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changeset 0:86c89c3bd99d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
author bgruening
date Fri, 20 Oct 2017 03:55:35 -0400
parents
children 1fbb1135da16
files augustus_training.xml extract_features.py macros.xml test-data/annot.gff3 test-data/arabidopsis_augustus.fa test-data/human_augustus.fa test-data/human_augustus_protein_codingseq_introns_cds_codingseq.fasta test-data/human_augustus_protein_codingseq_introns_cds_main.gtf test-data/human_augustus_protein_codingseq_introns_cds_protein.fasta test-data/human_augustus_utr-on.gff test-data/human_augustus_utr-on.gtf
diffstat 11 files changed, 817 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/augustus_training.xml	Fri Oct 20 03:55:35 2017 -0400
@@ -0,0 +1,43 @@
+<?xml version="1.0"?>
+<tool id="augustus_training" name="Train Augustus" profile="16.04" version="@VERSION@">
+    <description>ab-initio gene predictor</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+        <requirement type="package" version="2.31.9">maker</requirement>
+    </expand>
+    <command><![CDATA[
+        cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&
+
+        export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
+
+        maker2zff '${maker_gff}' &&
+
+        zff2gff3.pl genome.ann | perl -plne 's/\t(\S+)$/\t\.\t$1/' > genome.gff3 &&
+
+        autoAugTrain.pl --genome=${genome} --species=local --trainingset=genome.gff3 -v &&
+
+        cd 'augustus_dir/species/' && tar cvfz '${output_tar}' 'local'
+    ]]></command>
+    <inputs>
+        <param name="genome" type="data" format="fasta" label="Genome to annotate"/>
+        <param name="maker_gff" type="data" format="gff" label="Annotation to use for training"/>
+    </inputs>
+    <outputs>
+        <data name="output_tar" format="augustus" label="${tool.name} on ${on_string}: Augustus trained model"/>
+    </outputs>
+    <tests>
+        <test expect_failure="true">
+            <param name="genome" value="human_augustus.fa"/>
+            <param name="maker_gff" value="annot.gff3"/>
+            <assert_stderr>
+                <has_text text="Number of training genes is with 2 too low (at least 100 genes required)" />
+            </assert_stderr>
+        </test>
+    </tests>
+    <help><![CDATA[
+        This tool allows to train Augustus (the ab-initio gene predictor) based on a previous prediction (e.g. made with Maker).
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extract_features.py	Fri Oct 20 03:55:35 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 )
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Oct 20 03:55:35 2017 -0400
@@ -0,0 +1,20 @@
+<?xml version="1.0"?>
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@VERSION@">augustus</requirement>
+            <yield />
+        </requirements>
+    </xml>
+
+    <token name="@VERSION@">3.2.3</token>
+
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1093/bioinformatics/btg1080</citation>
+            <citation type="doi">10.1093/bioinformatics/btr010</citation>
+            <citation type="doi">10.1093/bioinformatics/btn013</citation>
+        </citations>
+    </xml>
+
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annot.gff3	Fri Oct 20 03:55:35 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
+###
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/arabidopsis_augustus.fa	Fri Oct 20 03:55:35 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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/human_augustus.fa	Fri Oct 20 03:55:35 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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/human_augustus_protein_codingseq_introns_cds_codingseq.fasta	Fri Oct 20 03:55:35 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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/human_augustus_protein_codingseq_introns_cds_main.gtf	Fri Oct 20 03:55:35 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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/human_augustus_protein_codingseq_introns_cds_protein.fasta	Fri Oct 20 03:55:35 2017 -0400
@@ -0,0 +1,13 @@
+>HS04636.g1
+MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYILTH
+FKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDS
+NEIVEKLLLRRKFIPDPQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKY
+QIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVGQEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRL
+ILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYHWHPLLPDTFQIHDQKYNYQQFIYNNSIL
+LEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGEKEMSAELEAL
+YGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKG
+CPFTSFSVPDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL
+>HS08198.g2
+MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGICWQ
+VRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQ
+IFYFPKYGFCEAADQFHVLDGECTAGASMAAW
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/human_augustus_utr-on.gff	Fri Oct 20 03:55:35 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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/human_augustus_utr-on.gtf	Fri Oct 20 03:55:35 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