# HG changeset patch
# User iuc
# Date 1508485715 14400
# Node ID fcdd4f5c6cfc4a80246ecd21855e47d2d31b0e45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
diff -r 000000000000 -r fcdd4f5c6cfc augustus_training.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/augustus_training.xml Fri Oct 20 03:48:35 2017 -0400
@@ -0,0 +1,43 @@
+
+
+ ab-initio gene predictor
+
+ macros.xml
+
+
+ maker
+
+ genome.gff3 &&
+
+ autoAugTrain.pl --genome=${genome} --species=local --trainingset=genome.gff3 -v &&
+
+ cd 'augustus_dir/species/' && tar cvfz '${output_tar}' 'local'
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r 000000000000 -r fcdd4f5c6cfc extract_features.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/extract_features.py Fri Oct 20 03:48:35 2017 -0400
@@ -0,0 +1,94 @@
+#!/usr/bin/env python
+
+import argparse
+import sys
+import textwrap
+
+
+def main( args ):
+ """
+ Extract the protein and coding section from an augustus gff, gtf file
+ Example file:
+HS04636 AUGUSTUS stop_codon 6901 6903 . + 0 Parent=g1.t1
+HS04636 AUGUSTUS transcription_end_site 8857 8857 . + . Parent=g1.t1
+# protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL
+# THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD
+# PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG
+# QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH
+# WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE
+# KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV
+# PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL]
+# end gene g1
+###
+#
+# ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----
+#
+# Predicted genes for sequence number 2 on both strands
+# start gene g2
+HS08198 AUGUSTUS gene 86 2344 1 + . ID=g2
+HS08198 AUGUSTUS transcript 86 2344 . + . ID=g2.t1;Parent=g2
+HS08198 AUGUSTUS transcription_start_site 86 86 . + . Parent=g2.t1
+HS08198 AUGUSTUS exon 86 582 . + . Parent=g2.t1
+HS08198 AUGUSTUS start_codon 445 447 . + 0 Parent=g2.t1
+ """
+ protein_seq = ''
+ coding_seq = ''
+ if args.protein:
+ po = open( args.protein, 'w+' )
+ if args.codingseq:
+ co = open( args.codingseq, 'w+' )
+
+ for line in sys.stdin:
+ # protein- and coding-sequence are stored as comments
+ if line.startswith('#'):
+ line = line[2:].strip()
+ if line.startswith('start gene'):
+ gene_name = line[11:].strip()
+
+ if protein_seq:
+ if line.endswith(']'):
+ protein_seq += line[:-1]
+ po.write( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( protein_seq, 80 ) ) ) )
+ protein_seq = ''
+ else:
+ protein_seq += line
+
+ if coding_seq:
+ if line.endswith(']'):
+ coding_seq += line[:-1]
+ co.write( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( coding_seq, 80 ) ) ) )
+ coding_seq = ''
+ else:
+ coding_seq += line
+
+ if args.protein and line.startswith('protein sequence = ['):
+ if line.endswith(']'):
+ protein_seq = line[20:-1]
+ po.write( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( protein_seq, 80 ) ) ) )
+ protein_seq = ''
+ else:
+ line = line[20:]
+ protein_seq = line
+
+ if args.codingseq and line.startswith('coding sequence = ['):
+ if line.endswith(']'):
+ coding_seq = line[19:-1]
+ co.write( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( coding_seq, 80 ) ) ) )
+ coding_seq = ''
+ else:
+ line = line[19:]
+ coding_seq = line
+
+ if args.codingseq:
+ co.close()
+ if args.protein:
+ po.close()
+
+
+if __name__ == '__main__':
+ parser = argparse.ArgumentParser()
+ parser.add_argument('-p', '--protein', help='Path to the protein file.')
+ parser.add_argument('-c', '--codingseq', help='Path to the coding file.')
+
+ args = parser.parse_args()
+ main( args )
diff -r 000000000000 -r fcdd4f5c6cfc macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Fri Oct 20 03:48:35 2017 -0400
@@ -0,0 +1,20 @@
+
+
+
+
+ augustus
+
+
+
+
+ 3.2.3
+
+
+
+ 10.1093/bioinformatics/btg1080
+ 10.1093/bioinformatics/btr010
+ 10.1093/bioinformatics/btn013
+
+
+
+
diff -r 000000000000 -r fcdd4f5c6cfc test-data/annot.gff3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annot.gff3 Fri Oct 20 03:48:35 2017 -0400
@@ -0,0 +1,41 @@
+##gff-version 3
+HS08198 maker gene 352 1848 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0;Name=maker-HS08198-exonerate_est2genome-gene-0.0
+HS08198 maker mRNA 352 1848 2869 + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1;Parent=maker-HS08198-exonerate_est2genome-gene-0.0;Name=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1;_AED=0.00;_eAED=0.00;_QI=70|1|1|1|0|0|7|0|192
+HS08198 maker exon 352 397 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:9;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198 maker exon 421 582 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:10;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198 maker exon 812 894 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:11;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198 maker exon 1053 1123 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:12;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198 maker exon 1208 1315 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:13;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198 maker exon 1587 1688 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:14;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198 maker exon 1772 1848 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:15;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198 maker five_prime_UTR 352 397 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198 maker five_prime_UTR 421 444 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198 maker CDS 445 582 . + 0 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198 maker CDS 812 894 . + 0 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198 maker CDS 1053 1123 . + 1 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198 maker CDS 1208 1315 . + 2 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198 maker CDS 1587 1688 . + 2 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198 maker CDS 1772 1848 . + 2 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+###
+HS04636 maker gene 1813 6903 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0;Name=maker-HS04636-exonerate_est2genome-gene-0.0
+HS04636 maker mRNA 1813 6903 8728 + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1;Parent=maker-HS04636-exonerate_est2genome-gene-0.0;Name=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1;_AED=0.00;_eAED=0.00;_QI=49|1|1|1|0|0|9|0|572
+HS04636 maker exon 1813 1934 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:0;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636 maker exon 2055 2198 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:1;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636 maker exon 2852 2995 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:2;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636 maker exon 3426 3607 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:3;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636 maker exon 4340 4423 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:4;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636 maker exon 4543 4789 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:5;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636 maker exon 5072 5358 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:6;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636 maker exon 5860 6007 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:7;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636 maker exon 6494 6903 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:8;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636 maker five_prime_UTR 1813 1861 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636 maker CDS 1862 1934 . + 0 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636 maker CDS 2055 2198 . + 2 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636 maker CDS 2852 2995 . + 2 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636 maker CDS 3426 3607 . + 2 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636 maker CDS 4340 4423 . + 0 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636 maker CDS 4543 4789 . + 0 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636 maker CDS 5072 5358 . + 2 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636 maker CDS 5860 6007 . + 0 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636 maker CDS 6494 6903 . + 2 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+###
diff -r 000000000000 -r fcdd4f5c6cfc test-data/arabidopsis_augustus.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/arabidopsis_augustus.fa Fri Oct 20 03:48:35 2017 -0400
@@ -0,0 +1,53 @@
+>arabidopsis
+ATATCATTCATGGGCCCCTACGCATTACTCGGTACCAATCTCGCTCTCTCTCTCTAAGTCTTGAAACTCTATCAAGAAT
+CTCAAGCCACCATTTTTTCTTCATCTTCATAAAGAGAAAGAGAGAGATCCTCTTGTTTGGCAAGAACCCAATTTGAGTT
+CTAAGTCCTGATTTGCTTAGCTCTTTTCTTTCCTTGATTTCATTCTATATAAAGTCAACGGAAAGATATACATATATAG
+TTTTCTTCCGATTCTAGGGTTTTCATATTTCCTCTAAATTTTCATGGTCAAAGAAGAAAATCTAAGAAACAATCGAACC
+AGCAAGAGAAAGAAGACTTCAATATCAACATCTCTCTCTCCCTCTCTCTCTCTTATATTATAAGGTGAGACCACAAGAA
+CTTTTGATTTTCTTTTTCCTTCTTCCCTTCTTTTAATATATTCTTTGAATTTTTTTTCACTAATTCATCTACCCTTTTT
+TATAATTGTGGCTAGATTTTTGTTTCGTTTCCTCTTTTTAATATTATCTCTCTAATGTATGTTGAAGATCTCGAGTTGA
+GTCATCATCATCGTCAATGGCTTTGAAAAACATCCGCAACAATTCACCAATTGAAGAACAAGAGAAAGGTTTAAACTTC
+ATCAAGATTCACTAAGACCCACTAAGAGCCAACTCAAAACTAAACGGAGCAAGGTTTTGCCAAAAACCAAAAAAAAAAA
+AAAAAAGATTCAAGAACCATCTCGTAAATCAAGATTTCTCCAAGGAAAATCAGATAAGTCATAATGGATCTATCCCTGG
+CTCCGACAACAACAACAAGTTCCGACCAAGAACAAGACAGAGACCAAGAATTAACCTCCAACATCGGAGCAAGCAGCAG
+CTCCGGTCCCAGCGGAAACAACAACAACCTTCCGATGATGATGATTCCACCTCCGGAGAAAGAACACATGTTCGACAAA
+GTGGTAACACCAAGCGACGTCGGAAAACTCAACAGACTCGTGATCCCTAAACAACACGCTGAGAGGTATTTCCCTCTAG
+ACTCCTCAAACAACCAAAACGGCACGCTTTTGAACTTCCAAGACAGAAACGGCAAGATGTGGAGATTCCGTTACTCGTA
+TTGGAACTCTAGCCAGAGCTACGTTATGACCAAAGGATGGAGCCGTTTCGTCAAAGAGAAAAAGCTCGATGCAGGAGAC
+ATTGTCTCTTTCCAACGAGGCATCGGAGATGAGTCAGAAAGATCCAAACTTTACATAGATTGGAGGCATAGACCCGACA
+TGAGCCTCGTTCAAGCACATCAGTTTGGTAATTTTGGTTTCAATTTCAATTTCCCGACCACTTCTCAATATTCCAACAG
+ATTTCATCCATTGCCAGAATATAACTCCGTCCCGATTCACCGGGGCTTAAACATCGGAAATCACCAACGTTCCTATTAT
+AACACCCAGCGTCAAGAGTTCGTAGGGTATGGTTATGGGAATTTAGCTGGAAGGTGTTACTACACGGGATCACCGTTGG
+ATCATAGGAACATTGTTGGATCAGAGCCGTTGGTTATAGACTCAGTCCCTGTGGTTCCCGGGAGATTAACTCCGGTGAT
+GTTACCGCCGCTTCCTCCGCCTCCTTCTACGGCGGGAAAGAGACTAAGGCTCTTTGGGGTGAATATGGAATGTGGCAAT
+GACTATAATCAACAAGAAGAGTCATGGTTGGTGCCACGTGGCGAAATTGGTGCATCTTCTTCTTCTTCTTCAGCTCTAC
+GACTAAATTTATCGACTGATCATGATGATGATAATGATGATGGTGATGATGGCGATGATGATCAATTTGCTAAGAAAGG
+GAAGTCTTCACTTTCTCTCAATTTCAATCCATGAGAAGTTTCATCATCTTCTTGTTTTGAATCTCTCTTTATATTGTTT
+CATTAGTAATTTTTCTAAGGGTATTAGATTCTAGCTAGTGAGAGGAAGAAAAAACGATCTTCTTCGTTTTTTTGGTTAT
+GATTTTTTTTTCCGACATGTTTCTTGATGTTCATCATCATTAGGCTTTTGTCACCATGTTGAAACTCGCATCTTTTCAA
+TTTTGTATATAA
+
+>arabidopsis2
+CTCCTCTGCCTCTCATCTCTTGTTCTCTCCGCCCATCTCTGCTCTCTTTTATTTTCCCAGAAAGTTTTTTTTTTTTTTT
+TCCGAATTCCGTTAATCTCATTGGGGTTTCCATTGATAGCAATGGCGACGGCTTTCGCTCCCACTAAGCTCACTGCCAC
+GGTTCCTCTGCATGGATCCCATGAGAATCGTCTCTTGCTCCCGATCCGATTGGCTCCTCCTTCTTCTTTCCTCGGATCC
+ACCCGTTCCCTCTCCCTTCGCAGACTCAATCACTCCAACGCCACCCGTCGATCTCCCGTCGTCTCTGTCCAGGAAGTTG
+TCAAGGAGAAGCAATCCACCAATAATACCAGCCTGGTACGCTTCCTCTCCTCGTCTCCTTCTTTTGGAATTTTACAAGT
+TGTGAGATTTGTTGTATTGATTTAAGTAATTTGAAATAGTTGATAACCAAAGAGGAAGGATTGGAGTTGTATGAAGATA
+TGATACTAGGTAGATCTTTCGAAGACATGTGTGCTCAAATGTATTACCGAGGCAAGATGTTTGGTTTTGTTCACTTGTA
+CAATGGCCAAGAGGCTGTTTCTACTGGCTTTATCAAGCTCCTTACCAAGTCTGACTCTGTCGTTAGTACCTACCGTGAC
+CATGTCCATGCCCTCAGCAAAGGTGTCTCTGCTCGTGCTGTTATGAGCGAGCTCTTCGGCAAGGTTACTGGATGCTGCA
+GAGGCCAAGGTGGATCCATGCACATGTTCTCCAAAGAACACAACATGCTTGGTGGCTTTGCTTTTATTGGTGAAGGCAT
+TCCTGTCGCCACTGGTGCTGCCTTTAGCTCCAAGTACAGGAGGGAAGTCTTGAAACAGGATTGTGATGATGTCACTGTC
+GCCTTTTTCGGAGATGGAACTTGTAACAACGGACAGTTCTTCGAGTGTCTCAACATGGCTGCTCTCTATAAACTGCCTA
+TTATCTTTGTTGTCGAGAATAACTTGTGGGCCATTGGGATGTCTCACTTGAGAGCCACTTCTGACCCCGAGATTTGGAA
+GAAAGGTCCTGCATTTGGGATGCCTGGTGTTCATGTTGACGGTATGGATGTCTTGAAGGTCAGGGAAGTCGCTAAAGAA
+GCTGTCACTAGAGCTAGAAGAGGAGAAGGTCCAACCTTGGTTGAATGTGAGACTTATAGATTCAGAGGACACTCCTTGG
+CTGATCCCGATGAGCTCCGTGATGCTGGTAAATATCGACTTCCTTCTGCTTCTTGATGCTTGTACTGATTATCTAAGGG
+TTGAAACAACCTTCTCTTTAATTTGAATTTTTTTTTGCAGCTGAGAAAGCCAAATACGCGGCTAGAGACCCAATCGCAG
+CATTGAAGAAGTATTTGATAGAGAACAAGCTTGCAAAGGAAGCAGAGCTAAAGTCAATAGAGAAAAAGATAGACGAGTT
+GGTGGAGGAAGCGGTTGAGTTTGCAGACGCTAGTCCACAGCCCGGTCGCAGTCAGTTGCTAGAGAATGTGTTTGCTGAT
+CCAAAAGGATTTGGAATTGGACCTGATGGACGGTACAGATGTGAGGACCCCAAGTTTACCGAAGGCACAGCTCAAGTCT
+GAGAAGACAAGTTTAACCATAAGCTGTCTACTGTCTCTTCGATGTTTCTATATATCTTATTAAGTTAAATGCTACAGAG
+AATCAGTTTGAATCATTTGCACTTTTTGCTTTTTGTTTGGTGTTACTAAACTATCACAAGGTTCTTCTTGTAGTTCGTT
+GGGTTTTCATTGGTTACCACTTACCAGAGAATTGTATTTTTTTTTTTAAAGATAATTATTTTGC
diff -r 000000000000 -r fcdd4f5c6cfc test-data/human_augustus.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/human_augustus.fa Fri Oct 20 03:48:35 2017 -0400
@@ -0,0 +1,200 @@
+>HS04636
+gagctcacattaactatttacagggtaactgcttaggaccagtattatgaggagaattta
+cctttcccgcctctctttccaagaaacaaggagggggtgaaggtacggagaacagtattt
+cttctgttgaaagcaacttagctacaaagataaattacagctatgtacactgaaggtagc
+tatttcattccacaaaataagagttttttaaaaagctatgtatgtatgtgctgcatatag
+agcagatatacagcctattaagcgtcgtcactaaaacataaaacatgtcagcctttctta
+accttactcgccccagtctgtcccgacgtgacttcctcgaccctctaaagacgtacagac
+cagacacggcggcggcggcgggagaggggattccctgcgcccccggacctcagggccgct
+cagattcctggagaggaagccaagtgtccttctgccctcccccggtatcccatccaaggc
+gatcagtccagaactggctctcggaagcgctcgggcaaagactgcgaagaagaaaagaca
+tctggcggaaacctgtgcgcctggggcggtggaactcggggaggagagggagggatcaga
+caggagagtggggactaccccctctgctcccaaattggggcagcttcctgggtttccgat
+tttctcatttccgtgggtaaaaaaccctgcccccaccgggcttacgcaatttttttaagg
+ggagaggagggaaaaaatttgtgggggggtacgaaaaggcggaaagaaacagtcattcac
+atgggcttggttttcagtcttataaaaaggaaggttctctcggttagcgaccaattgtca
+tacgacttgcagtgagcgtcaggagcacgtccaggaactcctcagcagcgcctccttcag
+ctccacagccagacgccctcagacagcaaagcctacccccgcgccgcgccctgcccgccg
+ctcggatgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacaggtg
+agtacctggcgccgcgcaccggggactccggttccacgcacccgggcagagtttccgctc
+tgacctcctgggtctatcccagtactccgacttctctccgaatagagaagctacgtgact
+tgggaaagagcttggaccgctagagtccgaaagaactccgtggatattccagctttccca
+caagcactgatcattatgagccagttacttaaccgatctgagacactctcacctcctaaa
+tagggatagatgatactaatttgcaggttgtcattatgataagacaggatctgatcaata
+tatgtgaattgtttatatttggaacctttttattgagtggaagaagttgttttaaatatt
+ctagtcagttctttcctgctcccaggaaagcccggattatgttttaagataagcaaaatg
+tcttaaaagtaagctgttttactttgaatttttccctaaatgttgattagtgtactagat
+ccattttaatttggaaagtgaagtgctacttatttgaacttcttaaaaatgctaatttta
+acatctaaagagttaactaagaaaagcttagtaacatgatgtaccaagttgaatatgctg
+ttatccttatttagaatagaaaattggtatttctacgttttatccattctaaggcaggtt
+aaaaaattgtatttccatgactacctatatatttcttgaatttattattgtaaagttgat
+tcatagtcaaacaattaaatgtttaaattaagattaagacactagagaatgatttatttg
+ctgtcctttaattgcagcaaatccttgctgttcccacccatgtcaaaaccgaggtgtatg
+tatgagtgtgggatttgaccagtataagtgcgattgtacccggacaggattctatggaga
+aaactgctcaacacgtaagtttgtcctttggttgcctcattaggagtggggctggataca
+gttatcattgtatagatttgtgtcttataatgagtcccattaatttctccctccctttct
+tcgtcttcttgcagcggaatttttgacaagaataaaattatttctgaaacccactccaaa
+cacagtgcactacatacttacccacttcaagggattttggaacgttgtgaataacattcc
+cttccttcgaaatgcaattatgagttatgtcttgacatgtaagtacaagtgtctttctaa
+ggtttttagccttctcaaagaaaaatatgctttataatactgtaagcctaatctaaaaac
+atatttccaagcttatcaaaaagactttaagatagcttttaagtttgccttccatcttaa
+tcgccaaaaatattgacatttagtcccatccagtttatacagtctgctcacaactctgta
+tacctcttctaacctttactgtttggtcagtttgtggaggtagcatggtccagctgttta
+ttgaatgcccatgggccacagaattgttctgaacatgtagcacccattaaaataaatttg
+gatttggatcagcaagaaaataactttccatgattctaaagtgggtgccatactcagcca
+ttcctttcataggcctcttggatagtgagcagatggctacctgaaaaatcaatattgcca
+gattataatgtgcagagtatatgtattttattaaagatgtatttcaagtggccattagac
+tataaagtgtagttgtttaaaaatagattttttttattttggagttacattcaacctcag
+gtgccactttccacattttacaataaaaataatggttgatttacttaacaaatgagaata
+aataaaacatttttttctttgaaaatttcagccagatcacatttgattgacagtccacca
+acttacaatgctgactatggctacaaaagctgggaagccttctctaacctctcctattat
+actagagcccttcctcctgtgcctgatgattgcccgactcccttgggtgtcaaaggtgag
+taagaagaatccattagagatgtattaactataagacgggctgcattgctgccaaaaaaa
+aaaattgaccttagactaccatttatttattaacaaaagcagtttttacttttagcatgg
+ttatctatgggtattttttaaagtatgagtctatataaactattatgtaaaagcaaatga
+gcgtcttggtataatgtcttaatattttcaaattatttctttagaaatgaaataattcta
+attaaaatagataaaatcattcagtaagaagttgttccaccatatcttagaactgttgtt
+tatattatgatcctattcacaattgtaattctcatataaatgaagaattcttggtagatt
+gacagtcaccatctcctttcttgaatacatagatggattcttaccttagctttctcattt
+ttcaggtaaaaagcagcttcctgattcaaatgagattgtggaaaaattgcttctaagaag
+aaagttcatccctgatccccagggctcaaacatgatgtttgcattctttgcccagcactt
+cacgcatcagtttttcaagacagatcataagcgagggccagctttcaccaacgggctggg
+ccatggggtaagatagagttaatatcttagagttagtaaaattataccaaatcatagtca
+agggctaacattaaaggagatatacagatagatagatccaaataacttatccactttttt
+taaaaagaagtcttatctataaaaaccttaaaggaattttccatttacttcactggtcta
+gtaaaattatacacacacacagacatgcacacacatatataaacattcacacacatacat
+atgtacaggtattgttatttgtaatttgacccttgtattttttagtttaaaatgttagta
+ctgcaaaatgttatgtcctcaaaaacacattgtaccatgattatgccgctttcaatattg
+taaagtgaggtttttgccgcattattattttttggatttcaatagcatagcttcaagtta
+ttcgtaagaattttttataaataatacatttttatacttttttataattaccatatcatc
+atagtgaagtatataatatatatgatataagctcaatatagtatattaattccgttaaac
+acaaagacatatcagtttgtagctttggtggataaacaaattaatttagcaattcatggc
+tatgaaaaatgtatattttatttaaaaattttaaagaaagctaaatgatcaaattattta
+atgatgaattatatgatagacactttatataagaaaaacttcaacagcaacaaattaaaa
+ttttttcatcattttctaggtggacttaaatcatatttacggtgaaactctggctagaca
+gcgtaaactgcgccttttcaaggatggaaaaatgaaatatcaggtatgcttcctttgact
+attaagacttagttattaccgcttatacccatattttaaaatccctaaaaatgtgttcct
+taactttttaactgatgtttatttatttatttatttttttagataattgatggagagatg
+tatcctcccacagtcaaagatactcaggcagagatgatctaccctcctcaagtccctgag
+catctacggtttgctgtggggcaggaggtctttggtctggtgcctggtctgatgatgtat
+gccacaatctggctgcgggaacacaacagagtatgcgatgtgcttaaacaggagcatcct
+gaatggggtgatgagcagttgttccagacaagcaggctaatactgataggtaaacaagaa
+aatgatttatataaaaccctcttccccagggaaaattagtgtgctatctttgttatgttt
+tgagtaaatgacaagatgtggtaaatgaaaactcacacattctatatacattaaatatgt
+aagcatgactgataaaatagctatcttttgatactgacaaggaagaaaacagaaatgaag
+gaatagcaaattttaaaaattgcattccagttgcttgaaagcttgtgatcagatgcaata
+aatgtttttattatttattttgtgcaaataggagagactattaagattgtgattgaagat
+tatgtgcaacacttgagtggctatcacttcaaactgaaatttgacccagaactacttttc
+aacaaacaattccagtaccaaaatcgtattgctgctgaatttaacaccctctatcactgg
+catccccttctgcctgacacctttcaaattcatgaccagaaatacaactatcaacagttt
+atctacaacaactctatattgctggaacatggaattacccagtttgttgaatcattcacc
+aggcaaattgctggcagggtaagcattattattgaaaaccaaaacaaaagactagtcagt
+aactttagaatttctgccacggaaattatttttcttaaacttactaaaagagtagttagt
+tatattgctagtaaaattattttattgatataagaagcctaactttgtttgaaaagtcta
+aacttttagtctagtctacagttgtcagacaaatagcaaattgtacccctaccttaaaaa
+tattttcaaaaagtatctataatcttataggaataaatattttaggcttgaatactagtg
+ttatttttgaaatgtaaaaaggcaaattagttctaggctggtgtcccattgaattttaag
+cagagctcctgttgaaatgtaggtaagcatctttccagcaaataaaaattgtctccgctg
+ggagtttcagttttacctgatttgtacctaaggcaagctgaatacaaacagtaaatatgc
+ctaaaattcttgttttacaactaattttactttccacaggttgctggtggtaggaatgtt
+ccacccgcagtacagaaagtatcacaggcttccattgaccagagcaggcagatgaaatac
+cagtcttttaatgagtaccgcaaacgctttatgctgaagccctatgaatcatttgaagaa
+cttacaggtaagaaacagtttctaaacttcttcgttttttgtttgtttgtttgtttttgt
+tgtttttggttttcttttcgagatggagccgccctctgtcacccaggctggagtgcagtg
+gcgccatctcggctcactgcaacctccgcctcctgggttcaagcaattctcctgcctcaa
+cttcctgagtagctgggactacaggctcacgtcgcacgcatggataattttttgtatttt
+cagtatagacggggtttcaccgtgttagccaggctggtctcaaactcctgacctagtgat
+ccgccggcttcggcctcccgaagtgctgggattacaggcgtgagccaccgcgcctggccc
+ctaaacttcttaaaagaatcaggggtcaaatggaaacagagaagttggcagcaaattgag
+caaaagaatcaaactgttttttattttgtgaagtttgacattggttgtatctctgtcttc
+atcgccttcacaggagaaaaggaaatgtctgcagagttggaagcactctatggtgacatc
+gatgctgtggagctgtatcctgcccttctggtagaaaagcctcggccagatgccatcttt
+ggtgaaaccatggtagaagttggagcaccattctccttgaaaggacttatgggtaatgtt
+atatgttctcctgcctactggaagccaagcacttttggtggagaagtgggttttcaaatc
+atcaacactgcctcaattcagtctctcatctgcaataacgtgaagggctgtccctttact
+tcattcagtgttccagatccagagctcattaaaacagtcaccatcaatgcaagttcttcc
+cgctccggactagatgatatcaatcccacagtactactaaaagaacgttcgactgaactg
+tagaagtctaatgatcatatttatttatttatatgaaccatgtctattaatttaattatt
+taataatatttatattaaactccttatgttacttaacatcttctgtaacagaagtcagta
+ctcctgttgcggagaaaggagtcatacttgtgaagacttttatgtcactactctaaagat
+tttgctgttgctgttaagtttggaaaacagtttttattctgttttataaaccagagagaa
+atgagttttgacgtctttttacttgaatttcaacttatattataagaacgaaagtaaaga
+tgtttgaatacttaaacactatcacaagatggcaaaatgctgaaagtttttacactgtcg
+atgtttccaatgcatcttccatgatgcattagaagtaactaatgtttgaaattttaaagt
+acttttggttatttttctgtcatcaaacaaaaacaggtatcagtgcattattaaatgaat
+atttaaattagacattaccagtaatttcatgtctactttttaaaatcagcaatgaaacaa
+taatttgaaatttctaaattcatagggtagaatcacctgtaaaagcttgtttgatttctt
+aaagttattaaacttgtacatataccaaaaagaagctgtcttggatttaaatctgtaaaa
+tcagatgaaattttactacaattgcttgttaaaatattttataagtgatgttcctttttc
+accaagagtataaacctttttagtgtgactgttaaaacttccttttaaatcaaaatgcca
+aatttattaaggtggtggagccactgcagtgttatctcaaaataagaatattttgttgag
+atattccagaatttgtttatatggctggtaacatgtaaaatctatatcagcaaaagggtc
+tacctttaaaataagcaataacaaagaagaaaaccaaattattgttcaaatttaggttta
+aacttttgaagcaaacttttttttatccttgtgcactgcaggcctggtactcagattttg
+ctatgaggttaatgaagtaccaagctgtgcttgaataacgatatgttttctcagattttc
+tgttgtacagtttaatttagcagtccatatcacattgcaaaagtagcaatgacctcataa
+aatacctcttcaaaatgcttaaattcatttcacacattaattttatctcagtcttgaagc
+caattcagtaggtgcattggaatcaagcctggctacctgcatgctgttccttttcttttc
+ttcttttagccattttgctaagagacacagtcttctcatcacttcgtttctcctattttg
+ttttactagttttaagatcagagttcactttctttggactctgcctatattttcttacct
+gaacttttgcaagttttcaggtaaacctcagctcaggactgctatttagctcctcttaag
+aagattaaaagagaaaaaaaaaggcccttttaaaaatagtatacacttattttaagtgaa
+aagcagagaattttatttatagctaattttagctatctgtaaccaagatggatgcaaaga
+ggctagtgcctcagagagaactgtacggggtttgtgactggaaaaagttacgttcccatt
+ctaattaatgccctttcttatttaaaaacaaaaccaaatgatatctaagtagttctcagc
+aataataataatgacgataatacttcttttccacatctcattgtcactgacatttaatgg
+tactgtatattacttaatttattgaagattattatttatgtcttattaggacactatggt
+tataaactgtgtttaagcctacaatcattgatttttttttgttatgtcacaatcagtata
+ttttctttggggttacctctctgaatattatgtaaacaatccaaagaaatgattgtatta
+agatttgtgaataaatttttagaaatctgattggcatattgagatatttaaggttgaatg
+tttgtccttaggataggcctatgtgctagcccacaaagaatattgtctcattagcctgaa
+tgtgccataagactgaccttttaaaatgttttgagggatctgtggatgcttcgttaattt
+gttcagccacaatttattgagaaaatattctgtgtcaagcactgtgggttttaatatttt
+taaatcaaacgctgattacagataatagtatttatataaataattgaaaaaaattttctt
+ttgggaagagggagaaaatgaaataaatatcattaaagataactcaggagaatcttcttt
+acaattttacgtttagaatgtttaaggttaagaaagaaatagtcaatatgcttgtataaa
+acactgttcactgttttttttaaaaaaaaaacttgatttgttattaacattgatctgctg
+acaaaacctgggaatttgggttgtgtatgcgaatgtttcagtgcctcagacaaatgtgta
+tttaacttatgtaaaagataagtctggaaataaatgtctgtttatttttgtactatttaa
+aaaaaaaaaaaaaaatcgatgtcgactcgagtc
+>HS08198
+agcgggcggcggtcgtgggcggggttgcaggcgaggctcaacgaacgctggtctgaccgt
+cggcgctccctgttgccgggccctgagcaagtggcttcatgaaccccgtgacgttggcca
+tggagataagaccactgggtgatggtttaaggaagataacgtgtaaagggctaaggactg
+tcggtggaaatcaggggtgcaggagaaatggataaacagccagaggtcaactcggacttt
+gtacataggacatggtgccaggccctgccaggaagtgcagatcgaagctaggctcacgag
+gaggctggaggtggggggtggggaggcaacggatggacatggacttcctgggctgggctc
+tgtgacagcagagtagactctgtcctgggacttggtggtgctacccttggcctcccacag
+tcctgccaccctgctgccgccaccatgctgccccctgggactgcgaccctcttgactctg
+ctcctggcagctggctcgctgggccagaagcctcagaggccacgccggcccgcatccccc
+atcagcaccatccagcccaaggccaattttgatgcgcagcaggtagaagttggggggggt
+agagggaggcaggtagaagttgtgggaggggtagagggagacaggtagaagttgttgcgg
+gggagagggaagcaggtgaagttgtggggggtgtagagggaagcaggtgaggggccctcc
+cacagtgccctcgagttctcccatggtctgcccccagtttgcagggacctggctccttgt
+ggctgtgggctccgcttgccgtttcctgcaggagcagggccaccgggccgaggccaccac
+actgcatgtggctccccagggcacagccatggctgtcagtaccttccgaaagctgtgagt
+cccagagcagccctgcaccctaaccccaaccctcctctcagcccccggacttcagccctg
+ctctggcccctgaccccaccccggctgtggcctggactaggattcctggttggggtctcc
+cagcctgtggtgcctcctccccgcccccccagggatgggatctgctggcaggtgcgccag
+ctctatggagacacaggggtcctcggccgcttcctgcttcaaggtgaggcaggggctgca
+ggtcatgtgggtgggggatgacgcagccactgtggctctctgacatggctactgtggctc
+tgcccagcccgaggcgcccgaggggctgtgcacgtggttgtcgctgagaccgactaccag
+agtttcgctgtcctgtacctggagcgggcggggcagctgtcagtgaagctctacggtatg
+tgggggccagcctctgtgaccaggcaggcgctcaagctctgcacactcactgggccaccc
+cgaggggctgggtgagccatggggacacacttcctttctcccatcctgatcctcctgcta
+agcaggggcccagggagtagtgacagacaggcctggtgtgggagcagggaggagggcccc
+gaggggcaggggacacacagaccccgttcccagagccctccacgccgcctggtgccagga
+ccccaggaaccctgtctgccctgcagcccgctcgctccctgtgagcgactcggtcctgag
+tgggtttgagcagcgggtccaggaggcccacctgactgaggaccagatcttctacttccc
+caagtacggtgagtgtccccagcaggtccccagctcagccacccccactctctggctgat
+gtccagcctgacccctgccttggcgccccaggcttctgcgaggctgcagaccagttccac
+gtcctggacggtgagtgcacagcgggggcaagcatggcggcgtggtgaggggggccactc
+gcaccggctgagtctcgtctctgctgcagaagtgaggaggtgaggccggcacacagctcc
+agtgctgagaagtcagtgccccgagagacgaccccaccagtggggtgcccgctgcctgtc
+ctccgtgaaaccagcctcagatcagggccctgccacccagggcaggggatcttctgccgg
+ctgccccagaggacagtgggtggagtggtacctacttattaaatgtctcagacccctctc
+tgactcttctgtccactctggaccggcgccagtaccaccaaggccctctctgcccccacc
+ccgcctctttaaaagcccggcgctccctgttggctggagtccacgcagggtcactgggcc
+gatttcggctcttgggatttgggaggggagatcctctctggcatatgccatcttgtgccc
+tgctggacctgggggcgtccacgtcactccaaggctgctcttgcctgggccatgcctgca
+gccc
diff -r 000000000000 -r fcdd4f5c6cfc test-data/human_augustus_protein_codingseq_introns_cds_codingseq.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/human_augustus_protein_codingseq_introns_cds_codingseq.fasta Fri Oct 20 03:48:35 2017 -0400
@@ -0,0 +1,33 @@
+>HS04636.g1
+atgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacagcaaatccttgctgttcccacccatgtca
+aaaccgaggtgtatgtatgagtgtgggatttgaccagtataagtgcgattgtacccggacaggattctatggagaaaact
+gctcaacaccggaatttttgacaagaataaaattatttctgaaacccactccaaacacagtgcactacatacttacccac
+ttcaagggattttggaacgttgtgaataacattcccttccttcgaaatgcaattatgagttatgtcttgacatccagatc
+acatttgattgacagtccaccaacttacaatgctgactatggctacaaaagctgggaagccttctctaacctctcctatt
+atactagagcccttcctcctgtgcctgatgattgcccgactcccttgggtgtcaaaggtaaaaagcagcttcctgattca
+aatgagattgtggaaaaattgcttctaagaagaaagttcatccctgatccccagggctcaaacatgatgtttgcattctt
+tgcccagcacttcacgcatcagtttttcaagacagatcataagcgagggccagctttcaccaacgggctgggccatgggg
+tggacttaaatcatatttacggtgaaactctggctagacagcgtaaactgcgccttttcaaggatggaaaaatgaaatat
+cagataattgatggagagatgtatcctcccacagtcaaagatactcaggcagagatgatctaccctcctcaagtccctga
+gcatctacggtttgctgtggggcaggaggtctttggtctggtgcctggtctgatgatgtatgccacaatctggctgcggg
+aacacaacagagtatgcgatgtgcttaaacaggagcatcctgaatggggtgatgagcagttgttccagacaagcaggcta
+atactgataggagagactattaagattgtgattgaagattatgtgcaacacttgagtggctatcacttcaaactgaaatt
+tgacccagaactacttttcaacaaacaattccagtaccaaaatcgtattgctgctgaatttaacaccctctatcactggc
+atccccttctgcctgacacctttcaaattcatgaccagaaatacaactatcaacagtttatctacaacaactctatattg
+ctggaacatggaattacccagtttgttgaatcattcaccaggcaaattgctggcagggttgctggtggtaggaatgttcc
+acccgcagtacagaaagtatcacaggcttccattgaccagagcaggcagatgaaataccagtcttttaatgagtaccgca
+aacgctttatgctgaagccctatgaatcatttgaagaacttacaggagaaaaggaaatgtctgcagagttggaagcactc
+tatggtgacatcgatgctgtggagctgtatcctgcccttctggtagaaaagcctcggccagatgccatctttggtgaaac
+catggtagaagttggagcaccattctccttgaaaggacttatgggtaatgttatatgttctcctgcctactggaagccaa
+gcacttttggtggagaagtgggttttcaaatcatcaacactgcctcaattcagtctctcatctgcaataacgtgaagggc
+tgtccctttacttcattcagtgttccagatccagagctcattaaaacagtcaccatcaatgcaagttcttcccgctccgg
+actagatgatatcaatcccacagtactactaaaagaacgttcgactgaactgtag
+>HS08198.g2
+atgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccacg
+ccggcccgcatcccccatcagcaccatccagcccaaggccaattttgatgcgcagcaggagcagggccaccgggccgagg
+ccaccacactgcatgtggctccccagggcacagccatggctgtcagtaccttccgaaagctggatgggatctgctggcag
+gtgcgccagctctatggagacacaggggtcctcggccgcttcctgcttcaagcccgaggcgcccgaggggctgtgcacgt
+ggttgtcgctgagaccgactaccagagtttcgctgtcctgtacctggagcgggcggggcagctgtcagtgaagctctacg
+cccgctcgctccctgtgagcgactcggtcctgagtgggtttgagcagcgggtccaggaggcccacctgactgaggaccag
+atcttctacttccccaagtacggcttctgcgaggctgcagaccagttccacgtcctggacggtgagtgcacagcgggggc
+aagcatggcggcgtggtga
diff -r 000000000000 -r fcdd4f5c6cfc test-data/human_augustus_protein_codingseq_introns_cds_main.gtf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/human_augustus_protein_codingseq_introns_cds_main.gtf Fri Oct 20 03:48:35 2017 -0400
@@ -0,0 +1,105 @@
+# This output was generated with AUGUSTUS (version 3.2.3).
+# AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de),
+# O. Keller, S. König, L. Gerischer and L. Romoth.
+# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
+# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
+# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
+# No extrinsic information on sequences given.
+# Initialising the parameters using config directory /home/bag/projects/code/galaxy/tool_deps/augustus/3.1/iuc/package_augustus_3_1/820bf3789c44/config/ ...
+# human version. Using default transition matrix.
+# Looks like /tmp/tmpboMLLQ/job_working_directory/000/6/task_0/dataset_9.dat is in fasta format.
+# We have hints for 0 sequences and for 0 of the sequences in the input set.
+#
+# ----- prediction on sequence number 1 (length = 9453, name = HS04636) -----
+#
+# Constraints/Hints:
+# (none)
+# Predicted genes for sequence number 1 on both strands
+# start gene HS04636.g1
+HS04636 AUGUSTUS gene 966 6903 1 + . HS04636.g1
+HS04636 AUGUSTUS transcript 966 6903 . + . HS04636.g1.t1
+HS04636 AUGUSTUS start_codon 966 968 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS intron 1018 1817 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS intron 1935 2054 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS intron 2199 2851 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS intron 2996 3425 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS intron 3608 4339 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS intron 4424 4542 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS intron 4790 5071 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS intron 5359 5859 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS intron 6008 6493 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS CDS 966 1017 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS CDS 1818 1934 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS CDS 2055 2198 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS CDS 2852 2995 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS CDS 3426 3607 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS CDS 4340 4423 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS CDS 4543 4789 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS CDS 5072 5358 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS CDS 5860 6007 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS CDS 6494 6903 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS stop_codon 6901 6903 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+# coding sequence = [atgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacagcaaatccttgctgttcccacccatgtc
+# aaaaccgaggtgtatgtatgagtgtgggatttgaccagtataagtgcgattgtacccggacaggattctatggagaaaactgctcaacaccggaattt
+# ttgacaagaataaaattatttctgaaacccactccaaacacagtgcactacatacttacccacttcaagggattttggaacgttgtgaataacattcc
+# cttccttcgaaatgcaattatgagttatgtcttgacatccagatcacatttgattgacagtccaccaacttacaatgctgactatggctacaaaagct
+# gggaagccttctctaacctctcctattatactagagcccttcctcctgtgcctgatgattgcccgactcccttgggtgtcaaaggtaaaaagcagctt
+# cctgattcaaatgagattgtggaaaaattgcttctaagaagaaagttcatccctgatccccagggctcaaacatgatgtttgcattctttgcccagca
+# cttcacgcatcagtttttcaagacagatcataagcgagggccagctttcaccaacgggctgggccatggggtggacttaaatcatatttacggtgaaa
+# ctctggctagacagcgtaaactgcgccttttcaaggatggaaaaatgaaatatcagataattgatggagagatgtatcctcccacagtcaaagatact
+# caggcagagatgatctaccctcctcaagtccctgagcatctacggtttgctgtggggcaggaggtctttggtctggtgcctggtctgatgatgtatgc
+# cacaatctggctgcgggaacacaacagagtatgcgatgtgcttaaacaggagcatcctgaatggggtgatgagcagttgttccagacaagcaggctaa
+# tactgataggagagactattaagattgtgattgaagattatgtgcaacacttgagtggctatcacttcaaactgaaatttgacccagaactacttttc
+# aacaaacaattccagtaccaaaatcgtattgctgctgaatttaacaccctctatcactggcatccccttctgcctgacacctttcaaattcatgacca
+# gaaatacaactatcaacagtttatctacaacaactctatattgctggaacatggaattacccagtttgttgaatcattcaccaggcaaattgctggca
+# gggttgctggtggtaggaatgttccacccgcagtacagaaagtatcacaggcttccattgaccagagcaggcagatgaaataccagtcttttaatgag
+# taccgcaaacgctttatgctgaagccctatgaatcatttgaagaacttacaggagaaaaggaaatgtctgcagagttggaagcactctatggtgacat
+# cgatgctgtggagctgtatcctgcccttctggtagaaaagcctcggccagatgccatctttggtgaaaccatggtagaagttggagcaccattctcct
+# tgaaaggacttatgggtaatgttatatgttctcctgcctactggaagccaagcacttttggtggagaagtgggttttcaaatcatcaacactgcctca
+# attcagtctctcatctgcaataacgtgaagggctgtccctttacttcattcagtgttccagatccagagctcattaaaacagtcaccatcaatgcaag
+# ttcttcccgctccggactagatgatatcaatcccacagtactactaaaagaacgttcgactgaactgtag]
+# protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL
+# THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD
+# PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG
+# QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH
+# WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE
+# KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV
+# PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL]
+# end gene HS04636.g1
+###
+#
+# ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----
+#
+# Constraints/Hints:
+# (none)
+# Predicted genes for sequence number 2 on both strands
+# start gene HS08198.g2
+HS08198 AUGUSTUS gene 445 1848 1 + . HS08198.g2
+HS08198 AUGUSTUS transcript 445 1848 . + . HS08198.g2.t1
+HS08198 AUGUSTUS start_codon 445 447 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198 AUGUSTUS intron 583 811 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198 AUGUSTUS intron 895 1052 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198 AUGUSTUS intron 1124 1207 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198 AUGUSTUS intron 1316 1586 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198 AUGUSTUS intron 1689 1771 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198 AUGUSTUS CDS 445 582 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198 AUGUSTUS CDS 812 894 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198 AUGUSTUS CDS 1053 1123 . + 1 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198 AUGUSTUS CDS 1208 1315 . + 2 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198 AUGUSTUS CDS 1587 1688 . + 2 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198 AUGUSTUS CDS 1772 1848 . + 2 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198 AUGUSTUS stop_codon 1846 1848 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+# coding sequence = [atgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccac
+# gccggcccgcatcccccatcagcaccatccagcccaaggccaattttgatgcgcagcaggagcagggccaccgggccgaggccaccacactgcatgtg
+# gctccccagggcacagccatggctgtcagtaccttccgaaagctggatgggatctgctggcaggtgcgccagctctatggagacacaggggtcctcgg
+# ccgcttcctgcttcaagcccgaggcgcccgaggggctgtgcacgtggttgtcgctgagaccgactaccagagtttcgctgtcctgtacctggagcggg
+# cggggcagctgtcagtgaagctctacgcccgctcgctccctgtgagcgactcggtcctgagtgggtttgagcagcgggtccaggaggcccacctgact
+# gaggaccagatcttctacttccccaagtacggcttctgcgaggctgcagaccagttccacgtcctggacggtgagtgcacagcgggggcaagcatggc
+# ggcgtggtga]
+# protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC
+# WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF
+# HVLDGECTAGASMAAW]
+# end gene HS08198.g2
+###
+# command line:
+# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=on --codingseq=on --introns=on --start=on --stop=on --cds=on --singlestrand=false /tmp/tmpboMLLQ/job_working_directory/000/6/task_0/dataset_9.dat --UTR=off --genemodel=complete --species=human
diff -r 000000000000 -r fcdd4f5c6cfc test-data/human_augustus_protein_codingseq_introns_cds_protein.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/human_augustus_protein_codingseq_introns_cds_protein.fasta Fri Oct 20 03:48:35 2017 -0400
@@ -0,0 +1,13 @@
+>HS04636.g1
+MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYILTH
+FKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDS
+NEIVEKLLLRRKFIPDPQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKY
+QIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVGQEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRL
+ILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYHWHPLLPDTFQIHDQKYNYQQFIYNNSIL
+LEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGEKEMSAELEAL
+YGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKG
+CPFTSFSVPDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL
+>HS08198.g2
+MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGICWQ
+VRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQ
+IFYFPKYGFCEAADQFHVLDGECTAGASMAAW
diff -r 000000000000 -r fcdd4f5c6cfc test-data/human_augustus_utr-on.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/human_augustus_utr-on.gff Fri Oct 20 03:48:35 2017 -0400
@@ -0,0 +1,106 @@
+##gff-version 3
+# This output was generated with AUGUSTUS (version 3.2.3).
+# AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de),
+# O. Keller, S. König, L. Gerischer and L. Romoth.
+# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
+# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
+# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
+# No extrinsic information on sequences given.
+# Initialising the parameters using config directory /home/bag/projects/code/galaxy/tool_deps/augustus/3.1/iuc/package_augustus_3_1/820bf3789c44/config/ ...
+# human version. Using default transition matrix.
+# Looks like /tmp/tmpboMLLQ/job_working_directory/000/4/task_0/dataset_5.dat is in fasta format.
+# We have hints for 0 sequences and for 0 of the sequences in the input set.
+#
+# ----- prediction on sequence number 1 (length = 9453, name = HS04636) -----
+#
+# Predicted genes for sequence number 1 on both strands
+# start gene HS04636.g1
+HS04636 AUGUSTUS gene 836 8857 1 + . ID=HS04636.g1
+HS04636 AUGUSTUS transcript 836 8857 . + . ID=HS04636.g1.t1;Parent=HS04636.g1
+HS04636 AUGUSTUS transcription_start_site 836 836 . + . Parent=HS04636.g1.t1
+HS04636 AUGUSTUS exon 836 1017 . + . Parent=HS04636.g1.t1
+HS04636 AUGUSTUS start_codon 966 968 . + 0 Parent=HS04636.g1.t1
+HS04636 AUGUSTUS CDS 966 1017 . + 0 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
+HS04636 AUGUSTUS CDS 1818 1934 . + 2 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
+HS04636 AUGUSTUS exon 1818 1934 . + . Parent=HS04636.g1.t1
+HS04636 AUGUSTUS CDS 2055 2198 . + 2 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
+HS04636 AUGUSTUS exon 2055 2198 . + . Parent=HS04636.g1.t1
+HS04636 AUGUSTUS CDS 2852 2995 . + 2 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
+HS04636 AUGUSTUS exon 2852 2995 . + . Parent=HS04636.g1.t1
+HS04636 AUGUSTUS CDS 3426 3607 . + 2 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
+HS04636 AUGUSTUS exon 3426 3607 . + . Parent=HS04636.g1.t1
+HS04636 AUGUSTUS CDS 4340 4423 . + 0 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
+HS04636 AUGUSTUS exon 4340 4423 . + . Parent=HS04636.g1.t1
+HS04636 AUGUSTUS CDS 4543 4789 . + 0 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
+HS04636 AUGUSTUS exon 4543 4789 . + . Parent=HS04636.g1.t1
+HS04636 AUGUSTUS CDS 5072 5358 . + 2 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
+HS04636 AUGUSTUS exon 5072 5358 . + . Parent=HS04636.g1.t1
+HS04636 AUGUSTUS CDS 5860 6007 . + 0 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
+HS04636 AUGUSTUS exon 5860 6007 . + . Parent=HS04636.g1.t1
+HS04636 AUGUSTUS CDS 6494 6903 . + 2 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
+HS04636 AUGUSTUS exon 6494 8857 . + . Parent=HS04636.g1.t1
+HS04636 AUGUSTUS transcription_end_site 8857 8857 . + . Parent=HS04636.g1.t1
+# coding sequence = [atgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacagcaaatccttgctgttcccacccatgtc
+# aaaaccgaggtgtatgtatgagtgtgggatttgaccagtataagtgcgattgtacccggacaggattctatggagaaaactgctcaacaccggaattt
+# ttgacaagaataaaattatttctgaaacccactccaaacacagtgcactacatacttacccacttcaagggattttggaacgttgtgaataacattcc
+# cttccttcgaaatgcaattatgagttatgtcttgacatccagatcacatttgattgacagtccaccaacttacaatgctgactatggctacaaaagct
+# gggaagccttctctaacctctcctattatactagagcccttcctcctgtgcctgatgattgcccgactcccttgggtgtcaaaggtaaaaagcagctt
+# cctgattcaaatgagattgtggaaaaattgcttctaagaagaaagttcatccctgatccccagggctcaaacatgatgtttgcattctttgcccagca
+# cttcacgcatcagtttttcaagacagatcataagcgagggccagctttcaccaacgggctgggccatggggtggacttaaatcatatttacggtgaaa
+# ctctggctagacagcgtaaactgcgccttttcaaggatggaaaaatgaaatatcagataattgatggagagatgtatcctcccacagtcaaagatact
+# caggcagagatgatctaccctcctcaagtccctgagcatctacggtttgctgtggggcaggaggtctttggtctggtgcctggtctgatgatgtatgc
+# cacaatctggctgcgggaacacaacagagtatgcgatgtgcttaaacaggagcatcctgaatggggtgatgagcagttgttccagacaagcaggctaa
+# tactgataggagagactattaagattgtgattgaagattatgtgcaacacttgagtggctatcacttcaaactgaaatttgacccagaactacttttc
+# aacaaacaattccagtaccaaaatcgtattgctgctgaatttaacaccctctatcactggcatccccttctgcctgacacctttcaaattcatgacca
+# gaaatacaactatcaacagtttatctacaacaactctatattgctggaacatggaattacccagtttgttgaatcattcaccaggcaaattgctggca
+# gggttgctggtggtaggaatgttccacccgcagtacagaaagtatcacaggcttccattgaccagagcaggcagatgaaataccagtcttttaatgag
+# taccgcaaacgctttatgctgaagccctatgaatcatttgaagaacttacaggagaaaaggaaatgtctgcagagttggaagcactctatggtgacat
+# cgatgctgtggagctgtatcctgcccttctggtagaaaagcctcggccagatgccatctttggtgaaaccatggtagaagttggagcaccattctcct
+# tgaaaggacttatgggtaatgttatatgttctcctgcctactggaagccaagcacttttggtggagaagtgggttttcaaatcatcaacactgcctca
+# attcagtctctcatctgcaataacgtgaagggctgtccctttacttcattcagtgttccagatccagagctcattaaaacagtcaccatcaatgcaag
+# ttcttcccgctccggactagatgatatcaatcccacagtactactaaaagaacgttcgactgaactgtag]
+# protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL
+# THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD
+# PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG
+# QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH
+# WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE
+# KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV
+# PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL]
+# end gene HS04636.g1
+###
+#
+# ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----
+#
+# Predicted genes for sequence number 2 on both strands
+# start gene HS08198.g2
+HS08198 AUGUSTUS gene 86 2105 1 + . ID=HS08198.g2
+HS08198 AUGUSTUS transcript 86 2105 . + . ID=HS08198.g2.t1;Parent=HS08198.g2
+HS08198 AUGUSTUS transcription_start_site 86 86 . + . Parent=HS08198.g2.t1
+HS08198 AUGUSTUS exon 86 582 . + . Parent=HS08198.g2.t1
+HS08198 AUGUSTUS start_codon 445 447 . + 0 Parent=HS08198.g2.t1
+HS08198 AUGUSTUS CDS 445 582 . + 0 ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1
+HS08198 AUGUSTUS CDS 812 894 . + 0 ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1
+HS08198 AUGUSTUS exon 812 894 . + . Parent=HS08198.g2.t1
+HS08198 AUGUSTUS CDS 1053 1123 . + 1 ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1
+HS08198 AUGUSTUS exon 1053 1123 . + . Parent=HS08198.g2.t1
+HS08198 AUGUSTUS CDS 1208 1315 . + 2 ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1
+HS08198 AUGUSTUS exon 1208 1315 . + . Parent=HS08198.g2.t1
+HS08198 AUGUSTUS CDS 1587 1688 . + 2 ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1
+HS08198 AUGUSTUS exon 1587 1688 . + . Parent=HS08198.g2.t1
+HS08198 AUGUSTUS CDS 1772 1848 . + 2 ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1
+HS08198 AUGUSTUS exon 1772 2105 . + . Parent=HS08198.g2.t1
+HS08198 AUGUSTUS transcription_end_site 2105 2105 . + . Parent=HS08198.g2.t1
+# coding sequence = [atgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccac
+# gccggcccgcatcccccatcagcaccatccagcccaaggccaattttgatgcgcagcaggagcagggccaccgggccgaggccaccacactgcatgtg
+# gctccccagggcacagccatggctgtcagtaccttccgaaagctggatgggatctgctggcaggtgcgccagctctatggagacacaggggtcctcgg
+# ccgcttcctgcttcaagcccgaggcgcccgaggggctgtgcacgtggttgtcgctgagaccgactaccagagtttcgctgtcctgtacctggagcggg
+# cggggcagctgtcagtgaagctctacgcccgctcgctccctgtgagcgactcggtcctgagtgggtttgagcagcgggtccaggaggcccacctgact
+# gaggaccagatcttctacttccccaagtacggcttctgcgaggctgcagaccagttccacgtcctggacggtgagtgcacagcgggggcaagcatggc
+# ggcgtggtga]
+# protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC
+# WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF
+# HVLDGECTAGASMAAW]
+# end gene HS08198.g2
+###
+# command line:
+# augustus --strand=both --noInFrameStop=false --gff3=on --uniqueGeneId=true --protein=on --codingseq=on --introns=off --stop=off --stop=off --cds=on --singlestrand=false /tmp/tmpboMLLQ/job_working_directory/000/4/task_0/dataset_5.dat --UTR=on --genemodel=complete --species=human
diff -r 000000000000 -r fcdd4f5c6cfc test-data/human_augustus_utr-on.gtf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/human_augustus_utr-on.gtf Fri Oct 20 03:48:35 2017 -0400
@@ -0,0 +1,109 @@
+# This output was generated with AUGUSTUS (version 3.2.3).
+# AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de),
+# O. Keller, S. König, L. Gerischer and L. Romoth.
+# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
+# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
+# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
+# No extrinsic information on sequences given.
+# Initialising the parameters using config directory /home/bag/projects/code/galaxy/tool_deps/augustus/3.1/iuc/package_augustus_3_1/820bf3789c44/config/ ...
+# human version. Using default transition matrix.
+# Looks like /tmp/tmpboMLLQ/job_working_directory/000/2/task_0/dataset_1.dat is in fasta format.
+# We have hints for 0 sequences and for 0 of the sequences in the input set.
+#
+# ----- prediction on sequence number 1 (length = 9453, name = HS04636) -----
+#
+# Constraints/Hints:
+# (none)
+# Predicted genes for sequence number 1 on both strands
+# start gene HS04636.g1
+HS04636 AUGUSTUS gene 836 8857 1 + . HS04636.g1
+HS04636 AUGUSTUS transcript 836 8857 . + . HS04636.g1.t1
+HS04636 AUGUSTUS tss 836 836 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS exon 836 1017 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS start_codon 966 968 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS CDS 966 1017 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS CDS 1818 1934 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS exon 1818 1934 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS CDS 2055 2198 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS exon 2055 2198 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS CDS 2852 2995 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS exon 2852 2995 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS CDS 3426 3607 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS exon 3426 3607 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS CDS 4340 4423 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS exon 4340 4423 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS CDS 4543 4789 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS exon 4543 4789 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS CDS 5072 5358 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS exon 5072 5358 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS CDS 5860 6007 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS exon 5860 6007 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS CDS 6494 6903 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS exon 6494 8857 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+HS04636 AUGUSTUS tts 8857 8857 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
+# coding sequence = [atgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacagcaaatccttgctgttcccacccatgtc
+# aaaaccgaggtgtatgtatgagtgtgggatttgaccagtataagtgcgattgtacccggacaggattctatggagaaaactgctcaacaccggaattt
+# ttgacaagaataaaattatttctgaaacccactccaaacacagtgcactacatacttacccacttcaagggattttggaacgttgtgaataacattcc
+# cttccttcgaaatgcaattatgagttatgtcttgacatccagatcacatttgattgacagtccaccaacttacaatgctgactatggctacaaaagct
+# gggaagccttctctaacctctcctattatactagagcccttcctcctgtgcctgatgattgcccgactcccttgggtgtcaaaggtaaaaagcagctt
+# cctgattcaaatgagattgtggaaaaattgcttctaagaagaaagttcatccctgatccccagggctcaaacatgatgtttgcattctttgcccagca
+# cttcacgcatcagtttttcaagacagatcataagcgagggccagctttcaccaacgggctgggccatggggtggacttaaatcatatttacggtgaaa
+# ctctggctagacagcgtaaactgcgccttttcaaggatggaaaaatgaaatatcagataattgatggagagatgtatcctcccacagtcaaagatact
+# caggcagagatgatctaccctcctcaagtccctgagcatctacggtttgctgtggggcaggaggtctttggtctggtgcctggtctgatgatgtatgc
+# cacaatctggctgcgggaacacaacagagtatgcgatgtgcttaaacaggagcatcctgaatggggtgatgagcagttgttccagacaagcaggctaa
+# tactgataggagagactattaagattgtgattgaagattatgtgcaacacttgagtggctatcacttcaaactgaaatttgacccagaactacttttc
+# aacaaacaattccagtaccaaaatcgtattgctgctgaatttaacaccctctatcactggcatccccttctgcctgacacctttcaaattcatgacca
+# gaaatacaactatcaacagtttatctacaacaactctatattgctggaacatggaattacccagtttgttgaatcattcaccaggcaaattgctggca
+# gggttgctggtggtaggaatgttccacccgcagtacagaaagtatcacaggcttccattgaccagagcaggcagatgaaataccagtcttttaatgag
+# taccgcaaacgctttatgctgaagccctatgaatcatttgaagaacttacaggagaaaaggaaatgtctgcagagttggaagcactctatggtgacat
+# cgatgctgtggagctgtatcctgcccttctggtagaaaagcctcggccagatgccatctttggtgaaaccatggtagaagttggagcaccattctcct
+# tgaaaggacttatgggtaatgttatatgttctcctgcctactggaagccaagcacttttggtggagaagtgggttttcaaatcatcaacactgcctca
+# attcagtctctcatctgcaataacgtgaagggctgtccctttacttcattcagtgttccagatccagagctcattaaaacagtcaccatcaatgcaag
+# ttcttcccgctccggactagatgatatcaatcccacagtactactaaaagaacgttcgactgaactgtag]
+# protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL
+# THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD
+# PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG
+# QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH
+# WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE
+# KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV
+# PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL]
+# end gene HS04636.g1
+###
+#
+# ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----
+#
+# Constraints/Hints:
+# (none)
+# Predicted genes for sequence number 2 on both strands
+# start gene HS08198.g2
+HS08198 AUGUSTUS gene 86 2105 1 + . HS08198.g2
+HS08198 AUGUSTUS transcript 86 2105 . + . HS08198.g2.t1
+HS08198 AUGUSTUS tss 86 86 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198 AUGUSTUS exon 86 582 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198 AUGUSTUS start_codon 445 447 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198 AUGUSTUS CDS 445 582 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198 AUGUSTUS CDS 812 894 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198 AUGUSTUS exon 812 894 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198 AUGUSTUS CDS 1053 1123 . + 1 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198 AUGUSTUS exon 1053 1123 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198 AUGUSTUS CDS 1208 1315 . + 2 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198 AUGUSTUS exon 1208 1315 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198 AUGUSTUS CDS 1587 1688 . + 2 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198 AUGUSTUS exon 1587 1688 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198 AUGUSTUS CDS 1772 1848 . + 2 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198 AUGUSTUS exon 1772 2105 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+HS08198 AUGUSTUS tts 2105 2105 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
+# coding sequence = [atgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccac
+# gccggcccgcatcccccatcagcaccatccagcccaaggccaattttgatgcgcagcaggagcagggccaccgggccgaggccaccacactgcatgtg
+# gctccccagggcacagccatggctgtcagtaccttccgaaagctggatgggatctgctggcaggtgcgccagctctatggagacacaggggtcctcgg
+# ccgcttcctgcttcaagcccgaggcgcccgaggggctgtgcacgtggttgtcgctgagaccgactaccagagtttcgctgtcctgtacctggagcggg
+# cggggcagctgtcagtgaagctctacgcccgctcgctccctgtgagcgactcggtcctgagtgggtttgagcagcgggtccaggaggcccacctgact
+# gaggaccagatcttctacttccccaagtacggcttctgcgaggctgcagaccagttccacgtcctggacggtgagtgcacagcgggggcaagcatggc
+# ggcgtggtga]
+# protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC
+# WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF
+# HVLDGECTAGASMAAW]
+# end gene HS08198.g2
+###
+# command line:
+# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=on --codingseq=on --introns=off --stop=off --stop=off --cds=on --singlestrand=false /tmp/tmpboMLLQ/job_working_directory/000/2/task_0/dataset_1.dat --UTR=on --genemodel=complete --species=human