| Next changeset 1:1de64ee71145 (2016-06-28) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d |
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added:
test-data/gencode/test.fa.transdecoder.bed test-data/gencode/test.fa.transdecoder.cds test-data/gencode/test.fa.transdecoder.gff3 test-data/gencode/test.fa.transdecoder.mRNA test-data/gencode/test.fa.transdecoder.pep test-data/raw/test.fa.transdecoder.bed test-data/raw/test.fa.transdecoder.cds test-data/raw/test.fa.transdecoder.gff3 test-data/raw/test.fa.transdecoder.mRNA test-data/raw/test.fa.transdecoder.pep test-data/strand/test.fa.transdecoder.bed test-data/strand/test.fa.transdecoder.cds test-data/strand/test.fa.transdecoder.gff3 test-data/strand/test.fa.transdecoder.mRNA test-data/strand/test.fa.transdecoder.pep test-data/test.fa test-data/top/test.fa.transdecoder.bed test-data/top/test.fa.transdecoder.cds test-data/top/test.fa.transdecoder.gff3 test-data/top/test.fa.transdecoder.mRNA test-data/top/test.fa.transdecoder.pep tool_dependencies.xml transdecoder.xml |
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| diff -r 000000000000 -r 8aef9a17faae test-data/gencode/test.fa.transdecoder.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gencode/test.fa.transdecoder.bed Fri Nov 20 06:49:25 2015 -0500 |
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| @@ -0,0 +1,7 @@ +track name='dataset_13.dat.transdecoder.gff3' +CUFF.36.1 0 1498 ID=CUFF.36.1|m.5;CUFF.36.1|g.5;ORF_CUFF.36.1|g.5_CUFF.36.1|m.5_type:complete_len:169_(+) 0 + 894 1401 0 1 1498 0 +CUFF.4.1 0 555 ID=CUFF.4.1|m.7;CUFF.4.1|g.7;ORF_CUFF.4.1|g.7_CUFF.4.1|m.7_type:3prime_partial_len:120_(+) 0 + 198 555 0 1 555 0 +CUFF.51.1 0 4342 ID=CUFF.51.1|m.2;CUFF.51.1|g.2;ORF_CUFF.51.1|g.2_CUFF.51.1|m.2_type:complete_len:347_(+) 0 + 316 1357 0 1 4342 0 +CUFF.51.1 0 4342 ID=CUFF.51.1|m.1;CUFF.51.1|g.1;ORF_CUFF.51.1|g.1_CUFF.51.1|m.1_type:complete_len:372_(+) 0 + 2631 3747 0 1 4342 0 +CUFF.57.1 0 3853 ID=CUFF.57.1|m.4;CUFF.57.1|g.4;ORF_CUFF.57.1|g.4_CUFF.57.1|m.4_type:complete_len:1032_(+) 0 + 188 3284 0 1 3853 0 +CUFF.9.1 0 804 ID=CUFF.9.1|m.8;CUFF.9.1|g.8;ORF_CUFF.9.1|g.8_CUFF.9.1|m.8_type:complete_len:156_(+) 0 + 172 640 0 1 804 0 |
| b |
| diff -r 000000000000 -r 8aef9a17faae test-data/gencode/test.fa.transdecoder.cds --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gencode/test.fa.transdecoder.cds Fri Nov 20 06:49:25 2015 -0500 |
| b |
| @@ -0,0 +1,118 @@ +>CUFF.36.1|m.5 CUFF.36.1|g.5 ORF CUFF.36.1|g.5 CUFF.36.1|m.5 type:complete len:169 (+) CUFF.36.1:895-1401(+) +ATGTCGCAAGACTCAGAATCGTTCATCCGGCAACTGTTTAAGGCATTTACGGATTTTAGT +ACTGACGTTGAGTCACTTAGAGGATTTTTAACGCCAGATTATCGACAGCTTGTCGATGGA +CGTGAATTGACACTTGACGATTTTATTTCTCATGCCAAAGCACTACGTACCCATCTTCAT +CGGCTCGACATCAACGTTCAACAAATTGTCTGTCAAGGTAACAAGGCTGCCACTGTGCAT +ATTGCCCATGCGATACGTTCCTCTGGCGAGTCCAGCAGAATCAAAGTCATTGCATTTTAC +AGTTTTAAAGACGGGCGTATTTCTTTGATCGATGAGTTGACGTACGTTCTTGAAGGTGGT +AATGCAGACAGAGAGCTTGGATCAGTACAATGACTTCAATTACCTTGACACTGCATTGCC +CACGTTATTCAACGTCCATCAGGAACCGGACAAATTATTCAGAGTCCTTTTGAACTACTT +CATAATTTTACAAATATTCAAGTGTAA +>CUFF.4.1|m.7 CUFF.4.1|g.7 ORF CUFF.4.1|g.7 CUFF.4.1|m.7 type:3prime_partial len:120 (+) CUFF.4.1:199-555(+) +ATGACTGCATTAATGAACCATATATATATCGATAATCCGCTTATAAGCAATTCAACTAAT +AACGTTACTCACGAGTTATTGATTGATCTCCATGAACTTTATAATGACGGAGAGATTTCC +AGGATAGTTCTACTCAGAACTTTGGTAACTCAATCTGCGGATGATGCTACATGGATAATC +AACTTGACAGATGATGTGCTTAATGGATTACCACTGCTGAAGAAGCGAGACCGATACACC +ACACAATGTCATAGTACAAATATGGCAAGCACATATGACTGTGACACTGGAGCCAATGCT +GTTGGAGCCCGAGGTGGAGCCACGTTAGCAGCCGACTATAGAGGTGATTGGGGGGGG +>CUFF.51.1|m.2 CUFF.51.1|g.2 ORF CUFF.51.1|g.2 CUFF.51.1|m.2 type:complete len:347 (+) CUFF.51.1:317-1357(+) +ATGGCACTTATGTTATCCAGGATTCCACGTCGTTTTTTTTTCTTATTTTTAACGGTCGGC +TTGATTGCTGGCGCGTTTCTATACTCGTTGATATATTTTGTGGACGTTGATTTGGTGTCG +AAGGTTAACCAGTTGTATGATCAGCAAATTGCACCCATGCTCTCCGATGCTATTGGCACT +CCATCCGTTAATCACTCGTTTGAGTTGGCGCCGTTAGACTCTCATTTGGTGGCCACAAGC +ACTACATTCCACGAGGCGTCATACGAGTCAGAGCCTCAGCAAAATCCTGCCAGTCAAAAT +ATTGTCTTATTACTAGTTAGTGATGGACACACTTCTTACAATAATGGAGCTAATACGTTT +GAAGAAGCTATACAGAACAGAGTTGACTATAGTACCAAACAAAACTACAACTTTGAGTAT +GTCAATGTTACTGGCCTCCCTATTCCCGCCGTTTGGTCCAAGATGCCCGCCGTCTTACAA +ACTATGAAGAAATACCCCAAAGCGGAATGGATCTGGTTGTTGGATCAGGATGCAATTATT +ACTAATACCCATCTTTCCCTTCAAGACTCCTTTTTGAAACCTGAGAACTTGCAAAAGACC +TTAATTACTAATACCATCCTCACTAAACGGCCTATAAATGCTAACGGGGATTTGCGTTAT +ACACCAAGTAATTATAGTTTAAAAGATATCGAAAATCTCATGGTCATAATCTCACAGGAT +CACAATGGATTAAACGCAGGTAGTATCTTGTTCCGTAATTCACCTGCTACTGCCTTGTTT +TTGGATATTTGGACAGATCCTGTTGTTGCAGAATGTGCGAAAGCCAATAATGAACAAGAC +ATGCTTGGATATTTGATTTCTAAGCATTCACAACTTGCTTCGCTGGTTGGCCTTATTCCT +CAAAGAAAAATAAATGCTTTTCACGAAGGTCCGGAAAATATGGAATGGCAAAAAGGTGAT +TTGGTAATTCACTTTGCTGGATGTTGGGTTGAAAACCGCTGCGATGAACTATGGCAAAAG +TTTTACGCCTTGATTGACTAA +>CUFF.51.1|m.1 CUFF.51.1|g.1 ORF CUFF.51.1|g.1 CUFF.51.1|m.1 type:complete len:372 (+) CUFF.51.1:2632-3747(+) +ATGTCTCGAATTTCACTTTCAAATTTTTTATCTCTTCCGCGTTACAAATTCCTGTTGTTT +TCTGTGGTTTTGATTATTGTGATGACAACCTTAGTGTTTAACGGACACGATTATAAGCAA +ACCCTTAATGACCGGCTTACTTCATTAAAAAACAACTTTGTTGAGGAAAATGATAATGCC +GTCTTAAAAGAAGAGCCTGGCAAATATACGTATATGAGTTTGTTTACTATGCCTTCTACT +GAAGAGGATTACTACTTCAACGCTACTAGGGTTTTAATTCACCGATTGAAATATCATCCT +ACTACCAAAAGTAAATACCCTATCCATATCCTTGCACTCCGTGGAGTAGATGAGTGGAAA +ATTGAACGTTTTCGAAAGGATGGTGCTTCTGTGATTGTTATAGACCCCATTGCTTCATCG +GATATTGTATACGATACATCCTCATTTAGTCAAGAAATATCTGCTAGATATGAACAAATG +TTTTCGAAGTTGCGAATTTTCGAACAAATACAATTTGACAAAATTTGCGTAATTGACAGT +GATATATTGATCATGAAGAACATTGATGATATATTTGATACTCCTTATATGTACCAACAA +ATTAATACCTTGAACTATACACGGCTACCTTCCTACACGAAGCCTGATGATGATACCGTC +TATCACTTCAATGAGGATTTTAAAGAATATGGTGCCAGTCGAAGCGAATTTTACCCTTAT +CTTCTCGCAGCCGTCTCTGATAGAGGAGAGCATCATAGTATACCTCCAGAAGATACTCCT +TATTTCAATGCTGGCTTAATGCTTATACGTCCAAGCGAGCTTCATTTTAACCGTATACTT +AAAATCGGAAGGTTTCCTTATATGTATGAGAATGCCAAAATGATGGAGCAAAGCTTGTTG +AATCTTGCATTTTCCTTGGACGGATGGTTTCCCTGGACTCGTCTTGATCCTTATTACAAT +GGCGTGTGGCCCTCAATTGACGAACGTCCTCTCTTAAAAACAGCACACGGAAAATTCTGG +AATATTGGTAGCTCAGAATTTGCACCAGTATATTTAGCTGACTGGTATGCTGCTTATGGC +GAAATGCTGTCTTTTCATAAGTATGAAACTCATTAA +>CUFF.57.1|m.4 CUFF.57.1|g.4 ORF CUFF.57.1|g.4 CUFF.57.1|m.4 type:complete len:1032 (+) CUFF.57.1:189-3284(+) +ATGTTCGATAGCTTTATGAAGAGAAATCAGCTAGCCTTAATCATGTTTCGTGCTTGCTCG +AAGTTGCAGTACCATGGAGTAAATACCAGCCTTTCGAGGCATTTGTTTCTTGCTAAAAGA +AATTTATCCATTTCTTCAGCTTGTCTAGAAGCTAAAAACTCCCAAAAGTTTCCTGCTCTT +GATACTTTTGAACCTCGACACATTGGACCTTCTAAAACGGATCAACAATATCAATTGGAG +TCACTAGGGTATAAGGATTTTGATTCTTTCCTCAAAGATGTAATTCCAGATTCTGTGCGA +ACACCTGAGAGCCAATTGATGGCTTTTGGGTCTGTGAATCCCAACGAAAAAAATCCTCCT +GTTAACTACTCCGAAAGCGAATTTACGACTCTGGCAAACAATGTGGCTAATCAAAATAAG +CTGATTAAGAGCTTCATTGGCATGGGATACTATAATGTAAAGCTTCCTGCTGCTATTCAG +CGTAATGTTCTTGAGAACCCTGAATGGTATACTCAATATACTCCATATCAGGCTGAAATT +TCTCAAGGGCGTCTGGAATCTATGATGAATTATCAAACCATGATTGCTGATCTCACAGGT +CTCAGCATTAGCAATGCTAGTTTACTGGATGAAGGAACTGCTGCTGGAGAAGCAATGGTT +ATGTTGATGGCCAACGACAAAAAGAAGCGCAAAACGTTTTTAGTGGACAAGAATATATAC +CCCAATACTCTGTCTGTTTTACGTACTCGTGCTTCTGGTTTTGGTATCAAAATTGAATTA +GACAATATCACTCCTGAACTCATTACGAAGTCTGCTAAGCATGTTTTTGGTATCTTTGTG +CAATACCCAGCGGCGGATGGCTCTATTTTTGACTATGGTCATTTAGCTGCTACAGCACGC +TCTTTTAATATGCACGTCGTAGCTGCCACCGATTTACTAGCTCTCACTATTTTGAAATCG +CCTGGGGAATGGGGTGCCGATGTTGCTGTTGGTTCCACTCAGCGCTTTGGTCTGCCCATG +GGCTATGGTGGCCCCCATGCCGGATTCTTTGCTTGTAGTGAAGAATTTAAACGAAAGATA +CCCGGTCGTCTTATTGGTCTCAGCAAAGATCGTTTAGAAAATCCCGCATACCGGTTGGCT +CTTCAAACAAGAGAACAACATATTCGTCGTGAAAAGGCTACAAGTAACATTTGCACGGCT +CAAGCTTTGTTAGCCAATATGTCTGCATTCTATGCTATTTACCATGGGCCAAATGGTCTC +CAAGAAATTGCAAACCGTATTTACGCTAGTACCTCCTTCTTAAAATCTGCTTTGGAATCT +TCAGGATATAAAATTGTTAATAAAAGTCATTTCTTTGACACATTAACTATCGAAGTTGAG +TCGGCTGACAAAGTTCTTGCGAAAGCACTTGATCACGGTTACAATTTAAGAAAGGTTGAT +GATTCACATGTTGGTCTTTCATTGGACGAGACCGTTTGCGATAAAGATATTCAAGCTTTG +TTTAGCATCTTTAATATAAATAAGAGTGTTGATCAGTATTATATGGAAATTGCAACGTCG +GAACCTAATGGAAATTCTGCTTCAACAGTCGATAATCTCAGCATTTGTTCTCTTCCTGAA +AACTTTAGACGAACAACCCTCTATTTACAACATCCCGTGTTTAACAGATACCATTCGGAA +ACTGAACTTATGCGTTATATTCATCATTTGCAGTCGAAGGATCTATCTTTAGCTCATGCC +ATGACCCCATTGGGTTCGTGCACAATGAAGTTGAATGCTGTCACCGAAATGATGCCAATC +ACAAATCCATTATTTGCCAACATTCATCCATATGTTCCAGAGGAACAAGCTAAAGGTTAT +CGTCATGTTATCGAAGATTTGCAGTTAATGTTAACGACCATCACCGGCTTTGATGCTGCA +TGCTTTCAACCAAATTCGGGAGCCGCTGGAGAATACACTGGCTTAAGTGTTATTCGAGCA +TATCAGCGGTCTATTGGTCAAGGTCATCGCAATATTTGCTTAATTCCTGTTTCGGCTCAC +GGTACTAATCCAGCTTCAGCTGCTATGGCTGGGTTTACTGTTATTCCTGTAAAATGTCTC +AATAACGGTTATTTGGATATGCAAGACTTAAAAGAAAAGGCCTCTAAACACGCCGACAAG +TTAGCTGCCTTTATGGTAACTTATCCTAGTACTTTTGGCATTTTTGAGCCTGATGTTAAG +GAAGCTTTGGAAGTAATTCACGAACATGGTGGTCAGGTTTACTTTGATGGTGCTAACATG +AATGCAATGGTTGGTTTATGCAAGGCTGGTGATATTGGTGCTGATGTTTGTCACTTAAAT +CTTCATAAGACATTTTGCATTCCTCACGGCGGTGGCGGTCCTGGTGTAGGTCCTATTTGT +GTAAAAAAGCATCTTGCTGATTTCCTACCATCTCATCCTGTAGTTTCATGCGGCGGTAAG +AATGGTATCACATCTGTTAGCTCTTCTCCTTTTGGCTCTGCTGGTATTTTACCTATCTCA +TGGGCATACATGAGAATGATGGGACTTGCCGGTTTGCGTGACGCTTCCAAAGCCGCTCTG +TTAAATGCCAATTATATGGCCAAGCGCCTGTCATCTCATTATAAACTTGTTTACACTAAT +AAGAACAACCTCTGTGCTCATGAGTTTATTCTAGATGCTCGCGAATTTAAAGCTACTGCG +GGTGTAGATGCAACTGATATAGCTAAACGTTTGCAAGATTACAGTTTCCATGCACCAACT +CTTTCCTGGCCTATTGCTAATACACTGATGATTGAGCCTACCGAGTCTGAGAGTATGTAT +GAGATGGACCGCTTCTGTGATGCTTTAATTTCTATTCGACAAGAAATTCGTGAAATTGAA +GAAGGTCTCCAGCCTAAGGACAATAACCTGCTCGTTAATGCTCCCCACCCTCAAAAGGAC +ATTGCATCTGAGAAATGGGATCGTCCTTATACTCGAGAGCGGGCTGTCTATCCTGTGCCT +CTTTTAAAGGAACGGAAATTCTGGCCTAGCGTTGCTCGATTAGATGATGCGTACGGTGAC +AAGAACTTATTTTGTACTTGTTCCCCAGTTGTTTAG +>CUFF.9.1|m.8 CUFF.9.1|g.8 ORF CUFF.9.1|g.8 CUFF.9.1|m.8 type:complete len:156 (+) CUFF.9.1:173-640(+) +ATGCCTATCAACCAAAAGTTTTATTCATATCTGGTAAAGCGAAATGGTGGTGAAGGTGAA +CCTGAATTTCGACTTCCTATGGGTTTTATTGGAATCACACTTTTTGAAATAGGAATTTTA +CTTTTCGGTTGGACTGCAAGATATAAGATTTTTTGGTTTGTGCCAACAATTGGATCAGCC +ATTATGGGTGGTGGGTACATTATGACTTCCAATCCCTTAAACATGTATGTGGTAGATTCA +TATGGAATTTACTCAGCCAGTGCGTCAGCGGGTGTAAAAATATTTCAACTATTATTAGGA +GCCATCTTTCCATTATTTGCTGAAAGTCTATTTCGTCGACTGAACTACGGATGGGGGTGT +ACTTTACTTGCCTTTATTTTATTAGCTTGTGGCTGTAGTCTTCCAATCTTATTCAAGTAT +GGAAAACAAATTAGAAATCTACGACCATTTGACCCCTCAAAATACTAG |
| b |
| diff -r 000000000000 -r 8aef9a17faae test-data/gencode/test.fa.transdecoder.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gencode/test.fa.transdecoder.gff3 Fri Nov 20 06:49:25 2015 -0500 |
| b |
| @@ -0,0 +1,41 @@ +CUFF.36.1 transdecoder gene 1 1498 . + . ID=CUFF.36.1|g.5;Name=ORF%20CUFF.36.1%7Cg.5%20CUFF.36.1%7Cm.5%20type%3Acomplete%20len%3A169%20%28%2B%29 +CUFF.36.1 transdecoder mRNA 1 1498 . + . ID=CUFF.36.1|m.5;Parent=CUFF.36.1|g.5;Name=ORF%20CUFF.36.1%7Cg.5%20CUFF.36.1%7Cm.5%20type%3Acomplete%20len%3A169%20%28%2B%29 +CUFF.36.1 transdecoder five_prime_UTR 1 894 . + . ID=CUFF.36.1|m.5.utr5p1;Parent=CUFF.36.1|m.5 +CUFF.36.1 transdecoder exon 1 1498 . + . ID=CUFF.36.1|m.5.exon1;Parent=CUFF.36.1|m.5 +CUFF.36.1 transdecoder CDS 895 1401 . + . ID=cds.CUFF.36.1|m.5;Parent=CUFF.36.1|m.5 +CUFF.36.1 transdecoder three_prime_UTR 1402 1498 . + . ID=CUFF.36.1|m.5.utr3p1;Parent=CUFF.36.1|m.5 + +CUFF.4.1 transdecoder gene 1 555 . + . ID=CUFF.4.1|g.7;Name=ORF%20CUFF.4.1%7Cg.7%20CUFF.4.1%7Cm.7%20type%3A3prime_partial%20len%3A120%20%28%2B%29 +CUFF.4.1 transdecoder mRNA 1 555 . + . ID=CUFF.4.1|m.7;Parent=CUFF.4.1|g.7;Name=ORF%20CUFF.4.1%7Cg.7%20CUFF.4.1%7Cm.7%20type%3A3prime_partial%20len%3A120%20%28%2B%29 +CUFF.4.1 transdecoder five_prime_UTR 1 198 . + . ID=CUFF.4.1|m.7.utr5p1;Parent=CUFF.4.1|m.7 +CUFF.4.1 transdecoder exon 1 555 . + . ID=CUFF.4.1|m.7.exon1;Parent=CUFF.4.1|m.7 +CUFF.4.1 transdecoder CDS 199 555 . + . ID=cds.CUFF.4.1|m.7;Parent=CUFF.4.1|m.7 + +CUFF.51.1 transdecoder gene 1 4342 . + . ID=CUFF.51.1|g.1;Name=ORF%20CUFF.51.1%7Cg.1%20CUFF.51.1%7Cm.1%20type%3Acomplete%20len%3A372%20%28%2B%29 +CUFF.51.1 transdecoder mRNA 1 4342 . + . ID=CUFF.51.1|m.1;Parent=CUFF.51.1|g.1;Name=ORF%20CUFF.51.1%7Cg.1%20CUFF.51.1%7Cm.1%20type%3Acomplete%20len%3A372%20%28%2B%29 +CUFF.51.1 transdecoder five_prime_UTR 1 2631 . + . ID=CUFF.51.1|m.1.utr5p1;Parent=CUFF.51.1|m.1 +CUFF.51.1 transdecoder exon 1 4342 . + . ID=CUFF.51.1|m.1.exon1;Parent=CUFF.51.1|m.1 +CUFF.51.1 transdecoder CDS 2632 3747 . + . ID=cds.CUFF.51.1|m.1;Parent=CUFF.51.1|m.1 +CUFF.51.1 transdecoder three_prime_UTR 3748 4342 . + . ID=CUFF.51.1|m.1.utr3p1;Parent=CUFF.51.1|m.1 + +CUFF.51.1 transdecoder gene 1 4342 . + . ID=CUFF.51.1|g.2;Name=ORF%20CUFF.51.1%7Cg.2%20CUFF.51.1%7Cm.2%20type%3Acomplete%20len%3A347%20%28%2B%29 +CUFF.51.1 transdecoder mRNA 1 4342 . + . ID=CUFF.51.1|m.2;Parent=CUFF.51.1|g.2;Name=ORF%20CUFF.51.1%7Cg.2%20CUFF.51.1%7Cm.2%20type%3Acomplete%20len%3A347%20%28%2B%29 +CUFF.51.1 transdecoder five_prime_UTR 1 316 . + . ID=CUFF.51.1|m.2.utr5p1;Parent=CUFF.51.1|m.2 +CUFF.51.1 transdecoder exon 1 4342 . + . ID=CUFF.51.1|m.2.exon1;Parent=CUFF.51.1|m.2 +CUFF.51.1 transdecoder CDS 317 1357 . + . ID=cds.CUFF.51.1|m.2;Parent=CUFF.51.1|m.2 +CUFF.51.1 transdecoder three_prime_UTR 1358 4342 . + . ID=CUFF.51.1|m.2.utr3p1;Parent=CUFF.51.1|m.2 + +CUFF.57.1 transdecoder gene 1 3853 . + . ID=CUFF.57.1|g.4;Name=ORF%20CUFF.57.1%7Cg.4%20CUFF.57.1%7Cm.4%20type%3Acomplete%20len%3A1032%20%28%2B%29 +CUFF.57.1 transdecoder mRNA 1 3853 . + . ID=CUFF.57.1|m.4;Parent=CUFF.57.1|g.4;Name=ORF%20CUFF.57.1%7Cg.4%20CUFF.57.1%7Cm.4%20type%3Acomplete%20len%3A1032%20%28%2B%29 +CUFF.57.1 transdecoder five_prime_UTR 1 188 . + . ID=CUFF.57.1|m.4.utr5p1;Parent=CUFF.57.1|m.4 +CUFF.57.1 transdecoder exon 1 3853 . + . ID=CUFF.57.1|m.4.exon1;Parent=CUFF.57.1|m.4 +CUFF.57.1 transdecoder CDS 189 3284 . + . ID=cds.CUFF.57.1|m.4;Parent=CUFF.57.1|m.4 +CUFF.57.1 transdecoder three_prime_UTR 3285 3853 . + . ID=CUFF.57.1|m.4.utr3p1;Parent=CUFF.57.1|m.4 + +CUFF.9.1 transdecoder gene 1 804 . + . ID=CUFF.9.1|g.8;Name=ORF%20CUFF.9.1%7Cg.8%20CUFF.9.1%7Cm.8%20type%3Acomplete%20len%3A156%20%28%2B%29 +CUFF.9.1 transdecoder mRNA 1 804 . + . ID=CUFF.9.1|m.8;Parent=CUFF.9.1|g.8;Name=ORF%20CUFF.9.1%7Cg.8%20CUFF.9.1%7Cm.8%20type%3Acomplete%20len%3A156%20%28%2B%29 +CUFF.9.1 transdecoder five_prime_UTR 1 172 . + . ID=CUFF.9.1|m.8.utr5p1;Parent=CUFF.9.1|m.8 +CUFF.9.1 transdecoder exon 1 804 . + . ID=CUFF.9.1|m.8.exon1;Parent=CUFF.9.1|m.8 +CUFF.9.1 transdecoder CDS 173 640 . + . ID=cds.CUFF.9.1|m.8;Parent=CUFF.9.1|m.8 +CUFF.9.1 transdecoder three_prime_UTR 641 804 . + . ID=CUFF.9.1|m.8.utr3p1;Parent=CUFF.9.1|m.8 + |
| b |
| diff -r 000000000000 -r 8aef9a17faae test-data/gencode/test.fa.transdecoder.mRNA --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gencode/test.fa.transdecoder.mRNA Fri Nov 20 06:49:25 2015 -0500 |
| b |
| b'@@ -0,0 +1,266 @@\n+>CUFF.36.1|m.5 CUFF.36.1|g.5 ORF CUFF.36.1|g.5 CUFF.36.1|m.5 type:complete len:169 (+) CUFF.36.1:895-1401(+)\n+TGACTAAGTGGCAATGATGCTCCTAATGAAACCACTGATCCTCGATCATCAGCAGTAGTA\n+TCAATAGCAGCATCAGCACCGTTAGACAGCTGTTTTTCTAAACCATTCAATGATTCATCT\n+GAAAAACGTGAACCCACTTTCGAATAGTGCTTTTCAAATTTCTTTCCCGTAATTAAGGAA\n+AGTAAATCCATGTGCAGTTAGTATTGAAAAGGAAAGAATAAATAAAAGTGGGTCAAAAGT\n+AACGCCAAACAAACGAAGGTTATCGAAATATATGCGAAGGAGAGATTTATATACTAGTCA\n+AATTTAAACAGCTGAGATTGCTTTAGTCATCGCGTTGTTCCAGATCGTGAACGAAAACAC\n+CGATTCGCTCGCTAAAGTAGATACGAAATGTCCAGCAGATTTTGCTTAATTAAAACATAA\n+ATATTGATGAGCAAGAGCAGCTCGTTATAAATCAGACCTCCAAGGATTTTATCAACTACT\n+CAACTGGTTATGTGAATAATGACTCAGTTAAATATTAAATGTACTCTAAACGGTTATCAT\n+ACAATTTATTAGGAGGATTATACCAGCTAGTAGGAATTTAACCATTTCAAATTTAAACCT\n+CTTTTTTTTCGTAACTTGGGGTCGTCATAATGAATAATTCTGTTTGTCGAATTTGAAGGG\n+AAAAACACACTTGTTATCTAATTCCAAAAAAAAATAAAAAATTTTTAAAAATTAGTGGGG\n+TTTTTTTTTCACCAATGTCTAATGATGTGTGATTTAAAAAAAAACGTGTGTAACGCATTG\n+TAGTATTACTTACCTTTGCATGATTAAAAGTATATGTTGATATCGACTATTTAGAGTACT\n+GTGCGACACATTACCCTATGTTTCCCACTCTTAATCACCAAAAATTTTTTCCGAATGTCG\n+CAAGACTCAGAATCGTTCATCCGGCAACTGTTTAAGGCATTTACGGATTTTAGTACTGAC\n+GTTGAGTCACTTAGAGGATTTTTAACGCCAGATTATCGACAGCTTGTCGATGGACGTGAA\n+TTGACACTTGACGATTTTATTTCTCATGCCAAAGCACTACGTACCCATCTTCATCGGCTC\n+GACATCAACGTTCAACAAATTGTCTGTCAAGGTAACAAGGCTGCCACTGTGCATATTGCC\n+CATGCGATACGTTCCTCTGGCGAGTCCAGCAGAATCAAAGTCATTGCATTTTACAGTTTT\n+AAAGACGGGCGTATTTCTTTGATCGATGAGTTGACGTACGTTCTTGAAGGTGGTAATGCA\n+GACAGAGAGCTTGGATCAGTACAATGACTTCAATTACCTTGACACTGCATTGCCCACGTT\n+ATTCAACGTCCATCAGGAACCGGACAAATTATTCAGAGTCCTTTTGAACTACTTCATAAT\n+TTTACAAATATTCAAGTGTAATTCGTAATATAATCAGTTTTATTCATCTTCGTTGTCTAA\n+AACTTTTATGTGCTGCAATATTTGGGGAATCTCGATTTGACATAATGATCCCAGTGCC\n+>CUFF.4.1|m.7 CUFF.4.1|g.7 ORF CUFF.4.1|g.7 CUFF.4.1|m.7 type:3prime_partial len:120 (+) CUFF.4.1:199-555(+)\n+CTCTTTTTAATATTTTACCGATGAGATTGCTATTATTAGTTACGTTGCTATCTATCGTTG\n+GTTACACTAATCAGTTGCTTTCCAACTGACCTCGAAGACGCTCCAGCTGTAATCTGGGTA\n+GCCCAATTTCCTCCAGATAACACTACACAGCACTATGAATTCAGATATATCGTAAATGAA\n+TTATATAATGCTAGCAAGATGACTGCATTAATGAACCATATATATATCGATAATCCGCTT\n+ATAAGCAATTCAACTAATAACGTTACTCACGAGTTATTGATTGATCTCCATGAACTTTAT\n+AATGACGGAGAGATTTCCAGGATAGTTCTACTCAGAACTTTGGTAACTCAATCTGCGGAT\n+GATGCTACATGGATAATCAACTTGACAGATGATGTGCTTAATGGATTACCACTGCTGAAG\n+AAGCGAGACCGATACACCACACAATGTCATAGTACAAATATGGCAAGCACATATGACTGT\n+GACACTGGAGCCAATGCTGTTGGAGCCCGAGGTGGAGCCACGTTAGCAGCCGACTATAGA\n+GGTGATTGGGGGGGG\n+>CUFF.51.1|m.1 CUFF.51.1|g.1 ORF CUFF.51.1|g.1 CUFF.51.1|m.1 type:complete len:372 (+) CUFF.51.1:2632-3747(+)\n+CGACGTTAATAAAATATTTAACAAAGCCTTTAAAAAATTAACGATAGCTAGTCAAAGGAA\n+GCTTAACGCGTATTCAGCCTCATTAAGACAATCAGGAAGCTTTTTTTTACCATCAGCATA\n+TACCTCTAACCCTTTGATTTATTTTTATATCTCGAGATTTCGTTCGTTATTTTATAGGTC\n+GTTTCGATAAGACCTTAATACAATCTGATTTAGTGGTTGTTTAAGATTTCGGAAAAGCCT\n+TTTTTTCAAAAAAAGTTTTCCAGTTATTGTTTCATTATTTCTAATTGATTTACTGAAGAA\n+TTGTTATAACCTAAAGATGGCACTTATGTTATCCAGGATTCCACGTCGTTTTTTTTTCTT\n+ATTTTTAACGGTCGGCTTGATTGCTGGCGCGTTTCTATACTCGTTGATATATTTTGTGGA\n+CGTTGATTTGGTGTCGAAGGTTAACCAGTTGTATGATCAGCAAATTGCACCCATGCTCTC\n+CGATGCTATTGGCACTCCATCCGTTAATCACTCGTTTGAGTTGGCGCCGTTAGACTCTCA\n+TTTGGTGGCCACAAGCACTACATTCCACGAGGCGTCATACGAGTCAGAGCCTCAGCAAAA\n+TCCTGCCAGTCAAAATATTGTCTTATTACTAGTTAGTGATGGACACACTTCTTACAATAA\n+TGGAGCTAATACGTTTGAAGAAGCTATACAGAACAGAGTTGACTATAGTACCAAACAAAA\n+CTACAACTTTGAGTATGTCAATGTTACTGGCCTCCCTATTCCCGCCGTTTGGTCCAAGAT\n+GCCCGCCGTCTTACAAACTATGAAGAAATACCCCAAAGCGGAATGGATCTGGTTGTTGGA\n+TCAGGATGCAATTATTACTAATACCCATCTTTCCCTTCAAGACTCCTTTTTGAAACCTGA\n+GAACTTGCAAAAGACCTTAATTACTAATACCATCCTCACTAAACGGCCTATAAATGCTAA\n+CGGGGATTTGCGTTATACACCAAGTAATTATAGTTTAAAAGATATCGAAAATCTCATGGT\n+CATAATCTCACAGGATCACAATGGATTAAACGCAGGTAGTATCTTGTTCCGTAATTCACC\n+TGCTACTGCCTTGTTTTTGGATATTTGGACAGATCCTGTTGTTGCAGAATGTGCGAAAGC\n+CAATAATGAACAAGACATGCTTGGATATTTGATTTCTAAGCATTCACAACTTGCTTCGCT\n+GGTTGGCCTTATTCCTCAAAGAAAAATAAATGCTTTTCACGAAGGTCCGGAAAATATGGA\n+ATGGCAAAAAGGTGATTTGGTAATTCACTTTGCTGGATGTTGGGTTGAAAACCGCTGCGA\n+TGAACTATGGCAAAAGTTTTACGCCTTGATTGACTAAGTTGCTTATTCATTATATCCGTC\n+TGTTTAATTTGTTTGTGTTTTAAAAAATTTTATATATATAAACAAAGCGCCGTATAATTT\n+TCCGTCAATCTTCCTTTCTTTATCTGAATCTCTAA'..b'GGACAAGA\n+ATATATACCCCAATACTCTGTCTGTTTTACGTACTCGTGCTTCTGGTTTTGGTATCAAAA\n+TTGAATTAGACAATATCACTCCTGAACTCATTACGAAGTCTGCTAAGCATGTTTTTGGTA\n+TCTTTGTGCAATACCCAGCGGCGGATGGCTCTATTTTTGACTATGGTCATTTAGCTGCTA\n+CAGCACGCTCTTTTAATATGCACGTCGTAGCTGCCACCGATTTACTAGCTCTCACTATTT\n+TGAAATCGCCTGGGGAATGGGGTGCCGATGTTGCTGTTGGTTCCACTCAGCGCTTTGGTC\n+TGCCCATGGGCTATGGTGGCCCCCATGCCGGATTCTTTGCTTGTAGTGAAGAATTTAAAC\n+GAAAGATACCCGGTCGTCTTATTGGTCTCAGCAAAGATCGTTTAGAAAATCCCGCATACC\n+GGTTGGCTCTTCAAACAAGAGAACAACATATTCGTCGTGAAAAGGCTACAAGTAACATTT\n+GCACGGCTCAAGCTTTGTTAGCCAATATGTCTGCATTCTATGCTATTTACCATGGGCCAA\n+ATGGTCTCCAAGAAATTGCAAACCGTATTTACGCTAGTACCTCCTTCTTAAAATCTGCTT\n+TGGAATCTTCAGGATATAAAATTGTTAATAAAAGTCATTTCTTTGACACATTAACTATCG\n+AAGTTGAGTCGGCTGACAAAGTTCTTGCGAAAGCACTTGATCACGGTTACAATTTAAGAA\n+AGGTTGATGATTCACATGTTGGTCTTTCATTGGACGAGACCGTTTGCGATAAAGATATTC\n+AAGCTTTGTTTAGCATCTTTAATATAAATAAGAGTGTTGATCAGTATTATATGGAAATTG\n+CAACGTCGGAACCTAATGGAAATTCTGCTTCAACAGTCGATAATCTCAGCATTTGTTCTC\n+TTCCTGAAAACTTTAGACGAACAACCCTCTATTTACAACATCCCGTGTTTAACAGATACC\n+ATTCGGAAACTGAACTTATGCGTTATATTCATCATTTGCAGTCGAAGGATCTATCTTTAG\n+CTCATGCCATGACCCCATTGGGTTCGTGCACAATGAAGTTGAATGCTGTCACCGAAATGA\n+TGCCAATCACAAATCCATTATTTGCCAACATTCATCCATATGTTCCAGAGGAACAAGCTA\n+AAGGTTATCGTCATGTTATCGAAGATTTGCAGTTAATGTTAACGACCATCACCGGCTTTG\n+ATGCTGCATGCTTTCAACCAAATTCGGGAGCCGCTGGAGAATACACTGGCTTAAGTGTTA\n+TTCGAGCATATCAGCGGTCTATTGGTCAAGGTCATCGCAATATTTGCTTAATTCCTGTTT\n+CGGCTCACGGTACTAATCCAGCTTCAGCTGCTATGGCTGGGTTTACTGTTATTCCTGTAA\n+AATGTCTCAATAACGGTTATTTGGATATGCAAGACTTAAAAGAAAAGGCCTCTAAACACG\n+CCGACAAGTTAGCTGCCTTTATGGTAACTTATCCTAGTACTTTTGGCATTTTTGAGCCTG\n+ATGTTAAGGAAGCTTTGGAAGTAATTCACGAACATGGTGGTCAGGTTTACTTTGATGGTG\n+CTAACATGAATGCAATGGTTGGTTTATGCAAGGCTGGTGATATTGGTGCTGATGTTTGTC\n+ACTTAAATCTTCATAAGACATTTTGCATTCCTCACGGCGGTGGCGGTCCTGGTGTAGGTC\n+CTATTTGTGTAAAAAAGCATCTTGCTGATTTCCTACCATCTCATCCTGTAGTTTCATGCG\n+GCGGTAAGAATGGTATCACATCTGTTAGCTCTTCTCCTTTTGGCTCTGCTGGTATTTTAC\n+CTATCTCATGGGCATACATGAGAATGATGGGACTTGCCGGTTTGCGTGACGCTTCCAAAG\n+CCGCTCTGTTAAATGCCAATTATATGGCCAAGCGCCTGTCATCTCATTATAAACTTGTTT\n+ACACTAATAAGAACAACCTCTGTGCTCATGAGTTTATTCTAGATGCTCGCGAATTTAAAG\n+CTACTGCGGGTGTAGATGCAACTGATATAGCTAAACGTTTGCAAGATTACAGTTTCCATG\n+CACCAACTCTTTCCTGGCCTATTGCTAATACACTGATGATTGAGCCTACCGAGTCTGAGA\n+GTATGTATGAGATGGACCGCTTCTGTGATGCTTTAATTTCTATTCGACAAGAAATTCGTG\n+AAATTGAAGAAGGTCTCCAGCCTAAGGACAATAACCTGCTCGTTAATGCTCCCCACCCTC\n+AAAAGGACATTGCATCTGAGAAATGGGATCGTCCTTATACTCGAGAGCGGGCTGTCTATC\n+CTGTGCCTCTTTTAAAGGAACGGAAATTCTGGCCTAGCGTTGCTCGATTAGATGATGCGT\n+ACGGTGACAAGAACTTATTTTGTACTTGTTCCCCAGTTGTTTAGCGGTCAAAAAGAGCTC\n+ACCTGCTAGATTACTTCAACCTTTTCCCAGTTAAGTTCAACCTAATTTTTACTCCATTTG\n+GTAGTTCGTTCAACACCAATTCCCACGTTTATATATAGACCAATTTTTTACTACATCTTG\n+TTAGACAATTCTTTCCGTTATCACTTTTTCGAATTTTTTTTAATTACGTTTTAATTTTGA\n+AGGTTAGAATTATCCTTTGCTGGAACATGAGGTTTTCAACAACCTTTTTTTAATCTGATA\n+ATCTAATTTTGCTAGTCATATAATTGCGACTTTCTGATAAAAACATTACCTATACTTTAT\n+AAATATGTCGTTTTTAAATATTAACTCCTATGTCTTACTTGCATCCTTGAAATTTACGAC\n+TAGAAATTTGGTGCTTTGGATTTTCGTTACATTAAGTAAGGCCATTGAATCGATATGACA\n+CGTAAATGTTAAATTTCAAAATATTTTGGAGAGCACCATGTATAATTTAAATATACGAAT\n+TTTTTCCTTTAAATTTGTGGTTCTTTTTTAAAAAATATCAAGACGAGTACTCGATTACTC\n+GTAAGTATTCAAG\n+>CUFF.9.1|m.8 CUFF.9.1|g.8 ORF CUFF.9.1|g.8 CUFF.9.1|m.8 type:complete len:156 (+) CUFF.9.1:173-640(+)\n+AGCGAAACAAACAAATCACGTTATAGACGGTGGCAGGGCCATAAAAGGTATTCCCTCGCT\n+TTAAAAAGAAACAATGTCAAAAAGCTTTCTTTATAAACTATTGGAAGATTGAAGACATTA\n+AAGAAGAAAAGTCCTGCTTACCCTTGGACTTTTTTCAGCAGTTTTCATTGCCATGCCTAT\n+CAACCAAAAGTTTTATTCATATCTGGTAAAGCGAAATGGTGGTGAAGGTGAACCTGAATT\n+TCGACTTCCTATGGGTTTTATTGGAATCACACTTTTTGAAATAGGAATTTTACTTTTCGG\n+TTGGACTGCAAGATATAAGATTTTTTGGTTTGTGCCAACAATTGGATCAGCCATTATGGG\n+TGGTGGGTACATTATGACTTCCAATCCCTTAAACATGTATGTGGTAGATTCATATGGAAT\n+TTACTCAGCCAGTGCGTCAGCGGGTGTAAAAATATTTCAACTATTATTAGGAGCCATCTT\n+TCCATTATTTGCTGAAAGTCTATTTCGTCGACTGAACTACGGATGGGGGTGTACTTTACT\n+TGCCTTTATTTTATTAGCTTGTGGCTGTAGTCTTCCAATCTTATTCAAGTATGGAAAACA\n+AATTAGAAATCTACGACCATTTGACCCCTCAAAATACTAGTTGATTTAACTGATCAAAGT\n+GAGGATTTTCACACACATTTTCAGAGTACTTGGAACGTGCCGAGCTGATTAAAAAACACC\n+GGTATTAACAAAAAATTTTATTTATGAAGCAATACGCTATTTCGTTATGAGAAACTTGAT\n+TCAATGAAACTATTATAAACCTTA\n' |
| b |
| diff -r 000000000000 -r 8aef9a17faae test-data/gencode/test.fa.transdecoder.pep --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gencode/test.fa.transdecoder.pep Fri Nov 20 06:49:25 2015 -0500 |
| b |
| @@ -0,0 +1,45 @@ +>CUFF.36.1|m.5 CUFF.36.1|g.5 ORF CUFF.36.1|g.5 CUFF.36.1|m.5 type:complete len:169 (+) CUFF.36.1:895-1401(+) +MSQDSESFIRQLFKAFTDFSTDVESLRGFLTPDYRQLVDGRELTLDDFISHAKALRTHLH +RLDINVQQIVCQGNKAATVHIAHAIRSSGESSRIKVIAFYSFKDGRISLIDELTYVLEGG +NADRELGSVQ*LQLP*HCIAHVIQRPSGTGQIIQSPFELLHNFTNIQV* +>CUFF.4.1|m.7 CUFF.4.1|g.7 ORF CUFF.4.1|g.7 CUFF.4.1|m.7 type:3prime_partial len:120 (+) CUFF.4.1:199-555(+) +MTALMNHIYIDNPLISNSTNNVTHELLIDLHELYNDGEISRIVLLRTLVTQSADDATWII +NLTDDVLNGLPLLKKRDRYTTQCHSTNMASTYDCDTGANAVGARGGATLAADYRGDWGG +>CUFF.51.1|m.2 CUFF.51.1|g.2 ORF CUFF.51.1|g.2 CUFF.51.1|m.2 type:complete len:347 (+) CUFF.51.1:317-1357(+) +MALMLSRIPRRFFFLFLTVGLIAGAFLYSLIYFVDVDLVSKVNQLYDQQIAPMLSDAIGT +PSVNHSFELAPLDSHLVATSTTFHEASYESEPQQNPASQNIVLLLVSDGHTSYNNGANTF +EEAIQNRVDYSTKQNYNFEYVNVTGLPIPAVWSKMPAVLQTMKKYPKAEWIWLLDQDAII +TNTHLSLQDSFLKPENLQKTLITNTILTKRPINANGDLRYTPSNYSLKDIENLMVIISQD +HNGLNAGSILFRNSPATALFLDIWTDPVVAECAKANNEQDMLGYLISKHSQLASLVGLIP +QRKINAFHEGPENMEWQKGDLVIHFAGCWVENRCDELWQKFYALID* +>CUFF.51.1|m.1 CUFF.51.1|g.1 ORF CUFF.51.1|g.1 CUFF.51.1|m.1 type:complete len:372 (+) CUFF.51.1:2632-3747(+) +MSRISLSNFLSLPRYKFLLFSVVLIIVMTTLVFNGHDYKQTLNDRLTSLKNNFVEENDNA +VLKEEPGKYTYMSLFTMPSTEEDYYFNATRVLIHRLKYHPTTKSKYPIHILALRGVDEWK +IERFRKDGASVIVIDPIASSDIVYDTSSFSQEISARYEQMFSKLRIFEQIQFDKICVIDS +DILIMKNIDDIFDTPYMYQQINTLNYTRLPSYTKPDDDTVYHFNEDFKEYGASRSEFYPY +LLAAVSDRGEHHSIPPEDTPYFNAGLMLIRPSELHFNRILKIGRFPYMYENAKMMEQSLL +NLAFSLDGWFPWTRLDPYYNGVWPSIDERPLLKTAHGKFWNIGSSEFAPVYLADWYAAYG +EMLSFHKYETH* +>CUFF.57.1|m.4 CUFF.57.1|g.4 ORF CUFF.57.1|g.4 CUFF.57.1|m.4 type:complete len:1032 (+) CUFF.57.1:189-3284(+) +MFDSFMKRNQLALIMFRACSKLQYHGVNTSLSRHLFLAKRNLSISSACLEAKNSQKFPAL +DTFEPRHIGPSKTDQQYQLESLGYKDFDSFLKDVIPDSVRTPESQLMAFGSVNPNEKNPP +VNYSESEFTTLANNVANQNKLIKSFIGMGYYNVKLPAAIQRNVLENPEWYTQYTPYQAEI +SQGRLESMMNYQTMIADLTGLSISNASLLDEGTAAGEAMVMLMANDKKKRKTFLVDKNIY +PNTLSVLRTRASGFGIKIELDNITPELITKSAKHVFGIFVQYPAADGSIFDYGHLAATAR +SFNMHVVAATDLLALTILKSPGEWGADVAVGSTQRFGLPMGYGGPHAGFFACSEEFKRKI +PGRLIGLSKDRLENPAYRLALQTREQHIRREKATSNICTAQALLANMSAFYAIYHGPNGL +QEIANRIYASTSFLKSALESSGYKIVNKSHFFDTLTIEVESADKVLAKALDHGYNLRKVD +DSHVGLSLDETVCDKDIQALFSIFNINKSVDQYYMEIATSEPNGNSASTVDNLSICSLPE +NFRRTTLYLQHPVFNRYHSETELMRYIHHLQSKDLSLAHAMTPLGSCTMKLNAVTEMMPI +TNPLFANIHPYVPEEQAKGYRHVIEDLQLMLTTITGFDAACFQPNSGAAGEYTGLSVIRA +YQRSIGQGHRNICLIPVSAHGTNPASAAMAGFTVIPVKCLNNGYLDMQDLKEKASKHADK +LAAFMVTYPSTFGIFEPDVKEALEVIHEHGGQVYFDGANMNAMVGLCKAGDIGADVCHLN +LHKTFCIPHGGGGPGVGPICVKKHLADFLPSHPVVSCGGKNGITSVSSSPFGSAGILPIS +WAYMRMMGLAGLRDASKAALLNANYMAKRLSSHYKLVYTNKNNLCAHEFILDAREFKATA +GVDATDIAKRLQDYSFHAPTLSWPIANTLMIEPTESESMYEMDRFCDALISIRQEIREIE +EGLQPKDNNLLVNAPHPQKDIASEKWDRPYTRERAVYPVPLLKERKFWPSVARLDDAYGD +KNLFCTCSPVV* +>CUFF.9.1|m.8 CUFF.9.1|g.8 ORF CUFF.9.1|g.8 CUFF.9.1|m.8 type:complete len:156 (+) CUFF.9.1:173-640(+) +MPINQKFYSYLVKRNGGEGEPEFRLPMGFIGITLFEIGILLFGWTARYKIFWFVPTIGSA +IMGGGYIMTSNPLNMYVVDSYGIYSASASAGVKIFQLLLGAIFPLFAESLFRRLNYGWGC +TLLAFILLACGCSLPILFKYGKQIRNLRPFDPSKY* |
| b |
| diff -r 000000000000 -r 8aef9a17faae test-data/raw/test.fa.transdecoder.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/raw/test.fa.transdecoder.bed Fri Nov 20 06:49:25 2015 -0500 |
| b |
| @@ -0,0 +1,7 @@ +track name='dataset_1.dat.transdecoder.gff3' +CUFF.36.1 0 1498 ID=CUFF.36.1|m.4;CUFF.36.1|g.4;ORF_CUFF.36.1|g.4_CUFF.36.1|m.4_type:complete_len:131_(+) 0 + 894 1287 0 1 1498 0 +CUFF.4.1 0 555 ID=CUFF.4.1|m.5;CUFF.4.1|g.5;ORF_CUFF.4.1|g.5_CUFF.4.1|m.5_type:3prime_partial_len:120_(+) 0 + 198 555 0 1 555 0 +CUFF.51.1 0 4342 ID=CUFF.51.1|m.2;CUFF.51.1|g.2;ORF_CUFF.51.1|g.2_CUFF.51.1|m.2_type:complete_len:347_(+) 0 + 316 1357 0 1 4342 0 +CUFF.51.1 0 4342 ID=CUFF.51.1|m.1;CUFF.51.1|g.1;ORF_CUFF.51.1|g.1_CUFF.51.1|m.1_type:complete_len:372_(+) 0 + 2631 3747 0 1 4342 0 +CUFF.57.1 0 3853 ID=CUFF.57.1|m.3;CUFF.57.1|g.3;ORF_CUFF.57.1|g.3_CUFF.57.1|m.3_type:complete_len:1032_(+) 0 + 188 3284 0 1 3853 0 +CUFF.9.1 0 804 ID=CUFF.9.1|m.6;CUFF.9.1|g.6;ORF_CUFF.9.1|g.6_CUFF.9.1|m.6_type:complete_len:156_(+) 0 + 172 640 0 1 804 0 |
| b |
| diff -r 000000000000 -r 8aef9a17faae test-data/raw/test.fa.transdecoder.cds --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/raw/test.fa.transdecoder.cds Fri Nov 20 06:49:25 2015 -0500 |
| b |
| @@ -0,0 +1,116 @@ +>CUFF.36.1|m.4 CUFF.36.1|g.4 ORF CUFF.36.1|g.4 CUFF.36.1|m.4 type:complete len:131 (+) CUFF.36.1:895-1287(+) +ATGTCGCAAGACTCAGAATCGTTCATCCGGCAACTGTTTAAGGCATTTACGGATTTTAGT +ACTGACGTTGAGTCACTTAGAGGATTTTTAACGCCAGATTATCGACAGCTTGTCGATGGA +CGTGAATTGACACTTGACGATTTTATTTCTCATGCCAAAGCACTACGTACCCATCTTCAT +CGGCTCGACATCAACGTTCAACAAATTGTCTGTCAAGGTAACAAGGCTGCCACTGTGCAT +ATTGCCCATGCGATACGTTCCTCTGGCGAGTCCAGCAGAATCAAAGTCATTGCATTTTAC +AGTTTTAAAGACGGGCGTATTTCTTTGATCGATGAGTTGACGTACGTTCTTGAAGGTGGT +AATGCAGACAGAGAGCTTGGATCAGTACAATGA +>CUFF.4.1|m.5 CUFF.4.1|g.5 ORF CUFF.4.1|g.5 CUFF.4.1|m.5 type:3prime_partial len:120 (+) CUFF.4.1:199-555(+) +ATGACTGCATTAATGAACCATATATATATCGATAATCCGCTTATAAGCAATTCAACTAAT +AACGTTACTCACGAGTTATTGATTGATCTCCATGAACTTTATAATGACGGAGAGATTTCC +AGGATAGTTCTACTCAGAACTTTGGTAACTCAATCTGCGGATGATGCTACATGGATAATC +AACTTGACAGATGATGTGCTTAATGGATTACCACTGCTGAAGAAGCGAGACCGATACACC +ACACAATGTCATAGTACAAATATGGCAAGCACATATGACTGTGACACTGGAGCCAATGCT +GTTGGAGCCCGAGGTGGAGCCACGTTAGCAGCCGACTATAGAGGTGATTGGGGGGGG +>CUFF.51.1|m.2 CUFF.51.1|g.2 ORF CUFF.51.1|g.2 CUFF.51.1|m.2 type:complete len:347 (+) CUFF.51.1:317-1357(+) +ATGGCACTTATGTTATCCAGGATTCCACGTCGTTTTTTTTTCTTATTTTTAACGGTCGGC +TTGATTGCTGGCGCGTTTCTATACTCGTTGATATATTTTGTGGACGTTGATTTGGTGTCG +AAGGTTAACCAGTTGTATGATCAGCAAATTGCACCCATGCTCTCCGATGCTATTGGCACT +CCATCCGTTAATCACTCGTTTGAGTTGGCGCCGTTAGACTCTCATTTGGTGGCCACAAGC +ACTACATTCCACGAGGCGTCATACGAGTCAGAGCCTCAGCAAAATCCTGCCAGTCAAAAT +ATTGTCTTATTACTAGTTAGTGATGGACACACTTCTTACAATAATGGAGCTAATACGTTT +GAAGAAGCTATACAGAACAGAGTTGACTATAGTACCAAACAAAACTACAACTTTGAGTAT +GTCAATGTTACTGGCCTCCCTATTCCCGCCGTTTGGTCCAAGATGCCCGCCGTCTTACAA +ACTATGAAGAAATACCCCAAAGCGGAATGGATCTGGTTGTTGGATCAGGATGCAATTATT +ACTAATACCCATCTTTCCCTTCAAGACTCCTTTTTGAAACCTGAGAACTTGCAAAAGACC +TTAATTACTAATACCATCCTCACTAAACGGCCTATAAATGCTAACGGGGATTTGCGTTAT +ACACCAAGTAATTATAGTTTAAAAGATATCGAAAATCTCATGGTCATAATCTCACAGGAT +CACAATGGATTAAACGCAGGTAGTATCTTGTTCCGTAATTCACCTGCTACTGCCTTGTTT +TTGGATATTTGGACAGATCCTGTTGTTGCAGAATGTGCGAAAGCCAATAATGAACAAGAC +ATGCTTGGATATTTGATTTCTAAGCATTCACAACTTGCTTCGCTGGTTGGCCTTATTCCT +CAAAGAAAAATAAATGCTTTTCACGAAGGTCCGGAAAATATGGAATGGCAAAAAGGTGAT +TTGGTAATTCACTTTGCTGGATGTTGGGTTGAAAACCGCTGCGATGAACTATGGCAAAAG +TTTTACGCCTTGATTGACTAA +>CUFF.51.1|m.1 CUFF.51.1|g.1 ORF CUFF.51.1|g.1 CUFF.51.1|m.1 type:complete len:372 (+) CUFF.51.1:2632-3747(+) +ATGTCTCGAATTTCACTTTCAAATTTTTTATCTCTTCCGCGTTACAAATTCCTGTTGTTT +TCTGTGGTTTTGATTATTGTGATGACAACCTTAGTGTTTAACGGACACGATTATAAGCAA +ACCCTTAATGACCGGCTTACTTCATTAAAAAACAACTTTGTTGAGGAAAATGATAATGCC +GTCTTAAAAGAAGAGCCTGGCAAATATACGTATATGAGTTTGTTTACTATGCCTTCTACT +GAAGAGGATTACTACTTCAACGCTACTAGGGTTTTAATTCACCGATTGAAATATCATCCT +ACTACCAAAAGTAAATACCCTATCCATATCCTTGCACTCCGTGGAGTAGATGAGTGGAAA +ATTGAACGTTTTCGAAAGGATGGTGCTTCTGTGATTGTTATAGACCCCATTGCTTCATCG +GATATTGTATACGATACATCCTCATTTAGTCAAGAAATATCTGCTAGATATGAACAAATG +TTTTCGAAGTTGCGAATTTTCGAACAAATACAATTTGACAAAATTTGCGTAATTGACAGT +GATATATTGATCATGAAGAACATTGATGATATATTTGATACTCCTTATATGTACCAACAA +ATTAATACCTTGAACTATACACGGCTACCTTCCTACACGAAGCCTGATGATGATACCGTC +TATCACTTCAATGAGGATTTTAAAGAATATGGTGCCAGTCGAAGCGAATTTTACCCTTAT +CTTCTCGCAGCCGTCTCTGATAGAGGAGAGCATCATAGTATACCTCCAGAAGATACTCCT +TATTTCAATGCTGGCTTAATGCTTATACGTCCAAGCGAGCTTCATTTTAACCGTATACTT +AAAATCGGAAGGTTTCCTTATATGTATGAGAATGCCAAAATGATGGAGCAAAGCTTGTTG +AATCTTGCATTTTCCTTGGACGGATGGTTTCCCTGGACTCGTCTTGATCCTTATTACAAT +GGCGTGTGGCCCTCAATTGACGAACGTCCTCTCTTAAAAACAGCACACGGAAAATTCTGG +AATATTGGTAGCTCAGAATTTGCACCAGTATATTTAGCTGACTGGTATGCTGCTTATGGC +GAAATGCTGTCTTTTCATAAGTATGAAACTCATTAA +>CUFF.57.1|m.3 CUFF.57.1|g.3 ORF CUFF.57.1|g.3 CUFF.57.1|m.3 type:complete len:1032 (+) CUFF.57.1:189-3284(+) +ATGTTCGATAGCTTTATGAAGAGAAATCAGCTAGCCTTAATCATGTTTCGTGCTTGCTCG +AAGTTGCAGTACCATGGAGTAAATACCAGCCTTTCGAGGCATTTGTTTCTTGCTAAAAGA +AATTTATCCATTTCTTCAGCTTGTCTAGAAGCTAAAAACTCCCAAAAGTTTCCTGCTCTT +GATACTTTTGAACCTCGACACATTGGACCTTCTAAAACGGATCAACAATATCAATTGGAG +TCACTAGGGTATAAGGATTTTGATTCTTTCCTCAAAGATGTAATTCCAGATTCTGTGCGA +ACACCTGAGAGCCAATTGATGGCTTTTGGGTCTGTGAATCCCAACGAAAAAAATCCTCCT +GTTAACTACTCCGAAAGCGAATTTACGACTCTGGCAAACAATGTGGCTAATCAAAATAAG +CTGATTAAGAGCTTCATTGGCATGGGATACTATAATGTAAAGCTTCCTGCTGCTATTCAG +CGTAATGTTCTTGAGAACCCTGAATGGTATACTCAATATACTCCATATCAGGCTGAAATT +TCTCAAGGGCGTCTGGAATCTATGATGAATTATCAAACCATGATTGCTGATCTCACAGGT +CTCAGCATTAGCAATGCTAGTTTACTGGATGAAGGAACTGCTGCTGGAGAAGCAATGGTT +ATGTTGATGGCCAACGACAAAAAGAAGCGCAAAACGTTTTTAGTGGACAAGAATATATAC +CCCAATACTCTGTCTGTTTTACGTACTCGTGCTTCTGGTTTTGGTATCAAAATTGAATTA +GACAATATCACTCCTGAACTCATTACGAAGTCTGCTAAGCATGTTTTTGGTATCTTTGTG +CAATACCCAGCGGCGGATGGCTCTATTTTTGACTATGGTCATTTAGCTGCTACAGCACGC +TCTTTTAATATGCACGTCGTAGCTGCCACCGATTTACTAGCTCTCACTATTTTGAAATCG +CCTGGGGAATGGGGTGCCGATGTTGCTGTTGGTTCCACTCAGCGCTTTGGTCTGCCCATG +GGCTATGGTGGCCCCCATGCCGGATTCTTTGCTTGTAGTGAAGAATTTAAACGAAAGATA +CCCGGTCGTCTTATTGGTCTCAGCAAAGATCGTTTAGAAAATCCCGCATACCGGTTGGCT +CTTCAAACAAGAGAACAACATATTCGTCGTGAAAAGGCTACAAGTAACATTTGCACGGCT +CAAGCTTTGTTAGCCAATATGTCTGCATTCTATGCTATTTACCATGGGCCAAATGGTCTC +CAAGAAATTGCAAACCGTATTTACGCTAGTACCTCCTTCTTAAAATCTGCTTTGGAATCT +TCAGGATATAAAATTGTTAATAAAAGTCATTTCTTTGACACATTAACTATCGAAGTTGAG +TCGGCTGACAAAGTTCTTGCGAAAGCACTTGATCACGGTTACAATTTAAGAAAGGTTGAT +GATTCACATGTTGGTCTTTCATTGGACGAGACCGTTTGCGATAAAGATATTCAAGCTTTG +TTTAGCATCTTTAATATAAATAAGAGTGTTGATCAGTATTATATGGAAATTGCAACGTCG +GAACCTAATGGAAATTCTGCTTCAACAGTCGATAATCTCAGCATTTGTTCTCTTCCTGAA +AACTTTAGACGAACAACCCTCTATTTACAACATCCCGTGTTTAACAGATACCATTCGGAA +ACTGAACTTATGCGTTATATTCATCATTTGCAGTCGAAGGATCTATCTTTAGCTCATGCC +ATGACCCCATTGGGTTCGTGCACAATGAAGTTGAATGCTGTCACCGAAATGATGCCAATC +ACAAATCCATTATTTGCCAACATTCATCCATATGTTCCAGAGGAACAAGCTAAAGGTTAT +CGTCATGTTATCGAAGATTTGCAGTTAATGTTAACGACCATCACCGGCTTTGATGCTGCA +TGCTTTCAACCAAATTCGGGAGCCGCTGGAGAATACACTGGCTTAAGTGTTATTCGAGCA +TATCAGCGGTCTATTGGTCAAGGTCATCGCAATATTTGCTTAATTCCTGTTTCGGCTCAC +GGTACTAATCCAGCTTCAGCTGCTATGGCTGGGTTTACTGTTATTCCTGTAAAATGTCTC +AATAACGGTTATTTGGATATGCAAGACTTAAAAGAAAAGGCCTCTAAACACGCCGACAAG +TTAGCTGCCTTTATGGTAACTTATCCTAGTACTTTTGGCATTTTTGAGCCTGATGTTAAG +GAAGCTTTGGAAGTAATTCACGAACATGGTGGTCAGGTTTACTTTGATGGTGCTAACATG +AATGCAATGGTTGGTTTATGCAAGGCTGGTGATATTGGTGCTGATGTTTGTCACTTAAAT +CTTCATAAGACATTTTGCATTCCTCACGGCGGTGGCGGTCCTGGTGTAGGTCCTATTTGT +GTAAAAAAGCATCTTGCTGATTTCCTACCATCTCATCCTGTAGTTTCATGCGGCGGTAAG +AATGGTATCACATCTGTTAGCTCTTCTCCTTTTGGCTCTGCTGGTATTTTACCTATCTCA +TGGGCATACATGAGAATGATGGGACTTGCCGGTTTGCGTGACGCTTCCAAAGCCGCTCTG +TTAAATGCCAATTATATGGCCAAGCGCCTGTCATCTCATTATAAACTTGTTTACACTAAT +AAGAACAACCTCTGTGCTCATGAGTTTATTCTAGATGCTCGCGAATTTAAAGCTACTGCG +GGTGTAGATGCAACTGATATAGCTAAACGTTTGCAAGATTACAGTTTCCATGCACCAACT +CTTTCCTGGCCTATTGCTAATACACTGATGATTGAGCCTACCGAGTCTGAGAGTATGTAT +GAGATGGACCGCTTCTGTGATGCTTTAATTTCTATTCGACAAGAAATTCGTGAAATTGAA +GAAGGTCTCCAGCCTAAGGACAATAACCTGCTCGTTAATGCTCCCCACCCTCAAAAGGAC +ATTGCATCTGAGAAATGGGATCGTCCTTATACTCGAGAGCGGGCTGTCTATCCTGTGCCT +CTTTTAAAGGAACGGAAATTCTGGCCTAGCGTTGCTCGATTAGATGATGCGTACGGTGAC +AAGAACTTATTTTGTACTTGTTCCCCAGTTGTTTAG +>CUFF.9.1|m.6 CUFF.9.1|g.6 ORF CUFF.9.1|g.6 CUFF.9.1|m.6 type:complete len:156 (+) CUFF.9.1:173-640(+) +ATGCCTATCAACCAAAAGTTTTATTCATATCTGGTAAAGCGAAATGGTGGTGAAGGTGAA +CCTGAATTTCGACTTCCTATGGGTTTTATTGGAATCACACTTTTTGAAATAGGAATTTTA +CTTTTCGGTTGGACTGCAAGATATAAGATTTTTTGGTTTGTGCCAACAATTGGATCAGCC +ATTATGGGTGGTGGGTACATTATGACTTCCAATCCCTTAAACATGTATGTGGTAGATTCA +TATGGAATTTACTCAGCCAGTGCGTCAGCGGGTGTAAAAATATTTCAACTATTATTAGGA +GCCATCTTTCCATTATTTGCTGAAAGTCTATTTCGTCGACTGAACTACGGATGGGGGTGT +ACTTTACTTGCCTTTATTTTATTAGCTTGTGGCTGTAGTCTTCCAATCTTATTCAAGTAT +GGAAAACAAATTAGAAATCTACGACCATTTGACCCCTCAAAATACTAG |
| b |
| diff -r 000000000000 -r 8aef9a17faae test-data/raw/test.fa.transdecoder.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/raw/test.fa.transdecoder.gff3 Fri Nov 20 06:49:25 2015 -0500 |
| b |
| @@ -0,0 +1,41 @@ +CUFF.36.1 transdecoder gene 1 1498 . + . ID=CUFF.36.1|g.4;Name=ORF%20CUFF.36.1%7Cg.4%20CUFF.36.1%7Cm.4%20type%3Acomplete%20len%3A131%20%28%2B%29 +CUFF.36.1 transdecoder mRNA 1 1498 . + . ID=CUFF.36.1|m.4;Parent=CUFF.36.1|g.4;Name=ORF%20CUFF.36.1%7Cg.4%20CUFF.36.1%7Cm.4%20type%3Acomplete%20len%3A131%20%28%2B%29 +CUFF.36.1 transdecoder five_prime_UTR 1 894 . + . ID=CUFF.36.1|m.4.utr5p1;Parent=CUFF.36.1|m.4 +CUFF.36.1 transdecoder exon 1 1498 . + . ID=CUFF.36.1|m.4.exon1;Parent=CUFF.36.1|m.4 +CUFF.36.1 transdecoder CDS 895 1287 . + . ID=cds.CUFF.36.1|m.4;Parent=CUFF.36.1|m.4 +CUFF.36.1 transdecoder three_prime_UTR 1288 1498 . + . ID=CUFF.36.1|m.4.utr3p1;Parent=CUFF.36.1|m.4 + +CUFF.4.1 transdecoder gene 1 555 . + . ID=CUFF.4.1|g.5;Name=ORF%20CUFF.4.1%7Cg.5%20CUFF.4.1%7Cm.5%20type%3A3prime_partial%20len%3A120%20%28%2B%29 +CUFF.4.1 transdecoder mRNA 1 555 . + . ID=CUFF.4.1|m.5;Parent=CUFF.4.1|g.5;Name=ORF%20CUFF.4.1%7Cg.5%20CUFF.4.1%7Cm.5%20type%3A3prime_partial%20len%3A120%20%28%2B%29 +CUFF.4.1 transdecoder five_prime_UTR 1 198 . + . ID=CUFF.4.1|m.5.utr5p1;Parent=CUFF.4.1|m.5 +CUFF.4.1 transdecoder exon 1 555 . + . ID=CUFF.4.1|m.5.exon1;Parent=CUFF.4.1|m.5 +CUFF.4.1 transdecoder CDS 199 555 . + . ID=cds.CUFF.4.1|m.5;Parent=CUFF.4.1|m.5 + +CUFF.51.1 transdecoder gene 1 4342 . + . ID=CUFF.51.1|g.2;Name=ORF%20CUFF.51.1%7Cg.2%20CUFF.51.1%7Cm.2%20type%3Acomplete%20len%3A347%20%28%2B%29 +CUFF.51.1 transdecoder mRNA 1 4342 . + . ID=CUFF.51.1|m.2;Parent=CUFF.51.1|g.2;Name=ORF%20CUFF.51.1%7Cg.2%20CUFF.51.1%7Cm.2%20type%3Acomplete%20len%3A347%20%28%2B%29 +CUFF.51.1 transdecoder five_prime_UTR 1 316 . + . ID=CUFF.51.1|m.2.utr5p1;Parent=CUFF.51.1|m.2 +CUFF.51.1 transdecoder exon 1 4342 . + . ID=CUFF.51.1|m.2.exon1;Parent=CUFF.51.1|m.2 +CUFF.51.1 transdecoder CDS 317 1357 . + . ID=cds.CUFF.51.1|m.2;Parent=CUFF.51.1|m.2 +CUFF.51.1 transdecoder three_prime_UTR 1358 4342 . + . ID=CUFF.51.1|m.2.utr3p1;Parent=CUFF.51.1|m.2 + +CUFF.51.1 transdecoder gene 1 4342 . + . ID=CUFF.51.1|g.1;Name=ORF%20CUFF.51.1%7Cg.1%20CUFF.51.1%7Cm.1%20type%3Acomplete%20len%3A372%20%28%2B%29 +CUFF.51.1 transdecoder mRNA 1 4342 . + . ID=CUFF.51.1|m.1;Parent=CUFF.51.1|g.1;Name=ORF%20CUFF.51.1%7Cg.1%20CUFF.51.1%7Cm.1%20type%3Acomplete%20len%3A372%20%28%2B%29 +CUFF.51.1 transdecoder five_prime_UTR 1 2631 . + . ID=CUFF.51.1|m.1.utr5p1;Parent=CUFF.51.1|m.1 +CUFF.51.1 transdecoder exon 1 4342 . + . ID=CUFF.51.1|m.1.exon1;Parent=CUFF.51.1|m.1 +CUFF.51.1 transdecoder CDS 2632 3747 . + . ID=cds.CUFF.51.1|m.1;Parent=CUFF.51.1|m.1 +CUFF.51.1 transdecoder three_prime_UTR 3748 4342 . + . ID=CUFF.51.1|m.1.utr3p1;Parent=CUFF.51.1|m.1 + +CUFF.57.1 transdecoder gene 1 3853 . + . ID=CUFF.57.1|g.3;Name=ORF%20CUFF.57.1%7Cg.3%20CUFF.57.1%7Cm.3%20type%3Acomplete%20len%3A1032%20%28%2B%29 +CUFF.57.1 transdecoder mRNA 1 3853 . + . ID=CUFF.57.1|m.3;Parent=CUFF.57.1|g.3;Name=ORF%20CUFF.57.1%7Cg.3%20CUFF.57.1%7Cm.3%20type%3Acomplete%20len%3A1032%20%28%2B%29 +CUFF.57.1 transdecoder five_prime_UTR 1 188 . + . ID=CUFF.57.1|m.3.utr5p1;Parent=CUFF.57.1|m.3 +CUFF.57.1 transdecoder exon 1 3853 . + . ID=CUFF.57.1|m.3.exon1;Parent=CUFF.57.1|m.3 +CUFF.57.1 transdecoder CDS 189 3284 . + . ID=cds.CUFF.57.1|m.3;Parent=CUFF.57.1|m.3 +CUFF.57.1 transdecoder three_prime_UTR 3285 3853 . + . ID=CUFF.57.1|m.3.utr3p1;Parent=CUFF.57.1|m.3 + +CUFF.9.1 transdecoder gene 1 804 . + . ID=CUFF.9.1|g.6;Name=ORF%20CUFF.9.1%7Cg.6%20CUFF.9.1%7Cm.6%20type%3Acomplete%20len%3A156%20%28%2B%29 +CUFF.9.1 transdecoder mRNA 1 804 . + . ID=CUFF.9.1|m.6;Parent=CUFF.9.1|g.6;Name=ORF%20CUFF.9.1%7Cg.6%20CUFF.9.1%7Cm.6%20type%3Acomplete%20len%3A156%20%28%2B%29 +CUFF.9.1 transdecoder five_prime_UTR 1 172 . + . ID=CUFF.9.1|m.6.utr5p1;Parent=CUFF.9.1|m.6 +CUFF.9.1 transdecoder exon 1 804 . + . ID=CUFF.9.1|m.6.exon1;Parent=CUFF.9.1|m.6 +CUFF.9.1 transdecoder CDS 173 640 . + . ID=cds.CUFF.9.1|m.6;Parent=CUFF.9.1|m.6 +CUFF.9.1 transdecoder three_prime_UTR 641 804 . + . ID=CUFF.9.1|m.6.utr3p1;Parent=CUFF.9.1|m.6 + |
| b |
| diff -r 000000000000 -r 8aef9a17faae test-data/raw/test.fa.transdecoder.mRNA --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/raw/test.fa.transdecoder.mRNA Fri Nov 20 06:49:25 2015 -0500 |
| b |
| b'@@ -0,0 +1,266 @@\n+>CUFF.36.1|m.4 CUFF.36.1|g.4 ORF CUFF.36.1|g.4 CUFF.36.1|m.4 type:complete len:131 (+) CUFF.36.1:895-1287(+)\n+TGACTAAGTGGCAATGATGCTCCTAATGAAACCACTGATCCTCGATCATCAGCAGTAGTA\n+TCAATAGCAGCATCAGCACCGTTAGACAGCTGTTTTTCTAAACCATTCAATGATTCATCT\n+GAAAAACGTGAACCCACTTTCGAATAGTGCTTTTCAAATTTCTTTCCCGTAATTAAGGAA\n+AGTAAATCCATGTGCAGTTAGTATTGAAAAGGAAAGAATAAATAAAAGTGGGTCAAAAGT\n+AACGCCAAACAAACGAAGGTTATCGAAATATATGCGAAGGAGAGATTTATATACTAGTCA\n+AATTTAAACAGCTGAGATTGCTTTAGTCATCGCGTTGTTCCAGATCGTGAACGAAAACAC\n+CGATTCGCTCGCTAAAGTAGATACGAAATGTCCAGCAGATTTTGCTTAATTAAAACATAA\n+ATATTGATGAGCAAGAGCAGCTCGTTATAAATCAGACCTCCAAGGATTTTATCAACTACT\n+CAACTGGTTATGTGAATAATGACTCAGTTAAATATTAAATGTACTCTAAACGGTTATCAT\n+ACAATTTATTAGGAGGATTATACCAGCTAGTAGGAATTTAACCATTTCAAATTTAAACCT\n+CTTTTTTTTCGTAACTTGGGGTCGTCATAATGAATAATTCTGTTTGTCGAATTTGAAGGG\n+AAAAACACACTTGTTATCTAATTCCAAAAAAAAATAAAAAATTTTTAAAAATTAGTGGGG\n+TTTTTTTTTCACCAATGTCTAATGATGTGTGATTTAAAAAAAAACGTGTGTAACGCATTG\n+TAGTATTACTTACCTTTGCATGATTAAAAGTATATGTTGATATCGACTATTTAGAGTACT\n+GTGCGACACATTACCCTATGTTTCCCACTCTTAATCACCAAAAATTTTTTCCGAATGTCG\n+CAAGACTCAGAATCGTTCATCCGGCAACTGTTTAAGGCATTTACGGATTTTAGTACTGAC\n+GTTGAGTCACTTAGAGGATTTTTAACGCCAGATTATCGACAGCTTGTCGATGGACGTGAA\n+TTGACACTTGACGATTTTATTTCTCATGCCAAAGCACTACGTACCCATCTTCATCGGCTC\n+GACATCAACGTTCAACAAATTGTCTGTCAAGGTAACAAGGCTGCCACTGTGCATATTGCC\n+CATGCGATACGTTCCTCTGGCGAGTCCAGCAGAATCAAAGTCATTGCATTTTACAGTTTT\n+AAAGACGGGCGTATTTCTTTGATCGATGAGTTGACGTACGTTCTTGAAGGTGGTAATGCA\n+GACAGAGAGCTTGGATCAGTACAATGACTTCAATTACCTTGACACTGCATTGCCCACGTT\n+ATTCAACGTCCATCAGGAACCGGACAAATTATTCAGAGTCCTTTTGAACTACTTCATAAT\n+TTTACAAATATTCAAGTGTAATTCGTAATATAATCAGTTTTATTCATCTTCGTTGTCTAA\n+AACTTTTATGTGCTGCAATATTTGGGGAATCTCGATTTGACATAATGATCCCAGTGCC\n+>CUFF.4.1|m.5 CUFF.4.1|g.5 ORF CUFF.4.1|g.5 CUFF.4.1|m.5 type:3prime_partial len:120 (+) CUFF.4.1:199-555(+)\n+CTCTTTTTAATATTTTACCGATGAGATTGCTATTATTAGTTACGTTGCTATCTATCGTTG\n+GTTACACTAATCAGTTGCTTTCCAACTGACCTCGAAGACGCTCCAGCTGTAATCTGGGTA\n+GCCCAATTTCCTCCAGATAACACTACACAGCACTATGAATTCAGATATATCGTAAATGAA\n+TTATATAATGCTAGCAAGATGACTGCATTAATGAACCATATATATATCGATAATCCGCTT\n+ATAAGCAATTCAACTAATAACGTTACTCACGAGTTATTGATTGATCTCCATGAACTTTAT\n+AATGACGGAGAGATTTCCAGGATAGTTCTACTCAGAACTTTGGTAACTCAATCTGCGGAT\n+GATGCTACATGGATAATCAACTTGACAGATGATGTGCTTAATGGATTACCACTGCTGAAG\n+AAGCGAGACCGATACACCACACAATGTCATAGTACAAATATGGCAAGCACATATGACTGT\n+GACACTGGAGCCAATGCTGTTGGAGCCCGAGGTGGAGCCACGTTAGCAGCCGACTATAGA\n+GGTGATTGGGGGGGG\n+>CUFF.51.1|m.2 CUFF.51.1|g.2 ORF CUFF.51.1|g.2 CUFF.51.1|m.2 type:complete len:347 (+) CUFF.51.1:317-1357(+)\n+CGACGTTAATAAAATATTTAACAAAGCCTTTAAAAAATTAACGATAGCTAGTCAAAGGAA\n+GCTTAACGCGTATTCAGCCTCATTAAGACAATCAGGAAGCTTTTTTTTACCATCAGCATA\n+TACCTCTAACCCTTTGATTTATTTTTATATCTCGAGATTTCGTTCGTTATTTTATAGGTC\n+GTTTCGATAAGACCTTAATACAATCTGATTTAGTGGTTGTTTAAGATTTCGGAAAAGCCT\n+TTTTTTCAAAAAAAGTTTTCCAGTTATTGTTTCATTATTTCTAATTGATTTACTGAAGAA\n+TTGTTATAACCTAAAGATGGCACTTATGTTATCCAGGATTCCACGTCGTTTTTTTTTCTT\n+ATTTTTAACGGTCGGCTTGATTGCTGGCGCGTTTCTATACTCGTTGATATATTTTGTGGA\n+CGTTGATTTGGTGTCGAAGGTTAACCAGTTGTATGATCAGCAAATTGCACCCATGCTCTC\n+CGATGCTATTGGCACTCCATCCGTTAATCACTCGTTTGAGTTGGCGCCGTTAGACTCTCA\n+TTTGGTGGCCACAAGCACTACATTCCACGAGGCGTCATACGAGTCAGAGCCTCAGCAAAA\n+TCCTGCCAGTCAAAATATTGTCTTATTACTAGTTAGTGATGGACACACTTCTTACAATAA\n+TGGAGCTAATACGTTTGAAGAAGCTATACAGAACAGAGTTGACTATAGTACCAAACAAAA\n+CTACAACTTTGAGTATGTCAATGTTACTGGCCTCCCTATTCCCGCCGTTTGGTCCAAGAT\n+GCCCGCCGTCTTACAAACTATGAAGAAATACCCCAAAGCGGAATGGATCTGGTTGTTGGA\n+TCAGGATGCAATTATTACTAATACCCATCTTTCCCTTCAAGACTCCTTTTTGAAACCTGA\n+GAACTTGCAAAAGACCTTAATTACTAATACCATCCTCACTAAACGGCCTATAAATGCTAA\n+CGGGGATTTGCGTTATACACCAAGTAATTATAGTTTAAAAGATATCGAAAATCTCATGGT\n+CATAATCTCACAGGATCACAATGGATTAAACGCAGGTAGTATCTTGTTCCGTAATTCACC\n+TGCTACTGCCTTGTTTTTGGATATTTGGACAGATCCTGTTGTTGCAGAATGTGCGAAAGC\n+CAATAATGAACAAGACATGCTTGGATATTTGATTTCTAAGCATTCACAACTTGCTTCGCT\n+GGTTGGCCTTATTCCTCAAAGAAAAATAAATGCTTTTCACGAAGGTCCGGAAAATATGGA\n+ATGGCAAAAAGGTGATTTGGTAATTCACTTTGCTGGATGTTGGGTTGAAAACCGCTGCGA\n+TGAACTATGGCAAAAGTTTTACGCCTTGATTGACTAAGTTGCTTATTCATTATATCCGTC\n+TGTTTAATTTGTTTGTGTTTTAAAAAATTTTATATATATAAACAAAGCGCCGTATAATTT\n+TCCGTCAATCTTCCTTTCTTTATCTGAATCTCTAAT'..b'GGACAAGA\n+ATATATACCCCAATACTCTGTCTGTTTTACGTACTCGTGCTTCTGGTTTTGGTATCAAAA\n+TTGAATTAGACAATATCACTCCTGAACTCATTACGAAGTCTGCTAAGCATGTTTTTGGTA\n+TCTTTGTGCAATACCCAGCGGCGGATGGCTCTATTTTTGACTATGGTCATTTAGCTGCTA\n+CAGCACGCTCTTTTAATATGCACGTCGTAGCTGCCACCGATTTACTAGCTCTCACTATTT\n+TGAAATCGCCTGGGGAATGGGGTGCCGATGTTGCTGTTGGTTCCACTCAGCGCTTTGGTC\n+TGCCCATGGGCTATGGTGGCCCCCATGCCGGATTCTTTGCTTGTAGTGAAGAATTTAAAC\n+GAAAGATACCCGGTCGTCTTATTGGTCTCAGCAAAGATCGTTTAGAAAATCCCGCATACC\n+GGTTGGCTCTTCAAACAAGAGAACAACATATTCGTCGTGAAAAGGCTACAAGTAACATTT\n+GCACGGCTCAAGCTTTGTTAGCCAATATGTCTGCATTCTATGCTATTTACCATGGGCCAA\n+ATGGTCTCCAAGAAATTGCAAACCGTATTTACGCTAGTACCTCCTTCTTAAAATCTGCTT\n+TGGAATCTTCAGGATATAAAATTGTTAATAAAAGTCATTTCTTTGACACATTAACTATCG\n+AAGTTGAGTCGGCTGACAAAGTTCTTGCGAAAGCACTTGATCACGGTTACAATTTAAGAA\n+AGGTTGATGATTCACATGTTGGTCTTTCATTGGACGAGACCGTTTGCGATAAAGATATTC\n+AAGCTTTGTTTAGCATCTTTAATATAAATAAGAGTGTTGATCAGTATTATATGGAAATTG\n+CAACGTCGGAACCTAATGGAAATTCTGCTTCAACAGTCGATAATCTCAGCATTTGTTCTC\n+TTCCTGAAAACTTTAGACGAACAACCCTCTATTTACAACATCCCGTGTTTAACAGATACC\n+ATTCGGAAACTGAACTTATGCGTTATATTCATCATTTGCAGTCGAAGGATCTATCTTTAG\n+CTCATGCCATGACCCCATTGGGTTCGTGCACAATGAAGTTGAATGCTGTCACCGAAATGA\n+TGCCAATCACAAATCCATTATTTGCCAACATTCATCCATATGTTCCAGAGGAACAAGCTA\n+AAGGTTATCGTCATGTTATCGAAGATTTGCAGTTAATGTTAACGACCATCACCGGCTTTG\n+ATGCTGCATGCTTTCAACCAAATTCGGGAGCCGCTGGAGAATACACTGGCTTAAGTGTTA\n+TTCGAGCATATCAGCGGTCTATTGGTCAAGGTCATCGCAATATTTGCTTAATTCCTGTTT\n+CGGCTCACGGTACTAATCCAGCTTCAGCTGCTATGGCTGGGTTTACTGTTATTCCTGTAA\n+AATGTCTCAATAACGGTTATTTGGATATGCAAGACTTAAAAGAAAAGGCCTCTAAACACG\n+CCGACAAGTTAGCTGCCTTTATGGTAACTTATCCTAGTACTTTTGGCATTTTTGAGCCTG\n+ATGTTAAGGAAGCTTTGGAAGTAATTCACGAACATGGTGGTCAGGTTTACTTTGATGGTG\n+CTAACATGAATGCAATGGTTGGTTTATGCAAGGCTGGTGATATTGGTGCTGATGTTTGTC\n+ACTTAAATCTTCATAAGACATTTTGCATTCCTCACGGCGGTGGCGGTCCTGGTGTAGGTC\n+CTATTTGTGTAAAAAAGCATCTTGCTGATTTCCTACCATCTCATCCTGTAGTTTCATGCG\n+GCGGTAAGAATGGTATCACATCTGTTAGCTCTTCTCCTTTTGGCTCTGCTGGTATTTTAC\n+CTATCTCATGGGCATACATGAGAATGATGGGACTTGCCGGTTTGCGTGACGCTTCCAAAG\n+CCGCTCTGTTAAATGCCAATTATATGGCCAAGCGCCTGTCATCTCATTATAAACTTGTTT\n+ACACTAATAAGAACAACCTCTGTGCTCATGAGTTTATTCTAGATGCTCGCGAATTTAAAG\n+CTACTGCGGGTGTAGATGCAACTGATATAGCTAAACGTTTGCAAGATTACAGTTTCCATG\n+CACCAACTCTTTCCTGGCCTATTGCTAATACACTGATGATTGAGCCTACCGAGTCTGAGA\n+GTATGTATGAGATGGACCGCTTCTGTGATGCTTTAATTTCTATTCGACAAGAAATTCGTG\n+AAATTGAAGAAGGTCTCCAGCCTAAGGACAATAACCTGCTCGTTAATGCTCCCCACCCTC\n+AAAAGGACATTGCATCTGAGAAATGGGATCGTCCTTATACTCGAGAGCGGGCTGTCTATC\n+CTGTGCCTCTTTTAAAGGAACGGAAATTCTGGCCTAGCGTTGCTCGATTAGATGATGCGT\n+ACGGTGACAAGAACTTATTTTGTACTTGTTCCCCAGTTGTTTAGCGGTCAAAAAGAGCTC\n+ACCTGCTAGATTACTTCAACCTTTTCCCAGTTAAGTTCAACCTAATTTTTACTCCATTTG\n+GTAGTTCGTTCAACACCAATTCCCACGTTTATATATAGACCAATTTTTTACTACATCTTG\n+TTAGACAATTCTTTCCGTTATCACTTTTTCGAATTTTTTTTAATTACGTTTTAATTTTGA\n+AGGTTAGAATTATCCTTTGCTGGAACATGAGGTTTTCAACAACCTTTTTTTAATCTGATA\n+ATCTAATTTTGCTAGTCATATAATTGCGACTTTCTGATAAAAACATTACCTATACTTTAT\n+AAATATGTCGTTTTTAAATATTAACTCCTATGTCTTACTTGCATCCTTGAAATTTACGAC\n+TAGAAATTTGGTGCTTTGGATTTTCGTTACATTAAGTAAGGCCATTGAATCGATATGACA\n+CGTAAATGTTAAATTTCAAAATATTTTGGAGAGCACCATGTATAATTTAAATATACGAAT\n+TTTTTCCTTTAAATTTGTGGTTCTTTTTTAAAAAATATCAAGACGAGTACTCGATTACTC\n+GTAAGTATTCAAG\n+>CUFF.9.1|m.6 CUFF.9.1|g.6 ORF CUFF.9.1|g.6 CUFF.9.1|m.6 type:complete len:156 (+) CUFF.9.1:173-640(+)\n+AGCGAAACAAACAAATCACGTTATAGACGGTGGCAGGGCCATAAAAGGTATTCCCTCGCT\n+TTAAAAAGAAACAATGTCAAAAAGCTTTCTTTATAAACTATTGGAAGATTGAAGACATTA\n+AAGAAGAAAAGTCCTGCTTACCCTTGGACTTTTTTCAGCAGTTTTCATTGCCATGCCTAT\n+CAACCAAAAGTTTTATTCATATCTGGTAAAGCGAAATGGTGGTGAAGGTGAACCTGAATT\n+TCGACTTCCTATGGGTTTTATTGGAATCACACTTTTTGAAATAGGAATTTTACTTTTCGG\n+TTGGACTGCAAGATATAAGATTTTTTGGTTTGTGCCAACAATTGGATCAGCCATTATGGG\n+TGGTGGGTACATTATGACTTCCAATCCCTTAAACATGTATGTGGTAGATTCATATGGAAT\n+TTACTCAGCCAGTGCGTCAGCGGGTGTAAAAATATTTCAACTATTATTAGGAGCCATCTT\n+TCCATTATTTGCTGAAAGTCTATTTCGTCGACTGAACTACGGATGGGGGTGTACTTTACT\n+TGCCTTTATTTTATTAGCTTGTGGCTGTAGTCTTCCAATCTTATTCAAGTATGGAAAACA\n+AATTAGAAATCTACGACCATTTGACCCCTCAAAATACTAGTTGATTTAACTGATCAAAGT\n+GAGGATTTTCACACACATTTTCAGAGTACTTGGAACGTGCCGAGCTGATTAAAAAACACC\n+GGTATTAACAAAAAATTTTATTTATGAAGCAATACGCTATTTCGTTATGAGAAACTTGAT\n+TCAATGAAACTATTATAAACCTTA\n' |
| b |
| diff -r 000000000000 -r 8aef9a17faae test-data/raw/test.fa.transdecoder.pep --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/raw/test.fa.transdecoder.pep Fri Nov 20 06:49:25 2015 -0500 |
| b |
| @@ -0,0 +1,45 @@ +>CUFF.36.1|m.4 CUFF.36.1|g.4 ORF CUFF.36.1|g.4 CUFF.36.1|m.4 type:complete len:131 (+) CUFF.36.1:895-1287(+) +MSQDSESFIRQLFKAFTDFSTDVESLRGFLTPDYRQLVDGRELTLDDFISHAKALRTHLH +RLDINVQQIVCQGNKAATVHIAHAIRSSGESSRIKVIAFYSFKDGRISLIDELTYVLEGG +NADRELGSVQ* +>CUFF.4.1|m.5 CUFF.4.1|g.5 ORF CUFF.4.1|g.5 CUFF.4.1|m.5 type:3prime_partial len:120 (+) CUFF.4.1:199-555(+) +MTALMNHIYIDNPLISNSTNNVTHELLIDLHELYNDGEISRIVLLRTLVTQSADDATWII +NLTDDVLNGLPLLKKRDRYTTQCHSTNMASTYDCDTGANAVGARGGATLAADYRGDWGG +>CUFF.51.1|m.2 CUFF.51.1|g.2 ORF CUFF.51.1|g.2 CUFF.51.1|m.2 type:complete len:347 (+) CUFF.51.1:317-1357(+) +MALMLSRIPRRFFFLFLTVGLIAGAFLYSLIYFVDVDLVSKVNQLYDQQIAPMLSDAIGT +PSVNHSFELAPLDSHLVATSTTFHEASYESEPQQNPASQNIVLLLVSDGHTSYNNGANTF +EEAIQNRVDYSTKQNYNFEYVNVTGLPIPAVWSKMPAVLQTMKKYPKAEWIWLLDQDAII +TNTHLSLQDSFLKPENLQKTLITNTILTKRPINANGDLRYTPSNYSLKDIENLMVIISQD +HNGLNAGSILFRNSPATALFLDIWTDPVVAECAKANNEQDMLGYLISKHSQLASLVGLIP +QRKINAFHEGPENMEWQKGDLVIHFAGCWVENRCDELWQKFYALID* +>CUFF.51.1|m.1 CUFF.51.1|g.1 ORF CUFF.51.1|g.1 CUFF.51.1|m.1 type:complete len:372 (+) CUFF.51.1:2632-3747(+) +MSRISLSNFLSLPRYKFLLFSVVLIIVMTTLVFNGHDYKQTLNDRLTSLKNNFVEENDNA +VLKEEPGKYTYMSLFTMPSTEEDYYFNATRVLIHRLKYHPTTKSKYPIHILALRGVDEWK +IERFRKDGASVIVIDPIASSDIVYDTSSFSQEISARYEQMFSKLRIFEQIQFDKICVIDS +DILIMKNIDDIFDTPYMYQQINTLNYTRLPSYTKPDDDTVYHFNEDFKEYGASRSEFYPY +LLAAVSDRGEHHSIPPEDTPYFNAGLMLIRPSELHFNRILKIGRFPYMYENAKMMEQSLL +NLAFSLDGWFPWTRLDPYYNGVWPSIDERPLLKTAHGKFWNIGSSEFAPVYLADWYAAYG +EMLSFHKYETH* +>CUFF.57.1|m.3 CUFF.57.1|g.3 ORF CUFF.57.1|g.3 CUFF.57.1|m.3 type:complete len:1032 (+) CUFF.57.1:189-3284(+) +MFDSFMKRNQLALIMFRACSKLQYHGVNTSLSRHLFLAKRNLSISSACLEAKNSQKFPAL +DTFEPRHIGPSKTDQQYQLESLGYKDFDSFLKDVIPDSVRTPESQLMAFGSVNPNEKNPP +VNYSESEFTTLANNVANQNKLIKSFIGMGYYNVKLPAAIQRNVLENPEWYTQYTPYQAEI +SQGRLESMMNYQTMIADLTGLSISNASLLDEGTAAGEAMVMLMANDKKKRKTFLVDKNIY +PNTLSVLRTRASGFGIKIELDNITPELITKSAKHVFGIFVQYPAADGSIFDYGHLAATAR +SFNMHVVAATDLLALTILKSPGEWGADVAVGSTQRFGLPMGYGGPHAGFFACSEEFKRKI +PGRLIGLSKDRLENPAYRLALQTREQHIRREKATSNICTAQALLANMSAFYAIYHGPNGL +QEIANRIYASTSFLKSALESSGYKIVNKSHFFDTLTIEVESADKVLAKALDHGYNLRKVD +DSHVGLSLDETVCDKDIQALFSIFNINKSVDQYYMEIATSEPNGNSASTVDNLSICSLPE +NFRRTTLYLQHPVFNRYHSETELMRYIHHLQSKDLSLAHAMTPLGSCTMKLNAVTEMMPI +TNPLFANIHPYVPEEQAKGYRHVIEDLQLMLTTITGFDAACFQPNSGAAGEYTGLSVIRA +YQRSIGQGHRNICLIPVSAHGTNPASAAMAGFTVIPVKCLNNGYLDMQDLKEKASKHADK +LAAFMVTYPSTFGIFEPDVKEALEVIHEHGGQVYFDGANMNAMVGLCKAGDIGADVCHLN +LHKTFCIPHGGGGPGVGPICVKKHLADFLPSHPVVSCGGKNGITSVSSSPFGSAGILPIS +WAYMRMMGLAGLRDASKAALLNANYMAKRLSSHYKLVYTNKNNLCAHEFILDAREFKATA +GVDATDIAKRLQDYSFHAPTLSWPIANTLMIEPTESESMYEMDRFCDALISIRQEIREIE +EGLQPKDNNLLVNAPHPQKDIASEKWDRPYTRERAVYPVPLLKERKFWPSVARLDDAYGD +KNLFCTCSPVV* +>CUFF.9.1|m.6 CUFF.9.1|g.6 ORF CUFF.9.1|g.6 CUFF.9.1|m.6 type:complete len:156 (+) CUFF.9.1:173-640(+) +MPINQKFYSYLVKRNGGEGEPEFRLPMGFIGITLFEIGILLFGWTARYKIFWFVPTIGSA +IMGGGYIMTSNPLNMYVVDSYGIYSASASAGVKIFQLLLGAIFPLFAESLFRRLNYGWGC +TLLAFILLACGCSLPILFKYGKQIRNLRPFDPSKY* |
| b |
| diff -r 000000000000 -r 8aef9a17faae test-data/strand/test.fa.transdecoder.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/strand/test.fa.transdecoder.bed Fri Nov 20 06:49:25 2015 -0500 |
| b |
| @@ -0,0 +1,7 @@ +track name='dataset_19.dat.transdecoder.gff3' +CUFF.36.1 0 1498 ID=CUFF.36.1|m.4;CUFF.36.1|g.4;ORF_CUFF.36.1|g.4_CUFF.36.1|m.4_type:complete_len:131_(+) 0 + 894 1287 0 1 1498 0 +CUFF.4.1 0 555 ID=CUFF.4.1|m.5;CUFF.4.1|g.5;ORF_CUFF.4.1|g.5_CUFF.4.1|m.5_type:3prime_partial_len:120_(+) 0 + 198 555 0 1 555 0 +CUFF.51.1 0 4342 ID=CUFF.51.1|m.1;CUFF.51.1|g.1;ORF_CUFF.51.1|g.1_CUFF.51.1|m.1_type:complete_len:372_(+) 0 + 2631 3747 0 1 4342 0 +CUFF.51.1 0 4342 ID=CUFF.51.1|m.2;CUFF.51.1|g.2;ORF_CUFF.51.1|g.2_CUFF.51.1|m.2_type:complete_len:347_(+) 0 + 316 1357 0 1 4342 0 +CUFF.57.1 0 3853 ID=CUFF.57.1|m.3;CUFF.57.1|g.3;ORF_CUFF.57.1|g.3_CUFF.57.1|m.3_type:complete_len:1032_(+) 0 + 188 3284 0 1 3853 0 +CUFF.9.1 0 804 ID=CUFF.9.1|m.6;CUFF.9.1|g.6;ORF_CUFF.9.1|g.6_CUFF.9.1|m.6_type:complete_len:156_(+) 0 + 172 640 0 1 804 0 |
| b |
| diff -r 000000000000 -r 8aef9a17faae test-data/strand/test.fa.transdecoder.cds --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/strand/test.fa.transdecoder.cds Fri Nov 20 06:49:25 2015 -0500 |
| b |
| @@ -0,0 +1,116 @@ +>CUFF.36.1|m.4 CUFF.36.1|g.4 ORF CUFF.36.1|g.4 CUFF.36.1|m.4 type:complete len:131 (+) CUFF.36.1:895-1287(+) +ATGTCGCAAGACTCAGAATCGTTCATCCGGCAACTGTTTAAGGCATTTACGGATTTTAGT +ACTGACGTTGAGTCACTTAGAGGATTTTTAACGCCAGATTATCGACAGCTTGTCGATGGA +CGTGAATTGACACTTGACGATTTTATTTCTCATGCCAAAGCACTACGTACCCATCTTCAT +CGGCTCGACATCAACGTTCAACAAATTGTCTGTCAAGGTAACAAGGCTGCCACTGTGCAT +ATTGCCCATGCGATACGTTCCTCTGGCGAGTCCAGCAGAATCAAAGTCATTGCATTTTAC +AGTTTTAAAGACGGGCGTATTTCTTTGATCGATGAGTTGACGTACGTTCTTGAAGGTGGT +AATGCAGACAGAGAGCTTGGATCAGTACAATGA +>CUFF.4.1|m.5 CUFF.4.1|g.5 ORF CUFF.4.1|g.5 CUFF.4.1|m.5 type:3prime_partial len:120 (+) CUFF.4.1:199-555(+) +ATGACTGCATTAATGAACCATATATATATCGATAATCCGCTTATAAGCAATTCAACTAAT +AACGTTACTCACGAGTTATTGATTGATCTCCATGAACTTTATAATGACGGAGAGATTTCC +AGGATAGTTCTACTCAGAACTTTGGTAACTCAATCTGCGGATGATGCTACATGGATAATC +AACTTGACAGATGATGTGCTTAATGGATTACCACTGCTGAAGAAGCGAGACCGATACACC +ACACAATGTCATAGTACAAATATGGCAAGCACATATGACTGTGACACTGGAGCCAATGCT +GTTGGAGCCCGAGGTGGAGCCACGTTAGCAGCCGACTATAGAGGTGATTGGGGGGGG +>CUFF.51.1|m.2 CUFF.51.1|g.2 ORF CUFF.51.1|g.2 CUFF.51.1|m.2 type:complete len:347 (+) CUFF.51.1:317-1357(+) +ATGGCACTTATGTTATCCAGGATTCCACGTCGTTTTTTTTTCTTATTTTTAACGGTCGGC +TTGATTGCTGGCGCGTTTCTATACTCGTTGATATATTTTGTGGACGTTGATTTGGTGTCG +AAGGTTAACCAGTTGTATGATCAGCAAATTGCACCCATGCTCTCCGATGCTATTGGCACT +CCATCCGTTAATCACTCGTTTGAGTTGGCGCCGTTAGACTCTCATTTGGTGGCCACAAGC +ACTACATTCCACGAGGCGTCATACGAGTCAGAGCCTCAGCAAAATCCTGCCAGTCAAAAT +ATTGTCTTATTACTAGTTAGTGATGGACACACTTCTTACAATAATGGAGCTAATACGTTT +GAAGAAGCTATACAGAACAGAGTTGACTATAGTACCAAACAAAACTACAACTTTGAGTAT +GTCAATGTTACTGGCCTCCCTATTCCCGCCGTTTGGTCCAAGATGCCCGCCGTCTTACAA +ACTATGAAGAAATACCCCAAAGCGGAATGGATCTGGTTGTTGGATCAGGATGCAATTATT +ACTAATACCCATCTTTCCCTTCAAGACTCCTTTTTGAAACCTGAGAACTTGCAAAAGACC +TTAATTACTAATACCATCCTCACTAAACGGCCTATAAATGCTAACGGGGATTTGCGTTAT +ACACCAAGTAATTATAGTTTAAAAGATATCGAAAATCTCATGGTCATAATCTCACAGGAT +CACAATGGATTAAACGCAGGTAGTATCTTGTTCCGTAATTCACCTGCTACTGCCTTGTTT +TTGGATATTTGGACAGATCCTGTTGTTGCAGAATGTGCGAAAGCCAATAATGAACAAGAC +ATGCTTGGATATTTGATTTCTAAGCATTCACAACTTGCTTCGCTGGTTGGCCTTATTCCT +CAAAGAAAAATAAATGCTTTTCACGAAGGTCCGGAAAATATGGAATGGCAAAAAGGTGAT +TTGGTAATTCACTTTGCTGGATGTTGGGTTGAAAACCGCTGCGATGAACTATGGCAAAAG +TTTTACGCCTTGATTGACTAA +>CUFF.51.1|m.1 CUFF.51.1|g.1 ORF CUFF.51.1|g.1 CUFF.51.1|m.1 type:complete len:372 (+) CUFF.51.1:2632-3747(+) +ATGTCTCGAATTTCACTTTCAAATTTTTTATCTCTTCCGCGTTACAAATTCCTGTTGTTT +TCTGTGGTTTTGATTATTGTGATGACAACCTTAGTGTTTAACGGACACGATTATAAGCAA +ACCCTTAATGACCGGCTTACTTCATTAAAAAACAACTTTGTTGAGGAAAATGATAATGCC +GTCTTAAAAGAAGAGCCTGGCAAATATACGTATATGAGTTTGTTTACTATGCCTTCTACT +GAAGAGGATTACTACTTCAACGCTACTAGGGTTTTAATTCACCGATTGAAATATCATCCT +ACTACCAAAAGTAAATACCCTATCCATATCCTTGCACTCCGTGGAGTAGATGAGTGGAAA +ATTGAACGTTTTCGAAAGGATGGTGCTTCTGTGATTGTTATAGACCCCATTGCTTCATCG +GATATTGTATACGATACATCCTCATTTAGTCAAGAAATATCTGCTAGATATGAACAAATG +TTTTCGAAGTTGCGAATTTTCGAACAAATACAATTTGACAAAATTTGCGTAATTGACAGT +GATATATTGATCATGAAGAACATTGATGATATATTTGATACTCCTTATATGTACCAACAA +ATTAATACCTTGAACTATACACGGCTACCTTCCTACACGAAGCCTGATGATGATACCGTC +TATCACTTCAATGAGGATTTTAAAGAATATGGTGCCAGTCGAAGCGAATTTTACCCTTAT +CTTCTCGCAGCCGTCTCTGATAGAGGAGAGCATCATAGTATACCTCCAGAAGATACTCCT +TATTTCAATGCTGGCTTAATGCTTATACGTCCAAGCGAGCTTCATTTTAACCGTATACTT +AAAATCGGAAGGTTTCCTTATATGTATGAGAATGCCAAAATGATGGAGCAAAGCTTGTTG +AATCTTGCATTTTCCTTGGACGGATGGTTTCCCTGGACTCGTCTTGATCCTTATTACAAT +GGCGTGTGGCCCTCAATTGACGAACGTCCTCTCTTAAAAACAGCACACGGAAAATTCTGG +AATATTGGTAGCTCAGAATTTGCACCAGTATATTTAGCTGACTGGTATGCTGCTTATGGC +GAAATGCTGTCTTTTCATAAGTATGAAACTCATTAA +>CUFF.57.1|m.3 CUFF.57.1|g.3 ORF CUFF.57.1|g.3 CUFF.57.1|m.3 type:complete len:1032 (+) CUFF.57.1:189-3284(+) +ATGTTCGATAGCTTTATGAAGAGAAATCAGCTAGCCTTAATCATGTTTCGTGCTTGCTCG +AAGTTGCAGTACCATGGAGTAAATACCAGCCTTTCGAGGCATTTGTTTCTTGCTAAAAGA +AATTTATCCATTTCTTCAGCTTGTCTAGAAGCTAAAAACTCCCAAAAGTTTCCTGCTCTT +GATACTTTTGAACCTCGACACATTGGACCTTCTAAAACGGATCAACAATATCAATTGGAG +TCACTAGGGTATAAGGATTTTGATTCTTTCCTCAAAGATGTAATTCCAGATTCTGTGCGA +ACACCTGAGAGCCAATTGATGGCTTTTGGGTCTGTGAATCCCAACGAAAAAAATCCTCCT +GTTAACTACTCCGAAAGCGAATTTACGACTCTGGCAAACAATGTGGCTAATCAAAATAAG +CTGATTAAGAGCTTCATTGGCATGGGATACTATAATGTAAAGCTTCCTGCTGCTATTCAG +CGTAATGTTCTTGAGAACCCTGAATGGTATACTCAATATACTCCATATCAGGCTGAAATT +TCTCAAGGGCGTCTGGAATCTATGATGAATTATCAAACCATGATTGCTGATCTCACAGGT +CTCAGCATTAGCAATGCTAGTTTACTGGATGAAGGAACTGCTGCTGGAGAAGCAATGGTT +ATGTTGATGGCCAACGACAAAAAGAAGCGCAAAACGTTTTTAGTGGACAAGAATATATAC +CCCAATACTCTGTCTGTTTTACGTACTCGTGCTTCTGGTTTTGGTATCAAAATTGAATTA +GACAATATCACTCCTGAACTCATTACGAAGTCTGCTAAGCATGTTTTTGGTATCTTTGTG +CAATACCCAGCGGCGGATGGCTCTATTTTTGACTATGGTCATTTAGCTGCTACAGCACGC +TCTTTTAATATGCACGTCGTAGCTGCCACCGATTTACTAGCTCTCACTATTTTGAAATCG +CCTGGGGAATGGGGTGCCGATGTTGCTGTTGGTTCCACTCAGCGCTTTGGTCTGCCCATG +GGCTATGGTGGCCCCCATGCCGGATTCTTTGCTTGTAGTGAAGAATTTAAACGAAAGATA +CCCGGTCGTCTTATTGGTCTCAGCAAAGATCGTTTAGAAAATCCCGCATACCGGTTGGCT +CTTCAAACAAGAGAACAACATATTCGTCGTGAAAAGGCTACAAGTAACATTTGCACGGCT +CAAGCTTTGTTAGCCAATATGTCTGCATTCTATGCTATTTACCATGGGCCAAATGGTCTC +CAAGAAATTGCAAACCGTATTTACGCTAGTACCTCCTTCTTAAAATCTGCTTTGGAATCT +TCAGGATATAAAATTGTTAATAAAAGTCATTTCTTTGACACATTAACTATCGAAGTTGAG +TCGGCTGACAAAGTTCTTGCGAAAGCACTTGATCACGGTTACAATTTAAGAAAGGTTGAT +GATTCACATGTTGGTCTTTCATTGGACGAGACCGTTTGCGATAAAGATATTCAAGCTTTG +TTTAGCATCTTTAATATAAATAAGAGTGTTGATCAGTATTATATGGAAATTGCAACGTCG +GAACCTAATGGAAATTCTGCTTCAACAGTCGATAATCTCAGCATTTGTTCTCTTCCTGAA +AACTTTAGACGAACAACCCTCTATTTACAACATCCCGTGTTTAACAGATACCATTCGGAA +ACTGAACTTATGCGTTATATTCATCATTTGCAGTCGAAGGATCTATCTTTAGCTCATGCC +ATGACCCCATTGGGTTCGTGCACAATGAAGTTGAATGCTGTCACCGAAATGATGCCAATC +ACAAATCCATTATTTGCCAACATTCATCCATATGTTCCAGAGGAACAAGCTAAAGGTTAT +CGTCATGTTATCGAAGATTTGCAGTTAATGTTAACGACCATCACCGGCTTTGATGCTGCA +TGCTTTCAACCAAATTCGGGAGCCGCTGGAGAATACACTGGCTTAAGTGTTATTCGAGCA +TATCAGCGGTCTATTGGTCAAGGTCATCGCAATATTTGCTTAATTCCTGTTTCGGCTCAC +GGTACTAATCCAGCTTCAGCTGCTATGGCTGGGTTTACTGTTATTCCTGTAAAATGTCTC +AATAACGGTTATTTGGATATGCAAGACTTAAAAGAAAAGGCCTCTAAACACGCCGACAAG +TTAGCTGCCTTTATGGTAACTTATCCTAGTACTTTTGGCATTTTTGAGCCTGATGTTAAG +GAAGCTTTGGAAGTAATTCACGAACATGGTGGTCAGGTTTACTTTGATGGTGCTAACATG +AATGCAATGGTTGGTTTATGCAAGGCTGGTGATATTGGTGCTGATGTTTGTCACTTAAAT +CTTCATAAGACATTTTGCATTCCTCACGGCGGTGGCGGTCCTGGTGTAGGTCCTATTTGT +GTAAAAAAGCATCTTGCTGATTTCCTACCATCTCATCCTGTAGTTTCATGCGGCGGTAAG +AATGGTATCACATCTGTTAGCTCTTCTCCTTTTGGCTCTGCTGGTATTTTACCTATCTCA +TGGGCATACATGAGAATGATGGGACTTGCCGGTTTGCGTGACGCTTCCAAAGCCGCTCTG +TTAAATGCCAATTATATGGCCAAGCGCCTGTCATCTCATTATAAACTTGTTTACACTAAT +AAGAACAACCTCTGTGCTCATGAGTTTATTCTAGATGCTCGCGAATTTAAAGCTACTGCG +GGTGTAGATGCAACTGATATAGCTAAACGTTTGCAAGATTACAGTTTCCATGCACCAACT +CTTTCCTGGCCTATTGCTAATACACTGATGATTGAGCCTACCGAGTCTGAGAGTATGTAT +GAGATGGACCGCTTCTGTGATGCTTTAATTTCTATTCGACAAGAAATTCGTGAAATTGAA +GAAGGTCTCCAGCCTAAGGACAATAACCTGCTCGTTAATGCTCCCCACCCTCAAAAGGAC +ATTGCATCTGAGAAATGGGATCGTCCTTATACTCGAGAGCGGGCTGTCTATCCTGTGCCT +CTTTTAAAGGAACGGAAATTCTGGCCTAGCGTTGCTCGATTAGATGATGCGTACGGTGAC +AAGAACTTATTTTGTACTTGTTCCCCAGTTGTTTAG +>CUFF.9.1|m.6 CUFF.9.1|g.6 ORF CUFF.9.1|g.6 CUFF.9.1|m.6 type:complete len:156 (+) CUFF.9.1:173-640(+) +ATGCCTATCAACCAAAAGTTTTATTCATATCTGGTAAAGCGAAATGGTGGTGAAGGTGAA +CCTGAATTTCGACTTCCTATGGGTTTTATTGGAATCACACTTTTTGAAATAGGAATTTTA +CTTTTCGGTTGGACTGCAAGATATAAGATTTTTTGGTTTGTGCCAACAATTGGATCAGCC +ATTATGGGTGGTGGGTACATTATGACTTCCAATCCCTTAAACATGTATGTGGTAGATTCA +TATGGAATTTACTCAGCCAGTGCGTCAGCGGGTGTAAAAATATTTCAACTATTATTAGGA +GCCATCTTTCCATTATTTGCTGAAAGTCTATTTCGTCGACTGAACTACGGATGGGGGTGT +ACTTTACTTGCCTTTATTTTATTAGCTTGTGGCTGTAGTCTTCCAATCTTATTCAAGTAT +GGAAAACAAATTAGAAATCTACGACCATTTGACCCCTCAAAATACTAG |
| b |
| diff -r 000000000000 -r 8aef9a17faae test-data/strand/test.fa.transdecoder.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/strand/test.fa.transdecoder.gff3 Fri Nov 20 06:49:25 2015 -0500 |
| b |
| @@ -0,0 +1,41 @@ +CUFF.36.1 transdecoder gene 1 1498 . + . ID=CUFF.36.1|g.4;Name=ORF%20CUFF.36.1%7Cg.4%20CUFF.36.1%7Cm.4%20type%3Acomplete%20len%3A131%20%28%2B%29 +CUFF.36.1 transdecoder mRNA 1 1498 . + . ID=CUFF.36.1|m.4;Parent=CUFF.36.1|g.4;Name=ORF%20CUFF.36.1%7Cg.4%20CUFF.36.1%7Cm.4%20type%3Acomplete%20len%3A131%20%28%2B%29 +CUFF.36.1 transdecoder five_prime_UTR 1 894 . + . ID=CUFF.36.1|m.4.utr5p1;Parent=CUFF.36.1|m.4 +CUFF.36.1 transdecoder exon 1 1498 . + . ID=CUFF.36.1|m.4.exon1;Parent=CUFF.36.1|m.4 +CUFF.36.1 transdecoder CDS 895 1287 . + . ID=cds.CUFF.36.1|m.4;Parent=CUFF.36.1|m.4 +CUFF.36.1 transdecoder three_prime_UTR 1288 1498 . + . ID=CUFF.36.1|m.4.utr3p1;Parent=CUFF.36.1|m.4 + +CUFF.4.1 transdecoder gene 1 555 . + . ID=CUFF.4.1|g.5;Name=ORF%20CUFF.4.1%7Cg.5%20CUFF.4.1%7Cm.5%20type%3A3prime_partial%20len%3A120%20%28%2B%29 +CUFF.4.1 transdecoder mRNA 1 555 . + . ID=CUFF.4.1|m.5;Parent=CUFF.4.1|g.5;Name=ORF%20CUFF.4.1%7Cg.5%20CUFF.4.1%7Cm.5%20type%3A3prime_partial%20len%3A120%20%28%2B%29 +CUFF.4.1 transdecoder five_prime_UTR 1 198 . + . ID=CUFF.4.1|m.5.utr5p1;Parent=CUFF.4.1|m.5 +CUFF.4.1 transdecoder exon 1 555 . + . ID=CUFF.4.1|m.5.exon1;Parent=CUFF.4.1|m.5 +CUFF.4.1 transdecoder CDS 199 555 . + . ID=cds.CUFF.4.1|m.5;Parent=CUFF.4.1|m.5 + +CUFF.51.1 transdecoder gene 1 4342 . + . ID=CUFF.51.1|g.1;Name=ORF%20CUFF.51.1%7Cg.1%20CUFF.51.1%7Cm.1%20type%3Acomplete%20len%3A372%20%28%2B%29 +CUFF.51.1 transdecoder mRNA 1 4342 . + . ID=CUFF.51.1|m.1;Parent=CUFF.51.1|g.1;Name=ORF%20CUFF.51.1%7Cg.1%20CUFF.51.1%7Cm.1%20type%3Acomplete%20len%3A372%20%28%2B%29 +CUFF.51.1 transdecoder five_prime_UTR 1 2631 . + . ID=CUFF.51.1|m.1.utr5p1;Parent=CUFF.51.1|m.1 +CUFF.51.1 transdecoder exon 1 4342 . + . ID=CUFF.51.1|m.1.exon1;Parent=CUFF.51.1|m.1 +CUFF.51.1 transdecoder CDS 2632 3747 . + . ID=cds.CUFF.51.1|m.1;Parent=CUFF.51.1|m.1 +CUFF.51.1 transdecoder three_prime_UTR 3748 4342 . + . ID=CUFF.51.1|m.1.utr3p1;Parent=CUFF.51.1|m.1 + +CUFF.51.1 transdecoder gene 1 4342 . + . ID=CUFF.51.1|g.2;Name=ORF%20CUFF.51.1%7Cg.2%20CUFF.51.1%7Cm.2%20type%3Acomplete%20len%3A347%20%28%2B%29 +CUFF.51.1 transdecoder mRNA 1 4342 . + . ID=CUFF.51.1|m.2;Parent=CUFF.51.1|g.2;Name=ORF%20CUFF.51.1%7Cg.2%20CUFF.51.1%7Cm.2%20type%3Acomplete%20len%3A347%20%28%2B%29 +CUFF.51.1 transdecoder five_prime_UTR 1 316 . + . ID=CUFF.51.1|m.2.utr5p1;Parent=CUFF.51.1|m.2 +CUFF.51.1 transdecoder exon 1 4342 . + . ID=CUFF.51.1|m.2.exon1;Parent=CUFF.51.1|m.2 +CUFF.51.1 transdecoder CDS 317 1357 . + . ID=cds.CUFF.51.1|m.2;Parent=CUFF.51.1|m.2 +CUFF.51.1 transdecoder three_prime_UTR 1358 4342 . + . ID=CUFF.51.1|m.2.utr3p1;Parent=CUFF.51.1|m.2 + +CUFF.57.1 transdecoder gene 1 3853 . + . ID=CUFF.57.1|g.3;Name=ORF%20CUFF.57.1%7Cg.3%20CUFF.57.1%7Cm.3%20type%3Acomplete%20len%3A1032%20%28%2B%29 +CUFF.57.1 transdecoder mRNA 1 3853 . + . ID=CUFF.57.1|m.3;Parent=CUFF.57.1|g.3;Name=ORF%20CUFF.57.1%7Cg.3%20CUFF.57.1%7Cm.3%20type%3Acomplete%20len%3A1032%20%28%2B%29 +CUFF.57.1 transdecoder five_prime_UTR 1 188 . + . ID=CUFF.57.1|m.3.utr5p1;Parent=CUFF.57.1|m.3 +CUFF.57.1 transdecoder exon 1 3853 . + . ID=CUFF.57.1|m.3.exon1;Parent=CUFF.57.1|m.3 +CUFF.57.1 transdecoder CDS 189 3284 . + . ID=cds.CUFF.57.1|m.3;Parent=CUFF.57.1|m.3 +CUFF.57.1 transdecoder three_prime_UTR 3285 3853 . + . ID=CUFF.57.1|m.3.utr3p1;Parent=CUFF.57.1|m.3 + +CUFF.9.1 transdecoder gene 1 804 . + . ID=CUFF.9.1|g.6;Name=ORF%20CUFF.9.1%7Cg.6%20CUFF.9.1%7Cm.6%20type%3Acomplete%20len%3A156%20%28%2B%29 +CUFF.9.1 transdecoder mRNA 1 804 . + . ID=CUFF.9.1|m.6;Parent=CUFF.9.1|g.6;Name=ORF%20CUFF.9.1%7Cg.6%20CUFF.9.1%7Cm.6%20type%3Acomplete%20len%3A156%20%28%2B%29 +CUFF.9.1 transdecoder five_prime_UTR 1 172 . + . ID=CUFF.9.1|m.6.utr5p1;Parent=CUFF.9.1|m.6 +CUFF.9.1 transdecoder exon 1 804 . + . ID=CUFF.9.1|m.6.exon1;Parent=CUFF.9.1|m.6 +CUFF.9.1 transdecoder CDS 173 640 . + . ID=cds.CUFF.9.1|m.6;Parent=CUFF.9.1|m.6 +CUFF.9.1 transdecoder three_prime_UTR 641 804 . + . ID=CUFF.9.1|m.6.utr3p1;Parent=CUFF.9.1|m.6 + |
| b |
| diff -r 000000000000 -r 8aef9a17faae test-data/strand/test.fa.transdecoder.mRNA --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/strand/test.fa.transdecoder.mRNA Fri Nov 20 06:49:25 2015 -0500 |
| b |
| b'@@ -0,0 +1,266 @@\n+>CUFF.36.1|m.4 CUFF.36.1|g.4 ORF CUFF.36.1|g.4 CUFF.36.1|m.4 type:complete len:131 (+) CUFF.36.1:895-1287(+)\n+TGACTAAGTGGCAATGATGCTCCTAATGAAACCACTGATCCTCGATCATCAGCAGTAGTA\n+TCAATAGCAGCATCAGCACCGTTAGACAGCTGTTTTTCTAAACCATTCAATGATTCATCT\n+GAAAAACGTGAACCCACTTTCGAATAGTGCTTTTCAAATTTCTTTCCCGTAATTAAGGAA\n+AGTAAATCCATGTGCAGTTAGTATTGAAAAGGAAAGAATAAATAAAAGTGGGTCAAAAGT\n+AACGCCAAACAAACGAAGGTTATCGAAATATATGCGAAGGAGAGATTTATATACTAGTCA\n+AATTTAAACAGCTGAGATTGCTTTAGTCATCGCGTTGTTCCAGATCGTGAACGAAAACAC\n+CGATTCGCTCGCTAAAGTAGATACGAAATGTCCAGCAGATTTTGCTTAATTAAAACATAA\n+ATATTGATGAGCAAGAGCAGCTCGTTATAAATCAGACCTCCAAGGATTTTATCAACTACT\n+CAACTGGTTATGTGAATAATGACTCAGTTAAATATTAAATGTACTCTAAACGGTTATCAT\n+ACAATTTATTAGGAGGATTATACCAGCTAGTAGGAATTTAACCATTTCAAATTTAAACCT\n+CTTTTTTTTCGTAACTTGGGGTCGTCATAATGAATAATTCTGTTTGTCGAATTTGAAGGG\n+AAAAACACACTTGTTATCTAATTCCAAAAAAAAATAAAAAATTTTTAAAAATTAGTGGGG\n+TTTTTTTTTCACCAATGTCTAATGATGTGTGATTTAAAAAAAAACGTGTGTAACGCATTG\n+TAGTATTACTTACCTTTGCATGATTAAAAGTATATGTTGATATCGACTATTTAGAGTACT\n+GTGCGACACATTACCCTATGTTTCCCACTCTTAATCACCAAAAATTTTTTCCGAATGTCG\n+CAAGACTCAGAATCGTTCATCCGGCAACTGTTTAAGGCATTTACGGATTTTAGTACTGAC\n+GTTGAGTCACTTAGAGGATTTTTAACGCCAGATTATCGACAGCTTGTCGATGGACGTGAA\n+TTGACACTTGACGATTTTATTTCTCATGCCAAAGCACTACGTACCCATCTTCATCGGCTC\n+GACATCAACGTTCAACAAATTGTCTGTCAAGGTAACAAGGCTGCCACTGTGCATATTGCC\n+CATGCGATACGTTCCTCTGGCGAGTCCAGCAGAATCAAAGTCATTGCATTTTACAGTTTT\n+AAAGACGGGCGTATTTCTTTGATCGATGAGTTGACGTACGTTCTTGAAGGTGGTAATGCA\n+GACAGAGAGCTTGGATCAGTACAATGACTTCAATTACCTTGACACTGCATTGCCCACGTT\n+ATTCAACGTCCATCAGGAACCGGACAAATTATTCAGAGTCCTTTTGAACTACTTCATAAT\n+TTTACAAATATTCAAGTGTAATTCGTAATATAATCAGTTTTATTCATCTTCGTTGTCTAA\n+AACTTTTATGTGCTGCAATATTTGGGGAATCTCGATTTGACATAATGATCCCAGTGCC\n+>CUFF.4.1|m.5 CUFF.4.1|g.5 ORF CUFF.4.1|g.5 CUFF.4.1|m.5 type:3prime_partial len:120 (+) CUFF.4.1:199-555(+)\n+CTCTTTTTAATATTTTACCGATGAGATTGCTATTATTAGTTACGTTGCTATCTATCGTTG\n+GTTACACTAATCAGTTGCTTTCCAACTGACCTCGAAGACGCTCCAGCTGTAATCTGGGTA\n+GCCCAATTTCCTCCAGATAACACTACACAGCACTATGAATTCAGATATATCGTAAATGAA\n+TTATATAATGCTAGCAAGATGACTGCATTAATGAACCATATATATATCGATAATCCGCTT\n+ATAAGCAATTCAACTAATAACGTTACTCACGAGTTATTGATTGATCTCCATGAACTTTAT\n+AATGACGGAGAGATTTCCAGGATAGTTCTACTCAGAACTTTGGTAACTCAATCTGCGGAT\n+GATGCTACATGGATAATCAACTTGACAGATGATGTGCTTAATGGATTACCACTGCTGAAG\n+AAGCGAGACCGATACACCACACAATGTCATAGTACAAATATGGCAAGCACATATGACTGT\n+GACACTGGAGCCAATGCTGTTGGAGCCCGAGGTGGAGCCACGTTAGCAGCCGACTATAGA\n+GGTGATTGGGGGGGG\n+>CUFF.51.1|m.2 CUFF.51.1|g.2 ORF CUFF.51.1|g.2 CUFF.51.1|m.2 type:complete len:347 (+) CUFF.51.1:317-1357(+)\n+CGACGTTAATAAAATATTTAACAAAGCCTTTAAAAAATTAACGATAGCTAGTCAAAGGAA\n+GCTTAACGCGTATTCAGCCTCATTAAGACAATCAGGAAGCTTTTTTTTACCATCAGCATA\n+TACCTCTAACCCTTTGATTTATTTTTATATCTCGAGATTTCGTTCGTTATTTTATAGGTC\n+GTTTCGATAAGACCTTAATACAATCTGATTTAGTGGTTGTTTAAGATTTCGGAAAAGCCT\n+TTTTTTCAAAAAAAGTTTTCCAGTTATTGTTTCATTATTTCTAATTGATTTACTGAAGAA\n+TTGTTATAACCTAAAGATGGCACTTATGTTATCCAGGATTCCACGTCGTTTTTTTTTCTT\n+ATTTTTAACGGTCGGCTTGATTGCTGGCGCGTTTCTATACTCGTTGATATATTTTGTGGA\n+CGTTGATTTGGTGTCGAAGGTTAACCAGTTGTATGATCAGCAAATTGCACCCATGCTCTC\n+CGATGCTATTGGCACTCCATCCGTTAATCACTCGTTTGAGTTGGCGCCGTTAGACTCTCA\n+TTTGGTGGCCACAAGCACTACATTCCACGAGGCGTCATACGAGTCAGAGCCTCAGCAAAA\n+TCCTGCCAGTCAAAATATTGTCTTATTACTAGTTAGTGATGGACACACTTCTTACAATAA\n+TGGAGCTAATACGTTTGAAGAAGCTATACAGAACAGAGTTGACTATAGTACCAAACAAAA\n+CTACAACTTTGAGTATGTCAATGTTACTGGCCTCCCTATTCCCGCCGTTTGGTCCAAGAT\n+GCCCGCCGTCTTACAAACTATGAAGAAATACCCCAAAGCGGAATGGATCTGGTTGTTGGA\n+TCAGGATGCAATTATTACTAATACCCATCTTTCCCTTCAAGACTCCTTTTTGAAACCTGA\n+GAACTTGCAAAAGACCTTAATTACTAATACCATCCTCACTAAACGGCCTATAAATGCTAA\n+CGGGGATTTGCGTTATACACCAAGTAATTATAGTTTAAAAGATATCGAAAATCTCATGGT\n+CATAATCTCACAGGATCACAATGGATTAAACGCAGGTAGTATCTTGTTCCGTAATTCACC\n+TGCTACTGCCTTGTTTTTGGATATTTGGACAGATCCTGTTGTTGCAGAATGTGCGAAAGC\n+CAATAATGAACAAGACATGCTTGGATATTTGATTTCTAAGCATTCACAACTTGCTTCGCT\n+GGTTGGCCTTATTCCTCAAAGAAAAATAAATGCTTTTCACGAAGGTCCGGAAAATATGGA\n+ATGGCAAAAAGGTGATTTGGTAATTCACTTTGCTGGATGTTGGGTTGAAAACCGCTGCGA\n+TGAACTATGGCAAAAGTTTTACGCCTTGATTGACTAAGTTGCTTATTCATTATATCCGTC\n+TGTTTAATTTGTTTGTGTTTTAAAAAATTTTATATATATAAACAAAGCGCCGTATAATTT\n+TCCGTCAATCTTCCTTTCTTTATCTGAATCTCTAAT'..b'GGACAAGA\n+ATATATACCCCAATACTCTGTCTGTTTTACGTACTCGTGCTTCTGGTTTTGGTATCAAAA\n+TTGAATTAGACAATATCACTCCTGAACTCATTACGAAGTCTGCTAAGCATGTTTTTGGTA\n+TCTTTGTGCAATACCCAGCGGCGGATGGCTCTATTTTTGACTATGGTCATTTAGCTGCTA\n+CAGCACGCTCTTTTAATATGCACGTCGTAGCTGCCACCGATTTACTAGCTCTCACTATTT\n+TGAAATCGCCTGGGGAATGGGGTGCCGATGTTGCTGTTGGTTCCACTCAGCGCTTTGGTC\n+TGCCCATGGGCTATGGTGGCCCCCATGCCGGATTCTTTGCTTGTAGTGAAGAATTTAAAC\n+GAAAGATACCCGGTCGTCTTATTGGTCTCAGCAAAGATCGTTTAGAAAATCCCGCATACC\n+GGTTGGCTCTTCAAACAAGAGAACAACATATTCGTCGTGAAAAGGCTACAAGTAACATTT\n+GCACGGCTCAAGCTTTGTTAGCCAATATGTCTGCATTCTATGCTATTTACCATGGGCCAA\n+ATGGTCTCCAAGAAATTGCAAACCGTATTTACGCTAGTACCTCCTTCTTAAAATCTGCTT\n+TGGAATCTTCAGGATATAAAATTGTTAATAAAAGTCATTTCTTTGACACATTAACTATCG\n+AAGTTGAGTCGGCTGACAAAGTTCTTGCGAAAGCACTTGATCACGGTTACAATTTAAGAA\n+AGGTTGATGATTCACATGTTGGTCTTTCATTGGACGAGACCGTTTGCGATAAAGATATTC\n+AAGCTTTGTTTAGCATCTTTAATATAAATAAGAGTGTTGATCAGTATTATATGGAAATTG\n+CAACGTCGGAACCTAATGGAAATTCTGCTTCAACAGTCGATAATCTCAGCATTTGTTCTC\n+TTCCTGAAAACTTTAGACGAACAACCCTCTATTTACAACATCCCGTGTTTAACAGATACC\n+ATTCGGAAACTGAACTTATGCGTTATATTCATCATTTGCAGTCGAAGGATCTATCTTTAG\n+CTCATGCCATGACCCCATTGGGTTCGTGCACAATGAAGTTGAATGCTGTCACCGAAATGA\n+TGCCAATCACAAATCCATTATTTGCCAACATTCATCCATATGTTCCAGAGGAACAAGCTA\n+AAGGTTATCGTCATGTTATCGAAGATTTGCAGTTAATGTTAACGACCATCACCGGCTTTG\n+ATGCTGCATGCTTTCAACCAAATTCGGGAGCCGCTGGAGAATACACTGGCTTAAGTGTTA\n+TTCGAGCATATCAGCGGTCTATTGGTCAAGGTCATCGCAATATTTGCTTAATTCCTGTTT\n+CGGCTCACGGTACTAATCCAGCTTCAGCTGCTATGGCTGGGTTTACTGTTATTCCTGTAA\n+AATGTCTCAATAACGGTTATTTGGATATGCAAGACTTAAAAGAAAAGGCCTCTAAACACG\n+CCGACAAGTTAGCTGCCTTTATGGTAACTTATCCTAGTACTTTTGGCATTTTTGAGCCTG\n+ATGTTAAGGAAGCTTTGGAAGTAATTCACGAACATGGTGGTCAGGTTTACTTTGATGGTG\n+CTAACATGAATGCAATGGTTGGTTTATGCAAGGCTGGTGATATTGGTGCTGATGTTTGTC\n+ACTTAAATCTTCATAAGACATTTTGCATTCCTCACGGCGGTGGCGGTCCTGGTGTAGGTC\n+CTATTTGTGTAAAAAAGCATCTTGCTGATTTCCTACCATCTCATCCTGTAGTTTCATGCG\n+GCGGTAAGAATGGTATCACATCTGTTAGCTCTTCTCCTTTTGGCTCTGCTGGTATTTTAC\n+CTATCTCATGGGCATACATGAGAATGATGGGACTTGCCGGTTTGCGTGACGCTTCCAAAG\n+CCGCTCTGTTAAATGCCAATTATATGGCCAAGCGCCTGTCATCTCATTATAAACTTGTTT\n+ACACTAATAAGAACAACCTCTGTGCTCATGAGTTTATTCTAGATGCTCGCGAATTTAAAG\n+CTACTGCGGGTGTAGATGCAACTGATATAGCTAAACGTTTGCAAGATTACAGTTTCCATG\n+CACCAACTCTTTCCTGGCCTATTGCTAATACACTGATGATTGAGCCTACCGAGTCTGAGA\n+GTATGTATGAGATGGACCGCTTCTGTGATGCTTTAATTTCTATTCGACAAGAAATTCGTG\n+AAATTGAAGAAGGTCTCCAGCCTAAGGACAATAACCTGCTCGTTAATGCTCCCCACCCTC\n+AAAAGGACATTGCATCTGAGAAATGGGATCGTCCTTATACTCGAGAGCGGGCTGTCTATC\n+CTGTGCCTCTTTTAAAGGAACGGAAATTCTGGCCTAGCGTTGCTCGATTAGATGATGCGT\n+ACGGTGACAAGAACTTATTTTGTACTTGTTCCCCAGTTGTTTAGCGGTCAAAAAGAGCTC\n+ACCTGCTAGATTACTTCAACCTTTTCCCAGTTAAGTTCAACCTAATTTTTACTCCATTTG\n+GTAGTTCGTTCAACACCAATTCCCACGTTTATATATAGACCAATTTTTTACTACATCTTG\n+TTAGACAATTCTTTCCGTTATCACTTTTTCGAATTTTTTTTAATTACGTTTTAATTTTGA\n+AGGTTAGAATTATCCTTTGCTGGAACATGAGGTTTTCAACAACCTTTTTTTAATCTGATA\n+ATCTAATTTTGCTAGTCATATAATTGCGACTTTCTGATAAAAACATTACCTATACTTTAT\n+AAATATGTCGTTTTTAAATATTAACTCCTATGTCTTACTTGCATCCTTGAAATTTACGAC\n+TAGAAATTTGGTGCTTTGGATTTTCGTTACATTAAGTAAGGCCATTGAATCGATATGACA\n+CGTAAATGTTAAATTTCAAAATATTTTGGAGAGCACCATGTATAATTTAAATATACGAAT\n+TTTTTCCTTTAAATTTGTGGTTCTTTTTTAAAAAATATCAAGACGAGTACTCGATTACTC\n+GTAAGTATTCAAG\n+>CUFF.9.1|m.6 CUFF.9.1|g.6 ORF CUFF.9.1|g.6 CUFF.9.1|m.6 type:complete len:156 (+) CUFF.9.1:173-640(+)\n+AGCGAAACAAACAAATCACGTTATAGACGGTGGCAGGGCCATAAAAGGTATTCCCTCGCT\n+TTAAAAAGAAACAATGTCAAAAAGCTTTCTTTATAAACTATTGGAAGATTGAAGACATTA\n+AAGAAGAAAAGTCCTGCTTACCCTTGGACTTTTTTCAGCAGTTTTCATTGCCATGCCTAT\n+CAACCAAAAGTTTTATTCATATCTGGTAAAGCGAAATGGTGGTGAAGGTGAACCTGAATT\n+TCGACTTCCTATGGGTTTTATTGGAATCACACTTTTTGAAATAGGAATTTTACTTTTCGG\n+TTGGACTGCAAGATATAAGATTTTTTGGTTTGTGCCAACAATTGGATCAGCCATTATGGG\n+TGGTGGGTACATTATGACTTCCAATCCCTTAAACATGTATGTGGTAGATTCATATGGAAT\n+TTACTCAGCCAGTGCGTCAGCGGGTGTAAAAATATTTCAACTATTATTAGGAGCCATCTT\n+TCCATTATTTGCTGAAAGTCTATTTCGTCGACTGAACTACGGATGGGGGTGTACTTTACT\n+TGCCTTTATTTTATTAGCTTGTGGCTGTAGTCTTCCAATCTTATTCAAGTATGGAAAACA\n+AATTAGAAATCTACGACCATTTGACCCCTCAAAATACTAGTTGATTTAACTGATCAAAGT\n+GAGGATTTTCACACACATTTTCAGAGTACTTGGAACGTGCCGAGCTGATTAAAAAACACC\n+GGTATTAACAAAAAATTTTATTTATGAAGCAATACGCTATTTCGTTATGAGAAACTTGAT\n+TCAATGAAACTATTATAAACCTTA\n' |
| b |
| diff -r 000000000000 -r 8aef9a17faae test-data/strand/test.fa.transdecoder.pep --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/strand/test.fa.transdecoder.pep Fri Nov 20 06:49:25 2015 -0500 |
| b |
| @@ -0,0 +1,45 @@ +>CUFF.36.1|m.4 CUFF.36.1|g.4 ORF CUFF.36.1|g.4 CUFF.36.1|m.4 type:complete len:131 (+) CUFF.36.1:895-1287(+) +MSQDSESFIRQLFKAFTDFSTDVESLRGFLTPDYRQLVDGRELTLDDFISHAKALRTHLH +RLDINVQQIVCQGNKAATVHIAHAIRSSGESSRIKVIAFYSFKDGRISLIDELTYVLEGG +NADRELGSVQ* +>CUFF.4.1|m.5 CUFF.4.1|g.5 ORF CUFF.4.1|g.5 CUFF.4.1|m.5 type:3prime_partial len:120 (+) CUFF.4.1:199-555(+) +MTALMNHIYIDNPLISNSTNNVTHELLIDLHELYNDGEISRIVLLRTLVTQSADDATWII +NLTDDVLNGLPLLKKRDRYTTQCHSTNMASTYDCDTGANAVGARGGATLAADYRGDWGG +>CUFF.51.1|m.1 CUFF.51.1|g.1 ORF CUFF.51.1|g.1 CUFF.51.1|m.1 type:complete len:372 (+) CUFF.51.1:2632-3747(+) +MSRISLSNFLSLPRYKFLLFSVVLIIVMTTLVFNGHDYKQTLNDRLTSLKNNFVEENDNA +VLKEEPGKYTYMSLFTMPSTEEDYYFNATRVLIHRLKYHPTTKSKYPIHILALRGVDEWK +IERFRKDGASVIVIDPIASSDIVYDTSSFSQEISARYEQMFSKLRIFEQIQFDKICVIDS +DILIMKNIDDIFDTPYMYQQINTLNYTRLPSYTKPDDDTVYHFNEDFKEYGASRSEFYPY +LLAAVSDRGEHHSIPPEDTPYFNAGLMLIRPSELHFNRILKIGRFPYMYENAKMMEQSLL +NLAFSLDGWFPWTRLDPYYNGVWPSIDERPLLKTAHGKFWNIGSSEFAPVYLADWYAAYG +EMLSFHKYETH* +>CUFF.51.1|m.2 CUFF.51.1|g.2 ORF CUFF.51.1|g.2 CUFF.51.1|m.2 type:complete len:347 (+) CUFF.51.1:317-1357(+) +MALMLSRIPRRFFFLFLTVGLIAGAFLYSLIYFVDVDLVSKVNQLYDQQIAPMLSDAIGT +PSVNHSFELAPLDSHLVATSTTFHEASYESEPQQNPASQNIVLLLVSDGHTSYNNGANTF +EEAIQNRVDYSTKQNYNFEYVNVTGLPIPAVWSKMPAVLQTMKKYPKAEWIWLLDQDAII +TNTHLSLQDSFLKPENLQKTLITNTILTKRPINANGDLRYTPSNYSLKDIENLMVIISQD +HNGLNAGSILFRNSPATALFLDIWTDPVVAECAKANNEQDMLGYLISKHSQLASLVGLIP +QRKINAFHEGPENMEWQKGDLVIHFAGCWVENRCDELWQKFYALID* +>CUFF.57.1|m.3 CUFF.57.1|g.3 ORF CUFF.57.1|g.3 CUFF.57.1|m.3 type:complete len:1032 (+) CUFF.57.1:189-3284(+) +MFDSFMKRNQLALIMFRACSKLQYHGVNTSLSRHLFLAKRNLSISSACLEAKNSQKFPAL +DTFEPRHIGPSKTDQQYQLESLGYKDFDSFLKDVIPDSVRTPESQLMAFGSVNPNEKNPP +VNYSESEFTTLANNVANQNKLIKSFIGMGYYNVKLPAAIQRNVLENPEWYTQYTPYQAEI +SQGRLESMMNYQTMIADLTGLSISNASLLDEGTAAGEAMVMLMANDKKKRKTFLVDKNIY +PNTLSVLRTRASGFGIKIELDNITPELITKSAKHVFGIFVQYPAADGSIFDYGHLAATAR +SFNMHVVAATDLLALTILKSPGEWGADVAVGSTQRFGLPMGYGGPHAGFFACSEEFKRKI +PGRLIGLSKDRLENPAYRLALQTREQHIRREKATSNICTAQALLANMSAFYAIYHGPNGL +QEIANRIYASTSFLKSALESSGYKIVNKSHFFDTLTIEVESADKVLAKALDHGYNLRKVD +DSHVGLSLDETVCDKDIQALFSIFNINKSVDQYYMEIATSEPNGNSASTVDNLSICSLPE +NFRRTTLYLQHPVFNRYHSETELMRYIHHLQSKDLSLAHAMTPLGSCTMKLNAVTEMMPI +TNPLFANIHPYVPEEQAKGYRHVIEDLQLMLTTITGFDAACFQPNSGAAGEYTGLSVIRA +YQRSIGQGHRNICLIPVSAHGTNPASAAMAGFTVIPVKCLNNGYLDMQDLKEKASKHADK +LAAFMVTYPSTFGIFEPDVKEALEVIHEHGGQVYFDGANMNAMVGLCKAGDIGADVCHLN +LHKTFCIPHGGGGPGVGPICVKKHLADFLPSHPVVSCGGKNGITSVSSSPFGSAGILPIS +WAYMRMMGLAGLRDASKAALLNANYMAKRLSSHYKLVYTNKNNLCAHEFILDAREFKATA +GVDATDIAKRLQDYSFHAPTLSWPIANTLMIEPTESESMYEMDRFCDALISIRQEIREIE +EGLQPKDNNLLVNAPHPQKDIASEKWDRPYTRERAVYPVPLLKERKFWPSVARLDDAYGD +KNLFCTCSPVV* +>CUFF.9.1|m.6 CUFF.9.1|g.6 ORF CUFF.9.1|g.6 CUFF.9.1|m.6 type:complete len:156 (+) CUFF.9.1:173-640(+) +MPINQKFYSYLVKRNGGEGEPEFRLPMGFIGITLFEIGILLFGWTARYKIFWFVPTIGSA +IMGGGYIMTSNPLNMYVVDSYGIYSASASAGVKIFQLLLGAIFPLFAESLFRRLNYGWGC +TLLAFILLACGCSLPILFKYGKQIRNLRPFDPSKY* |
| b |
| diff -r 000000000000 -r 8aef9a17faae test-data/test.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.fa Fri Nov 20 06:49:25 2015 -0500 |
| b |
| b'@@ -0,0 +1,10 @@\n+>CUFF.51.1 CUFF.51\n+CGACGTTAATAAAATATTTAACAAAGCCTTTAAAAAATTAACGATAGCTAGTCAAAGGAAGCTTAACGCGTATTCAGCCTCATTAAGACAATCAGGAAGCTTTTTTTTACCATCAGCATATACCTCTAACCCTTTGATTTATTTTTATATCTCGAGATTTCGTTCGTTATTTTATAGGTCGTTTCGATAAGACCTTAATACAATCTGATTTAGTGGTTGTTTAAGATTTCGGAAAAGCCTTTTTTTCAAAAAAAGTTTTCCAGTTATTGTTTCATTATTTCTAATTGATTTACTGAAGAATTGTTATAACCTAAAGATGGCACTTATGTTATCCAGGATTCCACGTCGTTTTTTTTTCTTATTTTTAACGGTCGGCTTGATTGCTGGCGCGTTTCTATACTCGTTGATATATTTTGTGGACGTTGATTTGGTGTCGAAGGTTAACCAGTTGTATGATCAGCAAATTGCACCCATGCTCTCCGATGCTATTGGCACTCCATCCGTTAATCACTCGTTTGAGTTGGCGCCGTTAGACTCTCATTTGGTGGCCACAAGCACTACATTCCACGAGGCGTCATACGAGTCAGAGCCTCAGCAAAATCCTGCCAGTCAAAATATTGTCTTATTACTAGTTAGTGATGGACACACTTCTTACAATAATGGAGCTAATACGTTTGAAGAAGCTATACAGAACAGAGTTGACTATAGTACCAAACAAAACTACAACTTTGAGTATGTCAATGTTACTGGCCTCCCTATTCCCGCCGTTTGGTCCAAGATGCCCGCCGTCTTACAAACTATGAAGAAATACCCCAAAGCGGAATGGATCTGGTTGTTGGATCAGGATGCAATTATTACTAATACCCATCTTTCCCTTCAAGACTCCTTTTTGAAACCTGAGAACTTGCAAAAGACCTTAATTACTAATACCATCCTCACTAAACGGCCTATAAATGCTAACGGGGATTTGCGTTATACACCAAGTAATTATAGTTTAAAAGATATCGAAAATCTCATGGTCATAATCTCACAGGATCACAATGGATTAAACGCAGGTAGTATCTTGTTCCGTAATTCACCTGCTACTGCCTTGTTTTTGGATATTTGGACAGATCCTGTTGTTGCAGAATGTGCGAAAGCCAATAATGAACAAGACATGCTTGGATATTTGATTTCTAAGCATTCACAACTTGCTTCGCTGGTTGGCCTTATTCCTCAAAGAAAAATAAATGCTTTTCACGAAGGTCCGGAAAATATGGAATGGCAAAAAGGTGATTTGGTAATTCACTTTGCTGGATGTTGGGTTGAAAACCGCTGCGATGAACTATGGCAAAAGTTTTACGCCTTGATTGACTAAGTTGCTTATTCATTATATCCGTCTGTTTAATTTGTTTGTGTTTTAAAAAATTTTATATATATAAACAAAGCGCCGTATAATTTTCCGTCAATCTTCCTTTCTTTATCTGAATCTCTAATAATGTTTACTATTTTTTAATCTTTACATACCTAATTAATATAGCGGTTGTGCCATAGCAATCAAAGTTTCAGGTTAGTTTTTTATAGCGAGATATCTGGGAGTTTTGTTTTACACAATCGTCCATCAATAATTGTTATATATTGTATATATTTCACATTGACTTTGAAGCTGTTTCTGTTGGTTCAACTAATTTGCTTTGGCAATTTACCAATGCAATATTGAAGATTGGAATAACAGTTTGGCGTTAATAAATCTTTTTAATAATTTGCATTTCACCGCAGCTGCCATTTTCTGTTAAATGCTGATAGAAGTTTTATTGAATCATTCGTGTCGGATTATACTAAGTTTTTATTTATCTTGTTTTTTGGCCCTACAAAGTATTGGTATGTCCTTATTTTATATTGATTACACTGGCTTTTGGCCTTATAAAGATATAGATTAGTTGCTAAGTCTAAAAGATGTATTTTTTAACGGTGGTTCCATTACGTCTGTGCACCCACTGTTTACACTTGTGTCTTTACAAACCTAGAAGCATTTTCCGATTAATGAGGTCTATCAGGTCAAGGAGAAAGAATATTTGAATAGATTTATCGACAAAATATATTTCGTTAAATTTACACAATATTTACTTTACCAATAAGCTAAATGGTATTTCCAATACTTTTCCAGCTAACAGTCAGATTTTTCACTGTTTGAAACAACTTCACCAAATTAATTCATTAGTGTCAATTTCTATTACATGCTTAAGCTCATAATTTTCAACATCCAGATAGCTCGAAAGTTGACACCATTACACACAAACTAAGATGATTGTGAAAAAACAAAGCGTTAGGATTTGTAAAAGGCAATTCCACAATTTGAATTACAATACTGTAACTGAATATAGCGCGGCACATGGTACAAACAACGTGCTGGTAATAAATTGACAAATGCAGAGCAACCCGCGTGATGAAACATAAATCTCGGATATTTTTTCTTTAAAGGGTTGTTAACGCAAGTCGTTTAAGGGTAAAAGAAATAAATAAATTTTAGAGGGTAACATCCTCATAAAGGGAGTCATCTTTAGAGCCTTTTTTCATTTTTTTAAGGCTTTCGAAAATTTCACGTGTCTCAAATTCTATTGTTTCAGCGGTTCGTTGAATTAATCTCTTATCATGTCTCGAATTTCACTTTCAAATTTTTTATCTCTTCCGCGTTACAAATTCCTGTTGTTTTCTGTGGTTTTGATTATTGTGATGACAACCTTAGTGTTTAACGGACACGATTATAAGCAAACCCTTAATGACCGGCTTACTTCATTAAAAAACAACTTTGTTGAGGAAAATGATAATGCCGTCTTAAAAGAAGAGCCTGGCAAATATACGTATATGAGTTTGTTTACTATGCCTTCTACTGAAGAGGATTACTACTTCAACGCTACTAGGGTTTTAATTCACCGATTGAAATATCATCCTACTACCAAAAGTAAATACCCTATCCATATCCTTGCACTCCGTGGAGTAGATGAGTGGAAAATTGAACGTTTTCGAAAGGATGGTGCTTCTGTGATTGTTATAGACCCCATTGCTTCATCGGATATTGTATACGATACATCCTCATTTAGTCAAGAAATATCTGCTAGATATGAACAAATGTTTTCGAAGTTGCGAATTTTCGAACAAATACAATTTGACAAAATTTGCGTAATTGACAGTGATATATTGATCATGAAGAACATTGATGATATATTTGATACTCCTTATATGTACCAACAAATTAATACCTTGAACTATACACGGCTACCTTCCTACACGAAGCCTGATGATGATACCGTCTATCACTTCAATGAGGATTTTAAAGAATATGGTGCCAGTCGAAGCGAATTTTACCCTTATCTTCTCGCAGCCGTCTCTGATAGAGGAGAGCATCATAGTATACCTCCAGAAGATACTCCTTATTTCAATGCTGGCTTAATGCTTATACGTCCAAGCGAGCTTCATTTTAACCGTATACTTAAAATCGGAAGGTTTCCTTATATGTATGAGAATGCCAAAATGATGGAGCAAAGCTTGTTGAATCTTGCATTTTCCTTGGACGGATGGTTTCCCTGGACTCGTCTTGATCCTTATTACAATGGCGTGTGGCCCTCAATTGACGAACGTCCTCTCTTAAAAACAGCACACGGAAAATTCTGGAATATTGGTAGCTCAGAATTTGCACCAGTATATTTAGCTGACTGGTATGCTGCTTATGGCGAAATGCTGTCTTTTCATAAGTATGAAACTCATTAAAGGAGGAATACCTTTCTTTTTTCTGTATTGTGACCTTATTTTACAATTAGAAGTTAAAATCTAATTGTATGTTATATATTTGAAAATTTCTTTAACTTATTACCATAATTTTATTTTAGACTTGCTATCCTTATTGTCTAAACGCACATTGTTTAGATCTCTTCAGCTTTCTTTGATTGCTGGCTATGTATACAACTTTATTACCTGCGTCTGT'..b'GCCAATTATATGGCCAAGCGCCTGTCATCTCATTATAAACTTGTTTACACTAATAAGAACAACCTCTGTGCTCATGAGTTTATTCTAGATGCTCGCGAATTTAAAGCTACTGCGGGTGTAGATGCAACTGATATAGCTAAACGTTTGCAAGATTACAGTTTCCATGCACCAACTCTTTCCTGGCCTATTGCTAATACACTGATGATTGAGCCTACCGAGTCTGAGAGTATGTATGAGATGGACCGCTTCTGTGATGCTTTAATTTCTATTCGACAAGAAATTCGTGAAATTGAAGAAGGTCTCCAGCCTAAGGACAATAACCTGCTCGTTAATGCTCCCCACCCTCAAAAGGACATTGCATCTGAGAAATGGGATCGTCCTTATACTCGAGAGCGGGCTGTCTATCCTGTGCCTCTTTTAAAGGAACGGAAATTCTGGCCTAGCGTTGCTCGATTAGATGATGCGTACGGTGACAAGAACTTATTTTGTACTTGTTCCCCAGTTGTTTAGCGGTCAAAAAGAGCTCACCTGCTAGATTACTTCAACCTTTTCCCAGTTAAGTTCAACCTAATTTTTACTCCATTTGGTAGTTCGTTCAACACCAATTCCCACGTTTATATATAGACCAATTTTTTACTACATCTTGTTAGACAATTCTTTCCGTTATCACTTTTTCGAATTTTTTTTAATTACGTTTTAATTTTGAAGGTTAGAATTATCCTTTGCTGGAACATGAGGTTTTCAACAACCTTTTTTTAATCTGATAATCTAATTTTGCTAGTCATATAATTGCGACTTTCTGATAAAAACATTACCTATACTTTATAAATATGTCGTTTTTAAATATTAACTCCTATGTCTTACTTGCATCCTTGAAATTTACGACTAGAAATTTGGTGCTTTGGATTTTCGTTACATTAAGTAAGGCCATTGAATCGATATGACACGTAAATGTTAAATTTCAAAATATTTTGGAGAGCACCATGTATAATTTAAATATACGAATTTTTTCCTTTAAATTTGTGGTTCTTTTTTAAAAAATATCAAGACGAGTACTCGATTACTCGTAAGTATTCAAG\n+>CUFF.36.1 CUFF.36\n+TGACTAAGTGGCAATGATGCTCCTAATGAAACCACTGATCCTCGATCATCAGCAGTAGTATCAATAGCAGCATCAGCACCGTTAGACAGCTGTTTTTCTAAACCATTCAATGATTCATCTGAAAAACGTGAACCCACTTTCGAATAGTGCTTTTCAAATTTCTTTCCCGTAATTAAGGAAAGTAAATCCATGTGCAGTTAGTATTGAAAAGGAAAGAATAAATAAAAGTGGGTCAAAAGTAACGCCAAACAAACGAAGGTTATCGAAATATATGCGAAGGAGAGATTTATATACTAGTCAAATTTAAACAGCTGAGATTGCTTTAGTCATCGCGTTGTTCCAGATCGTGAACGAAAACACCGATTCGCTCGCTAAAGTAGATACGAAATGTCCAGCAGATTTTGCTTAATTAAAACATAAATATTGATGAGCAAGAGCAGCTCGTTATAAATCAGACCTCCAAGGATTTTATCAACTACTCAACTGGTTATGTGAATAATGACTCAGTTAAATATTAAATGTACTCTAAACGGTTATCATACAATTTATTAGGAGGATTATACCAGCTAGTAGGAATTTAACCATTTCAAATTTAAACCTCTTTTTTTTCGTAACTTGGGGTCGTCATAATGAATAATTCTGTTTGTCGAATTTGAAGGGAAAAACACACTTGTTATCTAATTCCAAAAAAAAATAAAAAATTTTTAAAAATTAGTGGGGTTTTTTTTTCACCAATGTCTAATGATGTGTGATTTAAAAAAAAACGTGTGTAACGCATTGTAGTATTACTTACCTTTGCATGATTAAAAGTATATGTTGATATCGACTATTTAGAGTACTGTGCGACACATTACCCTATGTTTCCCACTCTTAATCACCAAAAATTTTTTCCGAATGTCGCAAGACTCAGAATCGTTCATCCGGCAACTGTTTAAGGCATTTACGGATTTTAGTACTGACGTTGAGTCACTTAGAGGATTTTTAACGCCAGATTATCGACAGCTTGTCGATGGACGTGAATTGACACTTGACGATTTTATTTCTCATGCCAAAGCACTACGTACCCATCTTCATCGGCTCGACATCAACGTTCAACAAATTGTCTGTCAAGGTAACAAGGCTGCCACTGTGCATATTGCCCATGCGATACGTTCCTCTGGCGAGTCCAGCAGAATCAAAGTCATTGCATTTTACAGTTTTAAAGACGGGCGTATTTCTTTGATCGATGAGTTGACGTACGTTCTTGAAGGTGGTAATGCAGACAGAGAGCTTGGATCAGTACAATGACTTCAATTACCTTGACACTGCATTGCCCACGTTATTCAACGTCCATCAGGAACCGGACAAATTATTCAGAGTCCTTTTGAACTACTTCATAATTTTACAAATATTCAAGTGTAATTCGTAATATAATCAGTTTTATTCATCTTCGTTGTCTAAAACTTTTATGTGCTGCAATATTTGGGGAATCTCGATTTGACATAATGATCCCAGTGCC\n+>CUFF.4.1 CUFF.4\n+CTCTTTTTAATATTTTACCGATGAGATTGCTATTATTAGTTACGTTGCTATCTATCGTTGGTTACACTAATCAGTTGCTTTCCAACTGACCTCGAAGACGCTCCAGCTGTAATCTGGGTAGCCCAATTTCCTCCAGATAACACTACACAGCACTATGAATTCAGATATATCGTAAATGAATTATATAATGCTAGCAAGATGACTGCATTAATGAACCATATATATATCGATAATCCGCTTATAAGCAATTCAACTAATAACGTTACTCACGAGTTATTGATTGATCTCCATGAACTTTATAATGACGGAGAGATTTCCAGGATAGTTCTACTCAGAACTTTGGTAACTCAATCTGCGGATGATGCTACATGGATAATCAACTTGACAGATGATGTGCTTAATGGATTACCACTGCTGAAGAAGCGAGACCGATACACCACACAATGTCATAGTACAAATATGGCAAGCACATATGACTGTGACACTGGAGCCAATGCTGTTGGAGCCCGAGGTGGAGCCACGTTAGCAGCCGACTATAGAGGTGATTGGGGGGGG\n+>CUFF.9.1 CUFF.9\n+AGCGAAACAAACAAATCACGTTATAGACGGTGGCAGGGCCATAAAAGGTATTCCCTCGCTTTAAAAAGAAACAATGTCAAAAAGCTTTCTTTATAAACTATTGGAAGATTGAAGACATTAAAGAAGAAAAGTCCTGCTTACCCTTGGACTTTTTTCAGCAGTTTTCATTGCCATGCCTATCAACCAAAAGTTTTATTCATATCTGGTAAAGCGAAATGGTGGTGAAGGTGAACCTGAATTTCGACTTCCTATGGGTTTTATTGGAATCACACTTTTTGAAATAGGAATTTTACTTTTCGGTTGGACTGCAAGATATAAGATTTTTTGGTTTGTGCCAACAATTGGATCAGCCATTATGGGTGGTGGGTACATTATGACTTCCAATCCCTTAAACATGTATGTGGTAGATTCATATGGAATTTACTCAGCCAGTGCGTCAGCGGGTGTAAAAATATTTCAACTATTATTAGGAGCCATCTTTCCATTATTTGCTGAAAGTCTATTTCGTCGACTGAACTACGGATGGGGGTGTACTTTACTTGCCTTTATTTTATTAGCTTGTGGCTGTAGTCTTCCAATCTTATTCAAGTATGGAAAACAAATTAGAAATCTACGACCATTTGACCCCTCAAAATACTAGTTGATTTAACTGATCAAAGTGAGGATTTTCACACACATTTTCAGAGTACTTGGAACGTGCCGAGCTGATTAAAAAACACCGGTATTAACAAAAAATTTTATTTATGAAGCAATACGCTATTTCGTTATGAGAAACTTGATTCAATGAAACTATTATAAACCTTA\n' |
| b |
| diff -r 000000000000 -r 8aef9a17faae test-data/top/test.fa.transdecoder.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/top/test.fa.transdecoder.bed Fri Nov 20 06:49:25 2015 -0500 |
| b |
| @@ -0,0 +1,7 @@ +track name='dataset_7.dat.transdecoder.gff3' +CUFF.36.1 0 1498 ID=CUFF.36.1|m.4;CUFF.36.1|g.4;ORF_CUFF.36.1|g.4_CUFF.36.1|m.4_type:complete_len:131_(+) 0 + 894 1287 0 1 1498 0 +CUFF.4.1 0 555 ID=CUFF.4.1|m.5;CUFF.4.1|g.5;ORF_CUFF.4.1|g.5_CUFF.4.1|m.5_type:3prime_partial_len:120_(+) 0 + 198 555 0 1 555 0 +CUFF.51.1 0 4342 ID=CUFF.51.1|m.2;CUFF.51.1|g.2;ORF_CUFF.51.1|g.2_CUFF.51.1|m.2_type:complete_len:347_(+) 0 + 316 1357 0 1 4342 0 +CUFF.51.1 0 4342 ID=CUFF.51.1|m.1;CUFF.51.1|g.1;ORF_CUFF.51.1|g.1_CUFF.51.1|m.1_type:complete_len:372_(+) 0 + 2631 3747 0 1 4342 0 +CUFF.57.1 0 3853 ID=CUFF.57.1|m.3;CUFF.57.1|g.3;ORF_CUFF.57.1|g.3_CUFF.57.1|m.3_type:complete_len:1032_(+) 0 + 188 3284 0 1 3853 0 +CUFF.9.1 0 804 ID=CUFF.9.1|m.6;CUFF.9.1|g.6;ORF_CUFF.9.1|g.6_CUFF.9.1|m.6_type:complete_len:156_(+) 0 + 172 640 0 1 804 0 |
| b |
| diff -r 000000000000 -r 8aef9a17faae test-data/top/test.fa.transdecoder.cds --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/top/test.fa.transdecoder.cds Fri Nov 20 06:49:25 2015 -0500 |
| b |
| @@ -0,0 +1,116 @@ +>CUFF.36.1|m.4 CUFF.36.1|g.4 ORF CUFF.36.1|g.4 CUFF.36.1|m.4 type:complete len:131 (+) CUFF.36.1:895-1287(+) +ATGTCGCAAGACTCAGAATCGTTCATCCGGCAACTGTTTAAGGCATTTACGGATTTTAGT +ACTGACGTTGAGTCACTTAGAGGATTTTTAACGCCAGATTATCGACAGCTTGTCGATGGA +CGTGAATTGACACTTGACGATTTTATTTCTCATGCCAAAGCACTACGTACCCATCTTCAT +CGGCTCGACATCAACGTTCAACAAATTGTCTGTCAAGGTAACAAGGCTGCCACTGTGCAT +ATTGCCCATGCGATACGTTCCTCTGGCGAGTCCAGCAGAATCAAAGTCATTGCATTTTAC +AGTTTTAAAGACGGGCGTATTTCTTTGATCGATGAGTTGACGTACGTTCTTGAAGGTGGT +AATGCAGACAGAGAGCTTGGATCAGTACAATGA +>CUFF.4.1|m.5 CUFF.4.1|g.5 ORF CUFF.4.1|g.5 CUFF.4.1|m.5 type:3prime_partial len:120 (+) CUFF.4.1:199-555(+) +ATGACTGCATTAATGAACCATATATATATCGATAATCCGCTTATAAGCAATTCAACTAAT +AACGTTACTCACGAGTTATTGATTGATCTCCATGAACTTTATAATGACGGAGAGATTTCC +AGGATAGTTCTACTCAGAACTTTGGTAACTCAATCTGCGGATGATGCTACATGGATAATC +AACTTGACAGATGATGTGCTTAATGGATTACCACTGCTGAAGAAGCGAGACCGATACACC +ACACAATGTCATAGTACAAATATGGCAAGCACATATGACTGTGACACTGGAGCCAATGCT +GTTGGAGCCCGAGGTGGAGCCACGTTAGCAGCCGACTATAGAGGTGATTGGGGGGGG +>CUFF.51.1|m.1 CUFF.51.1|g.1 ORF CUFF.51.1|g.1 CUFF.51.1|m.1 type:complete len:372 (+) CUFF.51.1:2632-3747(+) +ATGTCTCGAATTTCACTTTCAAATTTTTTATCTCTTCCGCGTTACAAATTCCTGTTGTTT +TCTGTGGTTTTGATTATTGTGATGACAACCTTAGTGTTTAACGGACACGATTATAAGCAA +ACCCTTAATGACCGGCTTACTTCATTAAAAAACAACTTTGTTGAGGAAAATGATAATGCC +GTCTTAAAAGAAGAGCCTGGCAAATATACGTATATGAGTTTGTTTACTATGCCTTCTACT +GAAGAGGATTACTACTTCAACGCTACTAGGGTTTTAATTCACCGATTGAAATATCATCCT +ACTACCAAAAGTAAATACCCTATCCATATCCTTGCACTCCGTGGAGTAGATGAGTGGAAA +ATTGAACGTTTTCGAAAGGATGGTGCTTCTGTGATTGTTATAGACCCCATTGCTTCATCG +GATATTGTATACGATACATCCTCATTTAGTCAAGAAATATCTGCTAGATATGAACAAATG +TTTTCGAAGTTGCGAATTTTCGAACAAATACAATTTGACAAAATTTGCGTAATTGACAGT +GATATATTGATCATGAAGAACATTGATGATATATTTGATACTCCTTATATGTACCAACAA +ATTAATACCTTGAACTATACACGGCTACCTTCCTACACGAAGCCTGATGATGATACCGTC +TATCACTTCAATGAGGATTTTAAAGAATATGGTGCCAGTCGAAGCGAATTTTACCCTTAT +CTTCTCGCAGCCGTCTCTGATAGAGGAGAGCATCATAGTATACCTCCAGAAGATACTCCT +TATTTCAATGCTGGCTTAATGCTTATACGTCCAAGCGAGCTTCATTTTAACCGTATACTT +AAAATCGGAAGGTTTCCTTATATGTATGAGAATGCCAAAATGATGGAGCAAAGCTTGTTG +AATCTTGCATTTTCCTTGGACGGATGGTTTCCCTGGACTCGTCTTGATCCTTATTACAAT +GGCGTGTGGCCCTCAATTGACGAACGTCCTCTCTTAAAAACAGCACACGGAAAATTCTGG +AATATTGGTAGCTCAGAATTTGCACCAGTATATTTAGCTGACTGGTATGCTGCTTATGGC +GAAATGCTGTCTTTTCATAAGTATGAAACTCATTAA +>CUFF.51.1|m.2 CUFF.51.1|g.2 ORF CUFF.51.1|g.2 CUFF.51.1|m.2 type:complete len:347 (+) CUFF.51.1:317-1357(+) +ATGGCACTTATGTTATCCAGGATTCCACGTCGTTTTTTTTTCTTATTTTTAACGGTCGGC +TTGATTGCTGGCGCGTTTCTATACTCGTTGATATATTTTGTGGACGTTGATTTGGTGTCG +AAGGTTAACCAGTTGTATGATCAGCAAATTGCACCCATGCTCTCCGATGCTATTGGCACT +CCATCCGTTAATCACTCGTTTGAGTTGGCGCCGTTAGACTCTCATTTGGTGGCCACAAGC +ACTACATTCCACGAGGCGTCATACGAGTCAGAGCCTCAGCAAAATCCTGCCAGTCAAAAT +ATTGTCTTATTACTAGTTAGTGATGGACACACTTCTTACAATAATGGAGCTAATACGTTT +GAAGAAGCTATACAGAACAGAGTTGACTATAGTACCAAACAAAACTACAACTTTGAGTAT +GTCAATGTTACTGGCCTCCCTATTCCCGCCGTTTGGTCCAAGATGCCCGCCGTCTTACAA +ACTATGAAGAAATACCCCAAAGCGGAATGGATCTGGTTGTTGGATCAGGATGCAATTATT +ACTAATACCCATCTTTCCCTTCAAGACTCCTTTTTGAAACCTGAGAACTTGCAAAAGACC +TTAATTACTAATACCATCCTCACTAAACGGCCTATAAATGCTAACGGGGATTTGCGTTAT +ACACCAAGTAATTATAGTTTAAAAGATATCGAAAATCTCATGGTCATAATCTCACAGGAT +CACAATGGATTAAACGCAGGTAGTATCTTGTTCCGTAATTCACCTGCTACTGCCTTGTTT +TTGGATATTTGGACAGATCCTGTTGTTGCAGAATGTGCGAAAGCCAATAATGAACAAGAC +ATGCTTGGATATTTGATTTCTAAGCATTCACAACTTGCTTCGCTGGTTGGCCTTATTCCT +CAAAGAAAAATAAATGCTTTTCACGAAGGTCCGGAAAATATGGAATGGCAAAAAGGTGAT +TTGGTAATTCACTTTGCTGGATGTTGGGTTGAAAACCGCTGCGATGAACTATGGCAAAAG +TTTTACGCCTTGATTGACTAA +>CUFF.57.1|m.3 CUFF.57.1|g.3 ORF CUFF.57.1|g.3 CUFF.57.1|m.3 type:complete len:1032 (+) CUFF.57.1:189-3284(+) +ATGTTCGATAGCTTTATGAAGAGAAATCAGCTAGCCTTAATCATGTTTCGTGCTTGCTCG +AAGTTGCAGTACCATGGAGTAAATACCAGCCTTTCGAGGCATTTGTTTCTTGCTAAAAGA +AATTTATCCATTTCTTCAGCTTGTCTAGAAGCTAAAAACTCCCAAAAGTTTCCTGCTCTT +GATACTTTTGAACCTCGACACATTGGACCTTCTAAAACGGATCAACAATATCAATTGGAG +TCACTAGGGTATAAGGATTTTGATTCTTTCCTCAAAGATGTAATTCCAGATTCTGTGCGA +ACACCTGAGAGCCAATTGATGGCTTTTGGGTCTGTGAATCCCAACGAAAAAAATCCTCCT +GTTAACTACTCCGAAAGCGAATTTACGACTCTGGCAAACAATGTGGCTAATCAAAATAAG +CTGATTAAGAGCTTCATTGGCATGGGATACTATAATGTAAAGCTTCCTGCTGCTATTCAG +CGTAATGTTCTTGAGAACCCTGAATGGTATACTCAATATACTCCATATCAGGCTGAAATT +TCTCAAGGGCGTCTGGAATCTATGATGAATTATCAAACCATGATTGCTGATCTCACAGGT +CTCAGCATTAGCAATGCTAGTTTACTGGATGAAGGAACTGCTGCTGGAGAAGCAATGGTT +ATGTTGATGGCCAACGACAAAAAGAAGCGCAAAACGTTTTTAGTGGACAAGAATATATAC +CCCAATACTCTGTCTGTTTTACGTACTCGTGCTTCTGGTTTTGGTATCAAAATTGAATTA +GACAATATCACTCCTGAACTCATTACGAAGTCTGCTAAGCATGTTTTTGGTATCTTTGTG +CAATACCCAGCGGCGGATGGCTCTATTTTTGACTATGGTCATTTAGCTGCTACAGCACGC +TCTTTTAATATGCACGTCGTAGCTGCCACCGATTTACTAGCTCTCACTATTTTGAAATCG +CCTGGGGAATGGGGTGCCGATGTTGCTGTTGGTTCCACTCAGCGCTTTGGTCTGCCCATG +GGCTATGGTGGCCCCCATGCCGGATTCTTTGCTTGTAGTGAAGAATTTAAACGAAAGATA +CCCGGTCGTCTTATTGGTCTCAGCAAAGATCGTTTAGAAAATCCCGCATACCGGTTGGCT +CTTCAAACAAGAGAACAACATATTCGTCGTGAAAAGGCTACAAGTAACATTTGCACGGCT +CAAGCTTTGTTAGCCAATATGTCTGCATTCTATGCTATTTACCATGGGCCAAATGGTCTC +CAAGAAATTGCAAACCGTATTTACGCTAGTACCTCCTTCTTAAAATCTGCTTTGGAATCT +TCAGGATATAAAATTGTTAATAAAAGTCATTTCTTTGACACATTAACTATCGAAGTTGAG +TCGGCTGACAAAGTTCTTGCGAAAGCACTTGATCACGGTTACAATTTAAGAAAGGTTGAT +GATTCACATGTTGGTCTTTCATTGGACGAGACCGTTTGCGATAAAGATATTCAAGCTTTG +TTTAGCATCTTTAATATAAATAAGAGTGTTGATCAGTATTATATGGAAATTGCAACGTCG +GAACCTAATGGAAATTCTGCTTCAACAGTCGATAATCTCAGCATTTGTTCTCTTCCTGAA +AACTTTAGACGAACAACCCTCTATTTACAACATCCCGTGTTTAACAGATACCATTCGGAA +ACTGAACTTATGCGTTATATTCATCATTTGCAGTCGAAGGATCTATCTTTAGCTCATGCC +ATGACCCCATTGGGTTCGTGCACAATGAAGTTGAATGCTGTCACCGAAATGATGCCAATC +ACAAATCCATTATTTGCCAACATTCATCCATATGTTCCAGAGGAACAAGCTAAAGGTTAT +CGTCATGTTATCGAAGATTTGCAGTTAATGTTAACGACCATCACCGGCTTTGATGCTGCA +TGCTTTCAACCAAATTCGGGAGCCGCTGGAGAATACACTGGCTTAAGTGTTATTCGAGCA +TATCAGCGGTCTATTGGTCAAGGTCATCGCAATATTTGCTTAATTCCTGTTTCGGCTCAC +GGTACTAATCCAGCTTCAGCTGCTATGGCTGGGTTTACTGTTATTCCTGTAAAATGTCTC +AATAACGGTTATTTGGATATGCAAGACTTAAAAGAAAAGGCCTCTAAACACGCCGACAAG +TTAGCTGCCTTTATGGTAACTTATCCTAGTACTTTTGGCATTTTTGAGCCTGATGTTAAG +GAAGCTTTGGAAGTAATTCACGAACATGGTGGTCAGGTTTACTTTGATGGTGCTAACATG +AATGCAATGGTTGGTTTATGCAAGGCTGGTGATATTGGTGCTGATGTTTGTCACTTAAAT +CTTCATAAGACATTTTGCATTCCTCACGGCGGTGGCGGTCCTGGTGTAGGTCCTATTTGT +GTAAAAAAGCATCTTGCTGATTTCCTACCATCTCATCCTGTAGTTTCATGCGGCGGTAAG +AATGGTATCACATCTGTTAGCTCTTCTCCTTTTGGCTCTGCTGGTATTTTACCTATCTCA +TGGGCATACATGAGAATGATGGGACTTGCCGGTTTGCGTGACGCTTCCAAAGCCGCTCTG +TTAAATGCCAATTATATGGCCAAGCGCCTGTCATCTCATTATAAACTTGTTTACACTAAT +AAGAACAACCTCTGTGCTCATGAGTTTATTCTAGATGCTCGCGAATTTAAAGCTACTGCG +GGTGTAGATGCAACTGATATAGCTAAACGTTTGCAAGATTACAGTTTCCATGCACCAACT +CTTTCCTGGCCTATTGCTAATACACTGATGATTGAGCCTACCGAGTCTGAGAGTATGTAT +GAGATGGACCGCTTCTGTGATGCTTTAATTTCTATTCGACAAGAAATTCGTGAAATTGAA +GAAGGTCTCCAGCCTAAGGACAATAACCTGCTCGTTAATGCTCCCCACCCTCAAAAGGAC +ATTGCATCTGAGAAATGGGATCGTCCTTATACTCGAGAGCGGGCTGTCTATCCTGTGCCT +CTTTTAAAGGAACGGAAATTCTGGCCTAGCGTTGCTCGATTAGATGATGCGTACGGTGAC +AAGAACTTATTTTGTACTTGTTCCCCAGTTGTTTAG +>CUFF.9.1|m.6 CUFF.9.1|g.6 ORF CUFF.9.1|g.6 CUFF.9.1|m.6 type:complete len:156 (+) CUFF.9.1:173-640(+) +ATGCCTATCAACCAAAAGTTTTATTCATATCTGGTAAAGCGAAATGGTGGTGAAGGTGAA +CCTGAATTTCGACTTCCTATGGGTTTTATTGGAATCACACTTTTTGAAATAGGAATTTTA +CTTTTCGGTTGGACTGCAAGATATAAGATTTTTTGGTTTGTGCCAACAATTGGATCAGCC +ATTATGGGTGGTGGGTACATTATGACTTCCAATCCCTTAAACATGTATGTGGTAGATTCA +TATGGAATTTACTCAGCCAGTGCGTCAGCGGGTGTAAAAATATTTCAACTATTATTAGGA +GCCATCTTTCCATTATTTGCTGAAAGTCTATTTCGTCGACTGAACTACGGATGGGGGTGT +ACTTTACTTGCCTTTATTTTATTAGCTTGTGGCTGTAGTCTTCCAATCTTATTCAAGTAT +GGAAAACAAATTAGAAATCTACGACCATTTGACCCCTCAAAATACTAG |
| b |
| diff -r 000000000000 -r 8aef9a17faae test-data/top/test.fa.transdecoder.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/top/test.fa.transdecoder.gff3 Fri Nov 20 06:49:25 2015 -0500 |
| b |
| @@ -0,0 +1,41 @@ +CUFF.36.1 transdecoder gene 1 1498 . + . ID=CUFF.36.1|g.4;Name=ORF%20CUFF.36.1%7Cg.4%20CUFF.36.1%7Cm.4%20type%3Acomplete%20len%3A131%20%28%2B%29 +CUFF.36.1 transdecoder mRNA 1 1498 . + . ID=CUFF.36.1|m.4;Parent=CUFF.36.1|g.4;Name=ORF%20CUFF.36.1%7Cg.4%20CUFF.36.1%7Cm.4%20type%3Acomplete%20len%3A131%20%28%2B%29 +CUFF.36.1 transdecoder five_prime_UTR 1 894 . + . ID=CUFF.36.1|m.4.utr5p1;Parent=CUFF.36.1|m.4 +CUFF.36.1 transdecoder exon 1 1498 . + . ID=CUFF.36.1|m.4.exon1;Parent=CUFF.36.1|m.4 +CUFF.36.1 transdecoder CDS 895 1287 . + . ID=cds.CUFF.36.1|m.4;Parent=CUFF.36.1|m.4 +CUFF.36.1 transdecoder three_prime_UTR 1288 1498 . + . ID=CUFF.36.1|m.4.utr3p1;Parent=CUFF.36.1|m.4 + +CUFF.4.1 transdecoder gene 1 555 . + . ID=CUFF.4.1|g.5;Name=ORF%20CUFF.4.1%7Cg.5%20CUFF.4.1%7Cm.5%20type%3A3prime_partial%20len%3A120%20%28%2B%29 +CUFF.4.1 transdecoder mRNA 1 555 . + . ID=CUFF.4.1|m.5;Parent=CUFF.4.1|g.5;Name=ORF%20CUFF.4.1%7Cg.5%20CUFF.4.1%7Cm.5%20type%3A3prime_partial%20len%3A120%20%28%2B%29 +CUFF.4.1 transdecoder five_prime_UTR 1 198 . + . ID=CUFF.4.1|m.5.utr5p1;Parent=CUFF.4.1|m.5 +CUFF.4.1 transdecoder exon 1 555 . + . ID=CUFF.4.1|m.5.exon1;Parent=CUFF.4.1|m.5 +CUFF.4.1 transdecoder CDS 199 555 . + . ID=cds.CUFF.4.1|m.5;Parent=CUFF.4.1|m.5 + +CUFF.51.1 transdecoder gene 1 4342 . + . ID=CUFF.51.1|g.2;Name=ORF%20CUFF.51.1%7Cg.2%20CUFF.51.1%7Cm.2%20type%3Acomplete%20len%3A347%20%28%2B%29 +CUFF.51.1 transdecoder mRNA 1 4342 . + . ID=CUFF.51.1|m.2;Parent=CUFF.51.1|g.2;Name=ORF%20CUFF.51.1%7Cg.2%20CUFF.51.1%7Cm.2%20type%3Acomplete%20len%3A347%20%28%2B%29 +CUFF.51.1 transdecoder five_prime_UTR 1 316 . + . ID=CUFF.51.1|m.2.utr5p1;Parent=CUFF.51.1|m.2 +CUFF.51.1 transdecoder exon 1 4342 . + . ID=CUFF.51.1|m.2.exon1;Parent=CUFF.51.1|m.2 +CUFF.51.1 transdecoder CDS 317 1357 . + . ID=cds.CUFF.51.1|m.2;Parent=CUFF.51.1|m.2 +CUFF.51.1 transdecoder three_prime_UTR 1358 4342 . + . ID=CUFF.51.1|m.2.utr3p1;Parent=CUFF.51.1|m.2 + +CUFF.51.1 transdecoder gene 1 4342 . + . ID=CUFF.51.1|g.1;Name=ORF%20CUFF.51.1%7Cg.1%20CUFF.51.1%7Cm.1%20type%3Acomplete%20len%3A372%20%28%2B%29 +CUFF.51.1 transdecoder mRNA 1 4342 . + . ID=CUFF.51.1|m.1;Parent=CUFF.51.1|g.1;Name=ORF%20CUFF.51.1%7Cg.1%20CUFF.51.1%7Cm.1%20type%3Acomplete%20len%3A372%20%28%2B%29 +CUFF.51.1 transdecoder five_prime_UTR 1 2631 . + . ID=CUFF.51.1|m.1.utr5p1;Parent=CUFF.51.1|m.1 +CUFF.51.1 transdecoder exon 1 4342 . + . ID=CUFF.51.1|m.1.exon1;Parent=CUFF.51.1|m.1 +CUFF.51.1 transdecoder CDS 2632 3747 . + . ID=cds.CUFF.51.1|m.1;Parent=CUFF.51.1|m.1 +CUFF.51.1 transdecoder three_prime_UTR 3748 4342 . + . ID=CUFF.51.1|m.1.utr3p1;Parent=CUFF.51.1|m.1 + +CUFF.57.1 transdecoder gene 1 3853 . + . ID=CUFF.57.1|g.3;Name=ORF%20CUFF.57.1%7Cg.3%20CUFF.57.1%7Cm.3%20type%3Acomplete%20len%3A1032%20%28%2B%29 +CUFF.57.1 transdecoder mRNA 1 3853 . + . ID=CUFF.57.1|m.3;Parent=CUFF.57.1|g.3;Name=ORF%20CUFF.57.1%7Cg.3%20CUFF.57.1%7Cm.3%20type%3Acomplete%20len%3A1032%20%28%2B%29 +CUFF.57.1 transdecoder five_prime_UTR 1 188 . + . ID=CUFF.57.1|m.3.utr5p1;Parent=CUFF.57.1|m.3 +CUFF.57.1 transdecoder exon 1 3853 . + . ID=CUFF.57.1|m.3.exon1;Parent=CUFF.57.1|m.3 +CUFF.57.1 transdecoder CDS 189 3284 . + . ID=cds.CUFF.57.1|m.3;Parent=CUFF.57.1|m.3 +CUFF.57.1 transdecoder three_prime_UTR 3285 3853 . + . ID=CUFF.57.1|m.3.utr3p1;Parent=CUFF.57.1|m.3 + +CUFF.9.1 transdecoder gene 1 804 . + . ID=CUFF.9.1|g.6;Name=ORF%20CUFF.9.1%7Cg.6%20CUFF.9.1%7Cm.6%20type%3Acomplete%20len%3A156%20%28%2B%29 +CUFF.9.1 transdecoder mRNA 1 804 . + . ID=CUFF.9.1|m.6;Parent=CUFF.9.1|g.6;Name=ORF%20CUFF.9.1%7Cg.6%20CUFF.9.1%7Cm.6%20type%3Acomplete%20len%3A156%20%28%2B%29 +CUFF.9.1 transdecoder five_prime_UTR 1 172 . + . ID=CUFF.9.1|m.6.utr5p1;Parent=CUFF.9.1|m.6 +CUFF.9.1 transdecoder exon 1 804 . + . ID=CUFF.9.1|m.6.exon1;Parent=CUFF.9.1|m.6 +CUFF.9.1 transdecoder CDS 173 640 . + . ID=cds.CUFF.9.1|m.6;Parent=CUFF.9.1|m.6 +CUFF.9.1 transdecoder three_prime_UTR 641 804 . + . ID=CUFF.9.1|m.6.utr3p1;Parent=CUFF.9.1|m.6 + |
| b |
| diff -r 000000000000 -r 8aef9a17faae test-data/top/test.fa.transdecoder.mRNA --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/top/test.fa.transdecoder.mRNA Fri Nov 20 06:49:25 2015 -0500 |
| b |
| b'@@ -0,0 +1,266 @@\n+>CUFF.36.1|m.4 CUFF.36.1|g.4 ORF CUFF.36.1|g.4 CUFF.36.1|m.4 type:complete len:131 (+) CUFF.36.1:895-1287(+)\n+TGACTAAGTGGCAATGATGCTCCTAATGAAACCACTGATCCTCGATCATCAGCAGTAGTA\n+TCAATAGCAGCATCAGCACCGTTAGACAGCTGTTTTTCTAAACCATTCAATGATTCATCT\n+GAAAAACGTGAACCCACTTTCGAATAGTGCTTTTCAAATTTCTTTCCCGTAATTAAGGAA\n+AGTAAATCCATGTGCAGTTAGTATTGAAAAGGAAAGAATAAATAAAAGTGGGTCAAAAGT\n+AACGCCAAACAAACGAAGGTTATCGAAATATATGCGAAGGAGAGATTTATATACTAGTCA\n+AATTTAAACAGCTGAGATTGCTTTAGTCATCGCGTTGTTCCAGATCGTGAACGAAAACAC\n+CGATTCGCTCGCTAAAGTAGATACGAAATGTCCAGCAGATTTTGCTTAATTAAAACATAA\n+ATATTGATGAGCAAGAGCAGCTCGTTATAAATCAGACCTCCAAGGATTTTATCAACTACT\n+CAACTGGTTATGTGAATAATGACTCAGTTAAATATTAAATGTACTCTAAACGGTTATCAT\n+ACAATTTATTAGGAGGATTATACCAGCTAGTAGGAATTTAACCATTTCAAATTTAAACCT\n+CTTTTTTTTCGTAACTTGGGGTCGTCATAATGAATAATTCTGTTTGTCGAATTTGAAGGG\n+AAAAACACACTTGTTATCTAATTCCAAAAAAAAATAAAAAATTTTTAAAAATTAGTGGGG\n+TTTTTTTTTCACCAATGTCTAATGATGTGTGATTTAAAAAAAAACGTGTGTAACGCATTG\n+TAGTATTACTTACCTTTGCATGATTAAAAGTATATGTTGATATCGACTATTTAGAGTACT\n+GTGCGACACATTACCCTATGTTTCCCACTCTTAATCACCAAAAATTTTTTCCGAATGTCG\n+CAAGACTCAGAATCGTTCATCCGGCAACTGTTTAAGGCATTTACGGATTTTAGTACTGAC\n+GTTGAGTCACTTAGAGGATTTTTAACGCCAGATTATCGACAGCTTGTCGATGGACGTGAA\n+TTGACACTTGACGATTTTATTTCTCATGCCAAAGCACTACGTACCCATCTTCATCGGCTC\n+GACATCAACGTTCAACAAATTGTCTGTCAAGGTAACAAGGCTGCCACTGTGCATATTGCC\n+CATGCGATACGTTCCTCTGGCGAGTCCAGCAGAATCAAAGTCATTGCATTTTACAGTTTT\n+AAAGACGGGCGTATTTCTTTGATCGATGAGTTGACGTACGTTCTTGAAGGTGGTAATGCA\n+GACAGAGAGCTTGGATCAGTACAATGACTTCAATTACCTTGACACTGCATTGCCCACGTT\n+ATTCAACGTCCATCAGGAACCGGACAAATTATTCAGAGTCCTTTTGAACTACTTCATAAT\n+TTTACAAATATTCAAGTGTAATTCGTAATATAATCAGTTTTATTCATCTTCGTTGTCTAA\n+AACTTTTATGTGCTGCAATATTTGGGGAATCTCGATTTGACATAATGATCCCAGTGCC\n+>CUFF.4.1|m.5 CUFF.4.1|g.5 ORF CUFF.4.1|g.5 CUFF.4.1|m.5 type:3prime_partial len:120 (+) CUFF.4.1:199-555(+)\n+CTCTTTTTAATATTTTACCGATGAGATTGCTATTATTAGTTACGTTGCTATCTATCGTTG\n+GTTACACTAATCAGTTGCTTTCCAACTGACCTCGAAGACGCTCCAGCTGTAATCTGGGTA\n+GCCCAATTTCCTCCAGATAACACTACACAGCACTATGAATTCAGATATATCGTAAATGAA\n+TTATATAATGCTAGCAAGATGACTGCATTAATGAACCATATATATATCGATAATCCGCTT\n+ATAAGCAATTCAACTAATAACGTTACTCACGAGTTATTGATTGATCTCCATGAACTTTAT\n+AATGACGGAGAGATTTCCAGGATAGTTCTACTCAGAACTTTGGTAACTCAATCTGCGGAT\n+GATGCTACATGGATAATCAACTTGACAGATGATGTGCTTAATGGATTACCACTGCTGAAG\n+AAGCGAGACCGATACACCACACAATGTCATAGTACAAATATGGCAAGCACATATGACTGT\n+GACACTGGAGCCAATGCTGTTGGAGCCCGAGGTGGAGCCACGTTAGCAGCCGACTATAGA\n+GGTGATTGGGGGGGG\n+>CUFF.51.1|m.1 CUFF.51.1|g.1 ORF CUFF.51.1|g.1 CUFF.51.1|m.1 type:complete len:372 (+) CUFF.51.1:2632-3747(+)\n+CGACGTTAATAAAATATTTAACAAAGCCTTTAAAAAATTAACGATAGCTAGTCAAAGGAA\n+GCTTAACGCGTATTCAGCCTCATTAAGACAATCAGGAAGCTTTTTTTTACCATCAGCATA\n+TACCTCTAACCCTTTGATTTATTTTTATATCTCGAGATTTCGTTCGTTATTTTATAGGTC\n+GTTTCGATAAGACCTTAATACAATCTGATTTAGTGGTTGTTTAAGATTTCGGAAAAGCCT\n+TTTTTTCAAAAAAAGTTTTCCAGTTATTGTTTCATTATTTCTAATTGATTTACTGAAGAA\n+TTGTTATAACCTAAAGATGGCACTTATGTTATCCAGGATTCCACGTCGTTTTTTTTTCTT\n+ATTTTTAACGGTCGGCTTGATTGCTGGCGCGTTTCTATACTCGTTGATATATTTTGTGGA\n+CGTTGATTTGGTGTCGAAGGTTAACCAGTTGTATGATCAGCAAATTGCACCCATGCTCTC\n+CGATGCTATTGGCACTCCATCCGTTAATCACTCGTTTGAGTTGGCGCCGTTAGACTCTCA\n+TTTGGTGGCCACAAGCACTACATTCCACGAGGCGTCATACGAGTCAGAGCCTCAGCAAAA\n+TCCTGCCAGTCAAAATATTGTCTTATTACTAGTTAGTGATGGACACACTTCTTACAATAA\n+TGGAGCTAATACGTTTGAAGAAGCTATACAGAACAGAGTTGACTATAGTACCAAACAAAA\n+CTACAACTTTGAGTATGTCAATGTTACTGGCCTCCCTATTCCCGCCGTTTGGTCCAAGAT\n+GCCCGCCGTCTTACAAACTATGAAGAAATACCCCAAAGCGGAATGGATCTGGTTGTTGGA\n+TCAGGATGCAATTATTACTAATACCCATCTTTCCCTTCAAGACTCCTTTTTGAAACCTGA\n+GAACTTGCAAAAGACCTTAATTACTAATACCATCCTCACTAAACGGCCTATAAATGCTAA\n+CGGGGATTTGCGTTATACACCAAGTAATTATAGTTTAAAAGATATCGAAAATCTCATGGT\n+CATAATCTCACAGGATCACAATGGATTAAACGCAGGTAGTATCTTGTTCCGTAATTCACC\n+TGCTACTGCCTTGTTTTTGGATATTTGGACAGATCCTGTTGTTGCAGAATGTGCGAAAGC\n+CAATAATGAACAAGACATGCTTGGATATTTGATTTCTAAGCATTCACAACTTGCTTCGCT\n+GGTTGGCCTTATTCCTCAAAGAAAAATAAATGCTTTTCACGAAGGTCCGGAAAATATGGA\n+ATGGCAAAAAGGTGATTTGGTAATTCACTTTGCTGGATGTTGGGTTGAAAACCGCTGCGA\n+TGAACTATGGCAAAAGTTTTACGCCTTGATTGACTAAGTTGCTTATTCATTATATCCGTC\n+TGTTTAATTTGTTTGTGTTTTAAAAAATTTTATATATATAAACAAAGCGCCGTATAATTT\n+TCCGTCAATCTTCCTTTCTTTATCTGAATCTCTAA'..b'GGACAAGA\n+ATATATACCCCAATACTCTGTCTGTTTTACGTACTCGTGCTTCTGGTTTTGGTATCAAAA\n+TTGAATTAGACAATATCACTCCTGAACTCATTACGAAGTCTGCTAAGCATGTTTTTGGTA\n+TCTTTGTGCAATACCCAGCGGCGGATGGCTCTATTTTTGACTATGGTCATTTAGCTGCTA\n+CAGCACGCTCTTTTAATATGCACGTCGTAGCTGCCACCGATTTACTAGCTCTCACTATTT\n+TGAAATCGCCTGGGGAATGGGGTGCCGATGTTGCTGTTGGTTCCACTCAGCGCTTTGGTC\n+TGCCCATGGGCTATGGTGGCCCCCATGCCGGATTCTTTGCTTGTAGTGAAGAATTTAAAC\n+GAAAGATACCCGGTCGTCTTATTGGTCTCAGCAAAGATCGTTTAGAAAATCCCGCATACC\n+GGTTGGCTCTTCAAACAAGAGAACAACATATTCGTCGTGAAAAGGCTACAAGTAACATTT\n+GCACGGCTCAAGCTTTGTTAGCCAATATGTCTGCATTCTATGCTATTTACCATGGGCCAA\n+ATGGTCTCCAAGAAATTGCAAACCGTATTTACGCTAGTACCTCCTTCTTAAAATCTGCTT\n+TGGAATCTTCAGGATATAAAATTGTTAATAAAAGTCATTTCTTTGACACATTAACTATCG\n+AAGTTGAGTCGGCTGACAAAGTTCTTGCGAAAGCACTTGATCACGGTTACAATTTAAGAA\n+AGGTTGATGATTCACATGTTGGTCTTTCATTGGACGAGACCGTTTGCGATAAAGATATTC\n+AAGCTTTGTTTAGCATCTTTAATATAAATAAGAGTGTTGATCAGTATTATATGGAAATTG\n+CAACGTCGGAACCTAATGGAAATTCTGCTTCAACAGTCGATAATCTCAGCATTTGTTCTC\n+TTCCTGAAAACTTTAGACGAACAACCCTCTATTTACAACATCCCGTGTTTAACAGATACC\n+ATTCGGAAACTGAACTTATGCGTTATATTCATCATTTGCAGTCGAAGGATCTATCTTTAG\n+CTCATGCCATGACCCCATTGGGTTCGTGCACAATGAAGTTGAATGCTGTCACCGAAATGA\n+TGCCAATCACAAATCCATTATTTGCCAACATTCATCCATATGTTCCAGAGGAACAAGCTA\n+AAGGTTATCGTCATGTTATCGAAGATTTGCAGTTAATGTTAACGACCATCACCGGCTTTG\n+ATGCTGCATGCTTTCAACCAAATTCGGGAGCCGCTGGAGAATACACTGGCTTAAGTGTTA\n+TTCGAGCATATCAGCGGTCTATTGGTCAAGGTCATCGCAATATTTGCTTAATTCCTGTTT\n+CGGCTCACGGTACTAATCCAGCTTCAGCTGCTATGGCTGGGTTTACTGTTATTCCTGTAA\n+AATGTCTCAATAACGGTTATTTGGATATGCAAGACTTAAAAGAAAAGGCCTCTAAACACG\n+CCGACAAGTTAGCTGCCTTTATGGTAACTTATCCTAGTACTTTTGGCATTTTTGAGCCTG\n+ATGTTAAGGAAGCTTTGGAAGTAATTCACGAACATGGTGGTCAGGTTTACTTTGATGGTG\n+CTAACATGAATGCAATGGTTGGTTTATGCAAGGCTGGTGATATTGGTGCTGATGTTTGTC\n+ACTTAAATCTTCATAAGACATTTTGCATTCCTCACGGCGGTGGCGGTCCTGGTGTAGGTC\n+CTATTTGTGTAAAAAAGCATCTTGCTGATTTCCTACCATCTCATCCTGTAGTTTCATGCG\n+GCGGTAAGAATGGTATCACATCTGTTAGCTCTTCTCCTTTTGGCTCTGCTGGTATTTTAC\n+CTATCTCATGGGCATACATGAGAATGATGGGACTTGCCGGTTTGCGTGACGCTTCCAAAG\n+CCGCTCTGTTAAATGCCAATTATATGGCCAAGCGCCTGTCATCTCATTATAAACTTGTTT\n+ACACTAATAAGAACAACCTCTGTGCTCATGAGTTTATTCTAGATGCTCGCGAATTTAAAG\n+CTACTGCGGGTGTAGATGCAACTGATATAGCTAAACGTTTGCAAGATTACAGTTTCCATG\n+CACCAACTCTTTCCTGGCCTATTGCTAATACACTGATGATTGAGCCTACCGAGTCTGAGA\n+GTATGTATGAGATGGACCGCTTCTGTGATGCTTTAATTTCTATTCGACAAGAAATTCGTG\n+AAATTGAAGAAGGTCTCCAGCCTAAGGACAATAACCTGCTCGTTAATGCTCCCCACCCTC\n+AAAAGGACATTGCATCTGAGAAATGGGATCGTCCTTATACTCGAGAGCGGGCTGTCTATC\n+CTGTGCCTCTTTTAAAGGAACGGAAATTCTGGCCTAGCGTTGCTCGATTAGATGATGCGT\n+ACGGTGACAAGAACTTATTTTGTACTTGTTCCCCAGTTGTTTAGCGGTCAAAAAGAGCTC\n+ACCTGCTAGATTACTTCAACCTTTTCCCAGTTAAGTTCAACCTAATTTTTACTCCATTTG\n+GTAGTTCGTTCAACACCAATTCCCACGTTTATATATAGACCAATTTTTTACTACATCTTG\n+TTAGACAATTCTTTCCGTTATCACTTTTTCGAATTTTTTTTAATTACGTTTTAATTTTGA\n+AGGTTAGAATTATCCTTTGCTGGAACATGAGGTTTTCAACAACCTTTTTTTAATCTGATA\n+ATCTAATTTTGCTAGTCATATAATTGCGACTTTCTGATAAAAACATTACCTATACTTTAT\n+AAATATGTCGTTTTTAAATATTAACTCCTATGTCTTACTTGCATCCTTGAAATTTACGAC\n+TAGAAATTTGGTGCTTTGGATTTTCGTTACATTAAGTAAGGCCATTGAATCGATATGACA\n+CGTAAATGTTAAATTTCAAAATATTTTGGAGAGCACCATGTATAATTTAAATATACGAAT\n+TTTTTCCTTTAAATTTGTGGTTCTTTTTTAAAAAATATCAAGACGAGTACTCGATTACTC\n+GTAAGTATTCAAG\n+>CUFF.9.1|m.6 CUFF.9.1|g.6 ORF CUFF.9.1|g.6 CUFF.9.1|m.6 type:complete len:156 (+) CUFF.9.1:173-640(+)\n+AGCGAAACAAACAAATCACGTTATAGACGGTGGCAGGGCCATAAAAGGTATTCCCTCGCT\n+TTAAAAAGAAACAATGTCAAAAAGCTTTCTTTATAAACTATTGGAAGATTGAAGACATTA\n+AAGAAGAAAAGTCCTGCTTACCCTTGGACTTTTTTCAGCAGTTTTCATTGCCATGCCTAT\n+CAACCAAAAGTTTTATTCATATCTGGTAAAGCGAAATGGTGGTGAAGGTGAACCTGAATT\n+TCGACTTCCTATGGGTTTTATTGGAATCACACTTTTTGAAATAGGAATTTTACTTTTCGG\n+TTGGACTGCAAGATATAAGATTTTTTGGTTTGTGCCAACAATTGGATCAGCCATTATGGG\n+TGGTGGGTACATTATGACTTCCAATCCCTTAAACATGTATGTGGTAGATTCATATGGAAT\n+TTACTCAGCCAGTGCGTCAGCGGGTGTAAAAATATTTCAACTATTATTAGGAGCCATCTT\n+TCCATTATTTGCTGAAAGTCTATTTCGTCGACTGAACTACGGATGGGGGTGTACTTTACT\n+TGCCTTTATTTTATTAGCTTGTGGCTGTAGTCTTCCAATCTTATTCAAGTATGGAAAACA\n+AATTAGAAATCTACGACCATTTGACCCCTCAAAATACTAGTTGATTTAACTGATCAAAGT\n+GAGGATTTTCACACACATTTTCAGAGTACTTGGAACGTGCCGAGCTGATTAAAAAACACC\n+GGTATTAACAAAAAATTTTATTTATGAAGCAATACGCTATTTCGTTATGAGAAACTTGAT\n+TCAATGAAACTATTATAAACCTTA\n' |
| b |
| diff -r 000000000000 -r 8aef9a17faae test-data/top/test.fa.transdecoder.pep --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/top/test.fa.transdecoder.pep Fri Nov 20 06:49:25 2015 -0500 |
| b |
| @@ -0,0 +1,45 @@ +>CUFF.36.1|m.4 CUFF.36.1|g.4 ORF CUFF.36.1|g.4 CUFF.36.1|m.4 type:complete len:131 (+) CUFF.36.1:895-1287(+) +MSQDSESFIRQLFKAFTDFSTDVESLRGFLTPDYRQLVDGRELTLDDFISHAKALRTHLH +RLDINVQQIVCQGNKAATVHIAHAIRSSGESSRIKVIAFYSFKDGRISLIDELTYVLEGG +NADRELGSVQ* +>CUFF.4.1|m.5 CUFF.4.1|g.5 ORF CUFF.4.1|g.5 CUFF.4.1|m.5 type:3prime_partial len:120 (+) CUFF.4.1:199-555(+) +MTALMNHIYIDNPLISNSTNNVTHELLIDLHELYNDGEISRIVLLRTLVTQSADDATWII +NLTDDVLNGLPLLKKRDRYTTQCHSTNMASTYDCDTGANAVGARGGATLAADYRGDWGG +>CUFF.51.1|m.2 CUFF.51.1|g.2 ORF CUFF.51.1|g.2 CUFF.51.1|m.2 type:complete len:347 (+) CUFF.51.1:317-1357(+) +MALMLSRIPRRFFFLFLTVGLIAGAFLYSLIYFVDVDLVSKVNQLYDQQIAPMLSDAIGT +PSVNHSFELAPLDSHLVATSTTFHEASYESEPQQNPASQNIVLLLVSDGHTSYNNGANTF +EEAIQNRVDYSTKQNYNFEYVNVTGLPIPAVWSKMPAVLQTMKKYPKAEWIWLLDQDAII +TNTHLSLQDSFLKPENLQKTLITNTILTKRPINANGDLRYTPSNYSLKDIENLMVIISQD +HNGLNAGSILFRNSPATALFLDIWTDPVVAECAKANNEQDMLGYLISKHSQLASLVGLIP +QRKINAFHEGPENMEWQKGDLVIHFAGCWVENRCDELWQKFYALID* +>CUFF.51.1|m.1 CUFF.51.1|g.1 ORF CUFF.51.1|g.1 CUFF.51.1|m.1 type:complete len:372 (+) CUFF.51.1:2632-3747(+) +MSRISLSNFLSLPRYKFLLFSVVLIIVMTTLVFNGHDYKQTLNDRLTSLKNNFVEENDNA +VLKEEPGKYTYMSLFTMPSTEEDYYFNATRVLIHRLKYHPTTKSKYPIHILALRGVDEWK +IERFRKDGASVIVIDPIASSDIVYDTSSFSQEISARYEQMFSKLRIFEQIQFDKICVIDS +DILIMKNIDDIFDTPYMYQQINTLNYTRLPSYTKPDDDTVYHFNEDFKEYGASRSEFYPY +LLAAVSDRGEHHSIPPEDTPYFNAGLMLIRPSELHFNRILKIGRFPYMYENAKMMEQSLL +NLAFSLDGWFPWTRLDPYYNGVWPSIDERPLLKTAHGKFWNIGSSEFAPVYLADWYAAYG +EMLSFHKYETH* +>CUFF.57.1|m.3 CUFF.57.1|g.3 ORF CUFF.57.1|g.3 CUFF.57.1|m.3 type:complete len:1032 (+) CUFF.57.1:189-3284(+) +MFDSFMKRNQLALIMFRACSKLQYHGVNTSLSRHLFLAKRNLSISSACLEAKNSQKFPAL +DTFEPRHIGPSKTDQQYQLESLGYKDFDSFLKDVIPDSVRTPESQLMAFGSVNPNEKNPP +VNYSESEFTTLANNVANQNKLIKSFIGMGYYNVKLPAAIQRNVLENPEWYTQYTPYQAEI +SQGRLESMMNYQTMIADLTGLSISNASLLDEGTAAGEAMVMLMANDKKKRKTFLVDKNIY +PNTLSVLRTRASGFGIKIELDNITPELITKSAKHVFGIFVQYPAADGSIFDYGHLAATAR +SFNMHVVAATDLLALTILKSPGEWGADVAVGSTQRFGLPMGYGGPHAGFFACSEEFKRKI +PGRLIGLSKDRLENPAYRLALQTREQHIRREKATSNICTAQALLANMSAFYAIYHGPNGL +QEIANRIYASTSFLKSALESSGYKIVNKSHFFDTLTIEVESADKVLAKALDHGYNLRKVD +DSHVGLSLDETVCDKDIQALFSIFNINKSVDQYYMEIATSEPNGNSASTVDNLSICSLPE +NFRRTTLYLQHPVFNRYHSETELMRYIHHLQSKDLSLAHAMTPLGSCTMKLNAVTEMMPI +TNPLFANIHPYVPEEQAKGYRHVIEDLQLMLTTITGFDAACFQPNSGAAGEYTGLSVIRA +YQRSIGQGHRNICLIPVSAHGTNPASAAMAGFTVIPVKCLNNGYLDMQDLKEKASKHADK +LAAFMVTYPSTFGIFEPDVKEALEVIHEHGGQVYFDGANMNAMVGLCKAGDIGADVCHLN +LHKTFCIPHGGGGPGVGPICVKKHLADFLPSHPVVSCGGKNGITSVSSSPFGSAGILPIS +WAYMRMMGLAGLRDASKAALLNANYMAKRLSSHYKLVYTNKNNLCAHEFILDAREFKATA +GVDATDIAKRLQDYSFHAPTLSWPIANTLMIEPTESESMYEMDRFCDALISIRQEIREIE +EGLQPKDNNLLVNAPHPQKDIASEKWDRPYTRERAVYPVPLLKERKFWPSVARLDDAYGD +KNLFCTCSPVV* +>CUFF.9.1|m.6 CUFF.9.1|g.6 ORF CUFF.9.1|g.6 CUFF.9.1|m.6 type:complete len:156 (+) CUFF.9.1:173-640(+) +MPINQKFYSYLVKRNGGEGEPEFRLPMGFIGITLFEIGILLFGWTARYKIFWFVPTIGSA +IMGGGYIMTSNPLNMYVVDSYGIYSASASAGVKIFQLLLGAIFPLFAESLFRRLNYGWGC +TLLAFILLACGCSLPILFKYGKQIRNLRPFDPSKY* |
| b |
| diff -r 000000000000 -r 8aef9a17faae tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Nov 20 06:49:25 2015 -0500 |
| b |
| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="transdecoder" version="2.0.1"> + <repository changeset_revision="1fb9f6beb8fb" name="package_transdecoder_2_0_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |
| b |
| diff -r 000000000000 -r 8aef9a17faae transdecoder.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/transdecoder.xml Fri Nov 20 06:49:25 2015 -0500 |
| [ |
| b'@@ -0,0 +1,171 @@\n+<tool id="transdecoder" name="TransDecoder" version="1.0">\n+ <description>Find coding regions within transcripts</description>\n+ <requirements>\n+ <requirement type="package" version="2.0.1">transdecoder</requirement>\n+ </requirements>\n+\n+ <stdio>\n+ <exit_code range="1:" level="fatal" description="Error occurred" />\n+ </stdio>\n+ \n+ <command><![CDATA[\n+ TransDecoder.LongOrfs -t "${input}"\n+ \n+ #if ($min_len):\n+ -m ${min_len}\n+ #end if\n+ \n+ ${adv.stranded}\n+ \n+ #if ($adv.gen_code):\n+ -G ${adv.gen_code}\n+ #end if\n+ \n+ &&\n+ \n+ TransDecoder.Predict -t "${input}"\n+ \n+ #if ($adv.retain_long_orfs):\n+ --retain_long_orfs ${adv.retain_long_orfs}\n+ #end if\n+\n+ #if str( $training_sect.training.training_selector ) == "training_top":\n+ #if ($training_sect.training.top_longest):\n+ -T ${training_sect.training.top_longest}\n+ #end if\n+ #else\n+ #if ($training_sect.training.train):\n+ --train ${training_sect.training.train}\n+ #end if\n+ #end if\n+ \n+ &&\n+\n+ out_prefix=`basename "${input}"`\n+\n+ mv `basename "${input}"`.transdecoder.pep transcript.transdecoder.pep &&\n+ mv `basename "${input}"`.transdecoder.cds transcript.transdecoder.cds &&\n+ mv `basename "${input}"`.transdecoder.bed transcript.transdecoder.bed &&\n+ mv `basename "${input}"`.transdecoder.gff3 transcript.transdecoder.gff3 &&\n+ mv `basename "${input}"`.transdecoder.mRNA transcript.transdecoder.mRNA\n+ ]]></command>\n+ \n+ <inputs>\n+ <param format="fasta" name="input" type="data" label="Transcripts"/>\n+ \n+ <param name="min_len" size="5" type="integer" optional=\'true\' value="100" label="Minimum protein length (default: 100aa)"/>\n+ \n+ <section name="adv" title="Advanced Options" expanded="False">\n+ <param name="stranded" type="boolean" checked="false" truevalue="-S" falsevalue="" label="Strand-specific" help="Only analyzes top strand"/>\n+ <param name="gen_code" type="select" label="Genetic code">\n+ <option value="universal" selected="True">universal</option>\n+ <option value="Euplotes">Euplotes</option>\n+ <option value="Tetrahymena">Tetrahymena</option>\n+ <option value="Candida">Candida</option>\n+ <option value="Acetabularia">Acetabularia</option>\n+ <option value="Mitochondrial-Canonical">Mitochondrial-Canonical</option>\n+ <option value="Mitochondrial-Vertebrates">Mitochondrial-Vertebrates</option>\n+ <option value="Mitochondrial-Arthropods">Mitochondrial-Arthropods</option>\n+ <option value="Mitochondrial-Echinoderms">Mitochondrial-Echinoderms</option>\n+ <option value="Mitochondrial-Molluscs">Mitochondrial-Molluscs</option>\n+ <option value="Mitochondrial-Ascidians">Mitochondrial-Ascidians</option>\n+ <option value="Mitochondrial-Nematodes">Mitochondrial-Nematodes</option>\n+ <option value="Mitochondrial-Platyhelminths">Mitochondrial-Platyhelminths</option>\n+ <option value="Mitochondrial-Yeasts">Mitochondrial-Yeasts</option>\n+ <option value="Mitochondrial-Euascomycetes">Mitochondrial-Euascomycetes</option>\n+ <option value="Mitochondrial-Protozoans">Mitochondrial-Protozoans</option>\n+ </param>\n+ \n+ <param name="retain_long_orfs" type="integer" optional="true" label="Retain long orfs" help="Retain all ORFs found that are equal or longer than these many nucleotides even if no other evidence marks it as coding (default: 900 bp => 300aa)" />\n+ </section>\n+ \n+ <section name="training_sect" title="Training Options" ex'..b'="transdecoder_gff3" file="raw/test.fa.transdecoder.gff3" compare="sim_size" />\n+ <output name="transdecoder_bed" file="raw/test.fa.transdecoder.bed" compare="sim_size" />\n+ <output name="transdecoder_cds" file="raw/test.fa.transdecoder.cds" compare="sim_size" />\n+ <output name="transdecoder_mRNA" file="raw/test.fa.transdecoder.mRNA" compare="sim_size" />\n+ <output name="transdecoder_pep" file="raw/test.fa.transdecoder.pep" compare="sim_size" />\n+ </test>\n+ <test>\n+ <param name="input" value="test.fa"/>\n+ <param name="training_selector" value="training_top"/>\n+ <param name="top_longest" value="10"/>\n+ <output name="transdecoder_gff3" file="top/test.fa.transdecoder.gff3" compare="sim_size" />\n+ <output name="transdecoder_bed" file="top/test.fa.transdecoder.bed" compare="sim_size" />\n+ <output name="transdecoder_cds" file="top/test.fa.transdecoder.cds" compare="sim_size" />\n+ <output name="transdecoder_mRNA" file="top/test.fa.transdecoder.mRNA" compare="sim_size" />\n+ <output name="transdecoder_pep" file="top/test.fa.transdecoder.pep" compare="sim_size" />\n+ </test>\n+ <test>\n+ <param name="input" value="test.fa"/>\n+ <param name="gen_code" value="Mitochondrial-Arthropods"/>\n+ <output name="transdecoder_gff3" file="gencode/test.fa.transdecoder.gff3" compare="sim_size" />\n+ <output name="transdecoder_bed" file="gencode/test.fa.transdecoder.bed" compare="sim_size" />\n+ <output name="transdecoder_cds" file="gencode/test.fa.transdecoder.cds" compare="sim_size" />\n+ <output name="transdecoder_mRNA" file="gencode/test.fa.transdecoder.mRNA" compare="sim_size" />\n+ <output name="transdecoder_pep" file="gencode/test.fa.transdecoder.pep" compare="sim_size" />\n+ </test>\n+ <test>\n+ <param name="input" value="test.fa"/>\n+ <param name="stranded" value="true"/>\n+ <output name="transdecoder_gff3" file="strand/test.fa.transdecoder.gff3" compare="sim_size" />\n+ <output name="transdecoder_bed" file="strand/test.fa.transdecoder.bed" compare="sim_size" />\n+ <output name="transdecoder_cds" file="strand/test.fa.transdecoder.cds" compare="sim_size" />\n+ <output name="transdecoder_mRNA" file="strand/test.fa.transdecoder.mRNA" compare="sim_size" />\n+ <output name="transdecoder_pep" file="strand/test.fa.transdecoder.pep" compare="sim_size" />\n+ </test>\n+ </tests>\n+ <help>\n+\n+**What it does**\n+\n+TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.\n+\n+TransDecoder identifies likely coding sequences based on the following criteria:\n+\n+ - a minimum length open reading frame (ORF) is found in a transcript sequence\n+\n+ - a log-likelihood score similar to what is computed by the GeneID software is > 0.\n+\n+ - the above coding score is greatest when the ORF is scored in the 1st reading frame as compared to scores in the other 5 reading frames.\n+\n+ - if a candidate ORF is found fully encapsulated by the coordinates of another candidate ORF, the longer one is reported. However, a single transcript can report multiple ORFs (allowing for operons, chimeras, etc).\n+\n+ - optional the putative peptide has a match to a Pfam domain above the noise cutoff score.\n+\n+The software is primarily maintained by Brian Haas at the Broad Institute and Alexie Papanicolaou at the Commonwealth Scientific and Industrial Research Organisation (CSIRO). It is integrated into other related software such as Trinity, PASA, EVidenceModeler, and Trinotate.\n+\n+ </help>\n+ <citations>\n+ <citation type="doi">10.1038/nprot.2013.084</citation>\n+ </citations>\n+</tool>\n' |