| Next changeset 1:9e61bc67866f (2018-03-16) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit aa771c525124559defacde367e17d782546677a5 |
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added:
test-data/Trinity.fasta test-data/Trinity.fasta.gene_to_trans_map test-data/Trinity.fasta.rnammer.gff test-data/Trinity.fasta.transdecoder.pep test-data/TrinotatePFAM.out test-data/signalp.out test-data/swissprot.blastp.outfmt6 test-data/swissprot.blastx.outfmt6 test-data/tmhmm.out test-data/trinotate_annotation_report.xls test-data/trinotate_annotation_report_minus_tmhmm_signalp.xls trinotate.xml |
| b |
| diff -r 000000000000 -r 499d87c45612 test-data/Trinity.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Trinity.fasta Tue Nov 15 09:17:29 2016 -0500 |
| [ |
| b'@@ -0,0 +1,472 @@\n+>TRINITY_DN596_c0_g1_i1 len=2082 path=[2085:0-470 2086:471-494 2087:495-2081] [-1, 2085, 2086, 2087, -2]\n+TGTGATTCGTGCCGCTCAACATTTCTTCAAGTGATTCCTAACATTGCTGTACATTCTCTTGAAAAGCGTTTTAACCTTTTCAATTCTGAAACTTGTAAAGAATGTCAGAGTATCGTATTCGAGTGACAACTGTGGACCAGAAGGTTGGTATTTTTCAAGTTCCTAGGACAAAAACGGTTTTAGAATTAAAGGAACTGATTGCTGTAACATTTGAAGCTCCTGCAGATCGATTAAAGTTGATTCACGCTGGTCGTGTATTGAGGAATGAAACTCCCCTCGAGGAAATTTTGCATGACGCTACTGATCTGGTCACTTTTCATCTTGTAATTGCGGTTTTTAATTCTACAAGCACAACCTTGCCATCAGCGACATCATCTTCTGTTCCTCAAAGTAGGACCAGCGAATTATCATCGACTAATTCAATTCCAACTCCTCGAATCACCAGTTTGAACCCGGAAGAATTGTCAAGACGTGAACGTGCCCAACGTTTATTACAGACATACAACAGTTTCCATGGATCTGGCTTAGGAGGACTTTTTCCAAACATACACCGGGAACTAGAAAGTCACGGATTTTCATTGCCAACCCATGAGCAATCATCACCCGTTGCTGAATCTCTGGATAATTCGGTATCGTCTGCTTTATCTCCACATTTGGAAACGCTGCGTCGCCGCAATCTCAGTATTCATCATCAACATATACAAGCTCACGAAATGGCACAAGAGTCCTTGGAGACCAGAAATCCAGGAAACATTTCTTCCTCGAGTGCTCCTTTAGCTAGTGATCAATCCCCGACTGTATCATCTAACCATATCCATGCATCCGGTAATTTGGCTTTAGGATCAAATTCGGGGTTAAATCCACGAAGCCCTAATTCTTTTTCTTCCCCATTGGACAATCCTGCACTTCATACTGTTGACTCAACCAACGTCAATGGTTCGCTTTCACCTCTATCAAATTCTTCATCTATCAATCAAGTTCACCAAAATGAAACTCATGGTTCTACCATCTCAGTACCTAACCCGAACTTAAGTCAAATGGGCCCTTCACACTCTTCTTCTGTGCCCTCAAATCTGTCACCAAATCCTGCCCAAAATGAAAATCCTAGTACAACCTCTATTCCATCAATAAATAATCAACCATTCCCGTCTGGTCTTTCTGCTTCTAACTCTAATTTTGCCTCTTCCTCGTTTATCCCTCAGAGCGTTCCGCAACTATTGCCTATATATTATCAAACTATCTTTTACAACGGTAACTATTATTTACAGCAGCTCCCATCTGCATCGCCTCCCACTATGTTTCGAGATCACTCATTTGCTCCTTTAGTTTCCCCTTCTATTGTTTCTCCGTATGGTGTTTTAGAAAATGAAGAAACTGGCGAATGTGCCTTTTTGTTTTCACCAAATGCCTCCCAACCCCATTTTCAGCCGAGAGCCCCCACGTTTGGCATTCCACGAAATGTGAGATCCCTCTTCACCTTACCGTTCTTCCATACTATCCGTAATATTGAGAGACATTTCCGATTATTTATTCGTTTAGCCCTGTTTTGTGTATTAACGACTTATAATGTTTCTCTCTCACAAACAATTTTGCTAACATCTATAATGTCTGTTGTGTTTTTGTTACAGACCGGTGCTCTAGCTCCATTCATCAATGACAATCCACTCATCCAGTCTGGTATGCGTCATATTCGTAATCTTCAAGATGAATACCGGCGGCGTCGAAACCGAACGGCTCAAAGAGTAGTTGAAATTCCTAATGAGACACAGACTGAAGATGAACAAGATGGTACAAATACGCCGGATAATAGGGCTGACGCTGAAGAACGCGAACTAACTCGAAGTCAAAGAATATACCGGACGGTAGTAAGAACCATAGTTGCCTTCGCATTAAGCTTTGTACCTCGAGCGTAACATTTTTTTCTTAAAAACAAAAGTGATAATATAGCTGTAAAGTCATTTTTCATTACTAATTAGAAATATTGTCTAAGCTTGCTATTAATAAAAGAGTTCTAGCTAGACTAAATTTTGACAGTGTCGAAATATCATTCCAAGGTACCCCATCAGATTAACAAATTTATAA\n+>TRINITY_DN549_c0_g1_i1 len=1522 path=[1525:0-44 1526:45-68 1527:69-1521] [-1, 1525, 1526, 1527, -2]\n+GTTTAACGGCTCGAATTTTATTACAACTTTACGTGCTCCTAGAGGTGATGCTACTGAGTCTCTACTCCTATGTGTCCCTTGGAAAGATCATATTGGGCAATATAATGAGGCCGGCGTTGCTTTAGCCATTAGTTTATTGAAATACTTCCAGGGATGGTCTCTTTGGTCGAAAGACATCATCTTGGTTATTTTTGATGATCCTGTTTATGGTCCATCGAGTTTTCTCACGTCTTATTTTGACCAAACGACGCCATATATATCTTACACACCATTGAAAATTCGTTCTGGTTCCATTCAAGCTGGTTTATCGCTTGAGCTAGTTACTACTGAAAATAACTCGGACGTGCTTGAAGTCCTTTACCAAGCTACCAATGGACAGTTGCCCAACCTTGACCTTTTCAATACTATTTCGAGAATCTTTATGCAACATTTTAATTATCCATTACGACTACAAGGATATGATTTCCATGCTAATTCGGGGTCCTCATACACATCCCGTCTAAAATCTTTGTGGATGGGTATGTTGACACAAGCAGTTTCGAATGTTACTAGTGCGCATGCACTATTTCCTCAATATAGAATTGACATGTTGACCTTGCGAATGAAAGTGAAAGACCCGTTTTCATTTGACATGTTTAGATTTGGTCAAGCCATTGAAAGCACATTTCGATCTCTTAACAATCTTCTTGAACACTTGCATCAATCTTTTTTCTTTTACTTCATCCTAGATCATTTGCATTTTATTAGTATCGGAAATTATATGCCTTCCATTTTAATTCTGGCTGCTAGTTTCATGCTCGGAGCTTACCGACATTGGATCAACCATGAAAAAAAAATAGATCTTTGGAGACCATTTTCTTTTTGGCTTTTTAGTATTTTTTGTACGATCGCCGCATATTATTTGGTATCTTCTTCTACTAAGATAACCGTTTTTATATTCCTCTATTTAATGCTCACTTTTATTGGTATTATCTTTTCAACTTTTATGACGAGTGAAGACGCTGAACTGGTTCTTTCTTACGATTTAATGTCAAAATCCCTTTTCATTTCCGTAGTGAGTACGTTAAATTTTTCTCTTTCTTTTGTTGTTGCAATTTTGCTTGTACCATTACAGTTTATTTCATTTAGATTTAATCGACGTCTTTCGTTACTTTTCGCAGTCTTGACATACTTTTCTACATTTATATTCCTTTGTTCTCTGTCTAAAATTTTGAATGGACCTTTGGTACCATTTTGGTTGTGGGCAAAAGAATATGAGTTGTTCAACTCTTGGTTAATGCCATCCGTGTTTATGATTTTAGTTTTACCTGAAATCATATTCTCAGTTACAAGTTTTTTTTCGCTTTGGAATGAACCGTCTGTGAAAACCAAGACAAAGACTTTGTGAGGGACTAAAAGGTACTATTGTATGAGTACTTATCATTATTTATTTTACGAACATCATTAAAAACTGTCTATAAAAAATATTACCGCAGAATTGTTACGTTCGCGGAAAGCTTTTAGAGGTAGAAATGCATTTCCG\n+>TRINITY_DN594_c0_g1_i1 len=1276 path=[1276:0-680 1281:681-768 1275:769-1275] [-1, 1276, 1281, 1275, -2]\n+GGTCTTATAGCTAGCATGAGACAAAGACGGCAACTCGCGGAATTCTTCATATAAACTT'..b'AGAGCTTTGTCTGCATTGCTCTTGGTCCTCCAACAAATTGTTGAGGGGATATCGTTTTTGTTATTCTTAAACGATACCGGTGTATCCGATTTTCATGAAATTGTTTCTTCTACCTCCATTGATATTCAAAAATCGTGTTCAAACATGACCTTTGGTGAGTTTTTTACTTCGAAACGGGGTCGAGAAGTAACTAAGGAACTCGTAAATTCTCTTGTCAATAGGCATCTGCAGTCTGGAGGGAATATTGATATGGTTAGTCAGCTTTTACGTAAAAAGTGTGGAAGTTTTTGCAGCGCTGATGATGTTTTAATTTTTAAAGCCGTGGAGTCTTTAAAAAAGGCTAAGGATACGGTCGACATTGAAGAGCGACAATCTCTTATAGAGTTATCCTACACCCTCTTTAAAAAGGCTGCACATGTCTTTACTCCCGAAGACCTTCGTTTAGCAGTTGAGGAATACAAGTCTTTGAACGCCTATACAACCGCGGTAAACTTAGCATTACACGTAGCAAGTGCGAGAGACGATCGAAATCAAGCTTTGTCTTACCTTGTCGATGGAATGCCTGAGAACGATCCTAGGCGTGAACCTTTCGAGAGCCGTACAAAGTGTTATTCGTACATTTTTGAGATTTTGGATTCTTTGGAATCTCAAATGTCAAATGATTCGAGTGCAATTAAGGTTGATGTATACGATACTATACAGCGTTCAAAGGATGAACTTTTTCATTATTGCTTTTATGATTGGTATTCATTTAAGGGGCTTACAGATCGCTTGATTGAGATAGATTCCCCTTACATACAGAGTTATCTGGAACGTAACAGCACCAAAGACATGAAAATTGCTGACTTACTATGGCAGTATTATGCTAAACGAGAACAGTATTATCAAGCTTCAATAGTCTTGTATGATTTGGCTACTACCCACCTTGCATTTAGCCTTGAACAACGCATTGAATATCTTACACGAGCCAAAGGTTTTGGTAGCTGCCACGTCCCTAATTCTCTTAGGCATAAAATGAATAAGGTTATGCTTAGTGTACTAGAGCAGCTAGACGTTGCTAGTATCCAAGATGATGTTTTAATAGCAATCCGTGGTGATATGCGTATTCCTACTTCAAAAAGAGAAGAATTGAGCAAACAATTGGATGGGGAAATTATACCCCTTAGCGATTTATTTAATAATTATGCTGATCCTCTGGGTTACGGTGAGATATGCTTGTCCATATTTCAGTGTGCTGATTACAGAGGAATTAACGAAATCTTAAACTGTTGGGAGTCTATTATTAAAACTACTCATGAGAATGCTATAATATCACCAGTTGGGTCATCCCCTGTCGAAGCAGTTTCCTCTACATTAAAAAATTTGACGCTGAGATTTTCACAATCTGAAAACGTTTTCCCTATTGAGCAAATAATTGACATTACTGAAAGATATGCGTTTGATCAACAAGGTGAAGCGGTAGCTACTGGTTGGGTTATTGATACATTCTTGGGAGCCGGCGTTTCTCATGAATTAATATTTATTGTACTAAACCAGCTCTACGATCGCAGAGAAAAGCCTTGGCAAGGAAAAGATAGGCTTTTTTTTCCTAATAAAAGAAGTTACCCATCTATTAAAATTATGGCATGAAGTGAGTGTAAGAGCCGGAGTTGCTCAAACCTCCAAACCCAGTTTTGATGCTCCTCTTGTTTTGGAAGCAATAGAGAAATACAAAAATGCGCTAGGTGCACCCGATACTGCCACGAAAAGTTGCAAAGAAAATTTAATATCTTTAGATTCTGAAATTCGTCAGACATACTAGTGAAAAGATAGCTTTTTATAACAACATTTTTTAAAAAGATGGTGTTTGGTATTTAATAAATGCAATGATTATATTGGATGGATTTGAAACCTTCACATAATTGGATGTTGTTAACTATCGCTATGACTGTTACATATAAAAAAACAATTTAGAAAATACTCTTTTACAGCACTTGCA\n+>TRINITY_DN59_c0_g1_i1 len=1951 path=[1953:0-1950] [-1, 1953, -2]\n+AGAACTTGACCGCAGCGCACATCAACTACACCTTGAGGCAATTCAAAATATGAAGTTTTCTACCGTAGGGTTTTTGTTTTCAACAATTTTATTCAAAAGTGCGTTTGCAGGATGGATGGATACACACATGAAAGATGAACATCACATTGATAAGTACACAGATGAATCTTTTTTTCGTCTTCACGATTTAGGAAAAAAGGGATACTGGTCAGATCAAGATATACTTAGTTTATATGGATTATTTGAAAATGATGAGGTCCCATTCGTCAAAAAGAATGAGGTTTTGGTTGATGTTCTAAAAAAATGCGATCCATCGGGCAATCGCCGGATAACACTTGATGAATTTCTTGCATTTCGTAAAAATGGAGGAGAGTTAACGGATTTTGGATTTCCAGGGCACCATGGTGATGAGGAAGAGGAATTTGAAATGCATCATGTGGAAAAATATCACCCAGCTGGCCTCGATGAACCAGATGAAAACTGGAATCATCCTGAAGATATCGAACATTTTCAAAAACACGATGAGATATTTCATGGTGATAAGAAACCTGAGGAACGACGCAAACATTTTGTAAAATACAATAATATCCCTGACAAGTATCGTCGTGTGAGCATTTAAATTTTCCCATTGATAGATTTACTTGCTTCTCCTTGGGACGTTTTATTTTTATTTTTATTTTTCCGTTTATTTTTGGATTGTCGTGTTCCGATATATATCCGTGTTTACAAACAATAGCTTCAACATTTTTGAACGGGTCCTTCCAATACTAATGCCATATCTTATTTCTTTGTCAATACAAAATCACTTTTGTTCGTTAAACTCATTTTGGTTTGCAGATATTATCATATTCTTACCAATTATACATACACTCACAATTTGTTTTACATTTCCGCTCCCTTCTTCAATAAGCTGATTGCTTATAAAAAATCAAACATTCATATGATTCAAGTTCAAATATTATCATCTGAAAACTGACAAGTTCCATTCATTACTATATTAATATCATTTATTCGTTAAACCGATATCATTAAAAATGGAAAATTAAAGAAATCAATTCATTTGCTTCCTTGAAGTCTAGAGTCGATCATAACGAGAGCTTCATGTTGAAGCTCTTTAAGTGCAGCTTGCTTAGTAATATAAGTGCGTAATGTTTCAACAGCCTTTGGTGTTTTTATGAACTTGTTAAATATTTCTTGATCTTTGGAATATACGATATTGCATATGCAAACTAATCCACGATGTTGAATTCCTTCATCTTGGTCGGTTAACATTCTGACTATGTAGTTAAAATCGTTCTGGAGACTTAAAATTTTCTTGCACCCTTCATCAACACTAGTAATTTGAACAAGAATTCCGCATGCTGCTAATCTCGTGGGAGTGTCTTCGGTATCTGAGAGTGCTAGTACAATGTGTAAACGAGTATTTTCAAAATCCGAGTCCTTGTCTCCTATAAACTTAATTAAGCAATAAGGTGATAAAGAAAGGTTGTTAATAAGTTCCGTGGTTGCCCTCTGAATTAAAGGATTTGTTTCTATAATTAGTTCATCCAATTCTCTCCAACATTCTTGAACTATGGCTTGCCGACTTTCTTCATCATGTGAAGCAAGATTTGTTAGCGCAAGTAACACTTCAAATTTCCCCAAGAGAATTGGATACTCAGTATCAGCAGAATTAGTACTTAGTAACTTTGACATAGGATGAATTGCTCGGTTCGATGGAAACGCCTTAGTAAATATACTATGAGGAGCCACACTGATAAGAATTTTCGCTAATGCAAAAGCCGCATTCGAATCCTGGGTTTGGATAAAACATTGTCTAGTAAGGAATTTCAATGCACCTATTTGTACTAGCTTGCGACGTGCCAGCTTGTAATTAGCCATGTGTACAAGTATCATTGCTAATAACCCGTTTAGGCTATTATAGTGCTTGGCCGCTGAAAAGAGTTTTGAC\n' |
| b |
| diff -r 000000000000 -r 499d87c45612 test-data/Trinity.fasta.gene_to_trans_map --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Trinity.fasta.gene_to_trans_map Tue Nov 15 09:17:29 2016 -0500 |
| b |
| b'@@ -0,0 +1,236 @@\n+TRINITY_DN596_c0_g1\tTRINITY_DN596_c0_g1_i1\n+TRINITY_DN549_c0_g1\tTRINITY_DN549_c0_g1_i1\n+TRINITY_DN594_c0_g1\tTRINITY_DN594_c0_g1_i1\n+TRINITY_DN594_c0_g2\tTRINITY_DN594_c0_g2_i1\n+TRINITY_DN591_c0_g1\tTRINITY_DN591_c0_g1_i1\n+TRINITY_DN540_c0_g1\tTRINITY_DN540_c0_g1_i1\n+TRINITY_DN540_c0_g2\tTRINITY_DN540_c0_g2_i1\n+TRINITY_DN597_c0_g1\tTRINITY_DN597_c0_g1_i1\n+TRINITY_DN597_c0_g2\tTRINITY_DN597_c0_g2_i1\n+TRINITY_DN547_c0_g1\tTRINITY_DN547_c0_g1_i1\n+TRINITY_DN542_c0_g1\tTRINITY_DN542_c0_g1_i1\n+TRINITY_DN542_c0_g2\tTRINITY_DN542_c0_g2_i1\n+TRINITY_DN599_c0_g1\tTRINITY_DN599_c0_g1_i1\n+TRINITY_DN599_c0_g2\tTRINITY_DN599_c0_g2_i1\n+TRINITY_DN592_c0_g1\tTRINITY_DN592_c0_g1_i1\n+TRINITY_DN592_c0_g2\tTRINITY_DN592_c0_g2_i1\n+TRINITY_DN543_c0_g1\tTRINITY_DN543_c0_g1_i1\n+TRINITY_DN543_c0_g2\tTRINITY_DN543_c0_g2_i1\n+TRINITY_DN595_c0_g1\tTRINITY_DN595_c0_g1_i1\n+TRINITY_DN595_c0_g2\tTRINITY_DN595_c0_g2_i1\n+TRINITY_DN590_c0_g1\tTRINITY_DN590_c0_g1_i1\n+TRINITY_DN541_c0_g1\tTRINITY_DN541_c0_g1_i1\n+TRINITY_DN541_c0_g2\tTRINITY_DN541_c0_g2_i1\n+TRINITY_DN548_c0_g1\tTRINITY_DN548_c0_g1_i1\n+TRINITY_DN548_c0_g2\tTRINITY_DN548_c0_g2_i1\n+TRINITY_DN545_c0_g1\tTRINITY_DN545_c0_g1_i1\n+TRINITY_DN545_c0_g2\tTRINITY_DN545_c0_g2_i1\n+TRINITY_DN546_c0_g1\tTRINITY_DN546_c0_g1_i1\n+TRINITY_DN546_c0_g2\tTRINITY_DN546_c0_g2_i1\n+TRINITY_DN544_c0_g1\tTRINITY_DN544_c0_g1_i1\n+TRINITY_DN544_c0_g2\tTRINITY_DN544_c0_g2_i1\n+TRINITY_DN598_c0_g1\tTRINITY_DN598_c0_g1_i1\n+TRINITY_DN598_c0_g2\tTRINITY_DN598_c0_g2_i1\n+TRINITY_DN593_c0_g1\tTRINITY_DN593_c0_g1_i1\n+TRINITY_DN593_c0_g2\tTRINITY_DN593_c0_g2_i1\n+TRINITY_DN5961_c0_g1\tTRINITY_DN5961_c0_g1_i1\n+TRINITY_DN5995_c0_g1\tTRINITY_DN5995_c0_g1_i1\n+TRINITY_DN5991_c0_g1\tTRINITY_DN5991_c0_g1_i1\n+TRINITY_DN5943_c0_g1\tTRINITY_DN5943_c0_g1_i1\n+TRINITY_DN5907_c0_g1\tTRINITY_DN5907_c0_g1_i1\n+TRINITY_DN5950_c0_g1\tTRINITY_DN5950_c0_g1_i1\n+TRINITY_DN5928_c0_g1\tTRINITY_DN5928_c0_g1_i1\n+TRINITY_DN5958_c0_g1\tTRINITY_DN5958_c0_g1_i1\n+TRINITY_DN5916_c0_g1\tTRINITY_DN5916_c0_g1_i1\n+TRINITY_DN5920_c0_g1\tTRINITY_DN5920_c0_g1_i1\n+TRINITY_DN5933_c0_g1\tTRINITY_DN5933_c0_g1_i1\n+TRINITY_DN5996_c0_g1\tTRINITY_DN5996_c0_g1_i1\n+TRINITY_DN5955_c0_g1\tTRINITY_DN5955_c0_g1_i1\n+TRINITY_DN5974_c0_g1\tTRINITY_DN5974_c0_g1_i1\n+TRINITY_DN5939_c0_g1\tTRINITY_DN5939_c0_g1_i1\n+TRINITY_DN5905_c0_g1\tTRINITY_DN5905_c0_g1_i1\n+TRINITY_DN5926_c0_g1\tTRINITY_DN5926_c0_g1_i1\n+TRINITY_DN5922_c0_g1\tTRINITY_DN5922_c0_g1_i1\n+TRINITY_DN5937_c0_g1\tTRINITY_DN5937_c0_g1_i1\n+TRINITY_DN5977_c0_g1\tTRINITY_DN5977_c0_g1_i1\n+TRINITY_DN5965_c0_g1\tTRINITY_DN5965_c0_g1_i1\n+TRINITY_DN5927_c0_g1\tTRINITY_DN5927_c0_g1_i1\n+TRINITY_DN5929_c0_g1\tTRINITY_DN5929_c0_g1_i1\n+TRINITY_DN5946_c0_g1\tTRINITY_DN5946_c0_g1_i1\n+TRINITY_DN5993_c0_g1\tTRINITY_DN5993_c0_g1_i1\n+TRINITY_DN5972_c0_g1\tTRINITY_DN5972_c0_g1_i1\n+TRINITY_DN5975_c0_g1\tTRINITY_DN5975_c0_g1_i1\n+TRINITY_DN5985_c0_g1\tTRINITY_DN5985_c0_g1_i1\n+TRINITY_DN5980_c0_g1\tTRINITY_DN5980_c0_g1_i1\n+TRINITY_DN5987_c0_g1\tTRINITY_DN5987_c0_g1_i1\n+TRINITY_DN5986_c0_g1\tTRINITY_DN5986_c0_g1_i1\n+TRINITY_DN5968_c0_g1\tTRINITY_DN5968_c0_g1_i1\n+TRINITY_DN5902_c0_g1\tTRINITY_DN5902_c0_g1_i1\n+TRINITY_DN5923_c0_g1\tTRINITY_DN5923_c0_g1_i1\n+TRINITY_DN5998_c0_g1\tTRINITY_DN5998_c0_g1_i1\n+TRINITY_DN5999_c0_g1\tTRINITY_DN5999_c0_g1_i1\n+TRINITY_DN5982_c0_g1\tTRINITY_DN5982_c0_g1_i1\n+TRINITY_DN5914_c0_g1\tTRINITY_DN5914_c0_g1_i1\n+TRINITY_DN5906_c0_g1\tTRINITY_DN5906_c0_g1_i1\n+TRINITY_DN5930_c0_g1\tTRINITY_DN5930_c0_g1_i1\n+TRINITY_DN5900_c0_g1\tTRINITY_DN5900_c0_g1_i1\n+TRINITY_DN5967_c0_g1\tTRINITY_DN5967_c0_g1_i1\n+TRINITY_DN5918_c0_g1\tTRINITY_DN5918_c0_g1_i1\n+TRINITY_DN5959_c0_g1\tTRINITY_DN5959_c0_g1_i1\n+TRINITY_DN5921_c0_g1\tTRINITY_DN5921_c0_g1_i1\n+TRINITY_DN5903_c0_g1\tTRINITY_DN5903_c0_g1_i1\n+TRINITY_DN5909_c0_g1\tTRINITY_DN5909_c0_g1_i1\n+TRINITY_DN5984_c0_g1\tTRINITY_DN5984_c0_g1_i1\n+TRINITY_DN5997_c0_g1\tTRINITY_DN5997_c0_g1_i1\n+TRINITY_DN5988_c0_g1\tTRINITY_DN5988_c0_g1_i1\n+TRINITY_DN5931_c0_g1\tTRINITY_DN5931_c0_g1_i1\n+TRINITY_DN5960_c0_g1\tTRINITY_DN5960_c0_g1_i1\n+TRINITY_DN5947_c0_g1\tTRINITY_DN5947_c0_g1_i1\n+TR'..b'c0_g1_i1\n+TRINITY_DN5479_c0_g1\tTRINITY_DN5479_c0_g1_i1\n+TRINITY_DN5417_c0_g1\tTRINITY_DN5417_c0_g1_i1\n+TRINITY_DN5413_c0_g1\tTRINITY_DN5413_c0_g1_i1\n+TRINITY_DN5402_c0_g1\tTRINITY_DN5402_c0_g1_i1\n+TRINITY_DN5478_c0_g1\tTRINITY_DN5478_c0_g1_i1\n+TRINITY_DN5403_c0_g1\tTRINITY_DN5403_c0_g1_i1\n+TRINITY_DN5401_c0_g1\tTRINITY_DN5401_c0_g1_i1\n+TRINITY_DN5438_c0_g1\tTRINITY_DN5438_c0_g1_i1\n+TRINITY_DN5496_c0_g1\tTRINITY_DN5496_c0_g1_i1\n+TRINITY_DN5429_c0_g1\tTRINITY_DN5429_c0_g1_i1\n+TRINITY_DN5455_c0_g1\tTRINITY_DN5455_c0_g1_i1\n+TRINITY_DN5450_c0_g1\tTRINITY_DN5450_c0_g1_i1\n+TRINITY_DN5480_c0_g1\tTRINITY_DN5480_c0_g1_i1\n+TRINITY_DN5482_c0_g1\tTRINITY_DN5482_c0_g1_i1\n+TRINITY_DN5405_c0_g1\tTRINITY_DN5405_c0_g1_i1\n+TRINITY_DN5447_c0_g1\tTRINITY_DN5447_c0_g1_i1\n+TRINITY_DN5465_c0_g1\tTRINITY_DN5465_c0_g1_i1\n+TRINITY_DN5477_c0_g1\tTRINITY_DN5477_c0_g1_i1\n+TRINITY_DN5460_c0_g1\tTRINITY_DN5460_c0_g1_i1\n+TRINITY_DN5492_c0_g1\tTRINITY_DN5492_c0_g1_i1\n+TRINITY_DN5425_c0_g1\tTRINITY_DN5425_c0_g1_i1\n+TRINITY_DN5452_c0_g1\tTRINITY_DN5452_c0_g1_i1\n+TRINITY_DN5404_c0_g1\tTRINITY_DN5404_c0_g1_i1\n+TRINITY_DN5420_c0_g1\tTRINITY_DN5420_c0_g1_i1\n+TRINITY_DN5494_c0_g1\tTRINITY_DN5494_c0_g1_i1\n+TRINITY_DN5475_c0_g1\tTRINITY_DN5475_c0_g1_i1\n+TRINITY_DN5427_c0_g1\tTRINITY_DN5427_c0_g1_i1\n+TRINITY_DN5411_c0_g1\tTRINITY_DN5411_c0_g1_i1\n+TRINITY_DN5467_c0_g1\tTRINITY_DN5467_c0_g1_i1\n+TRINITY_DN5412_c0_g1\tTRINITY_DN5412_c0_g1_i1\n+TRINITY_DN5439_c0_g1\tTRINITY_DN5439_c0_g1_i1\n+TRINITY_DN5466_c0_g1\tTRINITY_DN5466_c0_g1_i1\n+TRINITY_DN5470_c0_g1\tTRINITY_DN5470_c0_g1_i1\n+TRINITY_DN5422_c0_g1\tTRINITY_DN5422_c0_g1_i1\n+TRINITY_DN5473_c0_g1\tTRINITY_DN5473_c0_g1_i1\n+TRINITY_DN5457_c0_g1\tTRINITY_DN5457_c0_g1_i1\n+TRINITY_DN5485_c0_g1\tTRINITY_DN5485_c0_g1_i1\n+TRINITY_DN5436_c0_g1\tTRINITY_DN5436_c0_g1_i1\n+TRINITY_DN5433_c0_g1\tTRINITY_DN5433_c0_g1_i1\n+TRINITY_DN5445_c0_g1\tTRINITY_DN5445_c0_g1_i1\n+TRINITY_DN5419_c0_g1\tTRINITY_DN5419_c0_g1_i1\n+TRINITY_DN5481_c0_g1\tTRINITY_DN5481_c0_g1_i1\n+TRINITY_DN5431_c0_g1\tTRINITY_DN5431_c0_g1_i1\n+TRINITY_DN5409_c0_g1\tTRINITY_DN5409_c0_g1_i1\n+TRINITY_DN5459_c0_g1\tTRINITY_DN5459_c0_g1_i1\n+TRINITY_DN5449_c0_g1\tTRINITY_DN5449_c0_g1_i1\n+TRINITY_DN5424_c0_g1\tTRINITY_DN5424_c0_g1_i1\n+TRINITY_DN5464_c0_g1\tTRINITY_DN5464_c0_g1_i1\n+TRINITY_DN5418_c0_g1\tTRINITY_DN5418_c0_g1_i1\n+TRINITY_DN5423_c0_g1\tTRINITY_DN5423_c0_g1_i1\n+TRINITY_DN5484_c0_g1\tTRINITY_DN5484_c0_g1_i1\n+TRINITY_DN5483_c0_g1\tTRINITY_DN5483_c0_g1_i1\n+TRINITY_DN5458_c0_g1\tTRINITY_DN5458_c0_g1_i1\n+TRINITY_DN5491_c0_g1\tTRINITY_DN5491_c0_g1_i1\n+TRINITY_DN5428_c0_g1\tTRINITY_DN5428_c0_g1_i1\n+TRINITY_DN5488_c0_g1\tTRINITY_DN5488_c0_g1_i1\n+TRINITY_DN5456_c0_g1\tTRINITY_DN5456_c0_g1_i1\n+TRINITY_DN5463_c0_g1\tTRINITY_DN5463_c0_g1_i1\n+TRINITY_DN5444_c0_g1\tTRINITY_DN5444_c0_g1_i1\n+TRINITY_DN5440_c0_g1\tTRINITY_DN5440_c0_g1_i1\n+TRINITY_DN5489_c0_g1\tTRINITY_DN5489_c0_g1_i1\n+TRINITY_DN5469_c0_g1\tTRINITY_DN5469_c0_g1_i1\n+TRINITY_DN5410_c0_g1\tTRINITY_DN5410_c0_g1_i1\n+TRINITY_DN5441_c0_g1\tTRINITY_DN5441_c0_g1_i1\n+TRINITY_DN5430_c0_g1\tTRINITY_DN5430_c0_g1_i1\n+TRINITY_DN5435_c0_g1\tTRINITY_DN5435_c0_g1_i1\n+TRINITY_DN5414_c0_g1\tTRINITY_DN5414_c0_g1_i1\n+TRINITY_DN5432_c0_g1\tTRINITY_DN5432_c0_g1_i1\n+TRINITY_DN5454_c0_g1\tTRINITY_DN5454_c0_g1_i1\n+TRINITY_DN5474_c0_g1\tTRINITY_DN5474_c0_g1_i1\n+TRINITY_DN5406_c0_g1\tTRINITY_DN5406_c0_g1_i1\n+TRINITY_DN5472_c0_g1\tTRINITY_DN5472_c0_g1_i1\n+TRINITY_DN5497_c0_g1\tTRINITY_DN5497_c0_g1_i1\n+TRINITY_DN5426_c0_g1\tTRINITY_DN5426_c0_g1_i1\n+TRINITY_DN5486_c0_g1\tTRINITY_DN5486_c0_g1_i1\n+TRINITY_DN5468_c0_g1\tTRINITY_DN5468_c0_g1_i1\n+TRINITY_DN5434_c0_g1\tTRINITY_DN5434_c0_g1_i1\n+TRINITY_DN5400_c0_g1\tTRINITY_DN5400_c0_g1_i1\n+TRINITY_DN5476_c0_g1\tTRINITY_DN5476_c0_g1_i1\n+TRINITY_DN5490_c0_g1\tTRINITY_DN5490_c0_g1_i1\n+TRINITY_DN5443_c0_g1\tTRINITY_DN5443_c0_g1_i1\n+TRINITY_DN5471_c0_g1\tTRINITY_DN5471_c0_g1_i1\n+TRINITY_DN5407_c0_g1\tTRINITY_DN5407_c0_g1_i1\n+TRINITY_DN5498_c0_g1\tTRINITY_DN5498_c0_g1_i1\n+TRINITY_DN54_c0_g1\tTRINITY_DN54_c0_g1_i1\n+TRINITY_DN54_c0_g2\tTRINITY_DN54_c0_g2_i1\n+TRINITY_DN59_c0_g1\tTRINITY_DN59_c0_g1_i1\n' |
| b |
| diff -r 000000000000 -r 499d87c45612 test-data/Trinity.fasta.rnammer.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Trinity.fasta.rnammer.gff Tue Nov 15 09:17:29 2016 -0500 |
| b |
| @@ -0,0 +1,2 @@ +TRINITY_DN596_c0_g1_i1 RNAmmer rRNA 1 2082 3299.6 + . 28s_rRNA +TRINITY_DN549_c0_g1_i1 RNAmmer rRNA 1 1105 3299.6 + . 28s_rRNA |
| b |
| diff -r 000000000000 -r 499d87c45612 test-data/Trinity.fasta.transdecoder.pep --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Trinity.fasta.transdecoder.pep Tue Nov 15 09:17:29 2016 -0500 |
| b |
| b'@@ -0,0 +1,272 @@\n+>TRINITY_DN5404_c0_g1_i1|m.6938 TRINITY_DN5404_c0_g1_i1|g.6938 ORF TRINITY_DN5404_c0_g1_i1|g.6938 TRINITY_DN5404_c0_g1_i1|m.6938 type:internal len:115 (-) TRINITY_DN5404_c0_g1_i1:1-342(-)\n+QLSYAVFQAMLMKRYTSESVVADLLIPAGVNLPGAQEPNRGYFSPMHTYSSAVPGPISVPSAPYGRASSTIAEVSPMYGSHAAPYASTPSAAVGSSRGSTPASATVPISPARGF\n+>TRINITY_DN5409_c0_g1_i1|m.6942 TRINITY_DN5409_c0_g1_i1|g.6942 ORF TRINITY_DN5409_c0_g1_i1|g.6942 TRINITY_DN5409_c0_g1_i1|m.6942 type:internal len:202 (-) TRINITY_DN5409_c0_g1_i1:1-603(-)\n+ELFDNVVPKTVKNFASLCNGFEKDGRCLTYKGSRFHRVIKNFMLQGGDFTRGNGTGGESIYGEKFEDENFELKHDKPFLLSMANAGPNTNGSQFFITTVPTPHLDGKHVVFGKVIQGKSTVRTIENLETKNDDPVVPVVIEECGTCTKDQIEAPKPDVTGDSLEEFPDDYEGDKSETAIFKIASDLKGIANKQFAQQNLDT\n+>TRINITY_DN540_c0_g1_i1|m.650 TRINITY_DN540_c0_g1_i1|g.650 ORF TRINITY_DN540_c0_g1_i1|g.650 TRINITY_DN540_c0_g1_i1|m.650 type:complete len:407 (+) TRINITY_DN540_c0_g1_i1:350-1570(+)\n+MLSPSTAASQHHHHHSSSSSYAVSPTSPTSPTSSGPIGSNFDSASEHNGPVYPQDQQGPVIIPNSAISSTDPDDPETVVSLNVDEMIQRLIHVGYSRKSSKSVCLKNAEITSICMAVREIFLSQPTLLELTPPVKIVGDVHGQYSDLIRLFEMCGFPPSSNYLFLGDYVDRGKQSLETILLLFLYKIRYPENFFLLRGNHECANITRVYGFYDECKRRCNIKIWKTFINTFNCLPIASVVAGKIFCVHGGLSPSLSHMDDIREIPRPTDVPDYGLLNDLLWSDPADTENDWEDNERGVSFVFNKNVIRQFLAKHDFDLICRAHMVVEDGYEFFNDRTLCTVFSAPNYCGEFDNWGAVMSVNSELLCSFELIKPLDQAAIRRELKKSKRSGMAIYQSPPAEQVTQSV*\n+>TRINITY_DN540_c0_g2_i1|m.651 TRINITY_DN540_c0_g2_i1|g.651 ORF TRINITY_DN540_c0_g2_i1|g.651 TRINITY_DN540_c0_g2_i1|m.651 type:complete len:516 (+) TRINITY_DN540_c0_g2_i1:300-1847(+)\n+MGQGSSKHADSKLDSYPSFSRSDTQGSIKSLKSLKTVLGKGKDSNHDRRTSTDTTHSRHRYPETPPSLPPPPSPGILATSPAVLQKHQQEDSGNSSQSPTSPHPSNQPAMLSPSTAASQHHHHHSSSSSYAVSPTSPTSPTSSGPIGSNFDSASEHNGPVYPQDQQGPVIIPNSAISSTDPDDPETVVSLNVDEMIQRLIHVGYSRKSSKSVCLKNAEITSICMAVREIFLSQPTLLELTPPVKIVGDVHGQYSDLIRLFEMCGFPPSSNYLFLGDYVDRGKQSLETILLLFLYKIRYPENFFLLRGNHECANITRVYGFYDECKRRCNIKIWKTFINTFNCLPIASVVAGKIFCVHGGLSPSLSHMDDIREIPRPTDVPDYGLLNDLLWSDPADTENDWEDNERGVSFVFNKNVIRQFLAKHDFDLICRAHMVVEDGYEFFNDRTLCTVFSAPNYCGEFDNWGAVMSVNSELLCSFELIKPLDQAAIRRELKKSKRSGMAIYQSPPAEQVTQSV*\n+>TRINITY_DN540_c0_g2_i1|m.652 TRINITY_DN540_c0_g2_i1|g.652 ORF TRINITY_DN540_c0_g2_i1|g.652 TRINITY_DN540_c0_g2_i1|m.652 type:5prime_partial len:131 (+) TRINITY_DN540_c0_g2_i1:1-393(+)\n+LYYTSHHLLTHSSPRPYKFLNDCVLSAKQNIFIDQDYLKKRKSTNLRKISKNRKNLGTIGKPFNFGTKCKQRSLDFEVKKKIKIEQSGIVSRNLPLIEIQWDRGAVNTPTASSIPTHPFLGQTLKDPLSL*\n+>TRINITY_DN5419_c0_g1_i1|m.6941 TRINITY_DN5419_c0_g1_i1|g.6941 ORF TRINITY_DN5419_c0_g1_i1|g.6941 TRINITY_DN5419_c0_g1_i1|m.6941 type:complete len:116 (+) TRINITY_DN5419_c0_g1_i1:88-435(+)\n+MSLTSVLWNFVAKLAVDHGLNTNPDQVFQTVENVGKSFEKYETSFLKSLFNGNLGLSLPSAINILTLIIVLYFSLVIVNKTTSIALALFKTLAVISFFLLIGCLFAYWFINNGSF*\n+>TRINITY_DN541_c0_g1_i1|m.731 TRINITY_DN541_c0_g1_i1|g.731 ORF TRINITY_DN541_c0_g1_i1|g.731 TRINITY_DN541_c0_g1_i1|m.731 type:5prime_partial len:712 (+) TRINITY_DN541_c0_g1_i1:1-2136(+)\n+QAFSKVGKCEISQTNPSFSSGMRCLVRSADIQFKGICGLTRGFASFNKPPQTITEKIVQKFAQNIPENKYVRSGDYVTIKPKHCMSHDNSWPVALKFMGIGAKKVFDNRQIVCTLDHDVQNKSEANLRKYKNIESFAKGQGIDFYPAGRGIGHQIMVEQGYAMPGSMAVASDSHSNTYGGVGCLGTPIVRTDAAAIWATGQTWWQIPPIARVNLVGQLPKGLSGKDIIVSLCGAFNHDEVLNHAIEFYGEGLNSLSIESRLTIANMTTEWGALSGLFPTDEKLLAWYEDRLKFLGPNHPRVNRETLDAIKASPILADEGAFYAKHLILDLSTLSPAVSGPNSVKVYNSAATLEKKDILIKKAYLVSCTNGRLSDIHDAAETVKGKKVADGVEFYVGAASSEVEAAAQKNGDWQTLIDSGARTLPAGCGPCIGLGTGLLKDGEVGISATNRNFKGRMGSREALAYLASPAVVAASAIAGKIVAPEGFKNAVSLVSAVDITDKVNKQTASKSSTEAVDSETAIIDGFPSIVAGEIVFCDADNLNTDGIYPGRYTYRDDITKEEMAKVCMENYDSEFGKKTKKDDILVSGFNFGTGSSREQAATAILSRGIPLVVGGSFSDIFKRNSINNALLAIQLPDLVQKLRTAFANESKELTRRTGWHLKWDVRKSTVTVTTSDNKEMSWKIGELGNSVQSLFVRGGLEGWVKHEISKSN*\n+>TRINITY_DN541_c0_g1_i1|m.732 TRINITY_DN541_c0_g1_i1|g.732 ORF TRINITY_DN541_c0_g1_i1|g.732 TRINITY_DN541_c0_g1_i1|m.732 type:complete len:388 (-) TRINITY_DN541_c0_g1_i1:2423-3586(-)\n+MYNTKGHIAEITDGCWQPDSSQIFLTTGYDSTARIWDVNRTKSQLEVFVHVPEGSHTGLSRIPVTSCAWNPAKPDNFATAVLDGSIQFWQKGSRTKRPVMKIKDAHLPQQGISCLSFSQDGNYLLSRGEDNALRVWDLRNSNKCVNERIDILTPKAGGNAIFSPTQKLILAGSTAVNSMKAPLFVLDAMTLDTKATLFFDSKSTVTASVSAVSWNEKINQVSLGSADGNAYVLFSPNESIRGVKDAAMRPPKSKHIDDDLSSTVHINSLS'..b'AVNVEDDPEARLKRKEAIRLSQQYLSKLDSTKNQNK*\n+>TRINITY_DN5997_c0_g1_i1|m.826 TRINITY_DN5997_c0_g1_i1|g.826 ORF TRINITY_DN5997_c0_g1_i1|g.826 TRINITY_DN5997_c0_g1_i1|m.826 type:complete len:108 (+) TRINITY_DN5997_c0_g1_i1:78-401(+)\n+MGKRKAKAKVKPKRRAPPLDTTFTCLFCNHEKSVSCSLDKQSGVGNLHCKICGQSHQCLITALSAPIDVYSDWIDACDAVANQAKEVDNINDQEAYSPEAAYEEEKE*\n+>TRINITY_DN5998_c0_g1_i1|m.811 TRINITY_DN5998_c0_g1_i1|g.811 ORF TRINITY_DN5998_c0_g1_i1|g.811 TRINITY_DN5998_c0_g1_i1|m.811 type:5prime_partial len:266 (-) TRINITY_DN5998_c0_g1_i1:191-988(-)\n+VCGLDETRSSFKTLTTMCFGGDDNCGCQVFEDVNSSLEYCENMLLDDYDVYRTKLLHKAGYSHTLAVPGKHKQNISMAETFSPSPRHDLLRQVAMSSVKAETKELSKFEKYAKYEQPFPLLMQVFGEITTKREDFWLGLCPFFKKAFLRKGDLLWRKGDTPSKLVILETGMVKASYQMDRESLSENITCLCVVGELPFFSKTCYNATVVAELDSAVWILDREGWETMLKSSDKAEVIENEMLYLTLKMTRDKFNVFTNFALNLYR*\n+>TRINITY_DN5999_c0_g1_i1|m.812 TRINITY_DN5999_c0_g1_i1|g.812 ORF TRINITY_DN5999_c0_g1_i1|g.812 TRINITY_DN5999_c0_g1_i1|m.812 type:5prime_partial len:142 (+) TRINITY_DN5999_c0_g1_i1:2-427(+)\n+TARMPKNKGKGGKNRRRGKNENENEKRELTYAEEGQMYAQVTKMLGNGRIEAACFDGVKRLGHIRGKLRKKVWINQGDIILLSLREFQDEKGDVILKYTADEARTLKNQGELPETAKINETDTFGAEGEDDLDFEFDVDAI*\n+>TRINITY_DN599_c0_g1_i1|m.690 TRINITY_DN599_c0_g1_i1|g.690 ORF TRINITY_DN599_c0_g1_i1|g.690 TRINITY_DN599_c0_g1_i1|m.690 type:5prime_partial len:640 (+) TRINITY_DN599_c0_g1_i1:2-1921(+)\n+VVHNLDIPHDKSYKSNYLFSVVLSPHQASWNIYNSFDNSMVLWCPYGKNKTLICLLNFQSSLLSFEWISIISRALLFSPRPSLLISVPAFHIHLRLNFPCFKDTTRPHTNETFVTTDDITQLSRTSTLSLSTASPRLVHDLVMKSWDISEDQFVESCLGVLEVNPEWSGIVKTWSKSHTLGLCWRMYDRLEWINSFSSLKYVGLLAAKDLYQLELRPKLHYPNHVTFRDGSKMDEPTPVEGYLIRLTSSTGRKTRYGRMFHKELYFAIFNNFLFAIQPDSVLPLSMLSKSLNLDDKLPFLSNNENDKYVYEFDPFKIANCRASGLNETIDSSVRESFLLLLQAERKRELDMLTIADSFLDLSRVESVCPVEDVEERNIFEITMTNGMKLVFQSYCERTRNLWINKITEVASYWKQRLFLDLQEYHDVRETNINILHIEQSIEPDVACYLNHWEVAGCVASTLIYHYCSMLGCRVIRMQGTLFKKKDALFEKCFAILIPGQLVFFQDATRTKFGKLCTKTHYRKRYSISLKNAFIYTGLSTMDEFARGPNDPQPHISRLPRCYEDGWQSFDRDDMLSFVIWSSGGVDYDLRPHHSVPDTAYGMAKDKLSKPKRFMFLARTRQERDVWAKRISKEINRGHS*\n+>TRINITY_DN599_c0_g2_i1|m.691 TRINITY_DN599_c0_g2_i1|g.691 ORF TRINITY_DN599_c0_g2_i1|g.691 TRINITY_DN599_c0_g2_i1|m.691 type:complete len:966 (+) TRINITY_DN599_c0_g2_i1:572-3469(+)\n+MNEEDTDFAWLHNNSAEHLRFLSHRIFIGPIPSNFIHSTSGFFNKRFQNYTKRQICYNVASPNEPPIDFSFLMHKSTDENPDTPSNLDSPSTQNVGSTNNTRASQSLLRRSSSFFRRRHRKNGTHASTDNNPFSESSTLQPQTAERTSQQAVRSAITETTNPSVSVQNSNSTSTSSAAMIIPHRDSQNSLEIAPLISPESQLSSLHPSSSRRHLISTPHVNRGTQFKRSSSCRNSRQPLLSGVDKHLTSNFTDANLIIKQSVVLARIESTFTVLPSDYNDSAAQRVPRKTISPWSQCLLVARQTDVENSIRLDFISKKLRKRLNGDVVHNLDVPHDKSYKSNYLFSVVLSPHQASWNIYNSFDNSMVLWCPYGKNKTLICLLNFQSSLLSFEWISIISRALLFSPRPSLLISVPAFHIHLRLNFPCFKDTTRPHTNETFVTTDDITQLSRTSTLSLSTASPRLVHDLVMKSWDISEDQFVESCLGVLEVNPEWSGIVKTWSKSHTLGLCWRMYDRLEWINSFSSLKYVGLLAAKDLYQLELRPKLHYPNHVTFRDGSKMDEPTPVEGYLIRLTSSTGRKTRYGRMFHKELYFAIFNNFLFAIQPDSVLPLSMLSKSLNLDDKLPFLSNNENDKYVYEFDPFKIANCRASGLNETIDSSVRESFLLLLQAERKRELDMLTIADSFLDLSRVESVCPVEDVEERNIFEITMTNGMKLVFQSYCERTRNLWINKITEVASYWKQRLFLDLQEYHDVRETNINILHIEQSIEPDVACYLNHWEVAGCVASTLIYHYCSMLGCRVIRMQGTLFKKKDALFEKCFAILIPGQLVFFQDATRTKFGKLCTKTHYRKRYSISLKNAFIYTGLSTMDEFARGPNDPQPHISRLPRCYEDGWQSFDRDDMLSFVIWSSGGVDYDLRPHHSVPDTAYGMAKDKLSKPKRFMFLARTRQERDVWAKRISKEINRGHS*\n+>TRINITY_DN59_c0_g1_i1|m.8862 TRINITY_DN59_c0_g1_i1|g.8862 ORF TRINITY_DN59_c0_g1_i1|g.8862 TRINITY_DN59_c0_g1_i1|m.8862 type:5prime_partial len:298 (-) TRINITY_DN59_c0_g1_i1:1057-1950(-)\n+SKLFSAAKHYNSLNGLLAMILVHMANYKLARRKLVQIGALKFLTRQCFIQTQDSNAAFALAKILISVAPHSIFTKAFPSNRAIHPMSKLLSTNSADTEYPILLGKFEVLLALTNLASHDEESRQAIVQECWRELDELIIETNPLIQRATTELINNLSLSPYCLIKFIGDKDSDFENTRLHIVLALSDTEDTPTRLAACGILVQITSVDEGCKKILSLQNDFNYIVRMLTDQDEGIQHRGLVCICNIVYSKDQEIFNKFIKTPKAVETLRTYITKQAALKELQHEALVMIDSRLQGSK*\n+>TRINITY_DN59_c0_g1_i1|m.8863 TRINITY_DN59_c0_g1_i1|g.8863 ORF TRINITY_DN59_c0_g1_i1|g.8863 TRINITY_DN59_c0_g1_i1|m.8863 type:5prime_partial len:206 (+) TRINITY_DN59_c0_g1_i1:2-619(+)\n+ELDRSAHQLHLEAIQNMKFSTVGFLFSTILFKSAFAGWMDTHMKDEHHIDKYTDESFFRLHDLGKKGYWSDQDILSLYGLFENDEVPFVKKNEVLVDVLKKCDPSGNRRITLDEFLAFRKNGGELTDFGFPGHHGDEEEEFEMHHVEKYHPAGLDEPDENWNHPEDIEHFQKHDEIFHGDKKPEERRKHFVKYNNIPDKYRRVSI*\n' |
| b |
| diff -r 000000000000 -r 499d87c45612 test-data/TrinotatePFAM.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TrinotatePFAM.out Tue Nov 15 09:17:29 2016 -0500 |
| b |
| b'@@ -0,0 +1,816 @@\n+CSTF2_hinge PF14327.3 81 TRINITY_DN5404_c0_g1_i1|m.6938 - 114 0.00079 19.7 0.2 1 1 7.3e-08 0.0012 19.1 0.2 57 80 1 24 1 25 0.94 Hinge domain of cleavage stimulation factor subunit 2\n+Pro_isomerase PF00160.18 155 TRINITY_DN5409_c0_g1_i1|m.6942 - 201 8.4e-47 159.2 0.2 1 1 6.4e-51 1e-46 158.9 0.2 15 154 1 144 1 145 0.93 Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD\n+Metallophos PF00149.25 203 TRINITY_DN540_c0_g1_i1|m.650 - 407 2.4e-34 119.4 0.2 1 1 4.4e-38 3.6e-34 118.9 0.2 2 200 133 324 132 327 0.90 Calcineurin-like phosphoesterase\n+STPPase_N PF16891.2 48 TRINITY_DN540_c0_g1_i1|m.650 - 407 1.8e-19 69.7 0.1 1 1 4e-23 3.2e-19 68.9 0.1 1 47 83 130 83 131 0.97 Serine-threonine protein phosphatase N-terminal domain\n+Metallophos PF00149.25 203 TRINITY_DN540_c0_g2_i1|m.651 - 516 3.9e-34 118.8 0.2 1 1 7.6e-38 6.2e-34 118.1 0.2 2 200 242 433 241 436 0.90 Calcineurin-like phosphoesterase\n+STPPase_N PF16891.2 48 TRINITY_DN540_c0_g2_i1|m.651 - 516 2.4e-19 69.3 0.1 1 1 5.5e-23 4.5e-19 68.5 0.1 1 47 192 239 192 240 0.97 Serine-threonine protein phosphatase N-terminal domain\n+Apq12 PF12716.4 54 TRINITY_DN5419_c0_g1_i1|m.6941 - 116 1.8e-09 37.3 9.0 1 1 1.7e-13 2.8e-09 36.6 9.0 2 53 59 110 58 111 0.97 Nuclear pore assembly and biogenesis\n+Aconitase PF00330.17 458 TRINITY_DN541_c0_g1_i1|m.731 - 712 1.8e-106 356.7 0.0 1 1 2.4e-109 1.3e-105 353.9 0.0 12 458 73 478 55 478 0.89 Aconitase family (aconitate hydratase)\n+Aconitase_C PF00694.16 131 TRINITY_DN541_c0_g1_i1|m.731 - 712 1.5e-25 89.9 0.0 1 1 5.3e-29 2.9e-25 89.0 0.0 10 130 510 636 501 637 0.93 Aconitase C-terminal domain\n+DUF521 PF04412.10 402 TRINITY_DN541_c0_g1_i1|m.731 - 712 0.08 11.5 0.0 1 1 2.5e-05 0.14 10.7 0.0 297 358 365 427 345 449 0.86 Protein of unknown function (DUF521)\n+WD40 PF00400.29 38 TRINITY_DN541_c0_g1_i1|m.732 - 388 1.1e-13 51.3 2.1 1 5 1.3e-06 0.0052 17.5 0.1 8 38 5 37 1 37 0.82 WD domain, G-beta repeat\n+WD40 PF00400.29 38 TRINITY_DN541_c0_g1_i1|m.732 - 388 1.1e-13 51.3 2.1 2 5 0.0056 23 6.0 0.0 10 37 56 89 46 90 0.69 WD domain, G-beta repeat\n+WD40 PF00400.29 38 TRINITY_DN541_c0_g1_i1|m.732 - 388 1.1e-13 51.3 2.1 3 5 2.7e-08 0.00011 22.8 0.0 9 38 105 137 97 137 0.82 WD domain, G-beta repeat\n+WD40 PF00400.29 38 TRINITY_DN541_c0_g1_i1|m.732 - 388 1.1e-13 51.3 2.1 4 5 0.38 1.6e+03 0.1 0.0 18 29 162 173 143 177 0.81 WD domain, G-beta repeat\n+WD40 PF00400.29 38 TRINITY_DN541_c0_g1_i1|m.732 - 388 1.1e-13 51.3 2.1 5 5 2.6 1e+04 -2.5 0.0 13 33 209 229 201 232 0.52 WD domain, G-beta repeat\n+ANAPC4_WD40 PF12894.4 92 TRINITY_DN541_c0_g1_i1|m.732 - 388 0.0036 17.4 0.1 1 4 0.044 1.8e+02 2.4 0.0 38 75 8 46 2 72 0.68 Anaphase-promoting complex subunit 4 WD40 domain\n+ANAPC4_WD40 PF12894.4 92 TRINITY_DN541_c0_g1_i1|m.732 - 388 0.0036 17.4 0.1 2 4 0.37 1.5e+03 -0.6 0.0 39 66 62 90 37 108 0.74 Anaphase-promoting complex subunit 4 WD40 domain\n+ANAPC4_WD40 PF12894.4 92 TRINITY_DN541_c0_g1_i1|m.732 - 388 0.0036'..b'.1 0.3 1 4 3.7 1.5e+04 -3.6 0.0 62 97 336 369 317 370 0.64 PH domain\n+PH PF00169.26 106 TRINITY_DN599_c0_g2_i1|m.691 - 966 1.1e-07 32.1 0.3 2 4 0.28 1.2e+03 -0.1 0.0 4 45 566 608 565 677 0.54 PH domain\n+PH PF00169.26 106 TRINITY_DN599_c0_g2_i1|m.691 - 966 1.1e-07 32.1 0.3 3 4 0.00011 0.46 10.9 0.1 49 104 685 735 680 737 0.87 PH domain\n+PH PF00169.26 106 TRINITY_DN599_c0_g2_i1|m.691 - 966 1.1e-07 32.1 0.3 4 4 4.5e-06 0.018 15.4 0.0 3 105 803 960 801 961 0.91 PH domain\n+Spo7_2_N PF15407.3 64 TRINITY_DN599_c0_g2_i1|m.691 - 966 0.00078 18.9 0.0 1 1 7.3e-07 0.003 17.1 0.0 15 57 12 54 10 60 0.83 Sporulation protein family 7\n+PH_9 PF15410.3 119 TRINITY_DN599_c0_g2_i1|m.691 - 966 0.048 13.9 0.0 1 3 2.5 1e+04 -3.3 0.0 13 34 280 302 253 305 0.66 Pleckstrin homology domain\n+PH_9 PF15410.3 119 TRINITY_DN599_c0_g2_i1|m.691 - 966 0.048 13.9 0.0 2 3 0.00066 2.7 8.3 0.0 84 118 702 736 691 737 0.90 Pleckstrin homology domain\n+PH_9 PF15410.3 119 TRINITY_DN599_c0_g2_i1|m.691 - 966 0.048 13.9 0.0 3 3 0.11 4.3e+02 1.2 0.0 20 69 809 855 795 870 0.74 Pleckstrin homology domain\n+Adaptin_N PF01602.17 524 TRINITY_DN59_c0_g1_i1|m.8862 - 298 0.0028 16.2 0.5 1 1 1.1e-06 0.0046 15.4 0.5 171 308 107 260 53 276 0.75 Adaptin N terminal region\n+DUF2310 PF10071.6 255 TRINITY_DN59_c0_g1_i1|m.8862 - 298 0.065 12.4 0.0 1 1 2.6e-05 0.11 11.7 0.0 100 178 79 155 43 160 0.84 Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310)\n+Vac14_Fab1_bd PF12755.4 97 TRINITY_DN59_c0_g1_i1|m.8862 - 298 0.068 13.6 0.1 1 1 4.7e-05 0.19 12.2 0.1 22 86 172 237 161 258 0.87 Vacuolar 14 Fab1-binding region\n+UNC45-central PF11701.5 152 TRINITY_DN59_c0_g1_i1|m.8862 - 298 0.23 11.3 2.2 1 3 0.18 7.4e+02 -0.1 0.0 82 111 14 47 5 57 0.84 Myosin-binding striated muscle assembly central\n+UNC45-central PF11701.5 152 TRINITY_DN59_c0_g1_i1|m.8862 - 298 0.23 11.3 2.2 2 3 0.00095 3.9 7.3 0.1 101 136 107 142 49 153 0.84 Myosin-binding striated muscle assembly central\n+UNC45-central PF11701.5 152 TRINITY_DN59_c0_g1_i1|m.8862 - 298 0.23 11.3 2.2 3 3 0.056 2.3e+02 1.5 0.0 89 150 183 244 174 282 0.67 Myosin-binding striated muscle assembly central\n+EF-hand_7 PF13499.3 71 TRINITY_DN59_c0_g1_i1|m.8863 - 206 6.2e-05 23.2 0.3 1 1 2.5e-08 0.00014 22.1 0.3 7 69 57 118 51 120 0.85 EF-hand domain pair\n+EF-hand_6 PF13405.3 31 TRINITY_DN59_c0_g1_i1|m.8863 - 206 0.00015 21.3 0.2 1 2 0.00015 0.8 9.7 0.1 4 25 56 77 55 81 0.87 EF-hand domain\n+EF-hand_6 PF13405.3 31 TRINITY_DN59_c0_g1_i1|m.8863 - 206 0.00015 21.3 0.2 2 2 0.00029 1.6 8.7 0.0 3 25 96 118 94 123 0.86 EF-hand domain\n+EF-hand_1 PF00036.29 29 TRINITY_DN59_c0_g1_i1|m.8863 - 206 0.042 13.3 0.0 1 2 0.48 2.6e+03 -1.7 0.0 5 16 57 68 55 68 0.82 EF hand\n+EF-hand_1 PF00036.29 29 TRINITY_DN59_c0_g1_i1|m.8863 - 206 0.042 13.3 0.0 2 2 3.1e-05 0.17 11.4 0.0 4 25 97 118 94 121 0.87 EF hand\n' |
| b |
| diff -r 000000000000 -r 499d87c45612 test-data/signalp.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/signalp.out Tue Nov 15 09:17:29 2016 -0500 |
| b |
| @@ -0,0 +1,3 @@ +TRINITY_DN5906_c0_g1_i1|m.815 SignalP-4.0 SIGNAL 1 18 0.703 . . YES +TRINITY_DN593_c0_g1_i1|m.771 SignalP-4.0 SIGNAL 1 26 0.526 . . YES +TRINITY_DN5991_c0_g1_i1|m.781 SignalP-4.0 SIGNAL 1 25 0.688 . . YES |
| b |
| diff -r 000000000000 -r 499d87c45612 test-data/swissprot.blastp.outfmt6 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/swissprot.blastp.outfmt6 Tue Nov 15 09:17:29 2016 -0500 |
| b |
| b'@@ -0,0 +1,136 @@\n+TRINITY_DN5404_c0_g1_i1|m.6938\tYKCG_SCHPO\t100.00\t114\t0\t0\t1\t114\t198\t311\t1e-70\t 223\n+TRINITY_DN5409_c0_g1_i1|m.6942\tPPID_SCHPO\t100.00\t201\t0\t0\t1\t201\t22\t222\t3e-147\t 421\n+TRINITY_DN540_c0_g1_i1|m.650\tPPZ_SCHPO\t100.00\t406\t0\t0\t1\t406\t110\t515\t0.0\t 850\n+TRINITY_DN540_c0_g2_i1|m.651\tPPZ_SCHPO\t100.00\t515\t0\t0\t1\t515\t1\t515\t0.0\t 1068\n+TRINITY_DN5419_c0_g1_i1|m.6941\tAPQ12_SCHPO\t100.00\t115\t0\t0\t1\t115\t1\t115\t3e-75\t 224\n+TRINITY_DN541_c0_g1_i1|m.731\tLYS4_SCHPO\t100.00\t711\t0\t0\t1\t711\t11\t721\t0.0\t 1469\n+TRINITY_DN541_c0_g1_i1|m.732\tYIPH_SCHPO\t100.00\t387\t0\t0\t1\t387\t190\t576\t0.0\t 803\n+TRINITY_DN541_c0_g2_i1|m.735\tLYS4_SCHPO\t97.66\t128\t3\t0\t1\t128\t594\t721\t2e-79\t 254\n+TRINITY_DN541_c0_g2_i1|m.734\tYIPH_SCHPO\t100.00\t387\t0\t0\t1\t387\t190\t576\t0.0\t 803\n+TRINITY_DN5425_c0_g1_i1|m.6937\tGMH3_SCHPO\t100.00\t202\t0\t0\t1\t202\t39\t240\t5e-147\t 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361\n+TRINITY_DN595_c0_g2_i1|m.716\tPTH_SCHPO\t100.00\t153\t0\t0\t1\t153\t54\t206\t6e-110\t 318\n+TRINITY_DN5962_c0_g1_i1|m.834\tMU134_SCHPO\t100.00\t432\t0\t0\t1\t432\t1\t432\t0.0\t 894\n+TRINITY_DN5964_c0_g1_i1|m.859\tUTP25_SCHPO\t100.00\t652\t0\t0\t9\t660\t1\t652\t0.0\t 1356\n+TRINITY_DN5965_c0_g1_i1|m.801\tUBR1_SCHPO\t100.00\t645\t0\t0\t1\t645\t360\t1004\t0.0\t 1346\n+TRINITY_DN5967_c0_g1_i1|m.819\tCTR4_SCHPO\t100.00\t179\t0\t0\t1\t179\t111\t289\t5e-135\t 386\n+TRINITY_DN5968_c0_g1_i1|m.808\tYHAG_SCHPO\t100.00\t100\t0\t0\t1\t100\t21\t120\t3e-68\t 206\n+TRINITY_DN5969_c0_g1_i1|m.864\tVPS27_SCHPO\t100.00\t610\t0\t0\t1\t610\t1\t610\t0.0\t 1264\n+TRINITY_DN596_c0_g1_i1|m.607\tYB92_SCHPO\t100.00\t603\t0\t0\t1\t603\t1\t603\t0.0\t 1203\n+TRINITY_DN5970_c0_g1_i1|m.854\tTOR1_SCHPO\t100.00\t147\t0\t0\t1\t147\t303\t449\t1e-93\t 303\n+TRINITY_DN5971_c0_g1_i1|m.831\tGTR1_SCHPO\t100.00\t308\t0\t0\t1\t308\t1\t308\t0.0\t 638\n+TRINITY_DN5972_c0_g1_i1|m.803\tYNS9_SCHPO\t99.28\t417\t3\t0\t1\t417\t1\t417\t0.0\t 861\n+TRINITY_DN5973_c0_g1_i1|m.843\tISP7_SCHPO\t100.00\t397\t0\t0\t1\t397\t1\t397\t0.0\t 815\n+TRINITY_DN5974_c0_g1_i1|m.792\tNU211_SCHPO\t99.43\t176\t1\t0\t1\t176\t153\t328\t1e-108\t 346\n+TRINITY_DN5975_c0_g1_i1|m.804\tYOO2_SCHPO\t100.00\t189\t0\t0\t1\t189\t92\t280\t9e-128\t 382\n+TRINITY_DN5976_c0_g1_i1|m.869\tRL33A_SCHPO\t100.00\t108\t0\t0\t1\t108\t1\t108\t3e-75\t 224\n+TRINITY_DN5977_c0_g1_i1|m.800\tREXO3_SCHPO\t99.32\t147\t1\t0\t1\t147\t97\t243\t6e-97\t 296\n+TRINITY_DN597_c0_g1_i1|m.662\tKAPR_SCHPO\t100.00\t412\t0\t0\t1\t412\t1\t412\t0.0\t 843\n+TRINITY_DN597_c0_g2_i1|m.663\tKAPR_SCHPO\t100.00\t412\t0\t0\t1\t412\t1\t412\t0.0\t 843\n+TRINITY_DN5980_c0_g1_i1|m.807\tDBP4_SCHPO\t100.00\t735\t0\t0\t1\t735\t1\t735\t0.0\t 1514\n+TRINITY_DN5982_c0_g1_i1|m.813\tRCM1_SCHPO\t100.00\t460\t0\t0\t7\t466\t1\t460\t0.0\t 953\n+TRINITY_DN5983_c0_g1_i1|m.855\tYQ86_SCHPO\t100.00\t230\t0\t0\t1\t230\t1\t230\t1e-164\t 461\n+TRINITY_DN5985_c0_g1_i1|m.806\tDAM1_SCHPO\t100.00\t109\t0\t0\t1\t109\t1\t109\t3e-74\t 223\n+TRINITY_DN5985_c0_g1_i1|m.805\tYKP9_SCHPO\t100.00\t388\t0\t0\t1\t388\t1\t388\t0.0\t 815\n+TRINITY_DN5989_c0_g1_i1|m.829\tARF1_SCHPO\t100.00\t180\t0\t0\t1\t180\t1\t180\t1e-131\t 373\n+TRINITY_DN598_c0_g1_i1|m.767\tALLC_SCHPO\t100.00\t342\t0\t0\t1\t342\t1\t342\t0.0\t 712\n+TRINITY_DN598_c0_g2_i1|m.768\tALLC_SCHPO\t99.39\t165\t1\t0\t1\t165\t178\t342\t7e-116\t 338\n+TRINITY_DN598_c0_g2_i1|m.768\tALLC_SCHPO\t38.86\t175\t90\t5\t2\t160\t5\t178\t6e-26\t 105\n+TRINITY_DN5991_c0_g1_i1|m.781\tSLPI_SCHPO\t100.00\t659\t0\t0\t1\t659\t1\t659\t0.0\t 1345\n+TRINITY_DN5992_c0_g1_i1|m.853\tFOLD_SCHPO\t100.00\t417\t0\t0\t1\t417\t1\t417\t0.0\t 867\n+TRINITY_DN5994_c0_g1_i1|m.840\tSYG1_SCHPO\t99.27\t137\t1\t0\t1\t137\t329\t465\t1e-90\t 283\n+TRINITY_DN5996_c0_g1_i1|m.789\tBAG1B_SCHPO\t100.00\t206\t0\t0\t1\t206\t1\t206\t1e-149\t 421\n+TRINITY_DN5997_c0_g1_i1|m.826\tELOF1_SCHPO\t100.00\t107\t0\t0\t1\t107\t1\t107\t4e-75\t 224\n+TRINITY_DN5998_c0_g1_i1|m.811\tYA7B_SCHPO\t100.00\t265\t0\t0\t1\t265\t694\t958\t0.0\t 560\n+TRINITY_DN5999_c0_g1_i1|m.812\tIF1A_SCHPO\t100.00\t138\t0\t0\t4\t141\t1\t138\t4e-96\t 280\n+TRINITY_DN599_c0_g1_i1|m.690\tMUG56_SCHPO\t99.84\t639\t1\t0\t1\t639\t327\t965\t0.0\t 1342\n+TRINITY_DN599_c0_g2_i1|m.691\tMUG56_SCHPO\t100.00\t965\t0\t0\t1\t965\t1\t965\t0.0\t 2002\n+TRINITY_DN59_c0_g1_i1|m.8862\tRNG3_SCHPO\t100.00\t297\t0\t0\t1\t297\t450\t746\t0.0\t 612\n+TRINITY_DN59_c0_g1_i1|m.8863\tYCS3_SCHPO\t100.00\t189\t0\t0\t17\t205\t1\t189\t3e-137\t 389\n' |
| b |
| diff -r 000000000000 -r 499d87c45612 test-data/swissprot.blastx.outfmt6 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/swissprot.blastx.outfmt6 Tue Nov 15 09:17:29 2016 -0500 |
| b |
| b'@@ -0,0 +1,192 @@\n+TRINITY_DN596_c0_g1_i1\tYB92_SCHPO\t100.00\t603\t0\t0\t102\t1910\t1\t603\t0.0\t 1052\n+TRINITY_DN549_c0_g1_i1\tGAA1_SCHPO\t100.00\t454\t0\t0\t2\t1363\t121\t574\t0.0\t 919\n+TRINITY_DN594_c0_g1_i1\tERG27_SCHPO\t94.82\t309\t0\t1\t1275\t349\t46\t338\t0.0\t 566\n+TRINITY_DN594_c0_g2_i1\tERG27_SCHPO\t90.91\t176\t0\t1\t1207\t680\t46\t205\t2e-141\t 290\n+TRINITY_DN594_c0_g2_i1\tERG27_SCHPO\t100.00\t111\t0\t0\t681\t349\t228\t338\t2e-141\t 235\n+TRINITY_DN591_c0_g1_i1\tSYNM_SCHPO\t100.00\t335\t0\t0\t1742\t738\t107\t441\t0.0\t 702\n+TRINITY_DN540_c0_g1_i1\tPPZ_SCHPO\t100.00\t514\t0\t0\t26\t1567\t2\t515\t0.0\t 926\n+TRINITY_DN540_c0_g2_i1\tPPZ_SCHPO\t100.00\t515\t0\t0\t300\t1844\t1\t515\t0.0\t 928\n+TRINITY_DN597_c0_g1_i1\tKAPR_SCHPO\t100.00\t412\t0\t0\t202\t1437\t1\t412\t0.0\t 810\n+TRINITY_DN597_c0_g2_i1\tKAPR_SCHPO\t100.00\t412\t0\t0\t202\t1437\t1\t412\t0.0\t 810\n+TRINITY_DN542_c0_g1_i1\tTAF12_SCHPO\t100.00\t450\t0\t0\t125\t1474\t1\t450\t0.0\t 785\n+TRINITY_DN542_c0_g2_i1\tTAF12_SCHPO\t100.00\t383\t0\t0\t2\t1150\t68\t450\t0.0\t 649\n+TRINITY_DN599_c0_g1_i1\tMUG56_SCHPO\t99.84\t639\t1\t0\t2\t1918\t327\t965\t0.0\t 1302\n+TRINITY_DN599_c0_g2_i1\tMUG56_SCHPO\t100.00\t965\t0\t0\t572\t3466\t1\t965\t0.0\t 1837\n+TRINITY_DN592_c0_g1_i1\tHMCS_SCHPO\t100.00\t447\t0\t0\t92\t1432\t1\t447\t0.0\t 924\n+TRINITY_DN592_c0_g2_i1\tHMCS_SCHPO\t100.00\t447\t0\t0\t53\t1393\t1\t447\t0.0\t 924\n+TRINITY_DN543_c0_g1_i1\tPYRE_SCHPO\t99.17\t121\t1\t0\t284\t646\t86\t206\t3e-111\t 240\n+TRINITY_DN543_c0_g1_i1\tPYRE_SCHPO\t97.78\t90\t2\t0\t28\t297\t1\t90\t3e-111\t 184\n+TRINITY_DN543_c0_g2_i1\tPYRE_SCHPO\t100.00\t206\t0\t0\t28\t645\t1\t206\t4e-145\t 418\n+TRINITY_DN595_c0_g1_i1\tPTH_SCHPO\t99.43\t175\t1\t0\t201\t725\t32\t206\t3e-124\t 361\n+TRINITY_DN595_c0_g2_i1\tPTH_SCHPO\t98.87\t177\t2\t0\t421\t951\t30\t206\t3e-123\t 361\n+TRINITY_DN595_c0_g2_i1\tPTH_SCHPO\t96.97\t33\t1\t0\t287\t385\t1\t33\t1e-11\t67.0\n+TRINITY_DN590_c0_g1_i1\tYC5C_SCHPO\t100.00\t491\t0\t0\t138\t1610\t1\t491\t0.0\t 989\n+TRINITY_DN541_c0_g1_i1\tLYS4_SCHPO\t100.00\t711\t0\t0\t1\t2133\t11\t721\t0.0\t 1392\n+TRINITY_DN541_c0_g2_i1\tYIPH_SCHPO\t100.00\t482\t0\t0\t2137\t692\t90\t571\t0.0\t 983\n+TRINITY_DN541_c0_g2_i1\tYIPH_SCHPO\t98.77\t81\t1\t0\t2430\t2188\t11\t91\t9e-19\t94.7\n+TRINITY_DN548_c0_g1_i1\tDPH6_SCHPO\t100.00\t606\t0\t0\t72\t1889\t1\t606\t0.0\t 1256\n+TRINITY_DN548_c0_g2_i1\tDPH6_SCHPO\t100.00\t322\t0\t0\t72\t1037\t1\t322\t0.0\t 664\n+TRINITY_DN545_c0_g1_i1\tNSRP1_SCHPO\t100.00\t350\t0\t0\t163\t1212\t1\t350\t0.0\t 637\n+TRINITY_DN545_c0_g2_i1\tNSRP1_SCHPO\t100.00\t355\t0\t0\t163\t1227\t1\t355\t0.0\t 649\n+TRINITY_DN546_c0_g1_i1\tCTK1_SCHPO\t100.00\t161\t0\t0\t694\t1176\t1\t161\t2e-54\t 195\n+TRINITY_DN546_c0_g2_i1\tCTK1_SCHPO\t100.00\t585\t0\t0\t694\t2448\t1\t585\t0.0\t 962\n+TRINITY_DN544_c0_g1_i1\tIPK1_SCHPO\t100.00\t640\t0\t0\t898\t2817\t1\t640\t0.0\t 1299\n+TRINITY_DN544_c0_g2_i1\tIPK1_SCHPO\t100.00\t640\t0\t0\t2143\t4062\t1\t640\t0.0\t 1299\n+TRINITY_DN598_c0_g1_i1\tALLC_SCHPO\t100.00\t342\t0\t0\t442\t1467\t1\t342\t0.0\t 712\n+TRINITY_DN598_c0_g2_i1\tALLC_SCHPO\t99.39\t165\t1\t0\t2\t496\t178\t342\t4e-115\t 338\n+TRINITY_DN598_c0_g2_i1\tALLC_SCHPO\t38.86\t175\t90\t5\t5\t481\t5\t178\t2e-25\t 105\n+TRINITY_DN593_c0_g1_i1\tYEG7_SCHPO\t100.00\t505\t0\t0\t13\t1527\t1\t505\t0.0\t 904\n+TRINITY_DN593_c0_g2_i1\tYEG7_SCHPO\t99.24\t397\t3\t0\t2\t1192\t109\t505\t0.0\t 672\n+TRINITY_DN5991_c0_g1_i1\tSLPI_SCHPO\t100.00\t659\t0\t0\t34\t2010\t1\t659\t0.0\t 1239\n+TRINITY_DN5943_c0_g1_i1\tESF1_SCHPO\t100.00\t682\t0\t0\t14\t2059\t1\t682\t0.0\t 1103\n+TRINITY_DN5907_c0_g1_i1\tRUVB1_SCHPO\t100.00\t456\t0\t0\t46\t1413\t1\t456\t0.0\t 865\n+TRINITY_DN5928_c0_g1_i1\tVPS74_SCHPO\t100.00\t334\t0\t0\t401\t1402\t1\t334\t0.0\t 657\n+TRINITY_DN5916_c0_g1_i1\tYCN6_SCHPO\t100.00\t289\t0\t0\t7\t873\t1\t289\t0.0\t 581\n+TRINITY_DN5920_c0_g1_i1\tRSC4_SCHPO\t100.00\t542\t0\t0\t279\t1904\t1\t542\t0.0\t 1004\n+TRINITY_DN5933_c0_g1_i1\tRL32A_SCHPO\t100.00\t127\t0\t0\t25\t405\t1\t127\t3e-87\t 261\n+TRINITY_DN5996_c0_g1_i1\tBAG1B_SCHPO\t100.00\t206\t0\t0\t221\t838\t1\t206\t5e-141\t 408\n+TRINITY_DN5955_c0_g1_i1\tYD52_SCHPO\t100.00\t135\t0\t0\t370\t774\t38\t172\t1e-90\t 275\n+TRINITY_DN5974_c0_g1_i1\tNU211_SCHPO\t99.43\t176\t1\t0\t530\t3\t153\t328\t2e-97\t 314\n+TRINITY_DN5939_c0_g1_i1\tCDT2_SCHPO\t100.00\t490\t0\t0\t44\t1513\t1\t490\t0.0\t 959\n+TRINITY_DN5905_c0_g1_i1\tPPME1_SCHPO\t100.00\t341\t0\t0\t233\t1255\t1\t341\t0.0\t 709\n+TRINITY_DN5926_c0_g1_i1\tYBQ3_SCHPO\t100.00\t368\t0\t0\t279\t1382\t1\t368\t0.0\t 714\n+TRINITY_DN5922_c0_g1_i1\tRT51_SCHPO\t100.00\t303\t0\t0\t59\t96'..b'1_i1\tMU151_SCHPO\t100.00\t66\t0\t0\t236\t39\t81\t146\t1e-42\t 141\n+TRINITY_DN5413_c0_g1_i1\tMYO51_SCHPO\t100.00\t96\t0\t0\t1\t288\t486\t581\t1e-60\t 205\n+TRINITY_DN5402_c0_g1_i1\tNOG2_SCHPO\t96.00\t50\t2\t0\t210\t61\t218\t267\t5e-26\t 103\n+TRINITY_DN5450_c0_g1_i1\tYDAA_SCHPO\t100.00\t144\t0\t0\t120\t551\t1\t144\t3e-102\t 301\n+TRINITY_DN5480_c0_g1_i1\tRS26B_SCHPO\t81.82\t55\t8\t1\t191\t27\t1\t53\t2e-10\t57.0\n+TRINITY_DN5482_c0_g1_i1\tCUT12_SCHPO\t100.00\t77\t0\t0\t233\t3\t248\t324\t3e-48\t 165\n+TRINITY_DN5405_c0_g1_i1\tIES4_SCHPO\t100.00\t69\t0\t0\t207\t1\t1\t69\t7e-41\t 141\n+TRINITY_DN5477_c0_g1_i1\tATF31_SCHPO\t100.00\t77\t0\t0\t232\t2\t89\t165\t1e-47\t 156\n+TRINITY_DN5460_c0_g1_i1\tTR852_SCHPO\t100.00\t79\t0\t0\t238\t2\t530\t608\t1e-49\t 169\n+TRINITY_DN5492_c0_g1_i1\tUS108_SCHPO\t100.00\t55\t0\t0\t170\t6\t283\t337\t5e-30\t 112\n+TRINITY_DN5425_c0_g1_i1\tGMH3_SCHPO\t100.00\t202\t0\t0\t608\t3\t39\t240\t5e-147\t 419\n+TRINITY_DN5404_c0_g1_i1\tYKCG_SCHPO\t100.00\t114\t0\t0\t342\t1\t198\t311\t2e-70\t 223\n+TRINITY_DN5494_c0_g1_i1\tALR1_SCHPO\t100.00\t73\t0\t0\t219\t1\t222\t294\t7e-44\t 150\n+TRINITY_DN5467_c0_g1_i1\tPSD3_SCHPO\t100.00\t102\t0\t0\t306\t1\t310\t411\t5e-62\t 207\n+TRINITY_DN5439_c0_g1_i1\tYAMB_SCHPO\t100.00\t75\t0\t0\t1\t225\t2495\t2569\t4e-46\t 163\n+TRINITY_DN5422_c0_g1_i1\tSLD3_SCHPO\t100.00\t61\t0\t0\t334\t152\t639\t699\t1e-32\t 124\n+TRINITY_DN5473_c0_g1_i1\tTCG1_SCHPO\t100.00\t181\t0\t0\t543\t1\t145\t325\t2e-89\t 272\n+TRINITY_DN5457_c0_g1_i1\tSHK2_SCHPO\t100.00\t67\t0\t0\t2\t202\t115\t181\t4e-40\t 142\n+TRINITY_DN5445_c0_g1_i1\tMUG42_SCHPO\t100.00\t72\t0\t0\t1\t216\t44\t115\t3e-45\t 146\n+TRINITY_DN5419_c0_g1_i1\tAPQ12_SCHPO\t100.00\t115\t0\t0\t88\t432\t1\t115\t5e-74\t 224\n+TRINITY_DN5409_c0_g1_i1\tPPID_SCHPO\t100.00\t201\t0\t0\t603\t1\t22\t222\t7e-135\t 389\n+TRINITY_DN5459_c0_g1_i1\tCWF19_SCHPO\t100.00\t102\t0\t0\t306\t1\t190\t291\t7e-50\t 171\n+TRINITY_DN5424_c0_g1_i1\tERF1_SCHPO\t100.00\t78\t0\t0\t236\t3\t267\t344\t1e-48\t 164\n+TRINITY_DN5464_c0_g1_i1\tYOP2_SCHPO\t100.00\t133\t0\t0\t447\t49\t523\t655\t2e-88\t 278\n+TRINITY_DN5458_c0_g1_i1\tWIN1_SCHPO\t100.00\t82\t0\t0\t625\t870\t1\t82\t2e-32\t 132\n+TRINITY_DN5491_c0_g1_i1\tPSD3_SCHPO\t100.00\t48\t0\t0\t145\t2\t634\t681\t2e-24\t 100\n+TRINITY_DN5488_c0_g1_i1\tYAMB_SCHPO\t100.00\t83\t0\t0\t3\t251\t1904\t1986\t3e-48\t 170\n+TRINITY_DN5456_c0_g1_i1\tRS27_SCHPO\t90.14\t71\t7\t0\t2\t214\t5\t75\t8e-42\t 137\n+TRINITY_DN5463_c0_g1_i1\tYKV5_SCHPO\t100.00\t73\t0\t0\t1\t219\t116\t188\t3e-44\t 154\n+TRINITY_DN5444_c0_g1_i1\tTOR1_SCHPO\t100.00\t67\t0\t0\t1\t201\t104\t170\t4e-37\t 137\n+TRINITY_DN5440_c0_g1_i1\tDLP1_SCHPO\t100.00\t213\t0\t0\t639\t1\t45\t257\t5e-146\t 416\n+TRINITY_DN5469_c0_g1_i1\tRT07_SCHPO\t75.00\t116\t0\t1\t349\t2\t106\t192\t9e-48\t 159\n+TRINITY_DN5410_c0_g1_i1\tRPA43_SCHPO\t100.00\t67\t0\t0\t202\t2\t1\t67\t1e-40\t 138\n+TRINITY_DN5441_c0_g1_i1\tRSC4_SCHPO\t100.00\t80\t0\t0\t242\t3\t142\t221\t1e-48\t 166\n+TRINITY_DN5441_c0_g1_i1\tRSC4_SCHPO\t43.66\t71\t40\t0\t215\t3\t18\t88\t7e-12\t64.3\n+TRINITY_DN5430_c0_g1_i1\tECM1_SCHPO\t100.00\t23\t0\t0\t145\t77\t85\t107\t5e-06\t44.3\n+TRINITY_DN5435_c0_g1_i1\tYFE9_SCHPO\t100.00\t91\t0\t0\t274\t2\t448\t538\t1e-58\t 195\n+TRINITY_DN5432_c0_g1_i1\tYHV5_SCHPO\t100.00\t85\t0\t0\t15\t269\t1\t85\t3e-57\t 179\n+TRINITY_DN5454_c0_g1_i1\tYO29_SCHPO\t100.00\t80\t0\t0\t240\t1\t43\t122\t2e-56\t 181\n+TRINITY_DN5472_c0_g1_i1\tYF11_SCHPO\t100.00\t31\t0\t0\t2\t94\t69\t99\t3e-14\t67.8\n+TRINITY_DN5497_c0_g1_i1\tSFR1_SCHPO\t100.00\t193\t0\t0\t3\t581\t40\t232\t3e-135\t 387\n+TRINITY_DN5426_c0_g1_i1\tPDC4_SCHPO\t100.00\t72\t0\t0\t218\t3\t443\t514\t6e-43\t 150\n+TRINITY_DN5468_c0_g1_i1\tCDC37_SCHPO\t98.91\t92\t1\t0\t280\t5\t209\t300\t6e-41\t 145\n+TRINITY_DN5434_c0_g1_i1\tGCST_SCHPO\t100.00\t79\t0\t0\t238\t2\t4\t82\t2e-49\t 165\n+TRINITY_DN5443_c0_g1_i1\tYCUB_SCHPO\t100.00\t81\t0\t0\t243\t1\t1\t81\t2e-46\t 162\n+TRINITY_DN5471_c0_g1_i1\tRRG1_SCHPO\t100.00\t38\t0\t0\t214\t101\t266\t303\t3e-21\t88.6\n+TRINITY_DN5407_c0_g1_i1\tCSK2B_SCHPO\t100.00\t27\t0\t0\t81\t1\t14\t40\t2e-14\t68.9\n+TRINITY_DN5498_c0_g1_i1\tSRP2_SCHPO\t100.00\t23\t0\t0\t213\t145\t22\t44\t9e-10\t56.2\n+TRINITY_DN5498_c0_g1_i1\tSRP2_SCHPO\t100.00\t12\t0\t0\t91\t56\t44\t55\t9e-10\t26.2\n+TRINITY_DN54_c0_g1_i1\tNG06_SCHPO\t100.00\t1315\t0\t0\t49\t3993\t1\t1315\t0.0\t 2686\n+TRINITY_DN54_c0_g2_i1\tNG06_SCHPO\t100.00\t1245\t0\t0\t49\t3783\t1\t1245\t0.0\t 2543\n+TRINITY_DN54_c0_g2_i1\tNG06_SCHPO\t93.67\t79\t3\t1\t3758\t3994\t1239\t1315\t2e-35\t 151\n+TRINITY_DN59_c0_g1_i1\tRNG3_SCHPO\t100.00\t297\t0\t0\t1950\t1060\t450\t746\t0.0\t 612\n' |
| b |
| diff -r 000000000000 -r 499d87c45612 test-data/tmhmm.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tmhmm.out Tue Nov 15 09:17:29 2016 -0500 |
| b |
| b'@@ -0,0 +1,136 @@\n+TRINITY_DN5404_c0_g1_i1|m.6938\tlen=114\tExpAA=0.04\tFirst60=0.04\tPredHel=0\tTopology=o\n+TRINITY_DN5409_c0_g1_i1|m.6942\tlen=201\tExpAA=0.00\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN540_c0_g1_i1|m.650\tlen=406\tExpAA=0.43\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN540_c0_g2_i1|m.651\tlen=515\tExpAA=0.26\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN540_c0_g2_i1|m.652\tlen=130\tExpAA=0.00\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN5419_c0_g1_i1|m.6941\tlen=115\tExpAA=44.94\tFirst60=5.32\tPredHel=2\tTopology=o54-76i88-110o\n+TRINITY_DN541_c0_g1_i1|m.731\tlen=711\tExpAA=0.22\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN541_c0_g1_i1|m.732\tlen=387\tExpAA=0.04\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN541_c0_g2_i1|m.735\tlen=128\tExpAA=0.81\tFirst60=0.81\tPredHel=0\tTopology=o\n+TRINITY_DN541_c0_g2_i1|m.734\tlen=387\tExpAA=0.04\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN5425_c0_g1_i1|m.6937\tlen=202\tExpAA=0.01\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN542_c0_g1_i1|m.686\tlen=450\tExpAA=0.00\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN542_c0_g2_i1|m.687\tlen=383\tExpAA=0.00\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN543_c0_g1_i1|m.700\tlen=105\tExpAA=0.90\tFirst60=0.06\tPredHel=0\tTopology=o\n+TRINITY_DN543_c0_g1_i1|m.699\tlen=131\tExpAA=0.00\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN543_c0_g2_i1|m.701\tlen=224\tExpAA=0.34\tFirst60=0.03\tPredHel=0\tTopology=o\n+TRINITY_DN5440_c0_g1_i1|m.6945\tlen=213\tExpAA=0.03\tFirst60=0.01\tPredHel=0\tTopology=o\n+TRINITY_DN5442_c0_g1_i1|m.6933\tlen=102\tExpAA=0.00\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN544_c0_g1_i1|m.764\tlen=640\tExpAA=1.51\tFirst60=0.58\tPredHel=0\tTopology=o\n+TRINITY_DN544_c0_g2_i1|m.766\tlen=116\tExpAA=0.01\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN544_c0_g2_i1|m.765\tlen=640\tExpAA=1.51\tFirst60=0.58\tPredHel=0\tTopology=o\n+TRINITY_DN5450_c0_g1_i1|m.6936\tlen=147\tExpAA=0.00\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN5459_c0_g1_i1|m.6943\tlen=102\tExpAA=0.00\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN545_c0_g1_i1|m.745\tlen=354\tExpAA=0.00\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN545_c0_g2_i1|m.746\tlen=355\tExpAA=0.00\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN5462_c0_g1_i1|m.6934\tlen=150\tExpAA=0.00\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN5464_c0_g1_i1|m.6944\tlen=149\tExpAA=11.47\tFirst60=11.47\tPredHel=0\tTopology=o\n+TRINITY_DN5467_c0_g1_i1|m.6939\tlen=102\tExpAA=0.00\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN546_c0_g1_i1|m.753\tlen=168\tExpAA=0.00\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN546_c0_g2_i1|m.754\tlen=593\tExpAA=0.01\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN5473_c0_g1_i1|m.6940\tlen=181\tExpAA=0.00\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN548_c0_g1_i1|m.741\tlen=606\tExpAA=0.08\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN548_c0_g2_i1|m.742\tlen=322\tExpAA=0.12\tFirst60=0.01\tPredHel=0\tTopology=o\n+TRINITY_DN5497_c0_g1_i1|m.6946\tlen=193\tExpAA=0.00\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN549_c0_g1_i1|m.608\tlen=461\tExpAA=140.37\tFirst60=0.90\tPredHel=6\tTopology=i247-269o284-302i309-331o346-368i381-403o428-450i\n+TRINITY_DN54_c0_g1_i1|m.8839\tlen=1331\tExpAA=1.20\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN54_c0_g2_i1|m.8842\tlen=1274\tExpAA=2.42\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN5900_c0_g1_i1|m.818\tlen=123\tExpAA=0.00\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN5901_c0_g1_i1|m.835\tlen=496\tExpAA=0.04\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN5903_c0_g1_i1|m.823\tlen=466\tExpAA=0.70\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN5904_c0_g1_i1|m.856\tlen=251\tExpAA=0.00\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN5905_c0_g1_i1|m.794\tlen=341\tExpAA=0.22\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN5905_c0_g1_i1|m.795\tlen=295\tExpAA=0.01\tFirst60=0.01\tPredHel=0\tTopology=o\n+TRINITY_DN5906_c0_g1_i1|m.815\tlen=577\tExpAA=10.54\tFirst60=10.25\tPredHel=0\tTopology=o\n+TRINITY_DN5906_c0_g1_i1|m.816\tlen=427\tExpAA=0.04\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN5907_c0_g1_i1|m.784\tlen=471\tExpAA=2.14\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN5908_c0_g1_i1|m.865\tlen=364\tExpAA=22.32\tFirst60'..b'pAA=20.04\tFirst60=0.46\tPredHel=0\tTopology=o\n+TRINITY_DN5951_c0_g1_i1|m.851\tlen=167\tExpAA=42.16\tFirst60=18.65\tPredHel=2\tTopology=o22-39i88-110o\n+TRINITY_DN5952_c0_g1_i1|m.858\tlen=409\tExpAA=2.69\tFirst60=0.31\tPredHel=0\tTopology=o\n+TRINITY_DN5953_c0_g1_i1|m.832\tlen=517\tExpAA=0.00\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN5954_c0_g1_i1|m.845\tlen=151\tExpAA=0.00\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN5955_c0_g1_i1|m.790\tlen=172\tExpAA=2.05\tFirst60=0.26\tPredHel=0\tTopology=o\n+TRINITY_DN5956_c0_g1_i1|m.833\tlen=360\tExpAA=0.00\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN5957_c0_g1_i1|m.846\tlen=478\tExpAA=0.00\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN5959_c0_g1_i1|m.821\tlen=696\tExpAA=0.09\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN595_c0_g1_i1|m.715\tlen=181\tExpAA=0.01\tFirst60=0.01\tPredHel=0\tTopology=o\n+TRINITY_DN595_c0_g2_i1|m.716\tlen=153\tExpAA=0.00\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN5962_c0_g1_i1|m.834\tlen=432\tExpAA=7.61\tFirst60=0.35\tPredHel=0\tTopology=o\n+TRINITY_DN5964_c0_g1_i1|m.859\tlen=660\tExpAA=0.02\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN5965_c0_g1_i1|m.801\tlen=645\tExpAA=4.17\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN5967_c0_g1_i1|m.819\tlen=179\tExpAA=70.91\tFirst60=29.67\tPredHel=4\tTopology=i13-30o34-53i92-114o118-140i\n+TRINITY_DN5968_c0_g1_i1|m.808\tlen=100\tExpAA=0.02\tFirst60=0.02\tPredHel=0\tTopology=o\n+TRINITY_DN5969_c0_g1_i1|m.864\tlen=610\tExpAA=0.01\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN596_c0_g1_i1|m.607\tlen=603\tExpAA=26.01\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN5970_c0_g1_i1|m.854\tlen=147\tExpAA=0.58\tFirst60=0.56\tPredHel=0\tTopology=i\n+TRINITY_DN5971_c0_g1_i1|m.831\tlen=308\tExpAA=0.03\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN5972_c0_g1_i1|m.803\tlen=426\tExpAA=0.00\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN5973_c0_g1_i1|m.843\tlen=397\tExpAA=0.29\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN5974_c0_g1_i1|m.792\tlen=176\tExpAA=0.00\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN5975_c0_g1_i1|m.804\tlen=189\tExpAA=69.61\tFirst60=23.34\tPredHel=3\tTopology=o15-37i120-142o152-174i\n+TRINITY_DN5976_c0_g1_i1|m.869\tlen=108\tExpAA=0.00\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN5977_c0_g1_i1|m.800\tlen=152\tExpAA=0.00\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN597_c0_g1_i1|m.662\tlen=412\tExpAA=0.03\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN597_c0_g2_i1|m.663\tlen=412\tExpAA=0.03\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN5980_c0_g1_i1|m.807\tlen=735\tExpAA=0.05\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN5982_c0_g1_i1|m.813\tlen=466\tExpAA=0.05\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN5983_c0_g1_i1|m.855\tlen=230\tExpAA=0.00\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN5985_c0_g1_i1|m.806\tlen=109\tExpAA=0.03\tFirst60=0.00\tPredHel=0\tTopology=i\n+TRINITY_DN5985_c0_g1_i1|m.805\tlen=388\tExpAA=0.14\tFirst60=0.13\tPredHel=0\tTopology=o\n+TRINITY_DN5989_c0_g1_i1|m.829\tlen=180\tExpAA=0.03\tFirst60=0.03\tPredHel=0\tTopology=o\n+TRINITY_DN598_c0_g1_i1|m.767\tlen=342\tExpAA=0.00\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN598_c0_g2_i1|m.768\tlen=165\tExpAA=0.02\tFirst60=0.02\tPredHel=0\tTopology=o\n+TRINITY_DN5991_c0_g1_i1|m.781\tlen=659\tExpAA=15.54\tFirst60=6.83\tPredHel=0\tTopology=o\n+TRINITY_DN5992_c0_g1_i1|m.853\tlen=417\tExpAA=0.06\tFirst60=0.01\tPredHel=0\tTopology=o\n+TRINITY_DN5994_c0_g1_i1|m.840\tlen=137\tExpAA=81.27\tFirst60=32.80\tPredHel=4\tTopology=i23-45o50-72i79-96o100-122i\n+TRINITY_DN5996_c0_g1_i1|m.789\tlen=206\tExpAA=13.03\tFirst60=13.02\tPredHel=0\tTopology=o\n+TRINITY_DN5997_c0_g1_i1|m.826\tlen=107\tExpAA=0.00\tFirst60=0.00\tPredHel=0\tTopology=i\n+TRINITY_DN5998_c0_g1_i1|m.811\tlen=265\tExpAA=0.00\tFirst60=0.00\tPredHel=0\tTopology=o\n+TRINITY_DN5999_c0_g1_i1|m.812\tlen=141\tExpAA=0.00\tFirst60=0.00\tPredHel=0\tTopology=i\n+TRINITY_DN599_c0_g1_i1|m.690\tlen=639\tExpAA=1.13\tFirst60=0.30\tPredHel=0\tTopology=o\n+TRINITY_DN599_c0_g2_i1|m.691\tlen=965\tExpAA=1.92\tFirst60=1.63\tPredHel=0\tTopology=o\n+TRINITY_DN59_c0_g1_i1|m.8862\tlen=297\tExpAA=6.01\tFirst60=4.93\tPredHel=0\tTopology=o\n+TRINITY_DN59_c0_g1_i1|m.8863\tlen=205\tExpAA=13.90\tFirst60=13.90\tPredHel=0\tTopology=o\n' |
| b |
| diff -r 000000000000 -r 499d87c45612 test-data/trinotate_annotation_report.xls --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trinotate_annotation_report.xls Tue Nov 15 09:17:29 2016 -0500 |
| [ |
| b'@@ -0,0 +1,249 @@\n+#gene_id\ttranscript_id\tsprot_Top_BLASTX_hit\tRNAMMER\tprot_id\tprot_coords\tsprot_Top_BLASTP_hit\tPfam\tSignalP\tTmHMM\teggnog\tKegg\tgene_ontology_blast\tgene_ontology_pfam\ttranscript\tpeptide\n+TRINITY_DN596_c0_g1\tTRINITY_DN596_c0_g1_i1\tYB92_SCHPO^YB92_SCHPO^Q:102-1910,H:1-603^100%ID^E:0^RecName: Full=Uncharacterized ubiquitin-like protein C1E8.02;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces\t.\tTRINITY_DN596_c0_g1_i1|m.607\t102-1913[+]\tYB92_SCHPO^YB92_SCHPO^Q:1-603,H:1-603^100%ID^E:0^RecName: Full=Uncharacterized ubiquitin-like protein C1E8.02;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces\tPF13881.3^Rad60-SLD_2^Ubiquitin-2 like Rad60 SUMO-like^5-77^E:0.0063`PF00240.20^ubiquitin^Ubiquitin family^6-77^E:1.7e-13\t.\t.\t.\tKEGG:spo:SPBC1E8.02\tGO:0005783^cellular_component^endoplasmic reticulum`GO:0005789^cellular_component^endoplasmic reticulum membrane`GO:0016021^cellular_component^integral component of membrane`GO:0032446^biological_process^protein modification by small protein conjugation\tGO:0005515^molecular_function^protein binding\t.\t.\n+TRINITY_DN549_c0_g1\tTRINITY_DN549_c0_g1_i1\tGAA1_SCHPO^GAA1_SCHPO^Q:2-1363,H:121-574^100%ID^E:0^RecName: Full=GPI transamidase component gaa1;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces\t.\tTRINITY_DN549_c0_g1_i1|m.608\t2-1387[+]\tGAA1_SCHPO^GAA1_SCHPO^Q:1-461,H:121-581^100%ID^E:0^RecName: Full=GPI transamidase component gaa1;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces\tPF04114.11^Gaa1^Gaa1-like, GPI transamidase component^2-434^E:1.5e-135\t.\tExpAA=140.37^PredHel=6^Topology=i247-269o284-302i309-331o346-368i381-403o428-450i\t.\tKEGG:spo:SPAC1002.11`KO:K05289\tGO:0005783^cellular_component^endoplasmic reticulum`GO:0042765^cellular_component^GPI-anchor transamidase complex`GO:0016255^biological_process^attachment of GPI anchor to protein\tGO:0016021^cellular_component^integral component of membrane`GO:0042765^cellular_component^GPI-anchor transamidase complex\t.\t.\n+TRINITY_DN594_c0_g1\tTRINITY_DN594_c0_g1_i1\tERG27_SCHPO^ERG27_SCHPO^Q:1275-349,H:46-338^94.82%ID^E:0^RecName: Full=3-keto-steroid reductase;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces\t.\tTRINITY_DN594_c0_g1_i1|m.612\t346-1275[-]\tERG27_SCHPO^ERG27_SCHPO^Q:1-309,H:46-338^94.82%ID^E:0^RecName: Full=3-keto-steroid reductase;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces\t.\t.\t.\t.\tKEGG:spo:SPBC1709.07`KO:K09827\tGO:0005789^cellular_component^endoplasmic reticulum membrane`GO:0000253^molecular_function^3-keto sterol reductase activity`GO:0006696^biological_process^ergosterol biosynthetic process\t.\t.\t.\n+TRINITY_DN594_c0_g2\tTRINITY_DN594_c0_g2_i1\tERG27_SCHPO^ERG27_SCHPO^Q:1207-680,H:46-205^90.91%ID^E:2e-141^RecName: Full=3-keto-steroid reductase;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces`ERG27_SCHPO^ERG27_SCHPO^Q:681-349,H:228-338^100%ID^E:2e-141^RecName: Full=3-keto-steroid reductase;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces\t.\tTRINITY_DN594_c0_g2_i1|m.614\t346-651[-]\tERG27_SCHPO^ERG27_SCHPO^Q:1-101,H:238-338^100%ID^E:7e-68^RecName: Full=3-keto-steroid reductase;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces\t.\t.\t'..b'C890.06;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces\tPF08801.8^Nucleoporin_N^Nup133 N terminal like^76-527^E:2.3e-90`PF03177.11^Nucleoporin_C^Non-repetitive/WGA-negative nucleoporin C-terminal^771-1204^E:1.9e-52\t.\t.\t.\tKEGG:spo:SPAC890.06`KO:K14312\tGO:0005737^cellular_component^cytoplasm`GO:0005635^cellular_component^nuclear envelope`GO:0005643^cellular_component^nuclear pore`GO:0017056^molecular_function^structural constituent of nuclear pore`GO:0006913^biological_process^nucleocytoplasmic transport`GO:0006407^biological_process^rRNA export from nucleus\t.\t.\t.\n+TRINITY_DN54_c0_g2\tTRINITY_DN54_c0_g2_i1\tNG06_SCHPO^NG06_SCHPO^Q:49-3783,H:1-1245^100%ID^E:0^RecName: Full=Probable nucleoporin C890.06;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces`NG06_SCHPO^NG06_SCHPO^Q:3758-3994,H:1239-1315^93.67%ID^E:2e-35^RecName: Full=Probable nucleoporin C890.06;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces\t.\tTRINITY_DN54_c0_g2_i1|m.8842\t1-3825[+]\tNG06_SCHPO^NG06_SCHPO^Q:17-1261,H:1-1245^100%ID^E:0^RecName: Full=Probable nucleoporin C890.06;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces\tPF08801.8^Nucleoporin_N^Nup133 N terminal like^76-527^E:2.1e-90`PF03177.11^Nucleoporin_C^Non-repetitive/WGA-negative nucleoporin C-terminal^771-1204^E:1.8e-52\t.\t.\t.\tKEGG:spo:SPAC890.06`KO:K14312\tGO:0005737^cellular_component^cytoplasm`GO:0005635^cellular_component^nuclear envelope`GO:0005643^cellular_component^nuclear pore`GO:0017056^molecular_function^structural constituent of nuclear pore`GO:0006913^biological_process^nucleocytoplasmic transport`GO:0006407^biological_process^rRNA export from nucleus\t.\t.\t.\n+TRINITY_DN59_c0_g1\tTRINITY_DN59_c0_g1_i1\tRNG3_SCHPO^RNG3_SCHPO^Q:1950-1060,H:450-746^100%ID^E:0^RecName: Full=Ring assembly protein 3;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces\t.\tTRINITY_DN59_c0_g1_i1|m.8862\t1057-1950[-]\tRNG3_SCHPO^RNG3_SCHPO^Q:1-297,H:450-746^100%ID^E:0^RecName: Full=Ring assembly protein 3;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces\t.\t.\t.\t.\tKEGG:spo:SPCC613.04c\tGO:0005826^cellular_component^actomyosin contractile ring`GO:0005829^cellular_component^cytosol`GO:0005634^cellular_component^nucleus`GO:0005844^cellular_component^polysome`GO:0043234^cellular_component^protein complex`GO:0017022^molecular_function^myosin binding`GO:0000917^biological_process^barrier septum assembly`GO:0034613^biological_process^cellular protein localization`GO:1903475^biological_process^mitotic actomyosin contractile ring assembly\t.\t.\t.\n+TRINITY_DN59_c0_g1\tTRINITY_DN59_c0_g1_i1\tRNG3_SCHPO^RNG3_SCHPO^Q:1950-1060,H:450-746^100%ID^E:0^RecName: Full=Ring assembly protein 3;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces\t.\tTRINITY_DN59_c0_g1_i1|m.8863\t2-619[+]\tYCS3_SCHPO^YCS3_SCHPO^Q:17-205,H:1-189^100%ID^E:3e-137^RecName: Full=Uncharacterized calcium-binding protein C613.03;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces\t.\t.\t.\t.\tKEGG:spo:SPCC613.03\tGO:0005737^cellular_component^cytoplasm`GO:0005783^cellular_component^endoplasmic reticulum`GO:0005788^cellular_component^endoplasmic reticulum lumen`GO:0005794^cellular_component^Golgi apparatus`GO:0005796^cellular_component^Golgi lumen`GO:0005509^molecular_function^calcium ion binding\t.\t.\t.\n' |
| b |
| diff -r 000000000000 -r 499d87c45612 test-data/trinotate_annotation_report_minus_tmhmm_signalp.xls --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trinotate_annotation_report_minus_tmhmm_signalp.xls Tue Nov 15 09:17:29 2016 -0500 |
| [ |
| b'@@ -0,0 +1,249 @@\n+#gene_id\ttranscript_id\tsprot_Top_BLASTX_hit\tRNAMMER\tprot_id\tprot_coords\tsprot_Top_BLASTP_hit\tPfam\tSignalP\tTmHMM\teggnog\tKegg\tgene_ontology_blast\tgene_ontology_pfam\ttranscript\tpeptide\n+TRINITY_DN596_c0_g1\tTRINITY_DN596_c0_g1_i1\tYB92_SCHPO^YB92_SCHPO^Q:102-1910,H:1-603^100%ID^E:0^RecName: Full=Uncharacterized ubiquitin-like protein C1E8.02;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces\t.\tTRINITY_DN596_c0_g1_i1|m.607\t102-1913[+]\tYB92_SCHPO^YB92_SCHPO^Q:1-603,H:1-603^100%ID^E:0^RecName: Full=Uncharacterized ubiquitin-like protein C1E8.02;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces\tPF13881.3^Rad60-SLD_2^Ubiquitin-2 like Rad60 SUMO-like^5-77^E:0.0063`PF00240.20^ubiquitin^Ubiquitin family^6-77^E:1.7e-13\t.\t.\t.\tKEGG:spo:SPBC1E8.02\tGO:0005783^cellular_component^endoplasmic reticulum`GO:0005789^cellular_component^endoplasmic reticulum membrane`GO:0016021^cellular_component^integral component of membrane`GO:0032446^biological_process^protein modification by small protein conjugation\tGO:0005515^molecular_function^protein binding\tTGTGATTCGTGCCGCTCAACATTTCTTCAAGTGATTCCTAACATTGCTGTACATTCTCTTGAAAAGCGTTTTAACCTTTTCAATTCTGAAACTTGTAAAGAATGTCAGAGTATCGTATTCGAGTGACAACTGTGGACCAGAAGGTTGGTATTTTTCAAGTTCCTAGGACAAAAACGGTTTTAGAATTAAAGGAACTGATTGCTGTAACATTTGAAGCTCCTGCAGATCGATTAAAGTTGATTCACGCTGGTCGTGTATTGAGGAATGAAACTCCCCTCGAGGAAATTTTGCATGACGCTACTGATCTGGTCACTTTTCATCTTGTAATTGCGGTTTTTAATTCTACAAGCACAACCTTGCCATCAGCGACATCATCTTCTGTTCCTCAAAGTAGGACCAGCGAATTATCATCGACTAATTCAATTCCAACTCCTCGAATCACCAGTTTGAACCCGGAAGAATTGTCAAGACGTGAACGTGCCCAACGTTTATTACAGACATACAACAGTTTCCATGGATCTGGCTTAGGAGGACTTTTTCCAAACATACACCGGGAACTAGAAAGTCACGGATTTTCATTGCCAACCCATGAGCAATCATCACCCGTTGCTGAATCTCTGGATAATTCGGTATCGTCTGCTTTATCTCCACATTTGGAAACGCTGCGTCGCCGCAATCTCAGTATTCATCATCAACATATACAAGCTCACGAAATGGCACAAGAGTCCTTGGAGACCAGAAATCCAGGAAACATTTCTTCCTCGAGTGCTCCTTTAGCTAGTGATCAATCCCCGACTGTATCATCTAACCATATCCATGCATCCGGTAATTTGGCTTTAGGATCAAATTCGGGGTTAAATCCACGAAGCCCTAATTCTTTTTCTTCCCCATTGGACAATCCTGCACTTCATACTGTTGACTCAACCAACGTCAATGGTTCGCTTTCACCTCTATCAAATTCTTCATCTATCAATCAAGTTCACCAAAATGAAACTCATGGTTCTACCATCTCAGTACCTAACCCGAACTTAAGTCAAATGGGCCCTTCACACTCTTCTTCTGTGCCCTCAAATCTGTCACCAAATCCTGCCCAAAATGAAAATCCTAGTACAACCTCTATTCCATCAATAAATAATCAACCATTCCCGTCTGGTCTTTCTGCTTCTAACTCTAATTTTGCCTCTTCCTCGTTTATCCCTCAGAGCGTTCCGCAACTATTGCCTATATATTATCAAACTATCTTTTACAACGGTAACTATTATTTACAGCAGCTCCCATCTGCATCGCCTCCCACTATGTTTCGAGATCACTCATTTGCTCCTTTAGTTTCCCCTTCTATTGTTTCTCCGTATGGTGTTTTAGAAAATGAAGAAACTGGCGAATGTGCCTTTTTGTTTTCACCAAATGCCTCCCAACCCCATTTTCAGCCGAGAGCCCCCACGTTTGGCATTCCACGAAATGTGAGATCCCTCTTCACCTTACCGTTCTTCCATACTATCCGTAATATTGAGAGACATTTCCGATTATTTATTCGTTTAGCCCTGTTTTGTGTATTAACGACTTATAATGTTTCTCTCTCACAAACAATTTTGCTAACATCTATAATGTCTGTTGTGTTTTTGTTACAGACCGGTGCTCTAGCTCCATTCATCAATGACAATCCACTCATCCAGTCTGGTATGCGTCATATTCGTAATCTTCAAGATGAATACCGGCGGCGTCGAAACCGAACGGCTCAAAGAGTAGTTGAAATTCCTAATGAGACACAGACTGAAGATGAACAAGATGGTACAAATACGCCGGATAATAGGGCTGACGCTGAAGAACGCGAACTAACTCGAAGTCAAAGAATATACCGGACGGTAGTAAGAACCATAGTTGCCTTCGCATTAAGCTTTGTACCTCGAGCGTAACATTTTTTTCTTAAAAACAAAAGTGATAATATAGCTGTAAAGTCATTTTTCATTACTAATTAGAAATATTGTCTAAGCTTGCTATTAATAAAAGAGTTCTAGCTAGACTAAATTTTGACAGTGTCGAAATATCATTCCAAGGTACCCCATCAGATTAACAAATTTATAA\tMSEYRIRVTTVDQKVGIFQVPRTKTVLELKELIAVTFEAPADRLKLIHAGRVLRNETPLEEILHDATDLVTFHLVIAVFNSTSTTLPSATSSSVPQSRTSELSSTNSIPTPRITSLNPEELSRRERAQRLLQTYNSFHGSGLGGLFPNIHRELESHGFSLPTHEQSSPVAESLDNSVSSALSPHLETLRRRNLSIHHQHIQAHEMAQESLETRNPGNISSSSAPLASDQSPTVSSNHIHASGNLALGSNSGLNPRSPNSFSSPLDNPALHTVDSTNVNGSLSPLSNSSSINQVHQNETHGSTISVPNPNLSQMGPSHSSSVPSNLSPNPAQNENPSTTSIPSINNQPFPSGLSASNSNFASSSFIPQSVPQLLPIYYQTIFYNGNYYLQQLPSASPPTMFRDHSFAPLVSPSIVSPYGVLENEETGECAFLFSPNASQPHFQPRAPTFGIPRNVRSLFTLPFFHTIRNIERHFRLFIRLALFCVLTTYNVSLSQTILLTSIMSVVFLLQTGALAPFINDNPLIQSGMRHIRNLQDEYRRRRNRTAQRVVEIPNETQTEDEQDGTNTPDNRADAEERELTRSQRIYRTVVRTIVAFALSFVPRA*\n+TRINITY_DN549_c0_g1\tTRINITY_DN549_c0_g1_i1\tGAA1'..b'CATCAACACTAGTAATTTGAACAAGAATTCCGCATGCTGCTAATCTCGTGGGAGTGTCTTCGGTATCTGAGAGTGCTAGTACAATGTGTAAACGAGTATTTTCAAAATCCGAGTCCTTGTCTCCTATAAACTTAATTAAGCAATAAGGTGATAAAGAAAGGTTGTTAATAAGTTCCGTGGTTGCCCTCTGAATTAAAGGATTTGTTTCTATAATTAGTTCATCCAATTCTCTCCAACATTCTTGAACTATGGCTTGCCGACTTTCTTCATCATGTGAAGCAAGATTTGTTAGCGCAAGTAACACTTCAAATTTCCCCAAGAGAATTGGATACTCAGTATCAGCAGAATTAGTACTTAGTAACTTTGACATAGGATGAATTGCTCGGTTCGATGGAAACGCCTTAGTAAATATACTATGAGGAGCCACACTGATAAGAATTTTCGCTAATGCAAAAGCCGCATTCGAATCCTGGGTTTGGATAAAACATTGTCTAGTAAGGAATTTCAATGCACCTATTTGTACTAGCTTGCGACGTGCCAGCTTGTAATTAGCCATGTGTACAAGTATCATTGCTAATAACCCGTTTAGGCTATTATAGTGCTTGGCCGCTGAAAAGAGTTTTGAC\tSKLFSAAKHYNSLNGLLAMILVHMANYKLARRKLVQIGALKFLTRQCFIQTQDSNAAFALAKILISVAPHSIFTKAFPSNRAIHPMSKLLSTNSADTEYPILLGKFEVLLALTNLASHDEESRQAIVQECWRELDELIIETNPLIQRATTELINNLSLSPYCLIKFIGDKDSDFENTRLHIVLALSDTEDTPTRLAACGILVQITSVDEGCKKILSLQNDFNYIVRMLTDQDEGIQHRGLVCICNIVYSKDQEIFNKFIKTPKAVETLRTYITKQAALKELQHEALVMIDSRLQGSK*\n+TRINITY_DN59_c0_g1\tTRINITY_DN59_c0_g1_i1\tRNG3_SCHPO^RNG3_SCHPO^Q:1950-1060,H:450-746^100%ID^E:0^RecName: Full=Ring assembly protein 3;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces\t.\tTRINITY_DN59_c0_g1_i1|m.8863\t2-619[+]\tYCS3_SCHPO^YCS3_SCHPO^Q:17-205,H:1-189^100%ID^E:3e-137^RecName: Full=Uncharacterized calcium-binding protein C613.03;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces\t.\t.\t.\t.\tKEGG:spo:SPCC613.03\tGO:0005737^cellular_component^cytoplasm`GO:0005783^cellular_component^endoplasmic reticulum`GO:0005788^cellular_component^endoplasmic reticulum lumen`GO:0005794^cellular_component^Golgi apparatus`GO:0005796^cellular_component^Golgi lumen`GO:0005509^molecular_function^calcium ion binding\t.\tAGAACTTGACCGCAGCGCACATCAACTACACCTTGAGGCAATTCAAAATATGAAGTTTTCTACCGTAGGGTTTTTGTTTTCAACAATTTTATTCAAAAGTGCGTTTGCAGGATGGATGGATACACACATGAAAGATGAACATCACATTGATAAGTACACAGATGAATCTTTTTTTCGTCTTCACGATTTAGGAAAAAAGGGATACTGGTCAGATCAAGATATACTTAGTTTATATGGATTATTTGAAAATGATGAGGTCCCATTCGTCAAAAAGAATGAGGTTTTGGTTGATGTTCTAAAAAAATGCGATCCATCGGGCAATCGCCGGATAACACTTGATGAATTTCTTGCATTTCGTAAAAATGGAGGAGAGTTAACGGATTTTGGATTTCCAGGGCACCATGGTGATGAGGAAGAGGAATTTGAAATGCATCATGTGGAAAAATATCACCCAGCTGGCCTCGATGAACCAGATGAAAACTGGAATCATCCTGAAGATATCGAACATTTTCAAAAACACGATGAGATATTTCATGGTGATAAGAAACCTGAGGAACGACGCAAACATTTTGTAAAATACAATAATATCCCTGACAAGTATCGTCGTGTGAGCATTTAAATTTTCCCATTGATAGATTTACTTGCTTCTCCTTGGGACGTTTTATTTTTATTTTTATTTTTCCGTTTATTTTTGGATTGTCGTGTTCCGATATATATCCGTGTTTACAAACAATAGCTTCAACATTTTTGAACGGGTCCTTCCAATACTAATGCCATATCTTATTTCTTTGTCAATACAAAATCACTTTTGTTCGTTAAACTCATTTTGGTTTGCAGATATTATCATATTCTTACCAATTATACATACACTCACAATTTGTTTTACATTTCCGCTCCCTTCTTCAATAAGCTGATTGCTTATAAAAAATCAAACATTCATATGATTCAAGTTCAAATATTATCATCTGAAAACTGACAAGTTCCATTCATTACTATATTAATATCATTTATTCGTTAAACCGATATCATTAAAAATGGAAAATTAAAGAAATCAATTCATTTGCTTCCTTGAAGTCTAGAGTCGATCATAACGAGAGCTTCATGTTGAAGCTCTTTAAGTGCAGCTTGCTTAGTAATATAAGTGCGTAATGTTTCAACAGCCTTTGGTGTTTTTATGAACTTGTTAAATATTTCTTGATCTTTGGAATATACGATATTGCATATGCAAACTAATCCACGATGTTGAATTCCTTCATCTTGGTCGGTTAACATTCTGACTATGTAGTTAAAATCGTTCTGGAGACTTAAAATTTTCTTGCACCCTTCATCAACACTAGTAATTTGAACAAGAATTCCGCATGCTGCTAATCTCGTGGGAGTGTCTTCGGTATCTGAGAGTGCTAGTACAATGTGTAAACGAGTATTTTCAAAATCCGAGTCCTTGTCTCCTATAAACTTAATTAAGCAATAAGGTGATAAAGAAAGGTTGTTAATAAGTTCCGTGGTTGCCCTCTGAATTAAAGGATTTGTTTCTATAATTAGTTCATCCAATTCTCTCCAACATTCTTGAACTATGGCTTGCCGACTTTCTTCATCATGTGAAGCAAGATTTGTTAGCGCAAGTAACACTTCAAATTTCCCCAAGAGAATTGGATACTCAGTATCAGCAGAATTAGTACTTAGTAACTTTGACATAGGATGAATTGCTCGGTTCGATGGAAACGCCTTAGTAAATATACTATGAGGAGCCACACTGATAAGAATTTTCGCTAATGCAAAAGCCGCATTCGAATCCTGGGTTTGGATAAAACATTGTCTAGTAAGGAATTTCAATGCACCTATTTGTACTAGCTTGCGACGTGCCAGCTTGTAATTAGCCATGTGTACAAGTATCATTGCTAATAACCCGTTTAGGCTATTATAGTGCTTGGCCGCTGAAAAGAGTTTTGAC\tELDRSAHQLHLEAIQNMKFSTVGFLFSTILFKSAFAGWMDTHMKDEHHIDKYTDESFFRLHDLGKKGYWSDQDILSLYGLFENDEVPFVKKNEVLVDVLKKCDPSGNRRITLDEFLAFRKNGGELTDFGFPGHHGDEEEEFEMHHVEKYHPAGLDEPDENWNHPEDIEHFQKHDEIFHGDKKPEERRKHFVKYNNIPDKYRRVSI*\n' |
| b |
| diff -r 000000000000 -r 499d87c45612 trinotate.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/trinotate.xml Tue Nov 15 09:17:29 2016 -0500 |
| [ |
| b'@@ -0,0 +1,216 @@\n+<tool id="trinotate" name="Trinotate" version="3.0.1.0">\n+ <requirements>\n+ <requirement type="package" version="3.0.1">trinotate</requirement>\n+ <requirement type="package" version="1.18">gnu-wget</requirement>\n+ </requirements>\n+ <stdio>\n+ <exit_code range="1:" />\n+ </stdio>\n+ <version_command>\n+ <![CDATA[\n+ Trinotate version 3.0.1\n+ ]]>\n+ </version_command>\n+ <command><![CDATA[\n+\n+#if str($cond_download.select_download) == "yes":\n+ wget --no-verbose \'https://data.broadinstitute.org/Trinity/Trinotate_v3_RESOURCES/Trinotate_v3.sqlite.gz\' -O Trinotate.sqlite.gz &&\n+ gunzip Trinotate.sqlite.gz &&\n+#else:\n+ ln -s \'$cond_download.trinotate_sqlite_in\' Trinotate.sqlite\n+#end if\n+\n+Trinotate Trinotate.sqlite init --gene_trans_map \'$gene_trans_map\' --transcript_fasta $trinity --transdecoder_pep \'$transdecoder\' &&\n+#if $blastp:\n+ Trinotate Trinotate.sqlite LOAD_swissprot_blastp \'$blastp\' &&\n+#end if\n+#if $blastx:\n+ Trinotate Trinotate.sqlite LOAD_swissprot_blastx \'$blastx\' &&\n+#end if\n+#if $hmmscan:\n+ Trinotate Trinotate.sqlite LOAD_pfam \'$hmmscan\' &&\n+#end if\n+#if $tmhmm:\n+ Trinotate Trinotate.sqlite LOAD_tmhmm \'$tmhmm\' &&\n+#end if\n+#if $signalp:\n+ Trinotate Trinotate.sqlite LOAD_signalp \'$signalp\' &&\n+#end if\n+\n+Trinotate Trinotate.sqlite report -E $report_option.E --pfam_cutoff $report_option.pfam_cutoff $report_option.incl_pep $report_option.incl_trans > \'$trinotate_out\';\n+\n+ ]]></command>\n+ <inputs>\n+ <param name="trinity" type="data" format="fasta" optional="false" label="Transcripts" help="Trinity output: Assembled Transcripts" />\n+ <param name="transdecoder" type="data" format="fasta" optional="false" label="Peptides" help="Transdecoder output: transdecoder_pep" />\n+ <param name="gene_trans_map" type="data" format="tabular" optional="false" label="Genes to transcripts map" help="Genes to transcripts map output. Containing correspondance between gene ids and transcript ids based on the name of transcripts assembled by Trinity" />\n+ <param name="blastp" type="data" format="tabular" optional="true" label="BLASTP: Peptides vs Uniprot.SwissProt" help="[optional] NCBI BLAST+ blastp output. Output format: Tabular (standard 12 columns)" />\n+ <param name="blastx" type="data" format="tabular" optional="true" label="BLASTX: Transcripts vs Uniprot.SwissProt" help="[optional] NCBI BLAST+ blastx output. Output format: Tabular (standard 12 columns)" />\n+ <param name="hmmscan" type="data" format="txt" optional="true" label="HMMER hmmscan: Peptides vs PFAM" help="[optional] HMMER hmmscan output: Table of per-domain hits. Output format: Table of per-domain hits (--domtblout)" />\n+ <param name="tmhmm" type="data" format="tabular" optional="true" label="TMHMM on Peptides" help="[optional]"/>\n+ <param name="signalp" type="data" format="tabular" optional="true" label="SignalP on Peptides" help="[optional]" /> \n+\n+ <conditional name="cond_download">\n+ <param name="select_download" type="select" label="Let Galaxy downloading the Trinotate Pre-generated Resource SQLite database">\n+ <option value="yes" selected="True">Yes</option>\n+ <option value="no">No, I will provide it</option>\n+ </param>\n+ <when value="no">\n+ <param name="trinotate_sqlite_in" type="data" format="sqlite" optional="false" label="Trinotate Pre-generated Resource SQLite database" help="https://data.broadinstitute.org/Trinity/Trinotate_v3_RESOURCES/Trinotate_v3.sqlite.gz" />\n+ </when>\n+ <when value="yes" />\n+ </conditional>\n+ \n+ <section name="report_option" title="Report options" expanded="False">\n+ <param argument="-E" type="float" value="1e-5" label="Maximum E-value for reporting best blast hit and associated annotations." />\n+ <param argument="--pfam_cutoff"'..b'_trans_map" ftype="tabular" value="Trinity.fasta.gene_to_trans_map" />\n+ <param name="blastp" ftype="tabular" value="swissprot.blastp.outfmt6" />\n+ <param name="blastx" ftype="tabular" value="swissprot.blastx.outfmt6" />\n+ <param name="hmmscan" ftype="txt" value="TrinotatePFAM.out" />\n+ <section name="report_option">\n+ <param name="incl_pep" value="true" />\n+ <param name="incl_trans" value="true" />\n+ </section>\n+ <param name="keep_sqlite" value="true" />\n+ <output name="trinotate_out" file="trinotate_annotation_report_minus_tmhmm_signalp.xls" />\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+.. class:: infomark\n+\n+**What it does**\n+\n+Trinotate_ is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Trinotate makes use of a number of different well referenced methods for functional annotation including homology search to known sequence data (BLAST+/SwissProt), protein domain identification (HMMER/PFAM), protein signal peptide and transmembrane domain prediction (signalP/tmHMM), and leveraging various annotation databases (eggNOG/GO/Kegg databases). All functional annotation data derived from the analysis of transcripts is integrated into a SQLite database which allows fast efficient searching for terms with specific qualities related to a desired scientific hypothesis or a means to create a whole annotation report for a transcriptome.\n+\n+.. _Trinotate: https://trinotate.github.io/\n+\n+--------\n+\n+**Suggested upstream Galaxy tools**\n+\n+Transcripts\n+\n+ - Trinity: iuc/trinity_\n+\n+.. _trinity: https://toolshed.g2.bx.psu.edu/repository?repository_id=faf6028922d9220a\n+\n+Peptides\n+\n+ - TransDecoder: iuc/transdecoder_\n+\n+.. _transdecoder: https://toolshed.g2.bx.psu.edu/repository?repository_id=7a2a8151a50f8099\n+\n+Genes to transcripts map\n+\n+ - Generate gene to transcript map for Trinity assembly: iuc/trinity_gene_to_trans_map_\n+\n+.. _trinity_gene_to_trans_map: https://toolshed.g2.bx.psu.edu/repository?repository_id=faf6028922d9220a\n+\n+BLASTP: Peptides vs Uniprot.SwissProt\n+\n+ - NCBI BLAST+ blastp: devteam/ncbi_blast_plus_\n+\n+.. _ncbi_blast_plus: https://toolshed.g2.bx.psu.edu/repository?repository_id=1d92ebdf7e8d466c\n+\n+BLASTX: Transcripts vs Uniprot.SwissProt\n+\n+ - NCBI BLAST+ blastx: devteam/ncbi_blast_plus_\n+\n+.. _ncbi_blast_plus: https://toolshed.g2.bx.psu.edu/repository?repository_id=1d92ebdf7e8d466c\n+\n+HMMER hmmscan: Peptides vs PFAM\n+\n+ - HMMER hmmscan: iuc/hmmer_hmmscan_\n+\n+.. _hmmer_hmmscan: https://toolshed.g2.bx.psu.edu/repository?repository_id=a2cc4683090b1800\n+\n+TMHMM on Peptides\n+\n+ - TMHMM 2.0: peterjc/tmhmm_and_signalp_\n+\n+.. _tmhmm_and_signalp: https://toolshed.g2.bx.psu.edu/repository?repository_id=292389a45f1a238a\n+\n+SignalP on Peptides\n+\n+ - SignalP 3.0: peterjc/tmhmm_and_signalp_\n+\n+.. _tmhmm_and_signalp: https://toolshed.g2.bx.psu.edu/repository?repository_id=292389a45f1a238a\n+\n+\n+Trinotate Pre-generated Resource SQLite database\n+\n+- You can provide the SQLite database yourself, if Galaxy have trouble to download it : https://data.broadinstitute.org/Trinity/Trinotate_v3_RESOURCES/Trinotate_v3.sqlite.gz\n+\n+--------\n+\n+**Output**\n+\n+The output has the following column headers:\n+\n+\n+====== =======================\n+Column Description\n+------ -----------------------\n+ 0 #gene_id\n+ 1 transcript_id\n+ 2 sprot_Top_BLASTX_hit\n+ 3 RNAMMER\n+ 4 prot_id\n+ 5 prot_coords\n+ 6 sprot_Top_BLASTP_hit\n+ 7 custom_pombe_pep_BLASTX\n+ 8 custom_pombe_pep_BLASTP\n+ 9 Pfam\n+ 10 SignalP\n+ 11 TmHMM\n+ 12 eggnog\n+ 13 Kegg\n+ 14 gene_ontology_blast\n+ 15 gene_ontology_pfam\n+ 16 transcript\n+ 17 peptide\n+====== =======================\n+\n+ ]]></help>\n+ <citations>\n+ <citation type="doi">10.1038/nbt.1883</citation>\n+ </citations>\n+</tool>\n' |