Mercurial > repos > greg > assembly_post_processor
changeset 69:61f9552be416 draft
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--- a/assembly_post_processor.xml Thu May 25 09:11:26 2017 -0400 +++ b/assembly_post_processor.xml Tue Jun 06 08:31:58 2017 -0400 @@ -111,7 +111,7 @@ <param name="prediction_method" value="transdecoder"/> <output name="output_cds" file="transcripts.cds" ftype="fasta"/> <output name="output_cleaned_cds" file="transcripts.cleaned.cds" ftype="fasta"/> - <output name="output_cleaned._ep" file="transcripts.cleaned.pep" ftype="fasta"/> + <output name="output_cleaned_pep" file="transcripts.cleaned.pep" ftype="fasta"/> <output name="output_pep" file="transcripts.pep" ftype="fasta"/> </test> <test>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plant_tribes_scaffolds.loc Tue Jun 06 08:31:58 2017 -0400 @@ -0,0 +1,3 @@ +## Plant Tribes scaffolds +#Value Name Path Description +22Gv1.1 22Gv1.1 ${__HERE__}/test-data/tool-data/plant_tribes/scaffolds/22Gv1.1 22 plant genomes (Angiosperms clusters, version 1.1; 22Gv1.1)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/arabidopsis_thaliana.smat Tue Jun 06 08:31:58 2017 -0400 @@ -0,0 +1,8248 @@ +FORMAT: at.conf CODING REGION 6 3 1 s C+G: 0 42 +-2 1 4 -3 +1 1 0 -2 +1 0 2 -4 +-3 1 4 -4 +1 -1 2 -3 +1 0 2 -4 +1 0 1 -2 +-3 2 3 -2 +0 -1 3 -3 +1 -1 -2 0 +2 0 0 -3 +-2 -1 3 -1 +-1 0 2 -1 +1 0 1 -2 +0 -1 4 -4 +-3 2 4 -3 +-1 1 3 -4 +2 0 -1 -1 +2 1 -1 -2 +-3 2 3 -2 +1 -1 2 -3 +2 -4 2 -3 +1 -2 4 -4 +-2 1 3 -2 +0 -1 3 -3 +1 1 -1 -2 +2 0 -2 -1 +-3 1 3 -1 +0 0 3 -3 +1 -1 0 -1 +2 -1 1 -4 +-3 2 4 -4 +-1 -1 5 -5 +2 -2 1 -2 +2 0 0 -3 +-3 0 4 -2 +1 -2 3 -3 +3 -4 1 -3 +1 -3 2 -2 +-2 1 3 -2 +1 -3 3 -3 +1 -1 0 -1 +3 -2 -2 -2 +-3 0 3 -1 +0 -1 3 -3 +2 -1 0 -1 +2 -3 2 -3 +-2 1 4 -2 +1 -1 1 -2 +2 -1 0 -2 +2 2 -3 -2 +-3 1 4 -3 +1 -2 2 -2 +2 -2 2 -3 +2 -2 1 -3 +-3 2 3 -2 +1 -4 1 1 +2 -1 -1 -1 +1 -1 2 -2 +-3 0 4 -1 +-2 1 3 -3 +1 -1 0 -1 +0 0 3 -4 +-3 1 4 -4 +-1 -1 4 -4 +3 -2 -1 -3 +2 -1 1 -3 +-2 1 4 -4 +1 -2 2 -2 +3 -6 2 -4 +1 -2 2 -2 +-2 1 3 -1 +0 -3 4 -3 +2 -1 -1 0 +2 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3 +2 -2 -1 -1 +3 -3 -4 0 +3 -2 -4 0 +1 -2 -1 1 +2 -1 -3 0 +2 -2 -2 1 +0 -3 2 0 +-3 1 -2 3 +1 -2 0 0 +1 0 -3 1 +1 0 -3 1 +-1 -2 -1 2 +0 1 -2 1 +0 -2 -4 4 +0 -2 -1 2 +-3 0 0 2 +2 -3 1 -1 +2 -1 -3 1 +4 -3 -2 -2 +-1 0 -1 2 +2 -3 0 0 +2 -2 -1 1 +2 -4 0 0 +-2 0 -1 2 +1 -3 0 0 +0 0 -4 2 +-1 -4 -5 4 +-2 -2 -1 3 +1 -3 1 0 +0 -2 -4 3 +2 -4 -1 2 +-3 -2 -1 3 +2 -3 -2 1 +3 -2 -4 0 +2 -2 -3 1 +3 -3 -1 -1 +1 -2 -2 1 +2 -1 -3 1 +1 -1 -2 1 +-3 2 -2 2 +1 -4 -2 2 +2 -3 -4 2 +2 -3 -2 1 +1 -4 -1 2 +-1 -1 -2 3 +1 -1 -4 2 +0 -3 -1 2 +-2 -1 0 2 +1 -1 -1 0 +2 -1 -3 1 +2 -1 -2 0 +-2 1 -1 1 +1 0 -2 0 +2 -4 0 0 +1 -1 0 0 +-3 2 -1 2 +0 -2 0 1 +0 -1 -5 3 +1 -1 -1 1 +-3 0 0 3 +1 -2 -2 2 +2 -3 -2 1 +0 -4 -1 2 +-2 0 0 2 +2 -1 -1 -1 +0 2 -3 0 +2 0 -3 0 +-2 1 -1 2 +2 -1 -3 0 +2 -2 -3 1 +0 0 2 -2 +-4 3 -3 2 +-2 -1 -1 2 +-2 5 -4 0 +-2 2 -4 2 +-3 3 -3 2 +1 0 -2 1 +-2 2 -5 3 +1 -1 -1 0 +-4 3 -1 2 +1 -2 0 0 +-1 0 1 0 +2 -1 -2 0 +-4 2 -2 3 +1 -3 0 0 +-1 -8 5 -2 +1 -2 1 0 +-4 1 1 2 +0 -5 2 1 +-2 -2 2 1 +0 -4 -3 3 +-4 -2 1 3 +1 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+-1 0 -6 3 +0 -3 2 0 +-2 -2 0 3 +1 -2 -3 2 +1 -2 -4 3 +0 -3 -2 3 +-1 -2 -1 2 +1 -1 -1 0 +1 1 -4 1 +2 -1 -2 0 +-2 2 -2 1 +1 0 -2 1 +1 0 -3 1 +1 -3 1 0 +-5 3 -4 2 +1 -3 -1 2 +-1 2 -4 2 +1 -2 -2 2 +-3 2 -2 2 +0 0 -2 2 +-2 0 -5 4 +0 -1 -1 2 +-5 4 -2 1 +1 -3 1 0 +0 0 -3 2 +2 -1 -1 0 +-3 0 0 2 +1 -4 1 1 +1 -2 -2 2 +0 -4 0 2 +-3 0 -1 3 +1 -4 0 1 +-1 -1 -4 3 +1 -3 -1 1 +-3 -1 0 3 +1 -2 -2 2 +-1 -2 -3 3 +0 -4 -1 3 +-3 -1 1 3 +1 -2 -1 1 +1 -1 -5 2 +0 -1 -1 1 +-2 0 -1 2 +0 -1 -1 1 +0 0 -3 2 +1 -2 -2 2 +-5 2 -3 3 +0 -3 -1 2 +0 -1 -5 3 +0 -3 -1 3 +-1 -3 -1 3 +0 -1 -1 2 +-1 -1 -5 3 +-1 -3 0 2 +-4 -1 -1 3 +FORMAT: at.conf START PROFILE 1 12 7 s C+G: 42 100 +2 -3 0 0 +1 4 -4 -2 +6 -4 -1 -6 +8 -9 1 -9 +5 6 -14 -6 +6 -1 0 -11 +18 -100 -100 -100 +-38 -38 -39 18 +-49 -46 21 -44 +-3 -13 12 -10 +1 9 -4 -8 +-4 -7 6 2 +FORMAT: at.conf STOP PROFILE 1 12 6 s C+G: 42 100 +0 0 2 -2 +1 1 -3 1 +-4 2 -1 3 +-59 -62 -50 18 +10 -66 10 -68 +15 -64 -2 -70 +4 -8 -1 1 +2 -2 -2 0 +3 -1 -4 0 +2 -2 -3 1 +2 -3 -3 2 +2 -2 -3 2
--- a/test-data/assembly.fasta Thu May 25 09:11:26 2017 -0400 +++ b/test-data/assembly.fasta Tue Jun 06 08:31:58 2017 -0400 @@ -5,3 +5,69 @@ CCGGTATTCACCAGATCCAGAACACTGAGCCCTTGACTCTCAACGGCATCTTGCTCATTT AATTTAACACCTTCAACCCACTCCATTGTTAGCACCTTTCCACTCGTGTAATCCCAGAAA ATATCTGGGACAAGGATATCTTCCTTGTCTCCATATAATTTTTTAA +>contig_2 +CCTTTCCAAGGTACCCATCCCATCCAACAACATATATGCTATAAATGATAAGAAGTCCCC +GGAAGATGCAGCAGACGACTACGAAAACCGCCTCAAGGAACTCGTCTCCGAAAAAATCAT +ACCCGTTTCAACCATTAGCGGGTTCCCGAAGTTCGACCTCATGTTGCTTGGAATGGGGCC +CGACGGCCATGTGGCCTCTCTTTTCCCTTCTCACATGCAACGCTATGAGAAGGAGAAATG +GGTCACTTTCATAACTGACTCTCCCAAACCGCCTCCGTCGAGAATCACTTTTACGTTTCC +GATGATCAACTCGGCTTCGGAGATCGCTATGGTGGTTACCGGGGCTGATTTGGCTGGTAC +AACTAAGATAGCATTGGGTACTACGGGCAATGTTAAGCCGGGTGAGACTCCTTTGCCTTG +TACTGAAGTTTCGGCTGAGGGAGAGGTTACTTGGTTCTTGGACAAAGATGCTGCTTCACA +ACTGTTAAATTATGTGCGCTTTGATGATTAAAAACACGGGGTAATTGAACTCAAGGGATG +GTTGAGAATTGTAATATTTCTGTAAGTGTCGGGGGATGGTTGAAATGCTTTTTATTATGA +AGTGTTAAAATGTAAGATAAA +>contig_3 +CGGGGGCAAGGTTTACATGAAAGTACATCTACAGGACCTAGATAAGCATCATCACCTGAC +AAAAAGCCATACATAGTAACACTTGCTAGTTGATCTGTGAAAATGGTGCACGAGTCGTAA +CAGACGGCATTAGTTCCTTTCCTGTAACAGCAGATTCGTATGAATGGTTTTCTCGAAATT +CTTCTTCAAGTGCATCTATAGGCATGGCACGAAGTGACTCTATTGTGCCTTTGCTGGGAA +TATCCGGCTCGCTCCTAACTGGCGTGGACCCTGTAGGCTCGTAATCCATGTATTTTTGCC +TGAAAGTATCATTCGTGTGCTGTTCGATACAGGATACCTGCTGGGAATGATCTCTCTTAA +GGTTCTCAATTGTTTCTGAATGAGCTCTAGCAGTTGTCAGAATTTCAGAAACAGATGCCT +TCTCCTGCTCTGACAAGCCAGCAACAACAACTCCTTCATCCACA +>contig_4 +CTGACGATGTTCATATTCATGCCACTCTAAATGTATGCCATCCATGTTGAGGAGAAATGC +TTGTGTAAAGAAGAAACTGGAGTCAAGCGGTCCCGGTTTTACAGTTGAACGTTGCTCTAA +ATTAGTCAAAGTACCCGACTACCCGCTCATCAAACTGGCGAGCTCGTTTTCCTCGCCGCC +CTACTCGGTGTCTTGGCGGGGCACATGGGGGTGGCGTGTGGCGTGCGGGGATGCGACAAC +ATCATAAATTCATAATCGAAGG +>contig_5 +GTGAGAGTGTCGCCTTTTCCATGCTACCCCTTTCCAGATCTGACTTGTTCGAACCTTCCA +TCATCCGGTTCGACGTCAGCAGTCGGTCCTTCTTCTCCAAGCACGAGAGCAGACGGTGCG +AGAGCGAGCAAAGACTCGCCTGCCGCGCCTCTCGTGACCTGGCTCGCATCTCCAGGATTC +ATGGCTCCTTAGCTCGCCCTTCTTCGATACTTCGCTAGACGCCCGAGGACGTCATCGAAG +GCGAGGGTCGGCACAACGGAGTGCTCCTTGCATGATGTCGGGGCCTGGCATCACGCGGCA +TCGGCCAAATCGTCCCTCTCGACGTGCGTCACGGAGAGGGCCGAGCGCCGGGACGACCGC +GTGGAAGAGCCCGCGGGATGCGGGATCCCGCTTGACGTGTGTTTGTGGCGGACCACCG +>contig_6 +TATAACAATTCAAAATATTCCTATGAAAACCAAGACCAGAGGCAACACCGGTATAACCAA +AGCCAGAGGCAATATCCCTTTATTCTTCGGGAACAGAAAAATACACGATATGCTACAGAC +AAAAAAATAAATCCAAACCATTCTTCTGTGCATAAACATTGTAAAAGTTTATTAGACCGC +TGTAAAACTCGTAAATGAAATCCCTGGCAATTGAATCTGTTAAACCTGCTCC +>contig_7 +GAGAATGAGTGGTCTGGGGCTGAGTTTTTGAATGAAATGGCGGCAATGATGACTCAAAAT +AAATCCAATGAAAACGGAACCGGAACTTTTGAAGAACTGCAACAATTGTTCGATGAAATG +TTTCAGAGCGACATCGAGTCCTTCAATGGTTGTTCTTCATCATCCAATGAAACATGTAGC +AACTCGAACAAGAGGAATTCCATTGAGTCGAGCTCGGCTAATTTCAGACCCGAAAATGCG +AAACGAAAGCGGCGAGATTAGCGGGAAGAAGAATACTAGGAAAGGTAAAGGTGACG +>contig_8 +TGGCATGAAGTCGGCTCGACTCGTGCCCGCTCGTCTATAGACGAATTGAGCTAGATTCAC +TCATTCCATGAACTCGACTCGTTCATGAGTCGGCTCGTAGTTGTCCGGACTCGCTCCATG +GCCAGCTCTACAACAGACTGCCTGTATGTAGATGATTGTATTGATTTGTTCTTCTCTTGT +TTAAATCCAACCAAATATCAACATGATATTTGCAATTTC +>contig_9 +ACTTCGGTTAAAGGCAGATGAGGAGGCACAATGTTTGAATCAGATGCAGCGTATCATTTT +TGATGAAATTATGGAGCATGTGGAGTTAGAAAAGGGGGGCTTCTATTTCGTATATCGCCC +TGGGGGCAACGGAAAGACCTTGTGGTTGGCTATTATCTCAAAACTGAGAAGCGAGGGTAG +AATAGTTCTCGCAGTGGCTTCATCAGGTATAGCATTGCTTTTGGTTGAGGGTGGTAGAAC +AGCCCATTCTCGATTTAAAATACCCATAGATGTCAATGAATATAACAATTGTGAAATTAA +ACAGAACATCTACCTCGCTGAACTTATATGTCACACCAATTTGGTCATTTGGGATGAGGC +ACCTATGACTCAATATTTTGTCTTTGAGGCGGTTGA +>contig_10 +GGGGCATTGCCGCCGATTAATTCGAGCGCGAGGTTTCGCGTATCAGGCGGAATTGGGATT +TGGCGCCACAAAGAGCGCCACCTATGATTTCTGTGGCGGACGACTTCACGAACTCGGACG +GGACTATCTAACCAATCTTCCAAGTTCATTGCGACATCAGTATAAGGGCGTGATGAAGGT +TCGCTATCGTCGCTTGAGTTATTGATGGGGCCCAAATTGAGATCGAGGTTCATTGTAGTG +GTGTTCTCTTCTGCCATTTGAGAATTTCACAAGTTCTAACAAACGAAAACGCAAATCTTC +GGGACTAATATGCAGAATTTCCCTAAATAGAAGGGGTTTAAAA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/assembly_tgf.fasta Tue Jun 06 08:31:58 2017 -0400 @@ -0,0 +1,271 @@ +>contig_1 +CGATTAACCATGTGTACAACATGACCAATTATGGCCGATCTTGCTTGTTCAGGAGTCTCA +CTCATCATTCCAAAATCAAGAAAAGCAAGCTTCCCGTCAGGTGTAGCTAAGAGATTCCCT +GGGTGAGGATCTGCATGAAAATAGCCGTACTCAAGCAGCTGTCGAAGACTGCACTGTATG +CCGGTATTCACCAGATCCAGAACACTGAGCCCTTGACTCTCAACGGCATCTTGCTCATTT +AATTTAACACCTTCAACCCACTCCATTGTTAGCACCTTTCCACTCGTGTAATCCCAGAAA +ATATCTGGGACAAGGATATCTTCCTTGTCTCCATATAATTTTTTAA +>contig_2 +CCTTTCCAAGGTACCCATCCCATCCAACAACATATATGCTATAAATGATAAGAAGTCCCC +GGAAGATGCAGCAGACGACTACGAAAACCGCCTCAAGGAACTCGTCTCCGAAAAAATCAT +ACCCGTTTCAACCATTAGCGGGTTCCCGAAGTTCGACCTCATGTTGCTTGGAATGGGGCC +CGACGGCCATGTGGCCTCTCTTTTCCCTTCTCACATGCAACGCTATGAGAAGGAGAAATG +GGTCACTTTCATAACTGACTCTCCCAAACCGCCTCCGTCGAGAATCACTTTTACGTTTCC +GATGATCAACTCGGCTTCGGAGATCGCTATGGTGGTTACCGGGGCTGATTTGGCTGGTAC +AACTAAGATAGCATTGGGTACTACGGGCAATGTTAAGCCGGGTGAGACTCCTTTGCCTTG +TACTGAAGTTTCGGCTGAGGGAGAGGTTACTTGGTTCTTGGACAAAGATGCTGCTTCACA +ACTGTTAAATTATGTGCGCTTTGATGATTAAAAACACGGGGTAATTGAACTCAAGGGATG +GTTGAGAATTGTAATATTTCTGTAAGTGTCGGGGGATGGTTGAAATGCTTTTTATTATGA +AGTGTTAAAATGTAAGATAAA +>contig_3 +CGGGGGCAAGGTTTACATGAAAGTACATCTACAGGACCTAGATAAGCATCATCACCTGAC +AAAAAGCCATACATAGTAACACTTGCTAGTTGATCTGTGAAAATGGTGCACGAGTCGTAA +CAGACGGCATTAGTTCCTTTCCTGTAACAGCAGATTCGTATGAATGGTTTTCTCGAAATT +CTTCTTCAAGTGCATCTATAGGCATGGCACGAAGTGACTCTATTGTGCCTTTGCTGGGAA +TATCCGGCTCGCTCCTAACTGGCGTGGACCCTGTAGGCTCGTAATCCATGTATTTTTGCC +TGAAAGTATCATTCGTGTGCTGTTCGATACAGGATACCTGCTGGGAATGATCTCTCTTAA +GGTTCTCAATTGTTTCTGAATGAGCTCTAGCAGTTGTCAGAATTTCAGAAACAGATGCCT +TCTCCTGCTCTGACAAGCCAGCAACAACAACTCCTTCATCCACA +>contig_4 +CTGACGATGTTCATATTCATGCCACTCTAAATGTATGCCATCCATGTTGAGGAGAAATGC +TTGTGTAAAGAAGAAACTGGAGTCAAGCGGTCCCGGTTTTACAGTTGAACGTTGCTCTAA +ATTAGTCAAAGTACCCGACTACCCGCTCATCAAACTGGCGAGCTCGTTTTCCTCGCCGCC +CTACTCGGTGTCTTGGCGGGGCACATGGGGGTGGCGTGTGGCGTGCGGGGATGCGACAAC +ATCATAAATTCATAATCGAAGG +>contig_5 +GTGAGAGTGTCGCCTTTTCCATGCTACCCCTTTCCAGATCTGACTTGTTCGAACCTTCCA +TCATCCGGTTCGACGTCAGCAGTCGGTCCTTCTTCTCCAAGCACGAGAGCAGACGGTGCG +AGAGCGAGCAAAGACTCGCCTGCCGCGCCTCTCGTGACCTGGCTCGCATCTCCAGGATTC +ATGGCTCCTTAGCTCGCCCTTCTTCGATACTTCGCTAGACGCCCGAGGACGTCATCGAAG +GCGAGGGTCGGCACAACGGAGTGCTCCTTGCATGATGTCGGGGCCTGGCATCACGCGGCA +TCGGCCAAATCGTCCCTCTCGACGTGCGTCACGGAGAGGGCCGAGCGCCGGGACGACCGC +GTGGAAGAGCCCGCGGGATGCGGGATCCCGCTTGACGTGTGTTTGTGGCGGACCACCG +>contig_6 +TATAACAATTCAAAATATTCCTATGAAAACCAAGACCAGAGGCAACACCGGTATAACCAA +AGCCAGAGGCAATATCCCTTTATTCTTCGGGAACAGAAAAATACACGATATGCTACAGAC +AAAAAAATAAATCCAAACCATTCTTCTGTGCATAAACATTGTAAAAGTTTATTAGACCGC +TGTAAAACTCGTAAATGAAATCCCTGGCAATTGAATCTGTTAAACCTGCTCC +>contig_7 +GAGAATGAGTGGTCTGGGGCTGAGTTTTTGAATGAAATGGCGGCAATGATGACTCAAAAT +AAATCCAATGAAAACGGAACCGGAACTTTTGAAGAACTGCAACAATTGTTCGATGAAATG +TTTCAGAGCGACATCGAGTCCTTCAATGGTTGTTCTTCATCATCCAATGAAACATGTAGC +AACTCGAACAAGAGGAATTCCATTGAGTCGAGCTCGGCTAATTTCAGACCCGAAAATGCG +AAACGAAAGCGGCGAGATTAGCGGGAAGAAGAATACTAGGAAAGGTAAAGGTGACG +>contig_8 +TGGCATGAAGTCGGCTCGACTCGTGCCCGCTCGTCTATAGACGAATTGAGCTAGATTCAC +TCATTCCATGAACTCGACTCGTTCATGAGTCGGCTCGTAGTTGTCCGGACTCGCTCCATG +GCCAGCTCTACAACAGACTGCCTGTATGTAGATGATTGTATTGATTTGTTCTTCTCTTGT +TTAAATCCAACCAAATATCAACATGATATTTGCAATTTC +>contig_9 +ACTTCGGTTAAAGGCAGATGAGGAGGCACAATGTTTGAATCAGATGCAGCGTATCATTTT +TGATGAAATTATGGAGCATGTGGAGTTAGAAAAGGGGGGCTTCTATTTCGTATATCGCCC +TGGGGGCAACGGAAAGACCTTGTGGTTGGCTATTATCTCAAAACTGAGAAGCGAGGGTAG +AATAGTTCTCGCAGTGGCTTCATCAGGTATAGCATTGCTTTTGGTTGAGGGTGGTAGAAC +AGCCCATTCTCGATTTAAAATACCCATAGATGTCAATGAATATAACAATTGTGAAATTAA +ACAGAACATCTACCTCGCTGAACTTATATGTCACACCAATTTGGTCATTTGGGATGAGGC +ACCTATGACTCAATATTTTGTCTTTGAGGCGGTTGA +>contig_10 +GGGGCATTGCCGCCGATTAATTCGAGCGCGAGGTTTCGCGTATCAGGCGGAATTGGGATT +TGGCGCCACAAAGAGCGCCACCTATGATTTCTGTGGCGGACGACTTCACGAACTCGGACG +GGACTATCTAACCAATCTTCCAAGTTCATTGCGACATCAGTATAAGGGCGTGATGAAGGT +TCGCTATCGTCGCTTGAGTTATTGATGGGGCCCAAATTGAGATCGAGGTTCATTGTAGTG +GTGTTCTCTTCTGCCATTTGAGAATTTCACAAGTTCTAACAAACGAAAACGCAAATCTTC +GGGACTAATATGCAGAATTTCCCTAAATAGAAGGGGTTTAAAA +>contig_11 +CATTTATGGAAAGGGGATTCAAAATATGAGAACACTCTGGGGTGGCGTTGCTCCCGAATC +TCCCGTCGTTGTTGTTGGAGGCGGTGTTACTCCAGAATCTCCCGTCGTCGGAGGCATTGT +TCTAGGATCTCCCGCAGTGCTGCTTAAGTCGGATTTACTCCAAGCTCTCCCACCGCGGCT +CCTGAAGTCGGCGTTGTTCCAAAATCTCCCGTCGCCACTGTTGAAGTCGGGGTTGCTCCA +TGATATCCCGTCGGAGTTGCTCCGAATCTCCCGTTGTTGCTGCTGCAGTCGGTGTTGCTC +CAGAAACTCCCGCTGTGGCTATTGAAGTCGACCGCGGGAGATCCTGGGGCAACGCCGGCT +TCAGCAGTCGCCGGAGATTCTGAGGCAACGCCGCTTCCAGCAGCAGCGACGCGAGATCCG +GGAGCAACCGTGACTTTAGCAGCG +>contig_12 +GAATAATATTTTCCCACATAAACCTGATGCCTTGAATCTGATGGGGCTTTAATTTTATAC +AGATGCTTGGAGGGATTCTTACTGGCTCTTCACCTTCCTCTCTCACCACATTAATTATGT +AACCTGCAGAAATATCGCCCAGCAATTCTACACCAGTGCCATCAAATGAGCTCCTATTAC +TGACTGTAGATCTCATGATTACGGACTTGGTAGAAAACCGTGCTTCCAAAGATTTCAGCC +GCTCTTGACGTTCCTTTTCAATTGCAATTTTCTTCTTGGTCTCTTCCCCCCGCGATTTTG +ATCGCTATAGAGAACGTTTGGATGAGGATG +>contig_13 +AGCGACACATATCGCGCTCTCTCTCTCTCTTCAATAAATACGCAAACCCTACTACCATAG +TTTTCACGCCTTAAAATGTTTTCGCCTTATCGTTGATTGCTTCACGAGACGACACCTTGA +TTAGTTATTATTCCCGATCCATCCGCCTGTTTGTTTTTTACTGATTTAGTTGAGCGAAAG +CTTAATTGGGGGTGATCATCGGTCGCCGCGGAAAATGATGTCGTCTGGAAGGTACATGTC +ATACTCACCGTCTCCTTCCGCCCCTCACTCACCTCACATTGGCATCGCCGGCAGCGGCGG +GGGTATGCGTACTGCCGCCTCTGTGCTCATCGAGCAAGAAAAATACCTCTCAGAGTTGCT +GTCTGAACGCAACAAACTCAGTCCCTTCGTGGCTGTGCTGCCAAATAGTTATCGTTTGCT +GAACCAGG +>contig_14 +TGCTTGCCGCAACTATAAATAAATACCAAGAGGAAAAAATACAGAGAATGAAGAAGCTTA +AAGTACTAGTAACCACCATGTTGGAGCTATGGACTTTCTTGGACACACATAGTGAAGAGC +AACAATCGTTTGAACACGTTAAGTGTTATGTAGCCGCTGCTGCTGTTGATGAGCATGCAC +AAAAGGCATACGAGTTACCCGGAATTCTTTCTTTGGACTGCCTTAACAATGTTGAGACAG +AAGTTTCTCG +>contig_15 +TGTGTTTTCGGTTCGTGAAGTGTGTGTGTACAAAATTGCCGGATCTAATACTATCGTAGG +AGGAATGGGATATTGACGAGGAAGGAGGTGAAAAAGGTGTTAAAATGGAGGAGAAATTGG +TTTTTATGTGGGGGTACTTACCGGGGGCGCTGCCGCAGAGGATGCCGATTTTGTCTCCGA +TGGTGGTGCGGCTGCCGCATGGCGGCGGTTCATGGAAGGATGTATGTGGTGGAGGCTGTG +GTTTCGCCATGGCTATATCGGATTCTGGTAAGCTCATTACATGGGGGTCTACTGATGATT +TAGGTCAAAGCTACGTGACCTCTGGGAAACATGGGGAAATGCCAGAGCCTTTTCCACTAC +CC +>contig_16 +GGGGTTTTCCCACGGCGGCCACGATGGGTGGAAGCGGATGGGGTGGAGGATTCCGGTGTA +GGGTCCATAGAAGCAGATAGCTCAGCAATGGGATAGCCGGGAGAGATCGAATTGGTATTG +AAGGCAGTGGTAACAGCGGCAGCAGGTGTGGAGGAGGGACGGGAGCGTTTGGTGGCGCGT +GTGGTTGGGCCGGGAGAGGCTGATGAGGTGGATGCCTCTGTCCGCTTACGGCACCGAGTT +TCCATACAACCTACAAAATCGGAAATAGACGTCGCCGATTAATCGGCGGACATGCGCAAT +ATCAATCCCCAACTTCGTTGCATTTCAATTTCAC +>contig_17 +TGAGCGGCTACGGACAGGCCGAACTTTGGGTGGCTGCTATGCCATTATACATGCACGGTA +TACCTAAGCATCAGAAATTAGGATACACGTTGAACTTGTAAGCTCCAATCGAGGATTTAT +GTGATGATGAGATCGAGGGTTTCGCGCCACGAATAAGGGCTCCGATCACTCGGGGTTGTG +CTGCTGAATAAGGAAGAATTTTGATTTGATG +>contig_18 +GGTAACCTCATCCAATGCCAACCAAAGCGGGCACTTCTCTCCATCAATGGAAACGGGGTC +TAATTCCTTTATACTAACCATTTCAAGTGCCGAAGCATCAAGAAGCAAGCCCTGGTGAGG +CCTATTATCAACGACCATGTTGAGGTCGTGTTTGGATACCTCTTTTTTGCTTAATCCAAT +CTTTTCCACCATTTTCAAAACTCTCTCGAACCGTTTCTTGTCCTTCTTCTTACTGTTACT +ACTCAAATCCAAACCTTCCTGAACGTACAACGCGTAGAGTTCTCTTCGCCCGGATGAGAG +TGCAGCTAAAATGGGACCAACTCCATAGATCCCTTCACCTACTATTTTCGGCAATGTGGA +TTCCTTAGCTTCTTTCCATGTCTTTCTACCCCAATCTTCCTGCTTGTTCCATCTTCTCAC +CTCTGTTC +>contig_19 +ATACAAGAAAAGATACCCAGTCGTTCCAACTCTTCTTACAAGAATTCTGTGGTGGAGAAT +ATGTTTGGATGAAGCTCAAATGGTGGAGGGTAATGCTGCTGCAGCAACAGAACTGGCTGT +GCGTCTACATGCAAAACATCGTTGGTGTATAACAGGGACTCCCATACAACGGAAACTTGA +CGACCTGTATGGGCTTTTGAGATTCCTTCAATCAAGTCCATTCAATGTCCTCCGCTNG +>contig_20 +GGCTTACGCATCGATGCTCACGGATATGCCCTACAAGATTGGCAACGCGATCTGTTTCAA +CTTGATCTTGTACTTCATGACGAACCTTCGCCGCGAACCAGGAGCATTCTTCTTCTTCCT +GCTGATATCGTTCACGCTGACGCTTGTCATGTCGATGCTCTTCCGCACTATTGGATCCGT +TTCGCGTACACTGTCGCAGGCCATGGCTCCCGCAGCTATCCTTATCCTTGCGCTGGTCAT +TTACACTGGTTTCGTCATTCCTACCCGCTACATGTTGGGCTGGTCTCGTTGGATCAACTA +CTTGGATCA +>contig_21 +CGCCATATTAATGTGTCACTCGAATGCAAGTCTTTGGGTGCCAACCAGTGAGGCATAAAG +ACCCTTTTGCTCTAACAACTCAGAGTGTGTCCCCAGTTCTGAAATCTTCCCATCAGAGCA +TAAAGCAATTTGATCAGCATTTTGAACGGTGCTCAGCCTGTGAGCAATCACTAAAGTCGT +TCTTCCTTTCATCAAACGGTTCAAAGCATCCTGAACCAGACGTTCACTGACTGCGTCCAA +AGCACTGGTAGCCTCATCAAGAATCAAGATTGGAGCATTCTTGAGCAGAGCCCTTGCAAT +GGCTACCCTCTGTCTTTGTCCTCCACTTAACAACCCACCACGCTCACCAACTAATGTGTC +ATAACCCTGTGGCAACGCAATGATAAATTCATGAGCATTAGCTGCTTTAGCAGCTTTTAT +CACATCGACCTTGGAAACATAATCATCTGGGAGTCCGTAAGCAATATTTTCTCCAATGGA +AACCGAGAATAGAACAGGTTCCTGATTCACTATGGAAACC +>contig_22 +CCAGTTTCAATTATATTACATATGTAACCATGCACCACAGAGTGGGTATGGATGTCGCTA +ATATCAACAGGGAGCTGCTGAGTTGAGTTAACTAGTGAACACTTGGCACTAAGTACAAGA +TTGTTTCCTTCAACATCAAGAACCAATAATTCATCAAAATGATATCCTGGCTTCAAGACA +GACATCAATAGAGCAGCAAGTCCATGGTGGTCTGCCAAATGTTCAAGAG +>contig_23 +ATCCGTGATTCTTCAGGGTCGCCGGCGGCAAAGCTGGGGACTTTTTCGTCAGTTGGTTTG +GCTCCGGTTCAGGATCGGAATCGGATGAGGCATCTTCGAACGACGCGTTTTCTTCTGGGT +CGGATTCTGAATCCAACACGATTGGCTTCACCGGCTCCACATTATTGGACATTTTTTGTT +TCAAAACGGCGCAGTTTTTGCATGAGACTAGCA +>contig_24 +CGTTAAGTAAATTGTTCTCTTCCATTATAGAAGATATCTGAGACTGCAGCTTTTGTCCTT +CAGAAGCAAGCTTCTGAGTCAGCTCTTCTATTTCTTTTCTTGCACTAGTTAGTTCTTCAA +CAGTGCCGTCTTTCTCAGATGAAACAACGTTCAATTTCATCTGTATATCGTTTAGCTCGG +ATTTAAATGCACCCAACTCCTGACTGAGTTTCGAGTTTTCTGCAACAAGTGCCTCAGTCT +CCTTTATAAACATACTACCCTTGCTCTCCAATTCGCTTTCCAAATCCTTGGATTTTAACA +AGATTTGTTCGATTTCTAATTCACGGGTTTTC +>contig_25 +AGAAAATCAATCAGTACGAAAATCTCCATTAACCCAATCATCCCCCTTCCTTGCCTTTAT +CGATTTGTGATCAAAGTCGCCTTTTATCAATTTGTCCCCGTGCTCAGTTTCTTCCTCTCC +AGTTCATTCCCCCACCAATCGTTGCTAATTGATACCTAATCGCCTTTTTAACACCTCCTT +TTTTTGACTTAGTGCTTGATTTTCCTCGATCATAATCATTTCCAA +>contig_26 +AGAGGAAAGAAGGGGCGTCGGCAACAAAATTTGAAATTGAAAATATCTTCCCCGTCCGTC +ACTCCTTCTTGCGATCCCAAGAAAAAAGAGGAAAGAGGGGAGGCTACAACTTTTAGAGAG +AGGAAGCATAACGGTTGTGGCTTCTTGTTCTTGGAAGAAGAAACAATCGTTGTCGACAGG +TAGAGGGGATAATAATTGTTTAAAAAAATTGTTGGCAAAAAAAAAGTGAAAAATGAGAGA +AATAATAAGCATACA +>contig_27 +CCCACAACCCGGGCCCAAGACCCGGGCTATCCCGATAGCAAGTGCCCCACTTCCAGTCCC +TAAATCGGCCCACAAACCATTTTTCAGTTCCCCATTTTTCTTCACTGCATCTTCAACCAA +ATCCAAAATAACCTCCGTCTCAGGCCTGGGTATCAAAACACCTTCCTCAACACTCAATAT +CAAATCCCGCCAGTGTTCACAGCCCACCACGTACTGAAACGGCCTTCTTTCCTCAATCCT +CTGCTTCCACAGCTTGTAGAG +>contig_28 +CTTGGCTTTGATTAGGTGTTGTAGTTTGAGATCGCGCTGAATTATTGTTTGCTGTCACAA +GAACTGTTGGGGAGGAGGAGGAGCTGTCAAGGTGCGACGATCCTTGACGTTTTTCTTTAT +TCAGCACACTTTCTTCGAGTAATAGCATGGTCTGCGTGGATTCTAGGTCGGGTAATTTTT +CGCGATGCTTAATGATGCACGCATTTGGAGAAAATTGTG +>contig_29 +TGCTGGTAAATAGCTAGCAAAGTTAGGAGTAGTGATCGCAATTTCCGGACGATGAAGAAA +TCGAAGCTTCTGCAGAATTCGAAGGACTTACTTTCTAGGAGCTTCAATCCTGCTAAATGC +AAAACGTCTCTGAGGCTGGCGGGTTCAAGGTTGAAGCTATTGAGAAACAAGAAAGAGGTG +CAACTGAAGCAGATGAAGCGGGAAATAGCACAGTTGCTCGAGTCTGGACAGGATCAGACC +GCTCGAATTCGAGTCGAACATCTGATTAGGGAAGAGAAGATGATGGCTGCATATGATCTC +CTCGATATATACTGCGAGCTTGTTGTTGCACGTCTTCCAGTAATTGAGTCACAAAAGAAT +TGCCCCATTGACCTGAAAGAAGCAATTGCAAGTTTAGTATTTGCAGCACCAAGATGTGGA +GATGTACCCGAGTTTCTTGATGCAAGGAAGCAATTTTCAGCTAAATATGGAAAAGATTTC +ACTACTGCAGCCACAGAACTTCGTCCACAGTGCGGTGTAGGCCGCATGTTGGTTGAAAAA +TTATCTGCAACAGCGCCTGATGTACAGAGCAAAACTAAAATCTTGAATGCAATAGCTGAG +GAGCACAATGTTAAATGGGAACCCACATCATTTGGAGAGAACGACTCTGCACCTCTCAAT +GACCGACTGACTGGACCAAGTTCCTTTACGAAGGAGAGAGAACAGTACCCTGAACCTCCT +CATTTTGAAGCTGTACAAGTCCAAGCTCACCCGAGCAACAACACCTTGCATAGCTCGCCA +TCAAATTCTTCCCAGCAGGATGATAGAACCTCAGTTTTTGTTGAAACTTCTACTTTCAAG +ACACCATCG +>contig_30 +AAGGCTAGTGGACTTTTTTCAAGTAAAGATTCTGTTGATTCAACAGATAGCCACATGGAA +AATGTATGCTCTGATATTTTATCAATGAGCATCAACAAAAACCAAATTTTAGAGAATGGC +CATGTTCATAACAATAGAGGAGCAGCAATATTTGAGTTGTCTGGAGCTGCTACAAATGTA +ATTGAGGACGTTGGTTTGTCAGATGTCCAGTCTGACACCAGATTGGGAATGGCAAGTCAA +GTTTGCCAAGTTGATATGCATGAACCAGAGGGCGGTTTGTTGTCTTTTAAGAACCAAAGA +TTTAAGGATGCTGAGGTTGCTACCAATATAACACATGATTATTGTCATGTATCTCATCTG +TTAAAGCATTCTAACGTTCAAGTTCCTAAGTACATTAGTGGTAATGGTTCAGCCACTGTT +GATCTGAATAGGCAGACTGTAGATAGGAATAACAATTTTAAAGTTTCAACATCTAATT +>contig_31 +CCGTACTCAAGCTTTTAGTTTTATCCTCCTCATTATGACGTTTGCGTCTGTTTTCTTTTT +CAGACTTCTGGCTGCCTCTGTTAGTTAATCTTTCTGTATGCATCACATTTCTTTCGTCTC +TTCTTTTGTACTCTTTCTCAGAGTCACTGCTCATTCGCCGTTCTGTTTTCCTTTTCCTGT +GGACCTGTCCTTCATCGTTAACAAGCTGTTTTCTATCTATTTCGGATTTGACTCTGCCTC +TTTCAGAAGTTTTACCCTTTCTATATGACTCTCTGGCTTGCCTCTTATTTGATCCATTAT +ATGAATCCACACCTAAATGGCCATCTCTTTTTCTGTTGCTGTAATGTCGTCTTTCATTTT +CTCCTTCTCTCACTCTCTTGCTGCCTTCAGTCTTTTCCCATATACTCTTTAACTTGACAC +CACTTTCCCTATACTTTTCATCCTTATCCTGGACTAAATTGTCATTCTTACTATCCACTT +TTCTCCGGCAACTTACCTTCTGAAAATCATTTGAAGTATGTCTAACATCCATACGTTCAG +AAACCTCATTTATTTGCCGATGGTATTCTGGAAAATTAGAAATCTTTTCAATGTCACCAT +GCCCTGATGCACTATCAGCCACTCCAGAGCCACTGGCAACTTCTTTACCTGCATCTCCCT +TGTTATTTCTTCCGAGCATTATCTCATCATAGCTTAATGGCCTCGTTCTTGCACAAGTGC +CCTCCAAAAGATCATCCTGAGACACTCTACTTTCTAATTTCTCTATGTGTGGGCGGGATC +TAGTCATGGCGCTAACGGACTTCTACTATGTTTACGAGCATGAGGAACTGCCAGAGCGCG +GCCGGAGAGAATAAGCGTCGCCTGGTGGTTTTAC +>contig_32 +CACCGACACATCACAGAAATGGGGCTTTCCATGTTACTTCATTCACGAATGCCTTTGTCA +TATTGGGATGATGCTTTTTCTGCTGCAATTCACACAATCAACCGCCTACCTACTCTGATT +CTCAACAAAGTTTCTCCTTTTGAAGTACTCTTTGGACGCGCACCGGTGTATTCTAACTTT +CATCCTTTCGGCTGCAGAGTTTTTCCCTATGTTCGACCCACTGCTGAACACAAACTTGCT +CCACGCAGTCTGCCTTGTATCTTCATCGGCTACAGCGCTCACTATAAAGGC +>contig_33 +TTTTAATTCTATAGGGCGAAGTAATGCTGTCTTTTCAGCAACCTTTTGCCAATCGACAAA +GTCAATGAGCTCTTCATCCATTGATTCTTTTGCAGCAAGAAGAAGGATTTTCCTCCTTTC +TGCTTGAGTTAGTCGCTGAAGATGAAATATTCGATCCATTCTACCAGGACGCAGTAAAGC +CCCATCGATTTGTTTAAGATTCCGAGTAGTAGCCATCAAAACTACCCCATCTTGTTTCTC +AAACCCATCAAGCTCCACCAGAAGTTGATTGATGAAAGATTCGTGATCCAGCTTTTTGGT +CTGAAGGTCCTTCCCGCGGACACCAGCAAAGAGGTCAAAGTCTTCCACAAATATAATGAC +AGGAGCCAGATCCCGTGCTGCTTGAAACAATTCTCTAACGTTTGATGCACCTTGGCCCAC +AAACAGACCAGCTTCCAGCTGTTGGGCTTTTACTTCAACTAAAGGAACCTTCGCTTCCGC +TGCTATAGCCATTGCTAGGGATGTTTTACCTGTTCCTATCTCACCAACAATAAGAACACC +CCGAGGTGCCCGAGCTCCCATTTCTTGGAATGCACGAGGATTTTGTAGAAATGCCACAAC +TTCATTAATTTCTTC +>contig_34 +ACCCGTTGGACCCTCTCGTGATTCAAACTCAACTTGTTTCATAAAATAGCACAACACTGC +TCGGTACTGAAAACTGGAGGATCTTGTAGGTCAATAATACAAGTTACAACTCTTGTAATT +CCTCAACTGAGTGCACAGTCCAAAGTGGCCAATGGCATCAAGTAACAGATTACCAATAAG +ATAACAGTAGAAGTCAGATGAATATTCCTGTCTTGATTTTGTTTTCTCAACTGCTTCTAC +TTCCAATTAAGGAGAGACACAGTCGAAAATAGAATAAACCAAATATTTATCTGTAGGCTT +CCGGCAGGCGGTAACCACTGATCACTAAATTGTCGGCGAACATCTTGCCAGTTTTGGGCA +TCACATGCCAATGCATTGTTAAGTTGAAGTCTTTACCACGTAGATTGCTTCCTTGGTCAA +TAAAACGATACTTGTTAGTTGTCTGGATCTGAAATATTGCTTGCTCTTTGGAGGGTATAA +TAAGATCCCACAAGGAGACCTGATTCAGCGCATTTGTTGGGGTTTCA +>contig_35 +AATTCACAGCCTTCTCTTTCATCTCGAGATTGTCTACCTTCTGCAGATCGATATGTCGAT +GCTTTACAGAGGGATATCGAGGAAGGATAAACCTAGAGGACGTCAGCACGGGTTGACTCA +ACAGAAAAGGCAAGAGATAAAGGAAGCTTTTGAACTGTTTGACACCGATGGATCTGGAAC +TATTGATGCGAAAGAGTTGAACGTAGCAATGAGGGCTCTCGGTTTTGAAATGTCAGAAGA +GGAAATTACGAGAATGATAGCTGAAGTAGACAAAGACGGGAGTGGGGCGATTGACTTTGA +CGAGTTTTGTCACATGATGACAGCCAAATTCGGAGAAAGGGACACCAAAGAGGAGCTTAC +CAAGGCTTTTCAGATTATCGACAAAGATCAAAA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.pttgf Tue Jun 06 08:31:58 2017 -0400 @@ -0,0 +1,6 @@ +<html><head><h3>Targeted gene families: 1 items</h3></head> +<body><p/><table cellpadding="2"> +<tr><b>Directories</th></b> +<tr bgcolor="#D8D8D8"><td><a href="752" type="text/plain">752</a> +</td></tr> +</table></body></html>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/target_orthos.ids Tue Jun 06 08:31:58 2017 -0400 @@ -0,0 +1,5 @@ +213 +9300 +752 +4632 +4732
--- a/test-data/transcripts.cds Thu May 25 09:11:26 2017 -0400 +++ b/test-data/transcripts.cds Tue Jun 06 08:31:58 2017 -0400 @@ -1,2 +1,8 @@ >Gene.1::contig_1::g.1::m.1 type:internal len:115 contig_1:344-3(-) AAAAAATTATATGGAGACAAGGAAGATATCCTTGTCCCAGATATTTTCTGGGATTACACGAGTGGAAAGGTGCTAACAATGGAGTGGGTTGAAGGTGTTAAATTAAATGAGCAAGATGCCGTTGAGAGTCAAGGGCTCAGTGTTCTGGATCTGGTGAATACCGGCATACAGTGCAGTCTTCGACAGCTGCTTGAGTACGGCTATTTTCATGCAGATCCTCACCCAGGGAATCTCTTAGCTACACCTGACGGGAAGCTTGCTTTTCTTGATTTTGGAATGATGAGTGAGACTCCTGAACAAGCAAGATCGGCCATAATTGGTCATGTTGTACACATGGTTAAT +>Gene.2::contig_2::g.2::m.2 type:5prime_partial len:170 contig_2:2-511(+) +CTTTCCAAGGTACCCATCCCATCCAACAACATATATGCTATAAATGATAAGAAGTCCCCGGAAGATGCAGCAGACGACTACGAAAACCGCCTCAAGGAACTCGTCTCCGAAAAAATCATACCCGTTTCAACCATTAGCGGGTTCCCGAAGTTCGACCTCATGTTGCTTGGAATGGGGCCCGACGGCCATGTGGCCTCTCTTTTCCCTTCTCACATGCAACGCTATGAGAAGGAGAAATGGGTCACTTTCATAACTGACTCTCCCAAACCGCCTCCGTCGAGAATCACTTTTACGTTTCCGATGATCAACTCGGCTTCGGAGATCGCTATGGTGGTTACCGGGGCTGATTTGGCTGGTACAACTAAGATAGCATTGGGTACTACGGGCAATGTTAAGCCGGGTGAGACTCCTTTGCCTTGTACTGAAGTTTCGGCTGAGGGAGAGGTTACTTGGTTCTTGGACAAAGATGCTGCTTCACAACTGTTAAATTATGTGCGCTTTGATGATTAA +>Gene.3::contig_3::g.3::m.3 type:5prime_partial len:126 contig_3:463-86(-) +GTGGATGAAGGAGTTGTTGTTGCTGGCTTGTCAGAGCAGGAGAAGGCATCTGTTTCTGAAATTCTGACAACTGCTAGAGCTCATTCAGAAACAATTGAGAACCTTAAGAGAGATCATTCCCAGCAGGTATCCTGTATCGAACAGCACACGAATGATACTTTCAGGCAAAAATACATGGATTACGAGCCTACAGGGTCCACGCCAGTTAGGAGCGAGCCGGATATTCCCAGCAAAGGCACAATAGAGTCACTTCGTGCCATGCCTATAGATGCACTTGAAGAAGAATTTCGAGAAAACCATTCATACGAATCTGCTGTTACAGGAAAGGAACTAATGCCGTCTGTTACGACTCGTGCACCATTTTCACAGATCAACTAG +>Gene.4::contig_9::g.4::m.4 type:internal len:132 contig_9:2-394(+) +CTTCGGTTAAAGGCAGATGAGGAGGCACAATGTTTGAATCAGATGCAGCGTATCATTTTTGATGAAATTATGGAGCATGTGGAGTTAGAAAAGGGGGGCTTCTATTTCGTATATCGCCCTGGGGGCAACGGAAAGACCTTGTGGTTGGCTATTATCTCAAAACTGAGAAGCGAGGGTAGAATAGTTCTCGCAGTGGCTTCATCAGGTATAGCATTGCTTTTGGTTGAGGGTGGTAGAACAGCCCATTCTCGATTTAAAATACCCATAGATGTCAATGAATATAACAATTGTGAAATTAAACAGAACATCTACCTCGCTGAACTTATATGTCACACCAATTTGGTCATTTGGGATGAGGCACCTATGACTCAATATTTTGTCTTTGAGGCGGTT
--- a/test-data/transcripts.cleaned.cds Thu May 25 09:11:26 2017 -0400 +++ b/test-data/transcripts.cleaned.cds Tue Jun 06 08:31:58 2017 -0400 @@ -4,3 +4,23 @@ CCGGCATACAGTGCAGTCTTCGACAGCTGCTTGAGTACGGCTATTTTCATGCAGATCCTCACCCAGGGAATCTCTTAGCT ACACCTGACGGGAAGCTTGCTTTTCTTGATTTTGGAATGATGAGTGAGACTCCTGAACAAGCAAGATCGGCCATAATTGG TCATGTTGTACACATGGTTAAT +>contig_2 +CTTTCCAAGGTACCCATCCCATCCAACAACATATATGCTATAAATGATAAGAAGTCCCCGGAAGATGCAGCAGACGACTA +CGAAAACCGCCTCAAGGAACTCGTCTCCGAAAAAATCATACCCGTTTCAACCATTAGCGGGTTCCCGAAGTTCGACCTCA +TGTTGCTTGGAATGGGGCCCGACGGCCATGTGGCCTCTCTTTTCCCTTCTCACATGCAACGCTATGAGAAGGAGAAATGG +GTCACTTTCATAACTGACTCTCCCAAACCGCCTCCGTCGAGAATCACTTTTACGTTTCCGATGATCAACTCGGCTTCGGA +GATCGCTATGGTGGTTACCGGGGCTGATTTGGCTGGTACAACTAAGATAGCATTGGGTACTACGGGCAATGTTAAGCCGG +GTGAGACTCCTTTGCCTTGTACTGAAGTTTCGGCTGAGGGAGAGGTTACTTGGTTCTTGGACAAAGATGCTGCTTCACAA +CTGTTAAATTATGTGCGCTTTGATGAT +>contig_3 +GTGGATGAAGGAGTTGTTGTTGCTGGCTTGTCAGAGCAGGAGAAGGCATCTGTTTCTGAAATTCTGACAACTGCTAGAGC +TCATTCAGAAACAATTGAGAACCTTAAGAGAGATCATTCCCAGCAGGTATCCTGTATCGAACAGCACACGAATGATACTT +TCAGGCAAAAATACATGGATTACGAGCCTACAGGGTCCACGCCAGTTAGGAGCGAGCCGGATATTCCCAGCAAAGGCACA +ATAGAGTCACTTCGTGCCATGCCTATAGATGCACTTGAAGAAGAATTTCGAGAAAACCATTCATACGAATCTGCTGTTAC +AGGAAAGGAACTAATGCCGTCTGTTACGACTCGTGCACCATTTTCACAGATCAAC +>contig_9 +CTTCGGTTAAAGGCAGATGAGGAGGCACAATGTTTGAATCAGATGCAGCGTATCATTTTTGATGAAATTATGGAGCATGT +GGAGTTAGAAAAGGGGGGCTTCTATTTCGTATATCGCCCTGGGGGCAACGGAAAGACCTTGTGGTTGGCTATTATCTCAA +AACTGAGAAGCGAGGGTAGAATAGTTCTCGCAGTGGCTTCATCAGGTATAGCATTGCTTTTGGTTGAGGGTGGTAGAACA +GCCCATTCTCGATTTAAAATACCCATAGATGTCAATGAATATAACAATTGTGAAATTAAACAGAACATCTACCTCGCTGA +ACTTATATGTCACACCAATTTGGTCATTTGGGATGAGGCACCTATGACTCAATATTTTGTCTTTGAGGCGGTT
--- a/test-data/transcripts.cleaned.nr.cds Thu May 25 09:11:26 2017 -0400 +++ b/test-data/transcripts.cleaned.nr.cds Tue Jun 06 08:31:58 2017 -0400 @@ -1,6 +1,43 @@ >contig_1 -AAAAAATTATATGGAGACAAGGAAGATATCCTTGTCCCAGATATTTTCTGGGATTACACGAGTGGAAAGGTGCTAACAAT -GGAGTGGGTTGAAGGTGTTAAATTAAATGAGCAAGATGCCGTTGAGAGTCAAGGGCTCAGTGTTCTGGATCTGGTGAATA -CCGGCATACAGTGCAGTCTTCGACAGCTGCTTGAGTACGGCTATTTTCATGCAGATCCTCACCCAGGGAATCTCTTAGCT -ACACCTGACGGGAAGCTTGCTTTTCTTGATTTTGGAATGATGAGTGAGACTCCTGAACAAGCAAGATCGGCCATAATTGG -TCATGTTGTACACATGGTTAAT +NTTAAAAAATTATATGGAGACAAGGAAGATATCCTTGTCCCAGATATTTTCTGGGATTACACGAGTGGAAAGGTGCTAAC +AATGGAGTGGGTTGAAGGTGTTAAATTAAATGAGCAAGATGCCGTTGAGAGTCAAGGGCTCAGTGTTCTGGATCTGGTGA +ATACCGGCATACAGTGCAGTCTTCGACAGCTGCTTGAGTACGGCTATTTTCATGCAGATCCTCACCCAGGGAATCTCTTA +GCTACACCTGACGGGAAGCTTGCTTTTCTTGATTTTGGAATGATGAGTGAGACTCCTGAACAAGCAAGATCGGCCATAAT +TGGTCATGTTGTACACATGGTTAATCGN +>contig_10 +ATGGCAGAAGAGAACACCACTACAATGAACCTCGATCTCAATTTGGGCCCCATCAATAACTCAAGCGACGATAGCGAACC +TTCATCACGCCCTTATACTGATGTCGCAATGAACTTGGAAGATTGGTTAGATAGTCCCGTCCGAGTTCGTGAAGTCGTCC +GCCACAGAAATCATAGGTGGCGCTCTTTGTGGCGCCAAATCCCAATTCCGCCTGATACGCGAAACCTCGCGCTCGAATTA +ATCGGCGGCAATGCCCCN +>contig_2 +NNCCTTTCCAAGGTACCCATCCCATCCAACAACATATATGCTATAAATGATAAGAAGTCCCCGGAAGATGCAGCAGACGA +CTACGAAAACCGCCTCAAGGAACTCGTCTCCGAAAAAATCATACCCGTTTCAACCATTAGCGGGTTCCCGAAGTTCGACC +TCATGTTGCTTGGAATGGGGCCCGACGGCCATGTGGCCTCTCTTTTCCCTTCTCACATGCAACGCTATGAGAAGGAGAAA +TGGGTCACTTTCATAACTGACTCTCCCAAACCGCCTCCGTCGAGAATCACTTTTACGTTTCCGATGATCAACTCGGCTTC +GGAGATCGCTATGGTGGTTACCGGGGCTGATTTGGCTGGTACAACTAAGATAGCATTGGGTACTACGGGCAATGTTAAGC +CGGGTGAGACTCCTTTGCCTTGTACTGAAGTTTCGGCTGAGGGAGAGGTTACTTGGTTCTTGGACAAAGATGCTGCTTCA +CAACTGTTAAATTATGTGCGCTTTGATGAT +>contig_3 +NNTGTGGATGAAGGAGTTGTTGTTGCTGGCTTGTCAGAGCAGGAGAAGGCATCTGTTTCTGAAATTCTGACAACTGCTAG +AGCTCATTCAGAAACAATTGAGAACCTTAAGAGAGATCATTCCCAGCAGGTATCCTGTATCGAACAGCACACGAATGATA +CTTTCAGGCAAAAATACATGGATTACGAGCCTACAGGGTCCACGCCAGTTAGGAGCGAGCCGGATATTCCCAGCAAAGGC +ACAATAGAGTCACTTCGTGCCATGCCTATAGATGCACTTGAAGAAGAATTTCGAGAAAACCATTCATACGAATCTGCTGT +TACAGGAAAGGAACTAATGCCGTCTGTTACGACTCGTGCACCATTTTCACAGATCAAC +>contig_5 +NNCGGTGGTCCGCCACAAACACACGTCAAGCGGGATCCCGCATCCCGCGGGCTCTTCCACGCGGTCGTCCCGGCGCTCGG +CCCTCTCCGTGACGCACGTCGAGAGGGACGATTTGGCCGATGCCGCGTGATGCCAGGCCCCGACATCATCAAGGAGCACT +CCGTTGTGCCGACCCTCGCCTTCGATGACGTCCTCGGGCGTCTAGCGAAGTATCGAAGAAGGGCGAGCGGAGCCATGAAT +CCTGGAGATGCGAGCCAGGTCACGAGAGGCGCGGCAGGCGAGTCTTTGCTCGCTCTCGCACCGTCTGCTCTCGTGCTTGG +AGAAGAAGGACCGACTGCTGACGTCGAACCGGATGATGGAAGGTTCGAACAAGTCAGATCTGGAAAGGGGCATGGAAAAG +GCGACACTCTCACN +>contig_7 +GAGAATGAGTGGTCTGGGGCTGAGTTTTTGAATGAAATGGCGGCAATGATGACTCAAAATAAATCCAATGAAAACGGAAC +CGGAACTTTTGAAGAACTGCAACAATTGTTCGATGAAATGTTTCAGAGCGACATCGAGTCCTTCAATGGTTGTTCTTCAT +CATCCAATGAAACATGTAGCAACTCGAACAAGAGGAATTCCATTGAGTCGAGCTCGGCTAATTTCAGACCCGAAAATGGA +AACGAAAGCGGCGAGATTAGCGGGAAGAAGAATACTAGGAAAGGTAAAGGTGACGNN +>contig_9 +NNACTTCGGTTAAAGGCAGATGAGGAGGCACAATGTTTGAATCAGATGCAGCGTATCATTTTTGATGAAATTATGGAGCA +TGTGGAGTTAGAAAAGGGGGGCTTCTATTTCGTATATCGCCCTGGGGGCAACGGAAAGACCTTGTGGTTGGCTATTATCT +CAAAACTGAGAAGCGAGGGTAGAATAGTTCTCGCAGTGGCTTCATCAGGTATAGCATTGCTTTTGGTTGAGGGTGGTAGA +ACAGCCCATTCTCGATTTAAAATACCCATAGATGTCAATGAATATAACAATTGTGAAATTAAACAGAACATCTACCTCGC +TGAACTTATATGTCACACCAATTTGGTCATTTGGGATGAGGCACCTATGACTCAATATTTTGTCTTTGAGGCGGTTGAN
--- a/test-data/transcripts.cleaned.nr.pep Thu May 25 09:11:26 2017 -0400 +++ b/test-data/transcripts.cleaned.nr.pep Tue Jun 06 08:31:58 2017 -0400 @@ -1,3 +1,22 @@ >contig_1 -KKLYGDKEDILVPDIFWDYTSGKVLTMEWVEGVKLNEQDAVESQGLSVLDLVNTGIQCSLRQLLEYGYFHADPHPGNLLA -TPDGKLAFLDFGMMSETPEQARSAIIGHVVHMVN +XKKLYGDKEDILVPDIFWDYTSGKVLTMEWVEGVKLNEQDAVESQGLSVLDLVNTGIQCSLRQLLEYGYFHADPHPGNLL +ATPDGKLAFLDFGMMSETPEQARSAIIGHVVHMVNR +>contig_10 +MAEENTTTMNLDLNLGPINNSSDDSEPSSRPYTDVAMNLEDWLDSPVRVREVVRHRNHRWRSLWRQIPIPPDTRNLALEL +IGGNAP +>contig_2 +XLSKVPIPSNNIYAINDKKSPEDAADDYENRLKELVSEKIIPVSTISGFPKFDLMLLGMGPDGHVASLFPSHMQRYEKEK +WVTFITDSPKPPPSRITFTFPMINSASEIAMVVTGADLAGTTKIALGTTGNVKPGETPLPCTEVSAEGEVTWFLDKDAAS +QLLNYVRFDD +>contig_3 +XVDEGVVVAGLSEQEKASVSEILTTARAHSETIENLKRDHSQQVSCIEQHTNDTFRQKYMDYEPTGSTPVRSEPDIPSKG +TIESLRAMPIDALEEEFRENHSYESAVTGKELMPSVTTRAPFSQIN +>contig_5 +XGGPPQTHVKRDPASRGLFHAVVPALGPLRDARREGRFGRCRVMPGPDIIKEHSVVPTLAFDDVLGRLAKYRRRASGAMN +PGDASQVTRGAAGESLLALAPSALVLGEEGPTADVEPDDGRFEQVRSGKGHGKGDTLT +>contig_7 +ENEWSGAEFLNEMAAMMTQNKSNENGTGTFEELQQLFDEMFQSDIESFNGCSSSSNETCSNSNKRNSIESSSANFRPENG +NESGEISGKKNTRKGKGDX +>contig_9 +XLRLKADEEAQCLNQMQRIIFDEIMEHVELEKGGFYFVYRPGGNGKTLWLAIISKLRSEGRIVLAVASSGIALLLVEGGR +TAHSRFKIPIDVNEYNNCEIKQNIYLAELICHTNLVIWDEAPMTQYFVFEAVX
--- a/test-data/transcripts.cleaned.pep Thu May 25 09:11:26 2017 -0400 +++ b/test-data/transcripts.cleaned.pep Tue Jun 06 08:31:58 2017 -0400 @@ -1,3 +1,13 @@ >contig_1 KKLYGDKEDILVPDIFWDYTSGKVLTMEWVEGVKLNEQDAVESQGLSVLDLVNTGIQCSLRQLLEYGYFHADPHPGNLLA TPDGKLAFLDFGMMSETPEQARSAIIGHVVHMVN +>contig_2 +LSKVPIPSNNIYAINDKKSPEDAADDYENRLKELVSEKIIPVSTISGFPKFDLMLLGMGPDGHVASLFPSHMQRYEKEKW +VTFITDSPKPPPSRITFTFPMINSASEIAMVVTGADLAGTTKIALGTTGNVKPGETPLPCTEVSAEGEVTWFLDKDAASQ +LLNYVRFDD +>contig_3 +VDEGVVVAGLSEQEKASVSEILTTARAHSETIENLKRDHSQQVSCIEQHTNDTFRQKYMDYEPTGSTPVRSEPDIPSKGT +IESLRAMPIDALEEEFRENHSYESAVTGKELMPSVTTRAPFSQIN +>contig_9 +LRLKADEEAQCLNQMQRIIFDEIMEHVELEKGGFYFVYRPGGNGKTLWLAIISKLRSEGRIVLAVASSGIALLLVEGGRT +AHSRFKIPIDVNEYNNCEIKQNIYLAELICHTNLVIWDEAPMTQYFVFEAV
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcripts.cleaned_tgf.cds Tue Jun 06 08:31:58 2017 -0400 @@ -0,0 +1,102 @@ +>contig_1 +AAAAAATTATATGGAGACAAGGAAGATATCCTTGTCCCAGATATTTTCTGGGATTACACGAGTGGAAAGGTGCTAACAAT +GGAGTGGGTTGAAGGTGTTAAATTAAATGAGCAAGATGCCGTTGAGAGTCAAGGGCTCAGTGTTCTGGATCTGGTGAATA +CCGGCATACAGTGCAGTCTTCGACAGCTGCTTGAGTACGGCTATTTTCATGCAGATCCTCACCCAGGGAATCTCTTAGCT +ACACCTGACGGGAAGCTTGCTTTTCTTGATTTTGGAATGATGAGTGAGACTCCTGAACAAGCAAGATCGGCCATAATTGG +TCATGTTGTACACATGGTTAAT +>contig_11 +ATTTATGGAAAGGGGATTCAAAATATGAGAACACTCTGGGGTGGCGTTGCTCCCGAATCTCCCGTCGTTGTTGTTGGAGG +CGGTGTTACTCCAGAATCTCCCGTCGTCGGAGGCATTGTTCTAGGATCTCCCGCAGTGCTGCTTAAGTCGGATTTACTCC +AAGCTCTCCCACCGCGGCTCCTGAAGTCGGCGTTGTTCCAAAATCTCCCGTCGCCACTGTTGAAGTCGGGGTTGCTCCAT +GATATCCCGTCGGAGTTGCTCCGAATCTCCCGTTGTTGCTGCTGCAGTCGGTGTTGCTCCAGAAACTCCCGCTGTGGCTA +T +>contig_18 +ACAGAGGTGAGAAGATGGAACAAGCAGGAAGATTGGGGTAGAAAGACATGGAAAGAAGCTAAGGAATCCACATTGCCGAA +AATAGTAGGTGAAGGGATCTATGGAGTTGGTCCCATTTTAGCTGCACTCTCATCCGGGCGAAGAGAACTCTACGCGTTGT +ACGTTCAGGAAGGTTTGGATTTGAGTAGTAACAGTAAGAAGAAGGACAAGAAACGGTTCGAGAGAGTTTTGAAAATGGTG +GAAAAGATTGGATTAAGCAAAAAAGAGGTATCCAAACACGACCTCAACATGGTCGTTGATAATAGGCCTCACCAGGGCTT +GCTTCTTGATGCTTCGGCACTTGAAATGGTTAGTATAAAGGAATTAGACCCCGTTTCCATTGATGGAGAGAAGTGCCCGC +TTTGGTTGGCATTGGATGAGGTTACC +>contig_2 +CTTTCCAAGGTACCCATCCCATCCAACAACATATATGCTATAAATGATAAGAAGTCCCCGGAAGATGCAGCAGACGACTA +CGAAAACCGCCTCAAGGAACTCGTCTCCGAAAAAATCATACCCGTTTCAACCATTAGCGGGTTCCCGAAGTTCGACCTCA +TGTTGCTTGGAATGGGGCCCGACGGCCATGTGGCCTCTCTTTTCCCTTCTCACATGCAACGCTATGAGAAGGAGAAATGG +GTCACTTTCATAACTGACTCTCCCAAACCGCCTCCGTCGAGAATCACTTTTACGTTTCCGATGATCAACTCGGCTTCGGA +GATCGCTATGGTGGTTACCGGGGCTGATTTGGCTGGTACAACTAAGATAGCATTGGGTACTACGGGCAATGTTAAGCCGG +GTGAGACTCCTTTGCCTTGTACTGAAGTTTCGGCTGAGGGAGAGGTTACTTGGTTCTTGGACAAAGATGCTGCTTCACAA +CTGTTAAATTATGTGCGCTTTGATGAT +>contig_20 +GGCTTACGCATCGATGCTCACGGATATGCCCTACAAGATTGGCAACGCGATCTGTTTCAACTTGATCTTGTACTTCATGA +CGAACCTTCGCCGCGAACCAGGAGCATTCTTCTTCTTCCTGCTGATATCGTTCACGCTGACGCTTGTCATGTCGATGCTC +TTCCGCACTATTGGATCCGTTTCGCGTACACTGTCGCAGGCCATGGCTCCCGCAGCTATCCTTATCCTTGCGCTGGTCAT +TTACACTGGTTTCGTCATTCCTACCCGCTACATGTTGGGCTGGTCTCGTTGGATCAACTACTTGGATCA +>contig_21 +GTTTCCATAGTGAATCAGGAACCTGTTCTATTCTCGGTTTCCATTGGAGAAAATATTGCTTACGGACTCCCAGATGATTA +TGTTTCCAAGGTCGATGTGATAAAAGCTGCTAAAGCAGCTAATGCTCATGAATTTATCATTGCGTTGCCACAGGGTTATG +ACACATTAGTTGGTGAGCGTGGTGGGTTGTTAAGTGGAGGACAAAGACAGAGGGTAGCCATTGCAAGGGCTCTGCTCAAG +AATGCTCCAATCTTGATTCTTGATGAGGCTACCAGTGCTTTGGACGCAGTCAGTGAACGTCTGGTTCAGGATGCTTTGAA +CCGTTTGATGAAAGGAAGAACGACTTTAGTGATTGCTCACAGGCTGAGCACCGTTCAAAATGCTGATCAAATTGCTTTAT +GCTCTGATGGGAAGATTTCAGAACTGGGGACACACTCTGAGTTGTTAGAGCAAAAGGGTCTTTATGCCTCACTGGTTGGC +ACCCAAAGACTTGCATTCGAG +>contig_24 +AAAACCCGTGAATTAGAAATCGAACAAATCTTGTTAAAATCCAAGGATTTGGAAAGCGAATTGGAGAGCAAGGGTAGTAT +GTTTATAAAGGAGACTGAGGCACTTGTTGCAGAAAACTCGAAACTCAGTCAGGAGTTGGGTGCATTTAAATCCGAGCTAA +ACGATATACAGATGAAATTGAACGTTGTTTCATCTGAGAAAGACGGCACTGTTGAAGAACTAACTAGTGCAAGAAAAGAA +ATAGAAGAGCTGACTCAGAAGCTTGCTTCTGAAGGACAAAAGCTGCAGTCTCAGATATCTTCTATAATGGAAGAGAACAA +TTTACTTAAC +>contig_29 +ATGAAGAAATCGAAGCTTCTGCAGAATTCGAAGGACTTACTTTCTAGGAGCTTCAATCCTGCTAAATGCAAAACGTCTCT +GAGGCTGGCGGGTTCAAGGTTGAAGCTATTGAGAAACAAGAAAGAGGTGCAACTGAAGCAGATGAAGCGGGAAATAGCAC +AGTTGCTCGAGTCTGGACAGGATCAGACCGCTCGAATTCGAGTCGAACATCTGATTAGGGAAGAGAAGATGATGGCTGCA +TATGATCTCCTCGATATATACTGCGAGCTTGTTGTTGCACGTCTTCCAGTAATTGAGTCACAAAAGAATTGCCCCATTGA +CCTGAAAGAAGCAATTGCAAGTTTAGTATTTGCAGCACCAAGATGTGGAGATGTACCCGAGTTTCTTGATGCAAGGAAGC +AATTTTCAGCTAAATATGGAAAAGATTTCACTACTGCAGCCACAGAACTTCGTCCACAGTGCGGTGTAGGCCGCATGTTG +GTTGAAAAATTATCTGCAACAGCGCCTGATGTACAGAGCAAAACTAAAATCTTGAATGCAATAGCTGAGGAGCACAATGT +TAAATGGGAACCCACATCATTTGGAGAGAACGACTCTGCACCTCTCAATGACCGACTGACTGGACCAAGTTCCTTTACGA +AGGAGAGAGAACAGTACCCTGAACCTCCTCATTTTGAAGCTGTACAAGTCCAAGCTCACCCGAGCAACAACACCTTGCAT +AGCTCGCCATCAAATTCTTCCCAGCAGGATGATAGAACCTCAGTTTTTGTTGAAACTTCTACTTTCAAGACACCATCG +>contig_3 +GTGGATGAAGGAGTTGTTGTTGCTGGCTTGTCAGAGCAGGAGAAGGCATCTGTTTCTGAAATTCTGACAACTGCTAGAGC +TCATTCAGAAACAATTGAGAACCTTAAGAGAGATCATTCCCAGCAGGTATCCTGTATCGAACAGCACACGAATGATACTT +TCAGGCAAAAATACATGGATTACGAGCCTACAGGGTCCACGCCAGTTAGGAGCGAGCCGGATATTCCCAGCAAAGGCACA +ATAGAGTCACTTCGTGCCATGCCTATAGATGCACTTGAAGAAGAATTTCGAGAAAACCATTCATACGAATCTGCTGTTAC +AGGAAAGGAACTAATGCCGTCTGTTACGACTCGTGCACCATTTTCACAGATCAAC +>contig_30 +AAGGCTAGTGGACTTTTTTCAAGTAAAGATTCTGTTGATTCAACAGATAGCCACATGGAAAATGTATGCTCTGATATTTT +ATCAATGAGCATCAACAAAAACCAAATTTTAGAGAATGGCCATGTTCATAACAATAGAGGAGCAGCAATATTTGAGTTGT +CTGGAGCTGCTACAAATGTAATTGAGGACGTTGGTTTGTCAGATGTCCAGTCTGACACCAGATTGGGAATGGCAAGTCAA +GTTTGCCAAGTTGATATGCATGAACCAGAGGGCGGTTTGTTGTCTTTTAAGAACCAAAGATTTAAGGATGCTGAGGTTGC +TACCAATATAACACATGATTATTGTCATGTATCTCATCTGTTAAAGCATTCTAACGTTCAAGTTCCTAAGTACATTAGTG +GTAATGGTTCAGCCACTGTTGATCTGAATAGGCAGACTGTAGATAGGAATAACAATTTTAAAGTTTCAACATCTAAT +>contig_31 +ATGACTAGATCCCGCCCACACATAGAGAAATTAGAAAGTAGAGTGTCTCAGGATGATCTTTTGGAGGGCACTTGTGCAAG +AACGAGGCCATTAAGCTATGATGAGATAATGCTCGGAAGAAATAACAAGGGAGATGCAGGTAAAGAAGTTGCCAGTGGCT +CTGGAGTGGCTGATAGTGCATCAGGGCATGGTGACATTGAAAAGATTTCTAATTTTCCAGAATACCATCGGCAAATAAAT +GAGGTTTCTGAACGTATGGATGTTAGACATACTTCAAATGATTTTCAGAAGGTAAGTTGCCGGAGAAAAGTGGATAGTAA +GAATGACAATTTAGTCCAGGATAAGGATGAAAAGTATAGGGAAAGTGGTGTCAAGTTAAAGAGTATATGGGAAAAGACTG +AAGGCAGCAAGAGAGTGAGAGAAGGAGAAAATGAAAGACGACATTACAGCAACAGAAAAAGAGATGGCCATTTAGGTGTG +GATTCATATAATGGATCAAATAAGAGGCAAGCCAGAGAGTCATATAGAAAGGGTAAAACTTCTGAAAGAGGCAGAGTCAA +ATCCGAAATAGATAGAAAACAGCTTGTTAACGATGAAGGACAGGTCCACAGGAAAAGGAAAACAGAACGGCGAATGAGCA +GTGACTCTGAGAAAGAGTACAAAAGAAGAGACGAAAGAAATGTGATGCATACAGAAAGATTAACTAACAGAGGCAGCCAG +AAGTCTGAAAAAGAAAACAGACGCAAACGTCATAATGAGGAGGATAAAACTAAAAGCTTGAGTACG +>contig_33 +GAAGAAATTAATGAAGTTGTGGCATTTCTACAAAATCCTCGTGCATTCCAAGAAATGGGAGCTCGGGCACCTCGGGGTGT +TCTTATTGTTGGTGAGATAGGAACAGGTAAAACATCCCTAGCAATGGCTATAGCAGCGGAAGCGAAGGTTCCTTTAGTTG +AAGTAAAAGCCCAACAGCTGGAAGCTGGTCTGTTTGTGGGCCAAGGTGCATCAAACGTTAGAGAATTGTTTCAAGCAGCA +CGGGATCTGGCTCCTGTCATTATATTTGTGGAAGACTTTGACCTCTTTGCTGGTGTCCGCGGGAAGGACCTTCAGACCAA +AAAGCTGGATCACGAATCTTTCATCAATCAACTTCTGGTGGAGCTTGATGGGTTTGAGAAACAAGATGGGGTAGTTTTGA +TGGCTACTACTCGGAATCTTAAACAAATCGATGGGGCTTTACTGCGTCCTGGTAGAATGGATCGAATATTTCATCTTCAG +CGACTAACTCAAGCAGAAAGGAGGAAAATCCTTCTTCTTGCTGCAAAAGAATCAATGGATGAAGAGCTCATTGACTTTGT +CGATTGGCAAAAGGTTGCTGAAAAGACAGCATTACTTCGCCCTATAGAATTAAAA +>contig_35 +ATTCACAGCCTTCTCTTTCATCTCGAGATTGTCTACCTTCTGCAGATCGATATGTCGATGCTTTACAGAGGGATATCGAG +GAAGGATAAACCTAGAGGACGTCAGCACGGGTTGACTCAACAGAAAAGGCAAGAGATAAAGGAAGCTTTTGAACTGTTTG +ACACCGATGGATCTGGAACTATTGATGCGAAAGAGTTGAACGTAGCAATGAGGGCTCTCGGTTTTGAAATGTCAGAAGAG +GAAATTACGAGAATGATAGCTGAAGTAGACAAAGACGGGAGTGGGGCGATTGACTTTGACGAGTTTTGTCACATGATGAC +AGCCAAATTCGGAGAAAGGGACACCAAAGAGGAGCTTACCAAGGCTTTTCAGATTATCGACAAAGATCAA +>contig_9 +CTTCGGTTAAAGGCAGATGAGGAGGCACAATGTTTGAATCAGATGCAGCGTATCATTTTTGATGAAATTATGGAGCATGT +GGAGTTAGAAAAGGGGGGCTTCTATTTCGTATATCGCCCTGGGGGCAACGGAAAGACCTTGTGGTTGGCTATTATCTCAA +AACTGAGAAGCGAGGGTAGAATAGTTCTCGCAGTGGCTTCATCAGGTATAGCATTGCTTTTGGTTGAGGGTGGTAGAACA +GCCCATTCTCGATTTAAAATACCCATAGATGTCAATGAATATAACAATTGTGAAATTAAACAGAACATCTACCTCGCTGA +ACTTATATGTCACACCAATTTGGTCATTTGGGATGAGGCACCTATGACTCAATATTTTGTCTTTGAGGCGGTT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcripts.cleaned_tgf.pep Tue Jun 06 08:31:58 2017 -0400 @@ -0,0 +1,49 @@ +>contig_1 +KKLYGDKEDILVPDIFWDYTSGKVLTMEWVEGVKLNEQDAVESQGLSVLDLVNTGIQCSLRQLLEYGYFHADPHPGNLLA +TPDGKLAFLDFGMMSETPEQARSAIIGHVVHMVN +>contig_11 +IYGKGIQNMRTLWGGVAPESPVVVVGGGVTPESPVVGGIVLGSPAVLLKSDLLQALPPRLLKSALFQNLPSPLLKSGLLH +DIPSELLRISRCCCCSRCCSRNSRCGY +>contig_18 +TEVRRWNKQEDWGRKTWKEAKESTLPKIVGEGIYGVGPILAALSSGRRELYALYVQEGLDLSSNSKKKDKKRFERVLKMV +EKIGLSKKEVSKHDLNMVVDNRPHQGLLLDASALEMVSIKELDPVSIDGEKCPLWLALDEVT +>contig_2 +LSKVPIPSNNIYAINDKKSPEDAADDYENRLKELVSEKIIPVSTISGFPKFDLMLLGMGPDGHVASLFPSHMQRYEKEKW +VTFITDSPKPPPSRITFTFPMINSASEIAMVVTGADLAGTTKIALGTTGNVKPGETPLPCTEVSAEGEVTWFLDKDAASQ +LLNYVRFDD +>contig_20 +GLRIDAHGYALQDWQRDLFQLDLVLHDEPSPRTRSILLLPADIVHADACHVDALPHYWIRFAYTVAGHGSRSYPYPCAGH +LHWFRHSYPLHVGLVSLDQLLGS +>contig_21 +VSIVNQEPVLFSVSIGENIAYGLPDDYVSKVDVIKAAKAANAHEFIIALPQGYDTLVGERGGLLSGGQRQRVAIARALLK +NAPILILDEATSALDAVSERLVQDALNRLMKGRTTLVIAHRLSTVQNADQIALCSDGKISELGTHSELLEQKGLYASLVG +TQRLAFE +>contig_24 +KTRELEIEQILLKSKDLESELESKGSMFIKETEALVAENSKLSQELGAFKSELNDIQMKLNVVSSEKDGTVEELTSARKE +IEELTQKLASEGQKLQSQISSIMEENNLLN +>contig_29 +MKKSKLLQNSKDLLSRSFNPAKCKTSLRLAGSRLKLLRNKKEVQLKQMKREIAQLLESGQDQTARIRVEHLIREEKMMAA +YDLLDIYCELVVARLPVIESQKNCPIDLKEAIASLVFAAPRCGDVPEFLDARKQFSAKYGKDFTTAATELRPQCGVGRML +VEKLSATAPDVQSKTKILNAIAEEHNVKWEPTSFGENDSAPLNDRLTGPSSFTKEREQYPEPPHFEAVQVQAHPSNNTLH +SSPSNSSQQDDRTSVFVETSTFKTPS +>contig_3 +VDEGVVVAGLSEQEKASVSEILTTARAHSETIENLKRDHSQQVSCIEQHTNDTFRQKYMDYEPTGSTPVRSEPDIPSKGT +IESLRAMPIDALEEEFRENHSYESAVTGKELMPSVTTRAPFSQIN +>contig_30 +KASGLFSSKDSVDSTDSHMENVCSDILSMSINKNQILENGHVHNNRGAAIFELSGAATNVIEDVGLSDVQSDTRLGMASQ +VCQVDMHEPEGGLLSFKNQRFKDAEVATNITHDYCHVSHLLKHSNVQVPKYISGNGSATVDLNRQTVDRNNNFKVSTSN +>contig_31 +MTRSRPHIEKLESRVSQDDLLEGTCARTRPLSYDEIMLGRNNKGDAGKEVASGSGVADSASGHGDIEKISNFPEYHRQIN +EVSERMDVRHTSNDFQKVSCRRKVDSKNDNLVQDKDEKYRESGVKLKSIWEKTEGSKRVREGENERRHYSNRKRDGHLGV +DSYNGSNKRQARESYRKGKTSERGRVKSEIDRKQLVNDEGQVHRKRKTERRMSSDSEKEYKRRDERNVMHTERLTNRGSQ +KSEKENRRKRHNEEDKTKSLST +>contig_33 +EEINEVVAFLQNPRAFQEMGARAPRGVLIVGEIGTGKTSLAMAIAAEAKVPLVEVKAQQLEAGLFVGQGASNVRELFQAA +RDLAPVIIFVEDFDLFAGVRGKDLQTKKLDHESFINQLLVELDGFEKQDGVVLMATTRNLKQIDGALLRPGRMDRIFHLQ +RLTQAERRKILLLAAKESMDEELIDFVDWQKVAEKTALLRPIELK +>contig_35 +IHSLLFHLEIVYLLQIDMSMLYRGISRKDKPRGRQHGLTQQKRQEIKEAFELFDTDGSGTIDAKELNVAMRALGFEMSEE +EITRMIAEVDKDGSGAIDFDEFCHMMTAKFGERDTKEELTKAFQIIDKDQ +>contig_9 +LRLKADEEAQCLNQMQRIIFDEIMEHVELEKGGFYFVYRPGGNGKTLWLAIISKLRSEGRIVLAVASSGIALLLVEGGRT +AHSRFKIPIDVNEYNNCEIKQNIYLAELICHTNLVIWDEAPMTQYFVFEAV
--- a/test-data/transcripts.pep Thu May 25 09:11:26 2017 -0400 +++ b/test-data/transcripts.pep Tue Jun 06 08:31:58 2017 -0400 @@ -1,2 +1,8 @@ >Gene.1::contig_1::g.1::m.1 type:internal len:115 gc:universal contig_1:344-3(-) KKLYGDKEDILVPDIFWDYTSGKVLTMEWVEGVKLNEQDAVESQGLSVLDLVNTGIQCSLRQLLEYGYFHADPHPGNLLATPDGKLAFLDFGMMSETPEQARSAIIGHVVHMVN +>Gene.2::contig_2::g.2::m.2 type:5prime_partial len:170 gc:universal contig_2:2-511(+) +LSKVPIPSNNIYAINDKKSPEDAADDYENRLKELVSEKIIPVSTISGFPKFDLMLLGMGPDGHVASLFPSHMQRYEKEKWVTFITDSPKPPPSRITFTFPMINSASEIAMVVTGADLAGTTKIALGTTGNVKPGETPLPCTEVSAEGEVTWFLDKDAASQLLNYVRFDD* +>Gene.3::contig_3::g.3::m.3 type:5prime_partial len:126 gc:universal contig_3:463-86(-) +VDEGVVVAGLSEQEKASVSEILTTARAHSETIENLKRDHSQQVSCIEQHTNDTFRQKYMDYEPTGSTPVRSEPDIPSKGTIESLRAMPIDALEEEFRENHSYESAVTGKELMPSVTTRAPFSQIN* +>Gene.4::contig_9::g.4::m.4 type:internal len:132 gc:universal contig_9:2-394(+) +LRLKADEEAQCLNQMQRIIFDEIMEHVELEKGGFYFVYRPGGNGKTLWLAIISKLRSEGRIVLAVASSGIALLLVEGGRTAHSRFKIPIDVNEYNNCEIKQNIYLAELICHTNLVIWDEAPMTQYFVFEAV
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcripts2.cds Tue Jun 06 08:31:58 2017 -0400 @@ -0,0 +1,54 @@ +>contig_1; 91 1 346 minus strand +XTTAAAAAATTATATGGAGACAAGGAAGATATCCTTGTCCCAGATATTTTCTGGGATTAC +ACGAGTGGAAAGGTGCTAACAATGGAGTGGGTTGAAGGTGTTAAATTAAATGAGCAAGAT +GCCGTTGAGAGTCAAGGGCTCAGTGTTCTGGATCTGGTGAATACCGGCATACAGTGCAGT +CTTCGACAGCTGCTTGAGTACGGCTATTTTCATGCAGATCCTCACCCAGGGAATCTCTTA +GCTACACCTGACGGGAAGCTTGCTTTTCTTGATTTTGGAATGATGAGTGAGACTCCTGAA +CAAGCAAGATCGGCCATAATTGGTCATGTTGTACACATGGTTAATCGX +>contig_2 218 1 511 +XXCCTTTCCAAGGTACCCATCCCATCCAACAACATATATGCTATAAATGATAAGAAGTCC +CCGGAAGATGCAGCAGACGACTACGAAAACCGCCTCAAGGAACTCGTCTCCGAAAAAATC +ATACCCGTTTCAACCATTAGCGGGTTCCCGAAGTTCGACCTCATGTTGCTTGGAATGGGG +CCCGACGGCCATGTGGCCTCTCTTTTCCCTTCTCACATGCAACGCTATGAGAAGGAGAAA +TGGGTCACTTTCATAACTGACTCTCCCAAACCGCCTCCGTCGAGAATCACTTTTACGTTT +CCGATGATCAACTCGGCTTCGGAGATCGCTATGGTGGTTACCGGGGCTGATTTGGCTGGT +ACAACTAAGATAGCATTGGGTACTACGGGCAATGTTAAGCCGGGTGAGACTCCTTTGCCT +TGTACTGAAGTTTCGGCTGAGGGAGAGGTTACTTGGTTCTTGGACAAAGATGCTGCTTCA +CAACTGTTAAATTATGTGCGCTTTGATGATTAA +>contig_3; 134 1 379 minus strand +XXTGTGGATGAAGGAGTTGTTGTTGCTGGCTTGTCAGAGCAGGAGAAGGCATCTGTTTCT +GAAATTCTGACAACTGCTAGAGCTCATTCAGAAACAATTGAGAACCTTAAGAGAGATCAT +TCCCAGCAGGTATCCTGTATCGAACAGCACACGAATGATACTTTCAGGCAAAAATACATG +GATTACGAGCCTACAGGGTCCACGCCAGTTAGGAGCGAGCCGGATATTCCCAGCAAAGGC +ACAATAGAGTCACTTCGTGCCATGCCTATAGATGCACTTGAAGAAGAATTTCGAGAAAAC +CATTCATACGAATCTGCTGTTACAGGAAAGGAACTAATGCCGTCTGTTACGACTCGTGCA +CCATTTTCACAGATCAACTAG +>contig_5; -67 1 418 minus strand +XXCGGTGGTCCGCCACAAACACACGTCAAGCGGGATCCCGCATCCCGCGGGCTCTTCCAC +GCGGTCGTCCCGGCGCTCGGCCCTCTCCGTGACGCACGTCGAGAGGGACGATTTGGCCGA +TGCCGCGTGATGCCAGGCCCCGACATCATgCAAGGAGCACTCCGTTGTGCCGACCCTCGC +CTTCGATGACGTCCTCGGGCGTCTAGCGAAGTATCGAAGAAGGGCGAGCTAAGGAGCCAT +GAATCCTGGAGATGCGAGCCAGGTCACGAGAGGCGCGGCAGGCGAGTCTTTGCTCGCTCT +CGCACCGTCTGCTCTCGTGCTTGGAGAAGAAGGACCGACTGCTGACGTCGAACCGGATGA +TGGAAGGTTCGAACAAGTCAGATCTGGAAAGGGGTAGCATGGAAAAGGCGACACTCTCAC +X +>contig_7 103 1 296 +GAGAATGAGTGGTCTGGGGCTGAGTTTTTGAATGAAATGGCGGCAATGATGACTCAAAAT +AAATCCAATGAAAACGGAACCGGAACTTTTGAAGAACTGCAACAATTGTTCGATGAAATG +TTTCAGAGCGACATCGAGTCCTTCAATGGTTGTTCTTCATCATCCAATGAAACATGTAGC +AACTCGAACAAGAGGAATTCCATTGAGTCGAGCTCGGCTAATTTCAGACCCGAAAATGcG +AAACGAAAGCGGCGAGATTAGCGGGAAGAAGAATACTAGGAAAGGTAAAGGTGACGXX +>contig_9 34 1 396 +XXACTTCGGTTAAAGGCAGATGAGGAGGCACAATGTTTGAATCAGATGCAGCGTATCATT +TTTGATGAAATTATGGAGCATGTGGAGTTAGAAAAGGGGGGCTTCTATTTCGTATATCGC +CCTGGGGGCAACGGAAAGACCTTGTGGTTGGCTATTATCTCAAAACTGAGAAGCGAGGGT +AGAATAGTTCTCGCAGTGGCTTCATCAGGTATAGCATTGCTTTTGGTTGAGGGTGGTAGA +ACAGCCCATTCTCGATTTAAAATACCCATAGATGTCAATGAATATAACAATTGTGAAATT +AAACAGAACATCTACCTCGCTGAACTTATATGTCACACCAATTTGGTCATTTGGGATGAG +GCACCTATGACTCAATATTTTGTCTTTGAGGCGGTTGAX +>contig_10; 78 87 343 minus strand +ATGGCAGAAGAGAACACCACTACAATGAACCTCGATCTCAATTTGGGCCCCATCAATAAC +TCAAGCGACGATAGCGAACCTTCATCACGCCCTTATACTGATGTCGCAATGAACTTGGAA +GATTGGTTAGATAGTCCCGTCCGAGTTCGTGAAGTCGTCCGCCACAGAAATCATAGGTGG +CGCTCTTTGTGGCGCCAAATCCCAATTCCGCCTGATACGCGAAACCTCGCGCTCGAATTA +ATCGGCGGCAATGCCCCX
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcripts2.pep Tue Jun 06 08:31:58 2017 -0400 @@ -0,0 +1,25 @@ +>contig_1; 91 1 346 minus strand; translated +XKKLYGDKEDILVPDIFWDYTSGKVLTMEWVEGVKLNEQDAVESQGLSVLDLVNTGIQCS +LRQLLEYGYFHADPHPGNLLATPDGKLAFLDFGMMSETPEQARSAIIGHVVHMVNR +>contig_2 218 1 511 ; translated +XLSKVPIPSNNIYAINDKKSPEDAADDYENRLKELVSEKIIPVSTISGFPKFDLMLLGMG +PDGHVASLFPSHMQRYEKEKWVTFITDSPKPPPSRITFTFPMINSASEIAMVVTGADLAG +TTKIALGTTGNVKPGETPLPCTEVSAEGEVTWFLDKDAASQLLNYVRFDD +>contig_3; 134 1 379 minus strand; translated +XVDEGVVVAGLSEQEKASVSEILTTARAHSETIENLKRDHSQQVSCIEQHTNDTFRQKYM +DYEPTGSTPVRSEPDIPSKGTIESLRAMPIDALEEEFRENHSYESAVTGKELMPSVTTRA +PFSQIN +>contig_5; -67 1 418 minus strand; translated +XGGPPQTHVKRDPASRGLFHAVVPALGPLRDARREGRFGRCRVMPGPDIIKEHSVVPTLA +FDDVLGRLAKYRRRASXGAMNPGDASQVTRGAAGESLLALAPSALVLGEEGPTADVEPDD +GRFEQVRSGKGXHGKGDTLT +>contig_7 103 1 296 ; translated +ENEWSGAEFLNEMAAMMTQNKSNENGTGTFEELQQLFDEMFQSDIESFNGCSSSSNETCS +NSNKRNSIESSSANFRPENGNESGEISGKKNTRKGKGDX +>contig_9 34 1 396 ; translated +XLRLKADEEAQCLNQMQRIIFDEIMEHVELEKGGFYFVYRPGGNGKTLWLAIISKLRSEG +RIVLAVASSGIALLLVEGGRTAHSRFKIPIDVNEYNNCEIKQNIYLAELICHTNLVIWDE +APMTQYFVFEAVX +>contig_10; 78 87 343 minus strand; translated +MAEENTTTMNLDLNLGPINNSSDDSEPSSRPYTDVAMNLEDWLDSPVRVREVVRHRNHRW +RSLWRQIPIPPDTRNLALELIGGNAP
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcripts_tgf.cds Tue Jun 06 08:31:58 2017 -0400 @@ -0,0 +1,34 @@ +>Gene.1::contig_1::g.1::m.1 type:internal len:115 contig_1:344-3(-) +AAAAAATTATATGGAGACAAGGAAGATATCCTTGTCCCAGATATTTTCTGGGATTACACGAGTGGAAAGGTGCTAACAATGGAGTGGGTTGAAGGTGTTAAATTAAATGAGCAAGATGCCGTTGAGAGTCAAGGGCTCAGTGTTCTGGATCTGGTGAATACCGGCATACAGTGCAGTCTTCGACAGCTGCTTGAGTACGGCTATTTTCATGCAGATCCTCACCCAGGGAATCTCTTAGCTACACCTGACGGGAAGCTTGCTTTTCTTGATTTTGGAATGATGAGTGAGACTCCTGAACAAGCAAGATCGGCCATAATTGGTCATGTTGTACACATGGTTAAT +>Gene.2::contig_2::g.2::m.2 type:5prime_partial len:170 contig_2:2-511(+) +CTTTCCAAGGTACCCATCCCATCCAACAACATATATGCTATAAATGATAAGAAGTCCCCGGAAGATGCAGCAGACGACTACGAAAACCGCCTCAAGGAACTCGTCTCCGAAAAAATCATACCCGTTTCAACCATTAGCGGGTTCCCGAAGTTCGACCTCATGTTGCTTGGAATGGGGCCCGACGGCCATGTGGCCTCTCTTTTCCCTTCTCACATGCAACGCTATGAGAAGGAGAAATGGGTCACTTTCATAACTGACTCTCCCAAACCGCCTCCGTCGAGAATCACTTTTACGTTTCCGATGATCAACTCGGCTTCGGAGATCGCTATGGTGGTTACCGGGGCTGATTTGGCTGGTACAACTAAGATAGCATTGGGTACTACGGGCAATGTTAAGCCGGGTGAGACTCCTTTGCCTTGTACTGAAGTTTCGGCTGAGGGAGAGGTTACTTGGTTCTTGGACAAAGATGCTGCTTCACAACTGTTAAATTATGTGCGCTTTGATGATTAA +>Gene.3::contig_3::g.3::m.3 type:5prime_partial len:126 contig_3:463-86(-) +GTGGATGAAGGAGTTGTTGTTGCTGGCTTGTCAGAGCAGGAGAAGGCATCTGTTTCTGAAATTCTGACAACTGCTAGAGCTCATTCAGAAACAATTGAGAACCTTAAGAGAGATCATTCCCAGCAGGTATCCTGTATCGAACAGCACACGAATGATACTTTCAGGCAAAAATACATGGATTACGAGCCTACAGGGTCCACGCCAGTTAGGAGCGAGCCGGATATTCCCAGCAAAGGCACAATAGAGTCACTTCGTGCCATGCCTATAGATGCACTTGAAGAAGAATTTCGAGAAAACCATTCATACGAATCTGCTGTTACAGGAAAGGAACTAATGCCGTCTGTTACGACTCGTGCACCATTTTCACAGATCAACTAG +>Gene.4::contig_9::g.4::m.4 type:internal len:132 contig_9:2-394(+) +CTTCGGTTAAAGGCAGATGAGGAGGCACAATGTTTGAATCAGATGCAGCGTATCATTTTTGATGAAATTATGGAGCATGTGGAGTTAGAAAAGGGGGGCTTCTATTTCGTATATCGCCCTGGGGGCAACGGAAAGACCTTGTGGTTGGCTATTATCTCAAAACTGAGAAGCGAGGGTAGAATAGTTCTCGCAGTGGCTTCATCAGGTATAGCATTGCTTTTGGTTGAGGGTGGTAGAACAGCCCATTCTCGATTTAAAATACCCATAGATGTCAATGAATATAACAATTGTGAAATTAAACAGAACATCTACCTCGCTGAACTTATATGTCACACCAATTTGGTCATTTGGGATGAGGCACCTATGACTCAATATTTTGTCTTTGAGGCGGTT +>Gene.5::contig_11::g.5::m.5 type:5prime_partial len:108 contig_11:2-325(+) +ATTTATGGAAAGGGGATTCAAAATATGAGAACACTCTGGGGTGGCGTTGCTCCCGAATCTCCCGTCGTTGTTGTTGGAGGCGGTGTTACTCCAGAATCTCCCGTCGTCGGAGGCATTGTTCTAGGATCTCCCGCAGTGCTGCTTAAGTCGGATTTACTCCAAGCTCTCCCACCGCGGCTCCTGAAGTCGGCGTTGTTCCAAAATCTCCCGTCGCCACTGTTGAAGTCGGGGTTGCTCCATGATATCCCGTCGGAGTTGCTCCGAATCTCCCGTTGTTGCTGCTGCAGTCGGTGTTGCTCCAGAAACTCCCGCTGTGGCTATTGA +>Gene.6::contig_11::g.6::m.6 type:5prime_partial len:100 contig_11:443-144(-) +GCTGCTAAAGTCACGGTTGCTCCCGGATCTCGCGTCGCTGCTGCTGGAAGCGGCGTTGCCTCAGAATCTCCGGCGACTGCTGAAGCCGGCGTTGCCCCAGGATCTCCCGCGGTCGACTTCAATAGCCACAGCGGGAGTTTCTGGAGCAACACCGACTGCAGCAGCAACAACGGGAGATTCGGAGCAACTCCGACGGGATATCATGGAGCAACCCCGACTTCAACAGTGGCGACGGGAGATTTTGGAACAACGCCGACTTCAGGAGCCGCGGTGGGAGAGCTTGGAGTAAATCCGACTTAA +>Gene.7::contig_18::g.7::m.7 type:internal len:143 contig_18:426-1(-) +ACAGAGGTGAGAAGATGGAACAAGCAGGAAGATTGGGGTAGAAAGACATGGAAAGAAGCTAAGGAATCCACATTGCCGAAAATAGTAGGTGAAGGGATCTATGGAGTTGGTCCCATTTTAGCTGCACTCTCATCCGGGCGAAGAGAACTCTACGCGTTGTACGTTCAGGAAGGTTTGGATTTGAGTAGTAACAGTAAGAAGAAGGACAAGAAACGGTTCGAGAGAGTTTTGAAAATGGTGGAAAAGATTGGATTAAGCAAAAAAGAGGTATCCAAACACGACCTCAACATGGTCGTTGATAATAGGCCTCACCAGGGCTTGCTTCTTGATGCTTCGGCACTTGAAATGGTTAGTATAAAGGAATTAGACCCCGTTTCCATTGATGGAGAGAAGTGCCCGCTTTGGTTGGCATTGGATGAGGTTACC +>Gene.8::contig_20::g.8::m.8 type:internal len:104 contig_20:1-309(+) +GGCTTACGCATCGATGCTCACGGATATGCCCTACAAGATTGGCAACGCGATCTGTTTCAACTTGATCTTGTACTTCATGACGAACCTTCGCCGCGAACCAGGAGCATTCTTCTTCTTCCTGCTGATATCGTTCACGCTGACGCTTGTCATGTCGATGCTCTTCCGCACTATTGGATCCGTTTCGCGTACACTGTCGCAGGCCATGGCTCCCGCAGCTATCCTTATCCTTGCGCTGGTCATTTACACTGGTTTCGTCATTCCTACCCGCTACATGTTGGGCTGGTCTCGTTGGATCAACTACTTGGATCA +>Gene.9::contig_20::g.9::m.9 type:internal len:103 contig_20:2-307(+) +GCTTACGCATCGATGCTCACGGATATGCCCTACAAGATTGGCAACGCGATCTGTTTCAACTTGATCTTGTACTTCATGACGAACCTTCGCCGCGAACCAGGAGCATTCTTCTTCTTCCTGCTGATATCGTTCACGCTGACGCTTGTCATGTCGATGCTCTTCCGCACTATTGGATCCGTTTCGCGTACACTGTCGCAGGCCATGGCTCCCGCAGCTATCCTTATCCTTGCGCTGGTCATTTACACTGGTTTCGTCATTCCTACCCGCTACATGTTGGGCTGGTCTCGTTGGATCAACTACTTGGAT +>Gene.10::contig_20::g.10::m.10 type:internal len:103 contig_20:307-2(-) +ATCCAAGTAGTTGATCCAACGAGACCAGCCCAACATGTAGCGGGTAGGAATGACGAAACCAGTGTAAATGACCAGCGCAAGGATAAGGATAGCTGCGGGAGCCATGGCCTGCGACAGTGTACGCGAAACGGATCCAATAGTGCGGAAGAGCATCGACATGACAAGCGTCAGCGTGAACGATATCAGCAGGAAGAAGAAGAATGCTCCTGGTTCGCGGCGAAGGTTCGTCATGAAGTACAAGATCAAGTTGAAACAGATCGCGTTGCCAATCTTGTAGGGCATATCCGTGAGCATCGATGCGTAAGC +>Gene.11::contig_21::g.11::m.11 type:5prime_partial len:168 contig_21:519-16(-) +GTTTCCATAGTGAATCAGGAACCTGTTCTATTCTCGGTTTCCATTGGAGAAAATATTGCTTACGGACTCCCAGATGATTATGTTTCCAAGGTCGATGTGATAAAAGCTGCTAAAGCAGCTAATGCTCATGAATTTATCATTGCGTTGCCACAGGGTTATGACACATTAGTTGGTGAGCGTGGTGGGTTGTTAAGTGGAGGACAAAGACAGAGGGTAGCCATTGCAAGGGCTCTGCTCAAGAATGCTCCAATCTTGATTCTTGATGAGGCTACCAGTGCTTTGGACGCAGTCAGTGAACGTCTGGTTCAGGATGCTTTGAACCGTTTGATGAAAGGAAGAACGACTTTAGTGATTGCTCACAGGCTGAGCACCGTTCAAAATGCTGATCAAATTGCTTTATGCTCTGATGGGAAGATTTCAGAACTGGGGACACACTCTGAGTTGTTAGAGCAAAAGGGTCTTTATGCCTCACTGGTTGGCACCCAAAGACTTGCATTCGAGTGA +>Gene.12::contig_24::g.12::m.12 type:internal len:111 contig_24:331-2(-) +AAAACCCGTGAATTAGAAATCGAACAAATCTTGTTAAAATCCAAGGATTTGGAAAGCGAATTGGAGAGCAAGGGTAGTATGTTTATAAAGGAGACTGAGGCACTTGTTGCAGAAAACTCGAAACTCAGTCAGGAGTTGGGTGCATTTAAATCCGAGCTAAACGATATACAGATGAAATTGAACGTTGTTTCATCTGAGAAAGACGGCACTGTTGAAGAACTAACTAGTGCAAGAAAAGAAATAGAAGAGCTGACTCAGAAGCTTGCTTCTGAAGGACAAAAGCTGCAGTCTCAGATATCTTCTATAATGGAAGAGAACAATTTACTTAAC +>Gene.13::contig_29::g.13::m.13 type:3prime_partial len:267 contig_29:52-849(+) +ATGAAGAAATCGAAGCTTCTGCAGAATTCGAAGGACTTACTTTCTAGGAGCTTCAATCCTGCTAAATGCAAAACGTCTCTGAGGCTGGCGGGTTCAAGGTTGAAGCTATTGAGAAACAAGAAAGAGGTGCAACTGAAGCAGATGAAGCGGGAAATAGCACAGTTGCTCGAGTCTGGACAGGATCAGACCGCTCGAATTCGAGTCGAACATCTGATTAGGGAAGAGAAGATGATGGCTGCATATGATCTCCTCGATATATACTGCGAGCTTGTTGTTGCACGTCTTCCAGTAATTGAGTCACAAAAGAATTGCCCCATTGACCTGAAAGAAGCAATTGCAAGTTTAGTATTTGCAGCACCAAGATGTGGAGATGTACCCGAGTTTCTTGATGCAAGGAAGCAATTTTCAGCTAAATATGGAAAAGATTTCACTACTGCAGCCACAGAACTTCGTCCACAGTGCGGTGTAGGCCGCATGTTGGTTGAAAAATTATCTGCAACAGCGCCTGATGTACAGAGCAAAACTAAAATCTTGAATGCAATAGCTGAGGAGCACAATGTTAAATGGGAACCCACATCATTTGGAGAGAACGACTCTGCACCTCTCAATGACCGACTGACTGGACCAAGTTCCTTTACGAAGGAGAGAGAACAGTACCCTGAACCTCCTCATTTTGAAGCTGTACAAGTCCAAGCTCACCCGAGCAACAACACCTTGCATAGCTCGCCATCAAATTCTTCCCAGCAGGATGATAGAACCTCAGTTTTTGTTGAAACTTCTACTTTCAAGACACCATCG +>Gene.14::contig_30::g.14::m.14 type:internal len:160 contig_30:1-477(+) +AAGGCTAGTGGACTTTTTTCAAGTAAAGATTCTGTTGATTCAACAGATAGCCACATGGAAAATGTATGCTCTGATATTTTATCAATGAGCATCAACAAAAACCAAATTTTAGAGAATGGCCATGTTCATAACAATAGAGGAGCAGCAATATTTGAGTTGTCTGGAGCTGCTACAAATGTAATTGAGGACGTTGGTTTGTCAGATGTCCAGTCTGACACCAGATTGGGAATGGCAAGTCAAGTTTGCCAAGTTGATATGCATGAACCAGAGGGCGGTTTGTTGTCTTTTAAGAACCAAAGATTTAAGGATGCTGAGGTTGCTACCAATATAACACATGATTATTGTCATGTATCTCATCTGTTAAAGCATTCTAACGTTCAAGTTCCTAAGTACATTAGTGGTAATGGTTCAGCCACTGTTGATCTGAATAGGCAGACTGTAGATAGGAATAACAATTTTAAAGTTTCAACATCTAAT +>Gene.15::contig_31::g.15::m.15 type:3prime_partial len:263 contig_31:787-2(-) +ATGACTAGATCCCGCCCACACATAGAGAAATTAGAAAGTAGAGTGTCTCAGGATGATCTTTTGGAGGGCACTTGTGCAAGAACGAGGCCATTAAGCTATGATGAGATAATGCTCGGAAGAAATAACAAGGGAGATGCAGGTAAAGAAGTTGCCAGTGGCTCTGGAGTGGCTGATAGTGCATCAGGGCATGGTGACATTGAAAAGATTTCTAATTTTCCAGAATACCATCGGCAAATAAATGAGGTTTCTGAACGTATGGATGTTAGACATACTTCAAATGATTTTCAGAAGGTAAGTTGCCGGAGAAAAGTGGATAGTAAGAATGACAATTTAGTCCAGGATAAGGATGAAAAGTATAGGGAAAGTGGTGTCAAGTTAAAGAGTATATGGGAAAAGACTGAAGGCAGCAAGAGAGTGAGAGAAGGAGAAAATGAAAGACGACATTACAGCAACAGAAAAAGAGATGGCCATTTAGGTGTGGATTCATATAATGGATCAAATAAGAGGCAAGCCAGAGAGTCATATAGAAAGGGTAAAACTTCTGAAAGAGGCAGAGTCAAATCCGAAATAGATAGAAAACAGCTTGTTAACGATGAAGGACAGGTCCACAGGAAAAGGAAAACAGAACGGCGAATGAGCAGTGACTCTGAGAAAGAGTACAAAAGAAGAGACGAAAGAAATGTGATGCATACAGAAAGATTAACTAACAGAGGCAGCCAGAAGTCTGAAAAAGAAAACAGACGCAAACGTCATAATGAGGAGGATAAAACTAAAAGCTTGAGTACG +>Gene.16::contig_33::g.16::m.16 type:internal len:206 contig_33:615-1(-) +GAAGAAATTAATGAAGTTGTGGCATTTCTACAAAATCCTCGTGCATTCCAAGAAATGGGAGCTCGGGCACCTCGGGGTGTTCTTATTGTTGGTGAGATAGGAACAGGTAAAACATCCCTAGCAATGGCTATAGCAGCGGAAGCGAAGGTTCCTTTAGTTGAAGTAAAAGCCCAACAGCTGGAAGCTGGTCTGTTTGTGGGCCAAGGTGCATCAAACGTTAGAGAATTGTTTCAAGCAGCACGGGATCTGGCTCCTGTCATTATATTTGTGGAAGACTTTGACCTCTTTGCTGGTGTCCGCGGGAAGGACCTTCAGACCAAAAAGCTGGATCACGAATCTTTCATCAATCAACTTCTGGTGGAGCTTGATGGGTTTGAGAAACAAGATGGGGTAGTTTTGATGGCTACTACTCGGAATCTTAAACAAATCGATGGGGCTTTACTGCGTCCTGGTAGAATGGATCGAATATTTCATCTTCAGCGACTAACTCAAGCAGAAAGGAGGAAAATCCTTCTTCTTGCTGCAAAAGAATCAATGGATGAAGAGCTCATTGACTTTGTCGATTGGCAAAAGGTTGCTGAAAAGACAGCATTACTTCGCCCTATAGAATTAAAA +>Gene.17::contig_35::g.17::m.17 type:internal len:131 contig_35:2-391(+) +ATTCACAGCCTTCTCTTTCATCTCGAGATTGTCTACCTTCTGCAGATCGATATGTCGATGCTTTACAGAGGGATATCGAGGAAGGATAAACCTAGAGGACGTCAGCACGGGTTGACTCAACAGAAAAGGCAAGAGATAAAGGAAGCTTTTGAACTGTTTGACACCGATGGATCTGGAACTATTGATGCGAAAGAGTTGAACGTAGCAATGAGGGCTCTCGGTTTTGAAATGTCAGAAGAGGAAATTACGAGAATGATAGCTGAAGTAGACAAAGACGGGAGTGGGGCGATTGACTTTGACGAGTTTTGTCACATGATGACAGCCAAATTCGGAGAAAGGGACACCAAAGAGGAGCTTACCAAGGCTTTTCAGATTATCGACAAAGATCAA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcripts_tgf.cleaned.nr.cds Tue Jun 06 08:31:58 2017 -0400 @@ -0,0 +1,102 @@ +>contig_1 +AAAAAATTATATGGAGACAAGGAAGATATCCTTGTCCCAGATATTTTCTGGGATTACACGAGTGGAAAGGTGCTAACAAT +GGAGTGGGTTGAAGGTGTTAAATTAAATGAGCAAGATGCCGTTGAGAGTCAAGGGCTCAGTGTTCTGGATCTGGTGAATA +CCGGCATACAGTGCAGTCTTCGACAGCTGCTTGAGTACGGCTATTTTCATGCAGATCCTCACCCAGGGAATCTCTTAGCT +ACACCTGACGGGAAGCTTGCTTTTCTTGATTTTGGAATGATGAGTGAGACTCCTGAACAAGCAAGATCGGCCATAATTGG +TCATGTTGTACACATGGTTAAT +>contig_11 +ATTTATGGAAAGGGGATTCAAAATATGAGAACACTCTGGGGTGGCGTTGCTCCCGAATCTCCCGTCGTTGTTGTTGGAGG +CGGTGTTACTCCAGAATCTCCCGTCGTCGGAGGCATTGTTCTAGGATCTCCCGCAGTGCTGCTTAAGTCGGATTTACTCC +AAGCTCTCCCACCGCGGCTCCTGAAGTCGGCGTTGTTCCAAAATCTCCCGTCGCCACTGTTGAAGTCGGGGTTGCTCCAT +GATATCCCGTCGGAGTTGCTCCGAATCTCCCGTTGTTGCTGCTGCAGTCGGTGTTGCTCCAGAAACTCCCGCTGTGGCTA +T +>contig_18 +ACAGAGGTGAGAAGATGGAACAAGCAGGAAGATTGGGGTAGAAAGACATGGAAAGAAGCTAAGGAATCCACATTGCCGAA +AATAGTAGGTGAAGGGATCTATGGAGTTGGTCCCATTTTAGCTGCACTCTCATCCGGGCGAAGAGAACTCTACGCGTTGT +ACGTTCAGGAAGGTTTGGATTTGAGTAGTAACAGTAAGAAGAAGGACAAGAAACGGTTCGAGAGAGTTTTGAAAATGGTG +GAAAAGATTGGATTAAGCAAAAAAGAGGTATCCAAACACGACCTCAACATGGTCGTTGATAATAGGCCTCACCAGGGCTT +GCTTCTTGATGCTTCGGCACTTGAAATGGTTAGTATAAAGGAATTAGACCCCGTTTCCATTGATGGAGAGAAGTGCCCGC +TTTGGTTGGCATTGGATGAGGTTACC +>contig_2 +CTTTCCAAGGTACCCATCCCATCCAACAACATATATGCTATAAATGATAAGAAGTCCCCGGAAGATGCAGCAGACGACTA +CGAAAACCGCCTCAAGGAACTCGTCTCCGAAAAAATCATACCCGTTTCAACCATTAGCGGGTTCCCGAAGTTCGACCTCA +TGTTGCTTGGAATGGGGCCCGACGGCCATGTGGCCTCTCTTTTCCCTTCTCACATGCAACGCTATGAGAAGGAGAAATGG +GTCACTTTCATAACTGACTCTCCCAAACCGCCTCCGTCGAGAATCACTTTTACGTTTCCGATGATCAACTCGGCTTCGGA +GATCGCTATGGTGGTTACCGGGGCTGATTTGGCTGGTACAACTAAGATAGCATTGGGTACTACGGGCAATGTTAAGCCGG +GTGAGACTCCTTTGCCTTGTACTGAAGTTTCGGCTGAGGGAGAGGTTACTTGGTTCTTGGACAAAGATGCTGCTTCACAA +CTGTTAAATTATGTGCGCTTTGATGAT +>contig_20 +GGCTTACGCATCGATGCTCACGGATATGCCCTACAAGATTGGCAACGCGATCTGTTTCAACTTGATCTTGTACTTCATGA +CGAACCTTCGCCGCGAACCAGGAGCATTCTTCTTCTTCCTGCTGATATCGTTCACGCTGACGCTTGTCATGTCGATGCTC +TTCCGCACTATTGGATCCGTTTCGCGTACACTGTCGCAGGCCATGGCTCCCGCAGCTATCCTTATCCTTGCGCTGGTCAT +TTACACTGGTTTCGTCATTCCTACCCGCTACATGTTGGGCTGGTCTCGTTGGATCAACTACTTGGATCA +>contig_21 +GTTTCCATAGTGAATCAGGAACCTGTTCTATTCTCGGTTTCCATTGGAGAAAATATTGCTTACGGACTCCCAGATGATTA +TGTTTCCAAGGTCGATGTGATAAAAGCTGCTAAAGCAGCTAATGCTCATGAATTTATCATTGCGTTGCCACAGGGTTATG +ACACATTAGTTGGTGAGCGTGGTGGGTTGTTAAGTGGAGGACAAAGACAGAGGGTAGCCATTGCAAGGGCTCTGCTCAAG +AATGCTCCAATCTTGATTCTTGATGAGGCTACCAGTGCTTTGGACGCAGTCAGTGAACGTCTGGTTCAGGATGCTTTGAA +CCGTTTGATGAAAGGAAGAACGACTTTAGTGATTGCTCACAGGCTGAGCACCGTTCAAAATGCTGATCAAATTGCTTTAT +GCTCTGATGGGAAGATTTCAGAACTGGGGACACACTCTGAGTTGTTAGAGCAAAAGGGTCTTTATGCCTCACTGGTTGGC +ACCCAAAGACTTGCATTCGAG +>contig_24 +AAAACCCGTGAATTAGAAATCGAACAAATCTTGTTAAAATCCAAGGATTTGGAAAGCGAATTGGAGAGCAAGGGTAGTAT +GTTTATAAAGGAGACTGAGGCACTTGTTGCAGAAAACTCGAAACTCAGTCAGGAGTTGGGTGCATTTAAATCCGAGCTAA +ACGATATACAGATGAAATTGAACGTTGTTTCATCTGAGAAAGACGGCACTGTTGAAGAACTAACTAGTGCAAGAAAAGAA +ATAGAAGAGCTGACTCAGAAGCTTGCTTCTGAAGGACAAAAGCTGCAGTCTCAGATATCTTCTATAATGGAAGAGAACAA +TTTACTTAAC +>contig_29 +ATGAAGAAATCGAAGCTTCTGCAGAATTCGAAGGACTTACTTTCTAGGAGCTTCAATCCTGCTAAATGCAAAACGTCTCT +GAGGCTGGCGGGTTCAAGGTTGAAGCTATTGAGAAACAAGAAAGAGGTGCAACTGAAGCAGATGAAGCGGGAAATAGCAC +AGTTGCTCGAGTCTGGACAGGATCAGACCGCTCGAATTCGAGTCGAACATCTGATTAGGGAAGAGAAGATGATGGCTGCA +TATGATCTCCTCGATATATACTGCGAGCTTGTTGTTGCACGTCTTCCAGTAATTGAGTCACAAAAGAATTGCCCCATTGA +CCTGAAAGAAGCAATTGCAAGTTTAGTATTTGCAGCACCAAGATGTGGAGATGTACCCGAGTTTCTTGATGCAAGGAAGC +AATTTTCAGCTAAATATGGAAAAGATTTCACTACTGCAGCCACAGAACTTCGTCCACAGTGCGGTGTAGGCCGCATGTTG +GTTGAAAAATTATCTGCAACAGCGCCTGATGTACAGAGCAAAACTAAAATCTTGAATGCAATAGCTGAGGAGCACAATGT +TAAATGGGAACCCACATCATTTGGAGAGAACGACTCTGCACCTCTCAATGACCGACTGACTGGACCAAGTTCCTTTACGA +AGGAGAGAGAACAGTACCCTGAACCTCCTCATTTTGAAGCTGTACAAGTCCAAGCTCACCCGAGCAACAACACCTTGCAT +AGCTCGCCATCAAATTCTTCCCAGCAGGATGATAGAACCTCAGTTTTTGTTGAAACTTCTACTTTCAAGACACCATCG +>contig_3 +GTGGATGAAGGAGTTGTTGTTGCTGGCTTGTCAGAGCAGGAGAAGGCATCTGTTTCTGAAATTCTGACAACTGCTAGAGC +TCATTCAGAAACAATTGAGAACCTTAAGAGAGATCATTCCCAGCAGGTATCCTGTATCGAACAGCACACGAATGATACTT +TCAGGCAAAAATACATGGATTACGAGCCTACAGGGTCCACGCCAGTTAGGAGCGAGCCGGATATTCCCAGCAAAGGCACA +ATAGAGTCACTTCGTGCCATGCCTATAGATGCACTTGAAGAAGAATTTCGAGAAAACCATTCATACGAATCTGCTGTTAC +AGGAAAGGAACTAATGCCGTCTGTTACGACTCGTGCACCATTTTCACAGATCAAC +>contig_30 +AAGGCTAGTGGACTTTTTTCAAGTAAAGATTCTGTTGATTCAACAGATAGCCACATGGAAAATGTATGCTCTGATATTTT +ATCAATGAGCATCAACAAAAACCAAATTTTAGAGAATGGCCATGTTCATAACAATAGAGGAGCAGCAATATTTGAGTTGT +CTGGAGCTGCTACAAATGTAATTGAGGACGTTGGTTTGTCAGATGTCCAGTCTGACACCAGATTGGGAATGGCAAGTCAA +GTTTGCCAAGTTGATATGCATGAACCAGAGGGCGGTTTGTTGTCTTTTAAGAACCAAAGATTTAAGGATGCTGAGGTTGC +TACCAATATAACACATGATTATTGTCATGTATCTCATCTGTTAAAGCATTCTAACGTTCAAGTTCCTAAGTACATTAGTG +GTAATGGTTCAGCCACTGTTGATCTGAATAGGCAGACTGTAGATAGGAATAACAATTTTAAAGTTTCAACATCTAAT +>contig_31 +ATGACTAGATCCCGCCCACACATAGAGAAATTAGAAAGTAGAGTGTCTCAGGATGATCTTTTGGAGGGCACTTGTGCAAG +AACGAGGCCATTAAGCTATGATGAGATAATGCTCGGAAGAAATAACAAGGGAGATGCAGGTAAAGAAGTTGCCAGTGGCT +CTGGAGTGGCTGATAGTGCATCAGGGCATGGTGACATTGAAAAGATTTCTAATTTTCCAGAATACCATCGGCAAATAAAT +GAGGTTTCTGAACGTATGGATGTTAGACATACTTCAAATGATTTTCAGAAGGTAAGTTGCCGGAGAAAAGTGGATAGTAA +GAATGACAATTTAGTCCAGGATAAGGATGAAAAGTATAGGGAAAGTGGTGTCAAGTTAAAGAGTATATGGGAAAAGACTG +AAGGCAGCAAGAGAGTGAGAGAAGGAGAAAATGAAAGACGACATTACAGCAACAGAAAAAGAGATGGCCATTTAGGTGTG +GATTCATATAATGGATCAAATAAGAGGCAAGCCAGAGAGTCATATAGAAAGGGTAAAACTTCTGAAAGAGGCAGAGTCAA +ATCCGAAATAGATAGAAAACAGCTTGTTAACGATGAAGGACAGGTCCACAGGAAAAGGAAAACAGAACGGCGAATGAGCA +GTGACTCTGAGAAAGAGTACAAAAGAAGAGACGAAAGAAATGTGATGCATACAGAAAGATTAACTAACAGAGGCAGCCAG +AAGTCTGAAAAAGAAAACAGACGCAAACGTCATAATGAGGAGGATAAAACTAAAAGCTTGAGTACG +>contig_33 +GAAGAAATTAATGAAGTTGTGGCATTTCTACAAAATCCTCGTGCATTCCAAGAAATGGGAGCTCGGGCACCTCGGGGTGT +TCTTATTGTTGGTGAGATAGGAACAGGTAAAACATCCCTAGCAATGGCTATAGCAGCGGAAGCGAAGGTTCCTTTAGTTG +AAGTAAAAGCCCAACAGCTGGAAGCTGGTCTGTTTGTGGGCCAAGGTGCATCAAACGTTAGAGAATTGTTTCAAGCAGCA +CGGGATCTGGCTCCTGTCATTATATTTGTGGAAGACTTTGACCTCTTTGCTGGTGTCCGCGGGAAGGACCTTCAGACCAA +AAAGCTGGATCACGAATCTTTCATCAATCAACTTCTGGTGGAGCTTGATGGGTTTGAGAAACAAGATGGGGTAGTTTTGA +TGGCTACTACTCGGAATCTTAAACAAATCGATGGGGCTTTACTGCGTCCTGGTAGAATGGATCGAATATTTCATCTTCAG +CGACTAACTCAAGCAGAAAGGAGGAAAATCCTTCTTCTTGCTGCAAAAGAATCAATGGATGAAGAGCTCATTGACTTTGT +CGATTGGCAAAAGGTTGCTGAAAAGACAGCATTACTTCGCCCTATAGAATTAAAA +>contig_35 +ATTCACAGCCTTCTCTTTCATCTCGAGATTGTCTACCTTCTGCAGATCGATATGTCGATGCTTTACAGAGGGATATCGAG +GAAGGATAAACCTAGAGGACGTCAGCACGGGTTGACTCAACAGAAAAGGCAAGAGATAAAGGAAGCTTTTGAACTGTTTG +ACACCGATGGATCTGGAACTATTGATGCGAAAGAGTTGAACGTAGCAATGAGGGCTCTCGGTTTTGAAATGTCAGAAGAG +GAAATTACGAGAATGATAGCTGAAGTAGACAAAGACGGGAGTGGGGCGATTGACTTTGACGAGTTTTGTCACATGATGAC +AGCCAAATTCGGAGAAAGGGACACCAAAGAGGAGCTTACCAAGGCTTTTCAGATTATCGACAAAGATCAA +>contig_9 +CTTCGGTTAAAGGCAGATGAGGAGGCACAATGTTTGAATCAGATGCAGCGTATCATTTTTGATGAAATTATGGAGCATGT +GGAGTTAGAAAAGGGGGGCTTCTATTTCGTATATCGCCCTGGGGGCAACGGAAAGACCTTGTGGTTGGCTATTATCTCAA +AACTGAGAAGCGAGGGTAGAATAGTTCTCGCAGTGGCTTCATCAGGTATAGCATTGCTTTTGGTTGAGGGTGGTAGAACA +GCCCATTCTCGATTTAAAATACCCATAGATGTCAATGAATATAACAATTGTGAAATTAAACAGAACATCTACCTCGCTGA +ACTTATATGTCACACCAATTTGGTCATTTGGGATGAGGCACCTATGACTCAATATTTTGTCTTTGAGGCGGTT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcripts_tgf.cleaned.nr.pep Tue Jun 06 08:31:58 2017 -0400 @@ -0,0 +1,49 @@ +>contig_1 +KKLYGDKEDILVPDIFWDYTSGKVLTMEWVEGVKLNEQDAVESQGLSVLDLVNTGIQCSLRQLLEYGYFHADPHPGNLLA +TPDGKLAFLDFGMMSETPEQARSAIIGHVVHMVN +>contig_11 +IYGKGIQNMRTLWGGVAPESPVVVVGGGVTPESPVVGGIVLGSPAVLLKSDLLQALPPRLLKSALFQNLPSPLLKSGLLH +DIPSELLRISRCCCCSRCCSRNSRCGY +>contig_18 +TEVRRWNKQEDWGRKTWKEAKESTLPKIVGEGIYGVGPILAALSSGRRELYALYVQEGLDLSSNSKKKDKKRFERVLKMV +EKIGLSKKEVSKHDLNMVVDNRPHQGLLLDASALEMVSIKELDPVSIDGEKCPLWLALDEVT +>contig_2 +LSKVPIPSNNIYAINDKKSPEDAADDYENRLKELVSEKIIPVSTISGFPKFDLMLLGMGPDGHVASLFPSHMQRYEKEKW +VTFITDSPKPPPSRITFTFPMINSASEIAMVVTGADLAGTTKIALGTTGNVKPGETPLPCTEVSAEGEVTWFLDKDAASQ +LLNYVRFDD +>contig_20 +GLRIDAHGYALQDWQRDLFQLDLVLHDEPSPRTRSILLLPADIVHADACHVDALPHYWIRFAYTVAGHGSRSYPYPCAGH +LHWFRHSYPLHVGLVSLDQLLGS +>contig_21 +VSIVNQEPVLFSVSIGENIAYGLPDDYVSKVDVIKAAKAANAHEFIIALPQGYDTLVGERGGLLSGGQRQRVAIARALLK +NAPILILDEATSALDAVSERLVQDALNRLMKGRTTLVIAHRLSTVQNADQIALCSDGKISELGTHSELLEQKGLYASLVG +TQRLAFE +>contig_24 +KTRELEIEQILLKSKDLESELESKGSMFIKETEALVAENSKLSQELGAFKSELNDIQMKLNVVSSEKDGTVEELTSARKE +IEELTQKLASEGQKLQSQISSIMEENNLLN +>contig_29 +MKKSKLLQNSKDLLSRSFNPAKCKTSLRLAGSRLKLLRNKKEVQLKQMKREIAQLLESGQDQTARIRVEHLIREEKMMAA +YDLLDIYCELVVARLPVIESQKNCPIDLKEAIASLVFAAPRCGDVPEFLDARKQFSAKYGKDFTTAATELRPQCGVGRML +VEKLSATAPDVQSKTKILNAIAEEHNVKWEPTSFGENDSAPLNDRLTGPSSFTKEREQYPEPPHFEAVQVQAHPSNNTLH +SSPSNSSQQDDRTSVFVETSTFKTPS +>contig_3 +VDEGVVVAGLSEQEKASVSEILTTARAHSETIENLKRDHSQQVSCIEQHTNDTFRQKYMDYEPTGSTPVRSEPDIPSKGT +IESLRAMPIDALEEEFRENHSYESAVTGKELMPSVTTRAPFSQIN +>contig_30 +KASGLFSSKDSVDSTDSHMENVCSDILSMSINKNQILENGHVHNNRGAAIFELSGAATNVIEDVGLSDVQSDTRLGMASQ +VCQVDMHEPEGGLLSFKNQRFKDAEVATNITHDYCHVSHLLKHSNVQVPKYISGNGSATVDLNRQTVDRNNNFKVSTSN +>contig_31 +MTRSRPHIEKLESRVSQDDLLEGTCARTRPLSYDEIMLGRNNKGDAGKEVASGSGVADSASGHGDIEKISNFPEYHRQIN +EVSERMDVRHTSNDFQKVSCRRKVDSKNDNLVQDKDEKYRESGVKLKSIWEKTEGSKRVREGENERRHYSNRKRDGHLGV +DSYNGSNKRQARESYRKGKTSERGRVKSEIDRKQLVNDEGQVHRKRKTERRMSSDSEKEYKRRDERNVMHTERLTNRGSQ +KSEKENRRKRHNEEDKTKSLST +>contig_33 +EEINEVVAFLQNPRAFQEMGARAPRGVLIVGEIGTGKTSLAMAIAAEAKVPLVEVKAQQLEAGLFVGQGASNVRELFQAA +RDLAPVIIFVEDFDLFAGVRGKDLQTKKLDHESFINQLLVELDGFEKQDGVVLMATTRNLKQIDGALLRPGRMDRIFHLQ +RLTQAERRKILLLAAKESMDEELIDFVDWQKVAEKTALLRPIELK +>contig_35 +IHSLLFHLEIVYLLQIDMSMLYRGISRKDKPRGRQHGLTQQKRQEIKEAFELFDTDGSGTIDAKELNVAMRALGFEMSEE +EITRMIAEVDKDGSGAIDFDEFCHMMTAKFGERDTKEELTKAFQIIDKDQ +>contig_9 +LRLKADEEAQCLNQMQRIIFDEIMEHVELEKGGFYFVYRPGGNGKTLWLAIISKLRSEGRIVLAVASSGIALLLVEGGRT +AHSRFKIPIDVNEYNNCEIKQNIYLAELICHTNLVIWDEAPMTQYFVFEAV
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcripts_tgf.pep Tue Jun 06 08:31:58 2017 -0400 @@ -0,0 +1,34 @@ +>Gene.1::contig_1::g.1::m.1 type:internal len:115 gc:universal contig_1:344-3(-) +KKLYGDKEDILVPDIFWDYTSGKVLTMEWVEGVKLNEQDAVESQGLSVLDLVNTGIQCSLRQLLEYGYFHADPHPGNLLATPDGKLAFLDFGMMSETPEQARSAIIGHVVHMVN +>Gene.2::contig_2::g.2::m.2 type:5prime_partial len:170 gc:universal contig_2:2-511(+) +LSKVPIPSNNIYAINDKKSPEDAADDYENRLKELVSEKIIPVSTISGFPKFDLMLLGMGPDGHVASLFPSHMQRYEKEKWVTFITDSPKPPPSRITFTFPMINSASEIAMVVTGADLAGTTKIALGTTGNVKPGETPLPCTEVSAEGEVTWFLDKDAASQLLNYVRFDD* +>Gene.3::contig_3::g.3::m.3 type:5prime_partial len:126 gc:universal contig_3:463-86(-) +VDEGVVVAGLSEQEKASVSEILTTARAHSETIENLKRDHSQQVSCIEQHTNDTFRQKYMDYEPTGSTPVRSEPDIPSKGTIESLRAMPIDALEEEFRENHSYESAVTGKELMPSVTTRAPFSQIN* +>Gene.4::contig_9::g.4::m.4 type:internal len:132 gc:universal contig_9:2-394(+) +LRLKADEEAQCLNQMQRIIFDEIMEHVELEKGGFYFVYRPGGNGKTLWLAIISKLRSEGRIVLAVASSGIALLLVEGGRTAHSRFKIPIDVNEYNNCEIKQNIYLAELICHTNLVIWDEAPMTQYFVFEAV +>Gene.5::contig_11::g.5::m.5 type:5prime_partial len:108 gc:universal contig_11:2-325(+) +IYGKGIQNMRTLWGGVAPESPVVVVGGGVTPESPVVGGIVLGSPAVLLKSDLLQALPPRLLKSALFQNLPSPLLKSGLLHDIPSELLRISRCCCCSRCCSRNSRCGY* +>Gene.6::contig_11::g.6::m.6 type:5prime_partial len:100 gc:universal contig_11:443-144(-) +AAKVTVAPGSRVAAAGSGVASESPATAEAGVAPGSPAVDFNSHSGSFWSNTDCSSNNGRFGATPTGYHGATPTSTVATGDFGTTPTSGAAVGELGVNPT* +>Gene.7::contig_18::g.7::m.7 type:internal len:143 gc:universal contig_18:426-1(-) +TEVRRWNKQEDWGRKTWKEAKESTLPKIVGEGIYGVGPILAALSSGRRELYALYVQEGLDLSSNSKKKDKKRFERVLKMVEKIGLSKKEVSKHDLNMVVDNRPHQGLLLDASALEMVSIKELDPVSIDGEKCPLWLALDEVT +>Gene.8::contig_20::g.8::m.8 type:internal len:104 gc:universal contig_20:1-309(+) +GLRIDAHGYALQDWQRDLFQLDLVLHDEPSPRTRSILLLPADIVHADACHVDALPHYWIRFAYTVAGHGSRSYPYPCAGHLHWFRHSYPLHVGLVSLDQLLGS +>Gene.9::contig_20::g.9::m.9 type:internal len:103 gc:universal contig_20:2-307(+) +AYASMLTDMPYKIGNAICFNLILYFMTNLRREPGAFFFFLLISFTLTLVMSMLFRTIGSVSRTLSQAMAPAAILILALVIYTGFVIPTRYMLGWSRWINYLD +>Gene.10::contig_20::g.10::m.10 type:internal len:103 gc:universal contig_20:307-2(-) +IQVVDPTRPAQHVAGRNDETSVNDQRKDKDSCGSHGLRQCTRNGSNSAEEHRHDKRQRERYQQEEEECSWFAAKVRHEVQDQVETDRVANLVGHIREHRCVS +>Gene.11::contig_21::g.11::m.11 type:5prime_partial len:168 gc:universal contig_21:519-16(-) +VSIVNQEPVLFSVSIGENIAYGLPDDYVSKVDVIKAAKAANAHEFIIALPQGYDTLVGERGGLLSGGQRQRVAIARALLKNAPILILDEATSALDAVSERLVQDALNRLMKGRTTLVIAHRLSTVQNADQIALCSDGKISELGTHSELLEQKGLYASLVGTQRLAFE* +>Gene.12::contig_24::g.12::m.12 type:internal len:111 gc:universal contig_24:331-2(-) +KTRELEIEQILLKSKDLESELESKGSMFIKETEALVAENSKLSQELGAFKSELNDIQMKLNVVSSEKDGTVEELTSARKEIEELTQKLASEGQKLQSQISSIMEENNLLN +>Gene.13::contig_29::g.13::m.13 type:3prime_partial len:267 gc:universal contig_29:52-849(+) +MKKSKLLQNSKDLLSRSFNPAKCKTSLRLAGSRLKLLRNKKEVQLKQMKREIAQLLESGQDQTARIRVEHLIREEKMMAAYDLLDIYCELVVARLPVIESQKNCPIDLKEAIASLVFAAPRCGDVPEFLDARKQFSAKYGKDFTTAATELRPQCGVGRMLVEKLSATAPDVQSKTKILNAIAEEHNVKWEPTSFGENDSAPLNDRLTGPSSFTKEREQYPEPPHFEAVQVQAHPSNNTLHSSPSNSSQQDDRTSVFVETSTFKTPS +>Gene.14::contig_30::g.14::m.14 type:internal len:160 gc:universal contig_30:1-477(+) +KASGLFSSKDSVDSTDSHMENVCSDILSMSINKNQILENGHVHNNRGAAIFELSGAATNVIEDVGLSDVQSDTRLGMASQVCQVDMHEPEGGLLSFKNQRFKDAEVATNITHDYCHVSHLLKHSNVQVPKYISGNGSATVDLNRQTVDRNNNFKVSTSN +>Gene.15::contig_31::g.15::m.15 type:3prime_partial len:263 gc:universal contig_31:787-2(-) +MTRSRPHIEKLESRVSQDDLLEGTCARTRPLSYDEIMLGRNNKGDAGKEVASGSGVADSASGHGDIEKISNFPEYHRQINEVSERMDVRHTSNDFQKVSCRRKVDSKNDNLVQDKDEKYRESGVKLKSIWEKTEGSKRVREGENERRHYSNRKRDGHLGVDSYNGSNKRQARESYRKGKTSERGRVKSEIDRKQLVNDEGQVHRKRKTERRMSSDSEKEYKRRDERNVMHTERLTNRGSQKSEKENRRKRHNEEDKTKSLST +>Gene.16::contig_33::g.16::m.16 type:internal len:206 gc:universal contig_33:615-1(-) +EEINEVVAFLQNPRAFQEMGARAPRGVLIVGEIGTGKTSLAMAIAAEAKVPLVEVKAQQLEAGLFVGQGASNVRELFQAARDLAPVIIFVEDFDLFAGVRGKDLQTKKLDHESFINQLLVELDGFEKQDGVVLMATTRNLKQIDGALLRPGRMDRIFHLQRLTQAERRKILLLAAKESMDEELIDFVDWQKVAEKTALLRPIELK +>Gene.17::contig_35::g.17::m.17 type:internal len:131 gc:universal contig_35:2-391(+) +IHSLLFHLEIVYLLQIDMSMLYRGISRKDKPRGRQHGLTQQKRQEIKEAFELFDTDGSGTIDAKELNVAMRALGFEMSEEEITRMIAEVDKDGSGAIDFDEFCHMMTAKFGERDTKEELTKAFQIIDKDQ
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Tue Jun 06 08:31:58 2017 -0400 @@ -0,0 +1,6 @@ +<tables> + <table name="plant_tribes_scaffolds" comment_char="#"> + <columns>value, name, path, description</columns> + <file path="${__HERE__}/plant_tribes_scaffolds.loc" /> + </table> +</tables>