| Previous changeset 4:0db979fead3a (2017-06-01) Next changeset 6:d0d4cef4f967 (2021-02-01) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 860cdb41f79283c76d898404e5f28e2d506bed4d" |
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modified:
transdecoder.xml |
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added:
test-data/transcripts.fasta |
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removed:
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.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.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.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.pep |
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| diff -r 0db979fead3a -r c6334cb383ff test-data/gencode/test.fa.transdecoder.bed --- a/test-data/gencode/test.fa.transdecoder.bed Thu Jun 01 06:04:12 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,7 +0,0 @@ -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 |
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| diff -r 0db979fead3a -r c6334cb383ff test-data/gencode/test.fa.transdecoder.cds --- a/test-data/gencode/test.fa.transdecoder.cds Thu Jun 01 06:04:12 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,118 +0,0 @@ ->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 |
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| diff -r 0db979fead3a -r c6334cb383ff test-data/gencode/test.fa.transdecoder.gff3 --- a/test-data/gencode/test.fa.transdecoder.gff3 Thu Jun 01 06:04:12 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,41 +0,0 @@ -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 - |
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| diff -r 0db979fead3a -r c6334cb383ff test-data/gencode/test.fa.transdecoder.pep --- a/test-data/gencode/test.fa.transdecoder.pep Thu Jun 01 06:04:12 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,45 +0,0 @@ ->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 0db979fead3a -r c6334cb383ff test-data/raw/test.fa.transdecoder.bed --- a/test-data/raw/test.fa.transdecoder.bed Thu Jun 01 06:04:12 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,7 +0,0 @@ -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 0db979fead3a -r c6334cb383ff test-data/raw/test.fa.transdecoder.cds --- a/test-data/raw/test.fa.transdecoder.cds Thu Jun 01 06:04:12 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,116 +0,0 @@ ->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 0db979fead3a -r c6334cb383ff test-data/raw/test.fa.transdecoder.gff3 --- a/test-data/raw/test.fa.transdecoder.gff3 Thu Jun 01 06:04:12 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,41 +0,0 @@ -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 0db979fead3a -r c6334cb383ff test-data/raw/test.fa.transdecoder.pep --- a/test-data/raw/test.fa.transdecoder.pep Thu Jun 01 06:04:12 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,45 +0,0 @@ ->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 0db979fead3a -r c6334cb383ff test-data/strand/test.fa.transdecoder.bed --- a/test-data/strand/test.fa.transdecoder.bed Thu Jun 01 06:04:12 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,7 +0,0 @@ -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 0db979fead3a -r c6334cb383ff test-data/strand/test.fa.transdecoder.cds --- a/test-data/strand/test.fa.transdecoder.cds Thu Jun 01 06:04:12 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,116 +0,0 @@ ->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 0db979fead3a -r c6334cb383ff test-data/strand/test.fa.transdecoder.gff3 --- a/test-data/strand/test.fa.transdecoder.gff3 Thu Jun 01 06:04:12 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,41 +0,0 @@ -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 0db979fead3a -r c6334cb383ff test-data/strand/test.fa.transdecoder.pep --- a/test-data/strand/test.fa.transdecoder.pep Thu Jun 01 06:04:12 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,45 +0,0 @@ ->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 0db979fead3a -r c6334cb383ff test-data/test.fa --- a/test-data/test.fa Thu Jun 01 06:04:12 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,10 +0,0 @@\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 0db979fead3a -r c6334cb383ff test-data/top/test.fa.transdecoder.bed --- a/test-data/top/test.fa.transdecoder.bed Thu Jun 01 06:04:12 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,7 +0,0 @@ -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 0db979fead3a -r c6334cb383ff test-data/top/test.fa.transdecoder.cds --- a/test-data/top/test.fa.transdecoder.cds Thu Jun 01 06:04:12 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,116 +0,0 @@ ->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 0db979fead3a -r c6334cb383ff test-data/top/test.fa.transdecoder.gff3 --- a/test-data/top/test.fa.transdecoder.gff3 Thu Jun 01 06:04:12 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,41 +0,0 @@ -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 0db979fead3a -r c6334cb383ff test-data/top/test.fa.transdecoder.pep --- a/test-data/top/test.fa.transdecoder.pep Thu Jun 01 06:04:12 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,45 +0,0 @@ ->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 0db979fead3a -r c6334cb383ff test-data/transcripts.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcripts.fasta Thu Oct 08 12:33:46 2020 +0000 |
| [ |
| b'@@ -0,0 +1,10000 @@\n+>comp0_c0_seq1 len=796 path=[175:0-795]\n+AATTTTTCTATGTACAATATTGTAAGCAACATAACTGATCGGAACAGGAAAAGTAGATGA\n+GAAGAGGGAAACGGTTAGGATAGCGTGAAATTCAAGATCAATGCGAAAGAAATAAATTAT\n+AAGGGTTAAATAAGGCATAAATTAAGGAAGTCATCGAAACAAAACCTAAGAAAAAAACAC\n+AAGACAGCAGGGGAAAACAGTCATAGAGACCTAAGGGCCTCCAAGAACACCAACTTATTA\n+CGAAAGGTAAAACGAGGCAGTTGTTCTACATTAAGAATGGGATGATGGCACGACGGTTTG\n+CTGGATACTTCGGAAACTTTTTACAGTACCATTGATGGGCTTTTAATGCTCTTGGAAGCA\n+TCAACAGAATCTCTGACAGGAAGAACCACCAAAAAGGTTCGGCAGAAGGACCGGCTGCCA\n+AGTAGCATCCAAACCATTCAATCCATTCGCAAAAGTAATTGGGACACGAAACATACTGGA\n+AAAGCCCTCCATAGGGAATTCGATAATACGAATTCTCAGATTGTACGGTGTCAAGATTAT\n+CGGGATCCTTTTTTTTATTAGATGATCTTCTTAGGTCGTATAAGATGTTGTCGTGATACA\n+TATTTCCCAACCAACCCATTAACCAAAGAAACATACCAATGTATCGACGAATGATAGACA\n+CTGGATGATGCTGGACGCTAGCTTGAACCAAGTACAGACCTATTGACATACCGTTCAAAA\n+AGTTAAACAATACCGCAGAAACAAACACCGTCCAATGCATGGGTGAAACTTGTGGTGCCA\n+TCAAAAGAGGACTCAC\n+>comp3_c0_seq1 len=226 path=[84:0-225]\n+ACATCCATCCCCTTGGAGCAAGGGAGAGGGAGAGGGAAAGAGAAAGTGGGAGTCAGCAAC\n+ATTTCCTAATACTTTCCTTATTGAATGATTGTAAAGCGGGGAGAGATTAAGATGATAGAT\n+TCACAATAGTTAGGGGAGAAAAGTAGAAAGAAACAAATGATACTCTCAACCACTTTTTTT\n+CCTTTCCAACAGAGAATAAGAGAAAACAAGAGAAATTGAATATGAA\n+>comp5_c0_seq1 len=429 path=[73:0-428]\n+ATTCGGTTCAAGTGACTACAATACAATAACCACTATTTGCGAGATTAAACATACTATTAC\n+AGTAACCAACACATTTGAAATGTAAAAAATTGCCATAGTTGAAGCTATTCAGCGTCAGCG\n+AACATCTTCGGAGAGCTCAAATAATCTTAGCTCTTAAGATGGGGGTTTTTTCTGCCGAAT\n+ACTGTATCTGTTTGACTTTTATTTTTAATACGTTGGAGTAACCGCTGTATTCTTGTGCAA\n+CTTGGTGTTTTTGAAATTAACAATGGCACTGTTGATGAACGAAAGTGAATTATAATACAT\n+TTTTTGACAGTACCAATCTTATGGAAGTGCCTTGAAATCCTGTTACGTTACGTTTTAGCA\n+AGATCGCTTCTCTTATGATTTTCTTGTTTCAATGGTTTTCTACCCATAATCAATGAAATA\n+TGTTTACAA\n+>comp6_c0_seq1 len=584 path=[1:0-583]\n+GCGTTAAGTACCGCTTCTAGTAATCGACTCATAGATTTAAAAAATGACGAAGTTCCTATT\n+TTTCGCATTCCTTTAAGTGATTATGAAACAGATGACATGGATGACGGTACACCTCTCCAA\n+CGCCATGTTGCGACCCTGAACCAATATCAAAGTCCCATTTTTAATTTAGGCCCGGACATT\n+TTAGAAGATGAACCATCTTACTCTTCAAGAGCTTCCAGATCCCGTCAATCATCTCTCTCT\n+TCTCGATTATCTGAGTTACCTTCTAAACGCGCCAGCCTTGAGATTTTAAGGCGCGAAAAT\n+ACTTTCCCAGCCGATCCAATTCAGGAATTTGGTGAAAAAGCATACAATGAAAGAGAATTG\n+ATGGAAGAAATCTCAAATTTTGAACCCTTACTAGATGATAACTTGCTTGAAAATGCCAAC\n+GAAGCTGTCAATTCCCCAGTAGTAGACGCACCAATGGATGCTGATTCTGCTTTAGAAATA\n+CCCAATGATGAAGATAATGGGGAAATTCTAAATAAACTAAAAGATTCTCCGTTTAAAAAA\n+CCTAAAAGAAGATATTCCAAATCTTCAACACTTGTGCTACCGGT\n+>comp8_c0_seq1 len=439 path=[1:0-438]\n+ATTTATCTATAGCAGATGTAAAAGTTATATAATTTGATTAAGTTTTTAAATGAGGAAGTT\n+GCAATATTATCTGATTCCAAAGGTTTTCTGTAGCTGCAAAAGTTAAGCAGTAATGCTTTG\n+CTAACAATTGCCATTCTTCCAACTCATCAAGCATTTCTATGCTCATCGTTCTTTTCTTTT\n+CTTCTATGGGTATCCAGGTTTCTTCAATAGTTAAAAAATCTTCTGCAATTACTTCCGAGT\n+ATCCATAATCAAGAAACCTCATCCTTTGCTGCTCAGTTGTCTCATAACAATCGAGTGTTT\n+TAAGAATCACTCCTCTTGCCTAAATTTTGTTAGTTCTTAATCTGTGAAATGATATGCAAG\n+CATCGTACAGAAAGATTAGCCTTCATCATTTTTCCAAAGTTATCCATCCCCTGAATAGGT\n+TCATAAACAACAATGCCAG\n+>comp12_c0_seq1 len=447 path=[1:0-446]\n+TTTTGAACACTTTCAATGTCGTTGCTTTCATAATCAACCCAGCAGTGAGGATGAAAGAAA\n+GAAGCATCATTGAAGGGTATAACTTTTTCAAAGCTCATTTGTTCCAGCGGTCCGTTTATC\n+GCCATAGAATTGATAGCCACGTCTAGTAAAATCCATATGTCGCGTTTATGCAATTCTTGT\n+ATTAGCTCCATAAATTCTTCCTTTGTTCCAAAGTGGTGATTAAGCTCATAGAGGTTGGTT\n+GTCCAATATCCGTGATAGGACGAACCGTCAATATCATTTCCTTCAACATTTTCAAAGATT\n+GGTGAGATCCATATCTATCATTATGTTAATCAAGTATTTGGGTAAAAATACATACTGCGT\n+CAAATCCCATGCCTTGGATGTAATCTAGATGATTTCGAATTCCATTCCAAGTTCCCCCGC\n+AGTACATAAATCGAACGGGATCGCATG\n+>comp18_c0_seq1 len=402 path=[1:0-401]\n+ACATTTATAACCTTCGAATAAGCTTACGATAGAGTTTGTTTTAGATTTCTGTACTTGTTA\n+CTAATCTATGTAAGTTTTCTATGAATAAACCAATTTATATTTTAGCAAATCTATTTTTGT\n+AGAGCGATGCTTTCTCTCGTTTACCCAGGTTTCCCCAAATAGTCAAGTGAGCTTAAAGAG\n+ACGACGATCTACATGAAACTAGAAAACAACAAATGAACGTGACAATAAGATTAAATCATA\n+AATAAAAACAATGTTATTTCTGGAAATTAAACGAAAAATCATCACATTTAGGCAATATGC\n+AGAAGATTTTGTCAGATCACTGGATTTAAGTCGTAAATTTTGTTCCTTTCTTCTTTAGTC\n+AATCTTCCTATCTAGTGCGGGTTTTCTTATTAGTCTATGTAA\n+>comp19_c0_seq1 len=269 path=[155:0-268]\n+TGGCTTCTGCGCGAATCCCGATCACTGTGTACCTCCACGATCAACGAGAAGTAAAAGCAG\n+AATTTGGAGCGATAGACAGTAGTGAGTCAAAGTTGGCAGTTTCCAATCTACAAACCGATT\n+GGGGCGTTATTAACAGAGCGGTGATACGAACAGGAGACGTCGTGGGCATCGAATACAATT\n+TGGTGCAGGAAGAAGGAGAACTTTGATGAT'..b'CTTATACACATACAAGAACTGGCACATCTTTTTTCATGTACC\n+AAAAGGAGGCCTTTTATCGTGGACGTAGCTCAACAAGACAATTTAACAATACCCGATCTC\n+CATCTGGACGTTCAGCGTCGCGTTCTTCCAATTTCTCACATCGGTCTAGTAGTCGTGATT\n+CTTTTTCCTCGAATAGATCTTACTCGAGTTCGCTTTCCAGATCTCCAGAAGAACCATTGC\n+GAACAATTCTTGTGGAAAATTTGACGCGTAATGTCACTAAAGAACATATAGCAGAAATAT\n+TTGGGATTTATGGACTAATTGATCATATTTTCATGCCAATTTATAAAAAATCTGAATTGA\n+ATAAAGGGTATTGCTACATAGAATACGTATACCATGACCAGGCCGCAAACGCCGTCGATA\n+AGATGAACAACGCTGAGCTTGATGGTGAGGAGTTGTTTGTATCGATAAAACGTTTTCCTT\n+TTGAGTCACTACACAAAAACCATAAGCACTACGAAAACTCGTATCGACCATCAAGGTCAC\n+AAAACAATTCACATTACAACGATAAATCGTTTCATCGCTCCAGATATTCTCGGGCACGTA\n+GCCGATCTCCAGGTTCCAATATATCTGAATATTCTGATCAATCACCCCCCTATCACTCCT\n+ATAGACATCGTCCTTAATCCCGCAAATTGTGGCCTACTGAATAAAAAAGAAAAGTGAAAA\n+CAAATTTCCAGTTTGAAAGCTTTATTATGTCGTTGTTTGATACGTACCACTACTATTAAA\n+ATTTTTGTGAACGGTCGATCCTCTATAAATTATTTTTTGGGAAAATTTTACGAAGTATTT\n+ATCGGATGTGCAATTTTCATTGTTCTAAGTCCTATTAGAATTTAAAAGTGTTCGTCGTCA\n+AATTCATAACTTTTCGGTCGGATTCCCACCCTTTGTAGCATAAAGAGAATGCAACGACGG\n+AAATCTGTTTTTTTAAAATCATTGCTTTTATAGTAGTCCGGAATAATGAAATTAAAGATC\n+TCCCC\n+>comp874_c0_seq1 len=3229 path=[1:0-3228]\n+GGAAAGTGCGTAGGAATAGTTATACTGTTAGCGTTGAAGTGCCCAATTCCTTACGAAAAA\n+AGTTTCGCACGATTTATGTGGAATCGATTTGTGGCATATTTAGTAAGTTTATTCTTCAAA\n+AATATAATATAAGCTACAAAACAAGTTATCTTTTCCTTAATTATTGCATATGCGATTGCG\n+ATCATTTACGATGCTTTAAGTTGCGAGTGGAATGGAAAGTATCGCAGATCATTTCTTTCT\n+CGCAGGTCTCTCTAACGGATTTGTGAGTGTATCCAATTCTCAATTTCGAGCAGATAGACT\n+TGATGAAGACGCCATATCTGTTTCTAGTTCTATCATCCAAAACAATACAAGGAAGTCGCC\n+ATTAAAAAGAGTGTCAATCACTTCTGAGTCTTCTTTTTATAAAGAAAATACCTTTGCGCA\n+TCACAACACCACTGGATCCAATTCTGTGGGTCCAAAGAAGCCGTTTTTAGATTATCATCA\n+CTCAACATCTAACACACCGACCAAGAAAAAAAAGGATTCATTTGACCATGCCTCCGTTAC\n+GTCCTTACATCGTCGTAGCTTATCCTCTAATACTTCAACACCTCGAAAGTATCATTCCAG\n+AAAGCCATACTCCGAGCCTTCTGTCATCGATAAAGAGCATTTACAAAACCGCGTTAGTAT\n+CGGTACTACGCATACCCAAAATGATTTGTATCAGTCTTATGTTGCATATCCTGATGCCCT\n+GCCCTTATTCGCTGCTACCCATCCATTCGAGAGACGCTATCCTCCTTCTCTCCTCCATCA\n+ATTCCCTTCTTCCAAGGACATAAAAAATGAGACACCGACTATTGACCGTTGTGATTTCCC\n+TAATTATGTTCCGATGTTTGCTTTTCCTAACGACATAACTATAAAAGAATCGGATGTTAG\n+ACCTGTATCAACCTACCACTCTTTTGCTTTGACCAGTGACAATAACAGCCACTTGTATGG\n+GATTTGCGTGGTAGTTTGGGTTGCAATGCCTCAATCTATGCAAAATGACTTGGAAAAGGA\n+ATGTGAAGTTTGGAGAGCTAATAATACGACTGTGGAAGACCGTGAGGTTGCCGAGAAGCT\n+TTTATCCAGTTTAGAAACGGAGCGATCAAAACTTTCTTCATTATTATTAAAAATGCAAGA\n+AAAGGAACTTGAAGGGAGTGATTCCATCGATCCTATACTCTTGGAAAAGATTGATGTCTG\n+TGAAGAAAACATTATTCTTTATACTGAACTTCTTCGTCCTATGCGCTATAAATTACCTAG\n+ATTTGTTCATGGACTGACAAATAACAGGACTTTATGGATACCCAATGCTTATGGATTATT\n+GAGTAAGCATTCACATTTGCAGTCCTTTTGTCGGGATTGGCTTCGAATAGTATGCTCCTC\n+TATTCAAGCTGAAGATCTCGATTTTATCCCTTCGTCAGATTTAAATTCCCTTAAATCACT\n+AAACCTTCAATCGTTTGTAAAAAACATTTGCTGTGATGTTCCTTTGCCGCCGAAAGGACT\n+TCTGCAGTTGCAAGTTAATGTCGGCCCATTAAATCTTTACGCATTTAGGAGTCCAGTCAA\n+TGAAATCCCAGGTTGGAATGATGTTGACTTATATCCGTTATTTCGTGCATTAAGTATCCC\n+TAATATTCTTGTTCTTTTTGAGGCTGCTTTAATGGAAGCTAAAGTTATATTTTTGTCTGA\n+AAACTTAGGAATGCTGGGATATGCATCACAAGCTTTACTACATTTGCTTTATCCTCTTAC\n+GTGGCAAGGGCTTTATATTCCTGTTTTACCCAGGCGTTTGATATCTTGTTTTGAAGCTCC\n+TTGTTCGTACATTATTGGCACTCTATCGTACTTTTTTCATATGGACGACGTTCCTCTGGA\n+CAATATTCCGCTTGTTGTTTGTGACCTTGATAAAAATTCTGTATCTACGTTTGGGAAAAT\n+TGTTCGTCTTTCTCGCTCATTGCGATCTAAGTTACAGGCCCATCTGAAGCTTGCGGCGCC\n+ACTTCATGATAAATTTTATGTACCACATAGCCCTCCAAAGTACACAATGGAAACTTATCC\n+AAATAATGTCCTTTCGTTGAGTACAGTTACATGTTTTCCTTTGAGAGAAAAGTTTTCTAT\n+CCCAGCACTTTTGTCTTTTAGAAGCTCCAATTTTTCCAAAAGGCCTTATGTACTCTCTCC\n+TATCTTAAACGGTTTCCTTAAGCTTCAAGACAATCCTTCGAGTATTTATTTTGCGAAGCA\n+AACTGACTCGCGCCAGTCATCAGCTTCAAAACTTTTATATGCGCGTTTACAGGCGCCTGA\n+GCATGCTCGCAACTTTTCTTCTCCCCCTTTTACGAGACCTGCTTCTCCATCTTCTTCAAA\n+GTTTCGGTTTTCTTCTTCTTCTTTCCAATCGACGATAAGAAGAAATTCCCTCACATCACC\n+TTATTCGGTCCCTGAACTTCGTTCTTCTGAATCTAATCAAAATAAAGCTGGTTCTATTAA\n+CACCGGATCTGCTGTGAACCTTGTGAGTTCTAAGCCAGGAGAACAAAAAGTTCACATTAT\n+GTACAAAGAGGGGCATAAGCTGAGACGCATCTATAAAATGTTTCCCGCGGATAGCGCTGG\n+CTCCATTTGCGCTGTCTCAGGATATGCATTGGGTGACGTCCATGTTCAATGCGATAATTG\n+TGGGCTACGTGTTAATCTGGATTTCATAAAACATATATCAATGCCATGTGTTCCAGCATG\n+TTTTAATAGTCAGCAGATATTAGTGACATTTTTAAAATTCTTTATAAAAATCTTAGGGTC\n+ATATCGGAATTATTTACGCAAACCTCATATGTCTCGTGAAAATTTTGGTATTTCTAAAGG\n' |
| b |
| diff -r 0db979fead3a -r c6334cb383ff transdecoder.xml --- a/transdecoder.xml Thu Jun 01 06:04:12 2017 -0400 +++ b/transdecoder.xml Thu Oct 08 12:33:46 2020 +0000 |
| [ |
| b'@@ -1,134 +1,420 @@\n-<tool id="transdecoder" name="TransDecoder" version="3.0.1">\n- <description>Find coding regions within transcripts</description>\n+<tool id="transdecoder" name="TransDecoder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">\n+ <description>finds coding regions within transcripts</description>\n+ <macros>\n+ <token name="@TOOL_VERSION@">5.5.0</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n+ </macros>\n <requirements>\n- <requirement type="package" version="3.0.1">transdecoder</requirement>\n+ <requirement type="package" version="@TOOL_VERSION@">transdecoder</requirement>\n </requirements>\n-\n+ <version_command><![CDATA[TransDecoder.LongOrfs --version 2>&1 | grep \'TransDecoder.LongOrfs\' | cut -f 2 -d \' \']]></version_command>\n <command detect_errors="exit_code"><![CDATA[\n- TransDecoder.LongOrfs -t \'${input}\'\n- -m ${min_len}\n- ${adv.stranded}\n- -G ${adv.gen_code}\n- #if str($adv.partials)\n- -p ${adv.partials}\n- #end if\n- &&\n- TransDecoder.Predict --cpu \\${GALAXY_SLOTS:-1} -t \'${input}\'\n- --retain_long_orfs ${adv.retain_long_orfs}\n- ${adv.single_best_orf}\n- #if str( $training_sect.training.training_selector ) == "training_top":\n- -T ${training_sect.training.top_longest}\n- #else\n- --train \'${training_sect.training.train}\'\n- #end if\n- &&\n- mv `basename \'${input}\'`.transdecoder.pep \'$transdecoder_pep\' &&\n- mv `basename \'${input}\'`.transdecoder.cds \'$transdecoder_cds\' &&\n- mv `basename \'${input}\'`.transdecoder.bed \'$transdecoder_bed\' &&\n- mv `basename \'${input}\'`.transdecoder.gff3 \'$transdecoder_gff3\'\n+## initialize\n+ln -s \'${t}\' \'transcripts.fasta\' &&\n+\n+## run TransDecoder.LongOrfs\n+TransDecoder.LongOrfs\n+## Shared options\n+-t \'transcripts.fasta\'\n+-G \'${G}\'\n+## LongOrfs options\n+#if $lo.gene_trans_map\n+ --gene_trans_map \'${lo.gene_trans_map}\'\n+#end if\n+-m $lo.m\n+${lo.S}\n+-O \'output\' ## required, otherwise value of -t is used as output folder\n+\n+## run TransDecoder.Predict\n+#if $po.predict_cond.predict_sel == \'yes\'\n+ && TransDecoder.Predict\n+ ## Shared options\n+ -t \'transcripts.fasta\'\n+ -G \'${G}\'\n+ ## Predict options\n+ --retain_long_orfs_mode $po.predict_cond.mode_cond.mode_sel\n+ #if $po.predict_cond.mode_cond.mode_sel == \'strict\'\n+ --retain_long_orfs_length $po.predict_cond.mode_cond.retain_long_orfs_length\n+ #end if\n+ #if $po.predict_cond.retain_pfam_hits\n+ --retain_pfam_hits \'$po.predict_cond.retain_pfam_hits\'\n+ #end if\n+ #if $po.predict_cond.retain_blastp_hits\n+ --retain_blastp_hits \'$po.predict_cond.retain_blastp_hits\'\n+ #end if\n+ $po.predict_cond.single_best_only\n+ $po.predict_cond.no_refine_starts\n+ -T $po.predict_cond.T\n+ -O \'output\'\n+#end if\n+\n+## postprocessing\n+#if \'log\' in $oo.out\n+ |& tee \'$out_log\'\n+#end if\n ]]></command>\n <inputs>\n- <param name="input" argument="-t" type="data" format="fasta" label="Transcripts" />\n- <param name="min_len" argument="-m" type="integer" value="100" label="Minimum protein length" />\n- <section name="adv" title="Advanced Options" expanded="False">\n- <param name="stranded" argument="-S" type="boolean" truevalue="-S" falsevalue="" label="Strand-specific" help="Only analyzes top strand" />\n- <param name="gen_code" argument="-G" 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">Mitochondria'..b'e="out_lo_pep">\n+ <assert_contents>\n+ <has_n_lines n="772"/>\n+ <has_text_matching expression="c"/>\n+ </assert_contents>\n+ </output>\n </test>\n </tests>\n- <help>\n+ <help><![CDATA[\n+.. class:: infomark\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+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 minimum length open reading frame (ORF) is found in a transcript sequence.\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+ - a PSSM is built/trained/used to refine the start codon prediction.\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- </help>\n+*Step 1*: Extract long open reading frames\n+\n+By default, TransDecoder.LongOrfs will identify ORFs that are at least 100 amino acids long. You can lower this via the \'-m\' parameter, but know that the rate of false positive ORF predictions increases drastically with shorter minimum length criteria.\n+\n+*Step 2*: (optional and not part of this wrapper)\n+\n+The result "longest ORFs (PEP)" can be used to identify ORFs with homology to known proteins via BlastP or Pfam searches (`details <https://github.com/TransDecoder/TransDecoder/wiki#including-homology-searches-as-orf-retention-criteria>`_).\n+\n+*Step 3*: Predict the likely coding regions\n+\n+Optionally apply results of homology searches in this step and re-run the whole analysis.\n+\n+**Input**\n+\n+- FASTA file with transcripts\n+- (optional) gene-to-transcript identifier mapping file\n+- (optional) BLAST or Pfam database file (`details <https://github.com/TransDecoder/TransDecoder/wiki#including-homology-searches-as-orf-retention-criteria>`_)\n+\n+**Output**\n+\n+*LongOrfs*\n+\n+- longest ORFs (PEP/FASTA): all ORFs meeting the minimum length criteria, regardless of coding potential\n+- longest ORFs (GFF3): positions of all ORFs as found in the target transcripts\n+- longest ORFs (CDS/FASTA): the nucleotide coding sequence for all detected ORFs\n+\n+*Predict*\n+\n+- Results (PEP/FASTA): peptide sequences for the final candidate ORFs; all shorter candidates within longer ORFs were removed\n+- Results (CDS/FASTA): nucleotide sequences for coding regions of the final candidate ORFs\n+- Results (GFF3): positions within the target transcripts of the final selected ORFs\n+- Results (BED): BED-formatted file describing ORF positions, best for viewing using GenomeView or IGV\n+\n+*Other*\n+\n+- Log file\n+\n+.. class:: infomark\n+\n+**References**\n+\n+More information are available on `GitHub <https://github.com/TransDecoder/TransDecoder>`_.\n+ ]]></help>\n <citations>\n <citation type="doi">10.1038/nprot.2013.084</citation>\n </citations>\n-</tool>\n+</tool>\n\\ No newline at end of file\n' |