVDKLVKNLVNIGYKKVSRVLTQGEFSQRGD\n+ILDIFDMQSETPYRIEFFGDEIDGIRIFDVDSQKSLENLDEISISPASDIILSSEDYSRA\n+SQYIQTAIEQSTLEEQQSYLREVLADMQTEYRHPDLRKFLSCIYEQSWTLLDYLPKSSPL\n+FLDDFHKIADKQAQFEKEIADLLTDDLQKGKTVSSLKYFASTYAELRKYKPATFFSSFQK\n+GLGNVKFDALYQFTQHPMQEFFHQIPLLKDELTRYAKSNNTVVIQASSDVSLQTLQKNLQ\n+EYDIHLPVHAADKLVEGQQQVTIGQLASGFHLMDEKLVFITEKEIFNKKMKRKTRRTNIS\n+NAERIKDYSELAVGDYVVHHVHGIGQYLGIETIEISGIHRDYLTVQYQNSDRISIPVEQI\n+DLLSKYLASDGKAPKVNKLNDGRFQRTKQKVQKQVEDIADDLIKLYAERSQLKGFAFSPD\n+DENQVEFDNYFTHVETDDQLRSIDEIKKDMEKDSPMDRLLVGDVGFGKTEVAMRAAFKAV\n+NDGKQVAILVPTTVLAQQHYANFQERFAEFPVNVDVMSRFKTKAEQEKTLEKLKKGQVDI\n+LIGTHRLLSKDVVFADLGLLVIDEEQRFGVKHKERLKELKKKIDVLTLTATPIPRTLQMS\n+MLGIRDLSVIETPPTNRYP'..b'\n+DTDTVMYSIIALMTITYIVNRMMSGTQSSRNVMIISQKSEEIKDYITKVADRGVTELPII\n+GGFTGVDKRMLMTTISIPEMQKLETAVLEIDETAFMVVMPASQVRGRGFSLQKDHKHYDE\n+DILIPM\n+>Streptococcus_suis|ORF2902 length 565 aa, 1698 bp, from 1998923..2000620 of Streptococcus_suis\n+FQCNSLKIQVLSSTIKLIDRNRGETMLTVSDVSLRFSDRKLFDDVNIKFTAGNTYGLIGA\n+NGAGKSTFLKILAGDIEPSTGHISLGPDERLSVLRQNHFDYEDERVIDVVIMGNEQLYSI\n+MKEKDAIYMKEDFSDEDGVRAAELEGEFAELGGWEAESEASQLLQNLNISEDLHYQNMSE\n+LTNGEKVKVLLAKALFGKPDVLLLDEPTNGLDIQSINWLEDFLIDFENTVIVVSHDRHFL\n+NKVCTHMADLDFGKIKIFVGNYDFWKQSSELAAKLQADRNAKAEEKIKELQEFVARFSAN\n+ASKSKQATSRKKMLDKIELEEIIPSSRKYPFINFKSEREIGNDLLTVENLKVVIDGETIL\n+DNISFILRPGDKTALIGQNDIQTTALIRALMGDIEYEGTVKWGVTTSQSYLPKDNTRDFD\n+TNESILDWLRQFASKEEDDNTFLRGFLGRMLFSGDEVNKPVNVLSGGEKVRVMLSKLMLL\n+KSNVLVLDDPTNHLDLESISSLNDGLKAFKESIIFASHDHEFIQTLANHIIVISKNGVID\n+RIDETYDEFLENAEVQAKVQELWKA\n+>Streptococcus_suis|ORF2903 length 115 aa, 348 bp, from complement(1999705..2000052) of Streptococcus_suis\n+PIRAVLSPGRRIKLILSRIVSPSITTFKFSTVKRSLPISRSDLKLINGYLRLEGMISSNS\n+ILSNIFLREVACLDLEALAEKRATNSCSSLIFSSAFALRSACSLAASSLDCFQKS\n+>Streptococcus_suis|ORF2904 length 110 aa, 333 bp, from 1999974..2000306 of Streptococcus_suis\n+KLLLMVKRFLTISALSCAQVTRLLLLVKTTSKQLLSFVLLWAILNMKVLSSGVSLLVNPT\n+YQKTILVTLIQTNLSLIGSVNLPARKKMTIPSCAVSWDVCSSRVMRLTNL\n+>Streptococcus_suis|ORF2905 length 117 aa, 354 bp, from 2000502..2000855 of Streptococcus_suis\n+QTISSSFLKTVLSTESTKLMMNSWKMLKYKQKYKNFGKHNKKRLGLLPSLSSQSSCQHLS\n+AVVDCQICSCFTLQIWPLRLLRTKFALSPTSNCLPDSLSCAGVGVKQSGNRLFQLNN\n+>Streptococcus_suis|ORF2906 length 872 aa, 2619 bp, from 2000888..2003506 of Streptococcus_suis\n+PVKFFPTSFSFKSMKKIFTKTSIYYLLSFLIPLTIISIVLAFQGIWWGSDTTILASDGFH\n+QYVIFNQTLRNTLHGDGSLFYTFSSGLGLNFYALSSYYLGSFLSPIVFFFDLQSMPDAIY\n+LVTIVKFGLTGLSTYFSLKGIHKNLKEEWALLLATSFSLMSFSTSQLEINNWLDVFILLP\n+LVLLGLHRLLKKQGPILYYITLTCLFIQNYYFGYMVAIFLTLWTLVQLSWIDSQRIKRFI\n+NFTIVSILSALSSMFMLLPTYLDLKTHGETFTKIVNLKTEDSWYLDFFAKNLVGSFDTTK\n+FGSIPMISVGLVPLILALLFFTLKEIKPTVKLSYALFFTFIISSFYLQPLNLFWQGMHAP\n+NMFLYRYAWALSITVIYLAAETLVRLRQVSIKNFTLIVSFLLICFTSTFIFRDHYEFLTD\n+VNFLLTLEFLIAYFILFVAMIRYKSSLKWINIVLLFFTFLELGLHSHYQVQGISDEWHFP\n+SRSNYEEKLTDIDSIVKSTKTTTDSFYRIERLLPQTGNDSMKFNYNGISQFSSIRNRASS\n+SVLDKLGFRSDGTNLNLRYQNNTIIADSLFGVKYNLATTDPNKFGFTLNQSQSTINLYEN\n+SFNLGLALLTEGIYKDVNFTNLTLDNQTNFLNQLTGLSQKYYHTLSDVVSQNTVELSNRM\n+TVNKVDNEDAAKATFLVNIPANSQVYLNLPNLTFSNENQKKVVITVNNQSSEFTLDNAFS\n+FFNVGSFTTDVQVQVNVYFPENNQVSFDKPQFYRLDLLAFQQAISILQEKQVVTKTDGNK\n+VTVDFVTDKESSLLLTLPYDKGWNATIDGKPIKIQKAQDGFMKVDVSPGQTKLVLTFVPN\n+GFYLGLLISFGAVFVFFSYQFIGYYYSKNREY\n+>Streptococcus_suis|ORF2907 length 235 aa, 708 bp, from complement(2003907..2004614) of Streptococcus_suis\n+FHVKQGVKMNQKEYRVFEGLRIACSLTFISGYLNAFTFVTQGGRFAGVQSGNVISLAYFL\n+AKGDFAQVVNFSIPILFFVFGQFFTYLARRYFEKQTWSWHFGSSVMMLVLILLTIILSPI\n+MPASFTIASLAFVASIQVETFRRLRGAPYANVMMTGNVKNAAYLWFKGVIEKDSELRKTG\n+RNILLTIIGFMLGVIISTHLSFQFEEYALIGLILPVLYINYELWQEKRPTRGRSK\n+>Streptococcus_suis|ORF2908 length 180 aa, 543 bp, from complement(2004615..2005157) of Streptococcus_suis\n+PYPDFLKIFSVVCLWICYNYFMKIKLITVGKLKEKYLKEGIAEYSKRLGRFTKLDMIELP\n+DEKTPDKASQAENEQILKKEADRIMSKIGERDFVIALAIEGKQFPSEEFSQRISDIAVNG\n+YSDITFIIGGSLGLDSCIKKRANLLMSFGQLTLPHQLMKLVLIEQIYRAFMIQQGSPYHK\n+>Streptococcus_suis|ORF2909 length 413 aa, 1242 bp, from 2005223..2006464 of Streptococcus_suis\n+VIIKKEIVLLRKIKEMERIPYMKKYLKFAILFVIGFFGGLIGALSASFFQPQVQQANSAI\n+TSVSNVQYNNETSTTKAVEKVQNAVVSVINYQKSANNSLGVIFGNIESSDELAVAGEGSG\n+VIYKKYGQYAYIVTNTHVINNAEKIDILLASGEKISGELVGSDTYSDIAVIKISADKVTA\n+VAEFADSDTIKVGETAIAIGSPLGSVYANTVTQGIISSLSRTVTSQSKDGQTISTNAIQT\n+DTAINPGNSGGPLINTQGQVIGITSSKITSSSANSSGVAVEGLGFAIPANDAVAIINQLE\n+KTGQVSRPALGVHMVNLTTLSTSQLEKAGLSNTELTSGVVIVSTQSGLPADGKLETFDVI\n+TEIDGEAIQNKSDLQSALYKHQIGDTITVTYYRNNQKQTVDIKLTHSTEELSE\n+>Streptococcus_suis|ORF2910 length 256 aa, 771 bp, from 2006519..2007289 of Streptococcus_suis\n+GYMEELRTLNISEIHPNPYQPRIHFDEKELLELAQSIKENGLIQPIIVRKSSIIGYELLA\n+GERRLRASQLAGLTTIPAVVKELTDDDLLYQAIIENLQRSNLNPIEEAASYQKLISRGLT\n+HDEVAQIMGKSRPYISNLLRLLNLSSQTKQAVEEGKISQGHARQLVSFSEEKQAEWVQLI\n+LSKDLSVRTLEKLIAANKKKHTKLKQRDQFLKEQEDSLSKTLGTATKIIKKKNGSGEIRI\n+SFNDLDEFERIINNFK\n' |
| b |
| diff -r 9cff9a1176ea -r 922d69bd5258 test-data/get_orf_input.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/get_orf_input.fasta Tue Jan 29 10:19:01 2013 -0500 |
| b |
| @@ -0,0 +1,17 @@ +>alpha three forward CDS using table 1 +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +NNNNNNNNNNNNNNNNATGNATGNATGNNNNNNNNNNNNNNNNNNNNNNNN +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG +TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT +NNNNNNNNNNNNNNNNNTAANNTAGMNTGANNNNNNNNNNNNNNNNNNNNN +>beta three forward CDS using table 11 +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +NNNNNNNNNNNNNNNNNGTGNATANATTNNNNNNNNNNNNNNNNNNNNNNN +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG +TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT +NNNNNNNNNNNNNNNNNNTAANNTAGNNTGANNNNNNNNNNNNNNNNNNNN +TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT |
| b |
| diff -r 9cff9a1176ea -r 922d69bd5258 test-data/get_orf_input.t11_nuc_out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/get_orf_input.t11_nuc_out.fasta Tue Jan 29 10:19:01 2013 -0500 |
| b |
| @@ -0,0 +1,36 @@ +>alpha|CDS1 length 87 aa, 264 bp, from 68..331 of alpha three forward CDS using table 1 +ATGNATGNATGNNNNNNNNNNNNNNNNNNNNNNNNAAAAAAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +CCCCCCCCCCCCCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG +GGGGGGGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTN +NNNNNNNNNNNNNNNNTAANNTAG +>alpha|CDS2 length 84 aa, 255 bp, from 72..326 of alpha three forward CDS using table 1 +ATGNATGNNNNNNNNNNNNNNNNNNNNNNNNAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +CCCCCCCCCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG +GGGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNNNNN +NNNNNNNNNNNNTAA +>alpha|CDS3 length 86 aa, 261 bp, from 76..336 of alpha three forward CDS using table 1 +ATGNNNNNNNNNNNNNNNNNNNNNNNNAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +CCCCCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG +TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNNNNNNNNN +NNNNNNNNTAANNTAGMNTGA +>beta|CDS1 length 87 aa, 264 bp, from 69..332 of beta three forward CDS using table 11 +GTGNATANATTNNNNNNNNNNNNNNNNNNNNNNNAAAAAAAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +CCCCCCCCCCCCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG +GGGGGGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNN +NNNNNNNNNNNNNNNNTAANNTAG +>beta|CDS2 length 84 aa, 255 bp, from 73..327 of beta three forward CDS using table 11 +ATANATTNNNNNNNNNNNNNNNNNNNNNNNAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +CCCCCCCCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG +GGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNNNNNN +NNNNNNNNNNNNTAA +>beta|CDS3 length 86 aa, 261 bp, from 77..337 of beta three forward CDS using table 11 +ATTNNNNNNNNNNNNNNNNNNNNNNNAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +CCCCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGT +TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNNNNNNNNNN +NNNNNNNNTAANNTAGNNTGA |
| b |
| diff -r 9cff9a1176ea -r 922d69bd5258 test-data/get_orf_input.t11_open_nuc_out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/get_orf_input.t11_open_nuc_out.fasta Tue Jan 29 10:19:01 2013 -0500 |
| b |
| @@ -0,0 +1,39 @@ +>alpha|CDS1 length 87 aa, 264 bp, from 68..331 of alpha three forward CDS using table 1 +ATGNATGNATGNNNNNNNNNNNNNNNNNNNNNNNNAAAAAAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +CCCCCCCCCCCCCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG +GGGGGGGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTN +NNNNNNNNNNNNNNNNTAANNTAG +>alpha|CDS2 length 84 aa, 255 bp, from 72..326 of alpha three forward CDS using table 1 +ATGNATGNNNNNNNNNNNNNNNNNNNNNNNNAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +CCCCCCCCCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG +GGGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNNNNN +NNNNNNNNNNNNTAA +>alpha|CDS3 length 86 aa, 261 bp, from 76..336 of alpha three forward CDS using table 1 +ATGNNNNNNNNNNNNNNNNNNNNNNNNAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +CCCCCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG +TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNNNNNNNNN +NNNNNNNNTAANNTAGMNTGA +>beta|CDS1 length 87 aa, 264 bp, from 69..332 of beta three forward CDS using table 11 +GTGNATANATTNNNNNNNNNNNNNNNNNNNNNNNAAAAAAAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +CCCCCCCCCCCCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG +GGGGGGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNN +NNNNNNNNNNNNNNNNTAANNTAG +>beta|CDS2 length 84 aa, 255 bp, from 73..327 of beta three forward CDS using table 11 +ATANATTNNNNNNNNNNNNNNNNNNNNNNNAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +CCCCCCCCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG +GGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNNNNNN +NNNNNNNNNNNNTAA +>beta|CDS3 length 86 aa, 261 bp, from 77..337 of beta three forward CDS using table 11 +ATTNNNNNNNNNNNNNNNNNNNNNNNAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +CCCCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGT +TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNNNNNNNNNN +NNNNNNNNTAANNTAGNNTGA +>beta|CDS4 length 25 aa, 75 bp, from 334..408 of beta three forward CDS using table 11 +NTGANNNNNNNNNNNNNNNNNNNNTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT +TTTTTTTTTTTTTTT |
| b |
| diff -r 9cff9a1176ea -r 922d69bd5258 test-data/get_orf_input.t11_open_prot_out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/get_orf_input.t11_open_prot_out.fasta Tue Jan 29 10:19:01 2013 -0500 |
| b |
| @@ -0,0 +1,20 @@ +>alpha|CDS1 length 87 aa, 264 bp, from 68..331 of alpha three forward CDS using table 1 +MXXXXXXXXXXXKKKKKKKKKKKKKKKKNPPPPPPPPPPPPPPPPPGGGGGGGGGGGGGG +GGGFFFFFFFFFFFFFFFFXXXXXXXX +>alpha|CDS2 length 84 aa, 255 bp, from 72..326 of alpha three forward CDS using table 1 +MXXXXXXXXXXKKKKKKKKKKKKKKKKTPPPPPPPPPPPPPPPPRGGGGGGGGGGGGGGG +GVFFFFFFFFFFFFFFFFXXXXXX +>alpha|CDS3 length 86 aa, 261 bp, from 76..336 of alpha three forward CDS using table 1 +MXXXXXXXXKKKKKKKKKKKKKKKKKPPPPPPPPPPPPPPPPPGGGGGGGGGGGGGGGGG +FFFFFFFFFFFFFFFFFXXXXXXXXX +>beta|CDS1 length 87 aa, 264 bp, from 69..332 of beta three forward CDS using table 11 +MXXXXXXXXXXXKKKKKKKKKKKKKKKKTPPPPPPPPPPPPPPPPRGGGGGGGGGGGGGG +GGVFFFFFFFFFFFFFFFFXXXXXXXX +>beta|CDS2 length 84 aa, 255 bp, from 73..327 of beta three forward CDS using table 11 +MXXXXXXXXXKKKKKKKKKKKKKKKKKPPPPPPPPPPPPPPPPPGGGGGGGGGGGGGGGG +GFFFFFFFFFFFFFFFFFXXXXXX +>beta|CDS3 length 86 aa, 261 bp, from 77..337 of beta three forward CDS using table 11 +MXXXXXXXXKKKKKKKKKKKKKKKKNPPPPPPPPPPPPPPPPPGGGGGGGGGGGGGGGGG +FFFFFFFFFFFFFFFFXXXXXXXXXX +>beta|CDS4 length 25 aa, 75 bp, from 334..408 of beta three forward CDS using table 11 +MXXXXXXXFFFFFFFFFFFFFFFFF |
| b |
| diff -r 9cff9a1176ea -r 922d69bd5258 test-data/get_orf_input.t11_prot_out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/get_orf_input.t11_prot_out.fasta Tue Jan 29 10:19:01 2013 -0500 |
| b |
| @@ -0,0 +1,18 @@ +>alpha|CDS1 length 87 aa, 264 bp, from 68..331 of alpha three forward CDS using table 1 +MXXXXXXXXXXXKKKKKKKKKKKKKKKKNPPPPPPPPPPPPPPPPPGGGGGGGGGGGGGG +GGGFFFFFFFFFFFFFFFFXXXXXXXX +>alpha|CDS2 length 84 aa, 255 bp, from 72..326 of alpha three forward CDS using table 1 +MXXXXXXXXXXKKKKKKKKKKKKKKKKTPPPPPPPPPPPPPPPPRGGGGGGGGGGGGGGG +GVFFFFFFFFFFFFFFFFXXXXXX +>alpha|CDS3 length 86 aa, 261 bp, from 76..336 of alpha three forward CDS using table 1 +MXXXXXXXXKKKKKKKKKKKKKKKKKPPPPPPPPPPPPPPPPPGGGGGGGGGGGGGGGGG +FFFFFFFFFFFFFFFFFXXXXXXXXX +>beta|CDS1 length 87 aa, 264 bp, from 69..332 of beta three forward CDS using table 11 +MXXXXXXXXXXXKKKKKKKKKKKKKKKKTPPPPPPPPPPPPPPPPRGGGGGGGGGGGGGG +GGVFFFFFFFFFFFFFFFFXXXXXXXX +>beta|CDS2 length 84 aa, 255 bp, from 73..327 of beta three forward CDS using table 11 +MXXXXXXXXXKKKKKKKKKKKKKKKKKPPPPPPPPPPPPPPPPPGGGGGGGGGGGGGGGG +GFFFFFFFFFFFFFFFFFXXXXXX +>beta|CDS3 length 86 aa, 261 bp, from 77..337 of beta three forward CDS using table 11 +MXXXXXXXXKKKKKKKKKKKKKKKKNPPPPPPPPPPPPPPPPPGGGGGGGGGGGGGGGGG +FFFFFFFFFFFFFFFFXXXXXXXXXX |
| b |
| diff -r 9cff9a1176ea -r 922d69bd5258 test-data/get_orf_input.t1_nuc_out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/get_orf_input.t1_nuc_out.fasta Tue Jan 29 10:19:01 2013 -0500 |
| b |
| @@ -0,0 +1,18 @@ +>alpha|CDS1 length 87 aa, 264 bp, from 68..331 of alpha three forward CDS using table 1 +ATGNATGNATGNNNNNNNNNNNNNNNNNNNNNNNNAAAAAAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +CCCCCCCCCCCCCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG +GGGGGGGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTN +NNNNNNNNNNNNNNNNTAANNTAG +>alpha|CDS2 length 84 aa, 255 bp, from 72..326 of alpha three forward CDS using table 1 +ATGNATGNNNNNNNNNNNNNNNNNNNNNNNNAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +CCCCCCCCCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG +GGGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNNNNN +NNNNNNNNNNNNTAA +>alpha|CDS3 length 86 aa, 261 bp, from 76..336 of alpha three forward CDS using table 1 +ATGNNNNNNNNNNNNNNNNNNNNNNNNAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +CCCCCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG +TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNNNNNNNNN +NNNNNNNNTAANNTAGMNTGA |
| b |
| diff -r 9cff9a1176ea -r 922d69bd5258 test-data/get_orf_input.t1_prot_out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/get_orf_input.t1_prot_out.fasta Tue Jan 29 10:19:01 2013 -0500 |
| b |
| @@ -0,0 +1,9 @@ +>alpha|CDS1 length 87 aa, 264 bp, from 68..331 of alpha three forward CDS using table 1 +MXXXXXXXXXXXKKKKKKKKKKKKKKKKNPPPPPPPPPPPPPPPPPGGGGGGGGGGGGGG +GGGFFFFFFFFFFFFFFFFXXXXXXXX +>alpha|CDS2 length 84 aa, 255 bp, from 72..326 of alpha three forward CDS using table 1 +MXXXXXXXXXXKKKKKKKKKKKKKKKKTPPPPPPPPPPPPPPPPRGGGGGGGGGGGGGGG +GVFFFFFFFFFFFFFFFFXXXXXX +>alpha|CDS3 length 86 aa, 261 bp, from 76..336 of alpha three forward CDS using table 1 +MXXXXXXXXKKKKKKKKKKKKKKKKKPPPPPPPPPPPPPPPPPGGGGGGGGGGGGGGGGG +FFFFFFFFFFFFFFFFFXXXXXXXXX |
| b |
| diff -r 9cff9a1176ea -r 922d69bd5258 tools/filters/get_orfs_or_cdss.py --- a/tools/filters/get_orfs_or_cdss.py Thu Jan 19 10:17:10 2012 -0500 +++ b/tools/filters/get_orfs_or_cdss.py Tue Jan 29 10:19:01 2013 -0500 |
| [ |
| @@ -16,12 +16,12 @@ molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. -This script is copyright 2011 by Peter Cock, The James Hutton Institute +This script is copyright 2011-2013 by Peter Cock, The James Hutton Institute (formerly SCRI), Dundee, UK. All rights reserved. See accompanying text file for licence details (MIT/BSD style). -This is version 0.0.1 of the script. +This is version 0.0.2 of the script. """ import sys import re @@ -159,7 +159,7 @@ for frame in range(0,3) : for offset, n, t in break_up_frame(rc[frame:]): start = full_len - frame - offset #zero based - answer.append((start, start + len(n), -1, n ,t)) + answer.append((start - len(n), start, -1, n ,t)) answer.sort() return answer |
| b |
| diff -r 9cff9a1176ea -r 922d69bd5258 tools/filters/get_orfs_or_cdss.txt --- a/tools/filters/get_orfs_or_cdss.txt Thu Jan 19 10:17:10 2012 -0500 +++ b/tools/filters/get_orfs_or_cdss.txt Tue Jan 29 10:19:01 2013 -0500 |
| b |
| @@ -1,7 +1,7 @@ Galaxy tool to find ORFs or simple CDSs ======================================= -This tool is copyright 2011 by Peter Cock, The James Hutton Institute +This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below. @@ -15,9 +15,9 @@ * get_orfs_or_cdss.py (the Python script) * get_orfs_or_cdss.xml (the Galaxy tool definition) -The suggested location is in the Galaxy folder tools/filters next to the tool +If you are installing this manually (rather than via the Tool Shed), the +suggested location is in the Galaxy folder tools/filters next to the tool for calling sff_extract.py for converting SFF to FASTQ or FASTA + QUAL. - You will also need to modify the tools_conf.xml file to tell Galaxy to offer the tool. One suggested location is in the filters section. Simply add the line: @@ -25,13 +25,19 @@ You will also need to install Biopython 1.54 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. That's it. +FASTA files under the test-data directory. Then: + +./run_functional_tests.sh -id get_orfs_or_cdss + +That's it. History ======= v0.0.1 - Initial version. +v0.0.2 - Correct labelling issue on reverse strand. + - Use the new <stdio> settings in the XML wrappers to catch errors Developers @@ -43,7 +49,7 @@ For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use the following command from the Galaxy root folder: -tar -czf get_orfs_or_cdss.tar.gz tools/filters/get_orfs_or_cdss.* +tar -czf get_orfs_or_cdss.tar.gz tools/filters/get_orfs_or_cdss.* test-data/get_orf_input*.fasta Check this worked: @@ -51,6 +57,14 @@ filter/get_orfs_or_cdss.py filter/get_orfs_or_cdss.txt filter/get_orfs_or_cdss.xml +test-data/get_orf_input.Suis_ORF.nuc.fasta +test-data/get_orf_input.Suis_ORF.prot.fasta +test-data/get_orf_input.t11_nuc_out.fasta +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_nuc_out.fasta +test-data/get_orf_input.t1_prot_out.fasta Licence (MIT/BSD style) |
| b |
| diff -r 9cff9a1176ea -r 922d69bd5258 tools/filters/get_orfs_or_cdss.xml --- a/tools/filters/get_orfs_or_cdss.xml Thu Jan 19 10:17:10 2012 -0500 +++ b/tools/filters/get_orfs_or_cdss.xml Tue Jan 29 10:19:01 2013 -0500 |
| b |
| @@ -1,8 +1,13 @@ -<tool id="get_orfs_or_cdss" name="Get open reading frames (ORFs) or coding sequences (CDSs)" version="0.0.1"> +<tool id="get_orfs_or_cdss" name="Get open reading frames (ORFs) or coding sequences (CDSs)" version="0.0.2"> <description>e.g. to get peptides from ESTs</description> <command interpreter="python"> get_orfs_or_cdss.py $input_file $input_file.ext $table $ftype $ends $mode $min_len $strand $out_nuc_file $out_prot_file </command> + <stdio> + <!-- Anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> <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"> @@ -85,6 +90,17 @@ <output name="out_nuc_file" file="get_orf_input.t11_open_nuc_out.fasta" /> <output name="out_prot_file" file="get_orf_input.t11_open_prot_out.fasta" /> </test> + <test> + <param name="input_file" value="Ssuis.fasta" /> + <param name="table" value="11" /> + <param name="ftype" value="ORF" /> + <param name="ends" value="open" /> + <param name="mode" value="all" /> + <param name="min_len" value="100" /> + <param name="strand" value="both" /> + <output name="out_nuc_file" file="get_orf_input.Suis_ORF.nuc.fasta" /> + <output name="out_prot_file" file="get_orf_input.Suis_ORF.prot.fasta" /> + </test> </tests> <requirements> <requirement type="python-module">Bio</requirement> |