Repository 'augustus'
hg clone https://toolshed.g2.bx.psu.edu/repos/bgruening/augustus

Changeset 0:af307d3285c5 (2013-07-06)
Next changeset 1:e2b822d7408f (2013-12-05)
Commit message:
Uploaded
added:
augustus.xml
extract_features.py
readme.rst
test-data/arabidopsis_augustus.fa
test-data/arabidopsis_augustus_utr-off_singlestrand-on_mea-on.gtf
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
tool_conf.xml
tool_dependencies.xml
b
diff -r 000000000000 -r af307d3285c5 augustus.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/augustus.xml Sat Jul 06 10:07:41 2013 -0400
b
b'@@ -0,0 +1,246 @@\n+<tool id="augustus" name="Augustus" version="0.3">\n+    <description>gene prediction for eukaryotic genomes</description>\n+    <requirements>\n+        <requirement type="package" version="2.7">augustus</requirement>\n+        <requirement type="set_environment">AUGUSTUS_SCRIPT_PATH</requirement>\n+    </requirements>\n+    <command>\n+        ## please set export AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config\n+        ## or use the --AUGUSTUS_CONFIG_PATH=path if you are not installing through the toolshed\n+        ## Augustus writes the protein and coding sequences as comment into the gff/gtf file an external script is used to extract the sequences into additional files\n+\n+        augustus\n+            --strand=$strand\n+            $noInFrameStop\n+            $gff\n+            $protein\n+            $introns\n+            $start\n+            $stop\n+            $cds\n+            $codingseq\n+            $singlestrand\n+            $input_genome\n+            $mea\n+            $utr\n+            --genemodel=$genemodel\n+            --species=$organism\n+            ##--outfile=$output\n+        | tee $output \n+        #if $protein or $codingseq:\n+            | python \\$AUGUSTUS_SCRIPT_PATH/extract_features.py\n+                #if $protein:\n+                    --protein $protein_output\n+                #end if\n+                #if $codingseq:\n+                    --codingseq $codingseq_output\n+                #end if\n+        #end if\n+    </command>\n+    <inputs>\n+        <param name="input_genome" type="data" format="fasta" label="Genome Sequence"/>\n+        <param name="noInFrameStop" type="boolean" label="Don\'t report transcripts with in-frame stop codons (--noInFrameStop)" truevalue="--noInFrameStop=true" falsevalue="--noInFrameStop=false" checked="false" help="Otherwise, intron-spanning stop codons could occur" />\n+        <param name="singlestrand" type="boolean" label="Predict genes independently on each strand, allow overlapping genes on opposite strands (--singlestrand)" truevalue="--singlestrand=true" falsevalue="--singlestrand=false" checked="false" />\n+        <param name="mea" type="boolean" label="Using the maximum expected accuracy approach (--mea)" truevalue="--mea=1" falsevalue="" checked="false" help="MEA is an alternative decoding approach." />\n+        <param name="utr" type="boolean" label="Predict the untranslated regions in addition to the coding sequence (--UTR)" truevalue="--UTR=on" falsevalue="--UTR=off" checked="false" help="This currently works only for human, galdieria, toxoplasma and caenorhabditis." />\n+\n+        <param name="organism" label="Model Organism" type="select" multiple="false" format="text" help="Choose a specialised trainingset.">\n+            <option value="human">Homo sapiens</option>\n+            <option value="fly">Drosophila melanogaster</option>\n+            <option value="arabidopsis">Arabidopsis thaliana</option>\n+            <option value="brugia ">Brugia malayi</option>\n+            <option value="aedes">Aedes aegypti</option>\n+            <option value="tribolium2012">Tribolium castaneum</option>\n+            <option value="schistosoma">Schistosoma mansoni</option>\n+            <option value="tetrahymena">Tetrahymena thermophila</option>\n+            <option value="galdieria">Galdieria sulphuraria</option>\n+            <option value="maize">Zea mays</option>\n+            <option value="toxoplasma ">Toxoplasma gondii</option>\n+            <option value="caenorhabditis ">Caenorhabditis elegans</option>\n+            <option value="aspergillus_fumigatus">Aspergillus fumigatus</option>\n+            <option value="aspergillus_nidulans ">Aspergillus nidulans</option>\n+            <option value="aspergillus_oryzae ">Aspergillus oryzae</option>\n+            <option value="aspergillus_terreus">Aspergillus terreus</option>\n+            <option value="botrytis_cinerea ">Botrytis cinerea</option>\n+            <option value="candida_albicans ">Candida albicans</option>\n+   '..b'f_singlestrand-on_mea-on.gtf" ftype="gtf" lines_diff="2"/>\n+        </test>\n+        <test>\n+            <param name="input_genome" value="human_augustus.fa" ftype="fasta" />\n+            <param name="organism" value="human" />\n+            <param name="protein" value="--protein=on" />\n+            <param name="codingseq" value="--codingseq=on" />\n+            <param name="introns" value="--introns=on" />\n+            <param name="cds" value="--cds=on" />\n+            <output name="output" file="human_augustus_protein_codingseq_introns_cds_main.gtf" ftype="gff" lines_diff="2"/>\n+            <output name="codingseq_output" file="human_augustus_protein_codingseq_introns_cds_codingseq.fasta" ftype="fasta" />\n+            <output name="protein_output" file="human_augustus_protein_codingseq_introns_cds_protein.fasta" ftype="fasta" />\n+        </test>\n+    </tests>\n+    <help>\n+\n+**What it does**\n+\n+AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller.\n+It can be used as an ab initio program, which means it bases its prediction purely on the\n+sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources\n+such as EST, MS/MS, protein alignments and synthenic genomic alignments.\n+\n+-----\n+\n+**Parameters**\n+\n+Gene Model::\n+\n+    partial      : allow prediction of incomplete genes at the sequence boundaries (default)\n+    intronless   : only predict single-exon genes like in prokaryotes and some eukaryotes\n+    complete     : only predict complete genes\n+    atleastone   : predict at least one complete gene\n+    exactlyone   : predict exactly one complete gene\n+\n+\n+\n+**Example**\n+\n+Suppose you have the following DNA formatted sequences::\n+\n+    >Seq1\n+    cccgcggagcgggtaccacatcgctgcgcgatgtgcgagcgaacacccgggctgcgcccg\n+    ggtgttgcgctcccgctccgcgggagcgctggcgggacgctgcgcgtcccgctcaccaag\n+    cccgcttcgcgggcttggtgacgctccgtccgctgcgcttccggagttgcggggcttcgc\n+    cccgctaaccctgggcctcgcttcgctccgccttgggcctgcggcgggtccgctgcgctc\n+    ccccgcctcaagggcccttccggctgcgcctccaggacccaaccgcttgcgcgggcctgg\n+\n+Running this tool will produce this::\n+\n+    # ----- prediction on sequence number 1 (length = 1992969, name = scaffold1|size1992969) -----\n+    #\n+    # Constraints/Hints:\n+    # (none)\n+    # Predicted genes for sequence number 1 on both strands\n+    # start gene g1\n+    scaffold1|size1992969\tAUGUSTUS\tgene\t17453\t19382\t0.11\t+\t.\tg6\n+    scaffold1|size1992969\tAUGUSTUS\ttranscript\t17453\t19382\t0.11\t+\t.\tg6.t1\n+    scaffold1|size1992969\tAUGUSTUS\tstart_codon\t17453\t17455\t.\t+\t0\ttranscript_id "g6.t1"; gene_id "g6";\n+    scaffold1|size1992969\tAUGUSTUS\tintron\t17615\t17660\t0.38\t+\t.\ttranscript_id "g6.t1"; gene_id "g6";\n+    scaffold1|size1992969\tAUGUSTUS\tintron\t17708\t17772\t0.54\t+\t.\ttranscript_id "g6.t1"; gene_id "g6";\n+    scaffold1|size1992969\tAUGUSTUS\tintron\t17902\t18035\t0.58\t+\t.\ttranscript_id "g6.t1"; gene_id "g6";\n+    scaffold1|size1992969\tAUGUSTUS\tintron\t18313\t18367\t0.99\t+\t.\ttranscript_id "g6.t1"; gene_id "g6";\n+    scaffold1|size1992969\tAUGUSTUS\tintron\t19014\t19080\t0.44\t+\t.\ttranscript_id "g6.t1"; gene_id "g6";\n+    scaffold1|size1992969\tAUGUSTUS\tCDS\t17453\t17614\t0.55\t+\t0\ttranscript_id "g6.t1"; gene_id "g6";\n+    scaffold1|size1992969\tAUGUSTUS\tCDS\t17661\t17707\t0.38\t+\t0\ttranscript_id "g6.t1"; gene_id "g6";\n+    scaffold1|size1992969\tAUGUSTUS\tCDS\t17773\t17901\t0.54\t+\t1\ttranscript_id "g6.t1"; gene_id "g6";\n+    scaffold1|size1992969\tAUGUSTUS\tCDS\t18036\t18312\t0.52\t+\t1\ttranscript_id "g6.t1"; gene_id "g6";\n+    scaffold1|size1992969\tAUGUSTUS\tCDS\t18368\t19013\t0.99\t+\t0\ttranscript_id "g6.t1"; gene_id "g6";\n+    scaffold1|size1992969\tAUGUSTUS\tCDS\t19081\t19379\t0.31\t+\t2\ttranscript_id "g6.t1"; gene_id "g6";\n+    scaffold1|size1992969\tAUGUSTUS\tstop_codon\t19380\t19382\t.\t+\t0\ttranscript_id "g6.t1"; gene_id "g6";\n+\n+\n+**References**\n+\n+Mario Stanke and Stephan Waack (2003) \n+Gene Prediction with a Hidden-Markov Model and a new Intron Submodel. \n+Bioinformatics, Vol. 19, Suppl. 2, pages ii215-ii225\n+\n+\n+    </help>\n+</tool>\n'
b
diff -r 000000000000 -r af307d3285c5 extract_features.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/extract_features.py Sat Jul 06 10:07:41 2013 -0400
[
@@ -0,0 +1,93 @@
+#!/usr/bin/env python
+
+import os
+import sys
+import argparse
+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 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 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.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 )
+
b
diff -r 000000000000 -r af307d3285c5 readme.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.rst Sat Jul 06 10:07:41 2013 -0400
b
@@ -0,0 +1,83 @@
+Galaxy wrapper for Augustus
+===========================
+
+This wrapper is copyright 2012-2013 by Björn Grüning.
+
+This is a wrapper for the command line tool of Augustus_.
+
+.. _augustus: http://bioinf.uni-greifswald.de/augustus/
+
+AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.
+
+Oliver Keller, Martin Kollmar, Mario Stanke, Stephan Waack (2011)
+A novel hybrid gene prediction method employing protein multiple sequence alignments
+Bioinformatics, doi: 10.1093/bioinformatics/btr010
+
+Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008)
+Using native and syntenically mapped cDNA alignments to improve de novo gene finding
+Bioinformatics, doi: 10.1093/bioinformatics/btn013
+
+Mario Stanke and Stephan Waack (2003)
+Gene Prediction with a Hidden-Markov Model and a new Intron Submodel. 
+Bioinformatics, Vol. 19, Suppl. 2, pages ii215-ii225
+
+
+Installation
+============
+
+The recommended installation is by means of the toolshed_.
+If you need to install it manually here is a short introduction.
+
+.. _toolshed: http://toolshed.g2.bx.psu.edu/view/bjoern-gruening/augustus
+
+
+Install or downlaod augustus from::
+
+    http://bioinf.uni-greifswald.de/augustus/binaries/
+
+and follow the installation instructions or copy the binaries into your $PATH. To install the wrapper copy the augustus folder in the galaxy tools folder and modify the tools_conf.xml file to make the tool available to Galaxy.
+
+For example::
+
+  <section name="Gene Prediction" id="gene_prediction">
+    <tool file="gene_prediction/tools/augustus/augustus.xml" />
+  </section>
+
+
+Set the *AUGUSTUS_CONFIG_PATH* to /path_to_augustus/augustus/config with::
+
+  export AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config
+
+or modify the wrapper and use the following additional commandline switch::
+
+  --AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config
+
+
+History
+=======
+
+- v0.1: Initial public release
+- v0.2: Added tool_dependencies.xml file and update the augustus version (thanks to James Johnson)
+- v0.3: upgrade to augustus 2.7, added new organisms and new parameters, output additional sequence files
+
+Wrapper Licence (MIT/BSD style)
+===============================
+
+Permission to use, copy, modify, and distribute this software and its
+documentation with or without modifications and for any purpose and
+without fee is hereby granted, provided that any copyright notices
+appear in all copies and that both those copyright notices and this
+permission notice appear in supporting documentation, and that the
+names of the contributors or copyright holders not be used in
+advertising or publicity pertaining to distribution of the software
+without specific prior permission.
+
+THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
+WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
+CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
+OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
+OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
+OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
+OR PERFORMANCE OF THIS SOFTWARE.
+
b
diff -r 000000000000 -r af307d3285c5 test-data/arabidopsis_augustus.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/arabidopsis_augustus.fa Sat Jul 06 10:07:41 2013 -0400
b
@@ -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
b
diff -r 000000000000 -r af307d3285c5 test-data/arabidopsis_augustus_utr-off_singlestrand-on_mea-on.gtf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/arabidopsis_augustus_utr-off_singlestrand-on_mea-on.gtf Sat Jul 06 10:07:41 2013 -0400
[
@@ -0,0 +1,85 @@
+# This output was generated with AUGUSTUS (version 2.7).
+# AUGUSTUS is a gene prediction tool for eukaryotes written by Mario Stanke (mario.stanke@uni-greifswald.de)
+# and Oliver Keller (keller@cs.uni-goettingen.de).
+# 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.
+# arabidopsis version. Using default transition matrix.
+# We have hints for 0 sequences and for 0 of the sequences in the input set.
+#
+# ----- prediction on sequence number 1 (length = 2066, name = arabidopsis) -----
+#
+# Constraints/Hints:
+# (none)
+# Predicted genes for sequence number 1 on both strands
+# start gene g1
+arabidopsis AUGUSTUS gene 775 1851 0 + . g1
+arabidopsis AUGUSTUS transcript 775 1851 . + . g1.t1
+arabidopsis AUGUSTUS start_codon 775 777 . + 0 transcript_id "g1.t1"; gene_id "g1";
+arabidopsis AUGUSTUS CDS 775 1851 0.99 + 0 transcript_id "g1.t1"; gene_id "g1";
+arabidopsis AUGUSTUS stop_codon 1849 1851 . + 0 transcript_id "g1.t1"; gene_id "g1";
+# protein sequence = [MDLSLAPTTTTSSDQEQDRDQELTSNIGASSSSGPSGNNNNLPMMMIPPPEKEHMFDKVVTPSDVGKLNRLVIPKQHA
+# ERYFPLDSSNNQNGTLLNFQDRNGKMWRFRYSYWNSSQSYVMTKGWSRFVKEKKLDAGDIVSFQRGIGDESERSKLYIDWRHRPDMSLVQAHQFGNFG
+# FNFNFPTTSQYSNRFHPLPEYNSVPIHRGLNIGNHQRSYYNTQRQEFVGYGYGNLAGRCYYTGSPLDHRNIVGSEPLVIDSVPVVPGRLTPVMLPPLP
+# PPPSTAGKRLRLFGVNMECGNDYNQQEESWLVPRGEIGASSSSSSALRLNLSTDHDDDNDDGDDGDDDQFAKKGKSSLSLNFNP]
+# end gene g1
+###
+# start gene g2
+arabidopsis AUGUSTUS gene 841 1661 . - . g2
+arabidopsis AUGUSTUS transcript 841 1661 . - . g2.t1
+arabidopsis AUGUSTUS stop_codon 841 843 . - 0 transcript_id "g2.t1"; gene_id "g2";
+arabidopsis AUGUSTUS intron 1024 1101 0.75 - . transcript_id "g2.t1"; gene_id "g2";
+arabidopsis AUGUSTUS intron 1193 1325 0.03 - . transcript_id "g2.t1"; gene_id "g2";
+arabidopsis AUGUSTUS intron 1416 1512 0.85 - . transcript_id "g2.t1"; gene_id "g2";
+arabidopsis AUGUSTUS CDS 841 1023 0.87 - 0 transcript_id "g2.t1"; gene_id "g2";
+arabidopsis AUGUSTUS CDS 1102 1192 0.78 - 1 transcript_id "g2.t1"; gene_id "g2";
+arabidopsis AUGUSTUS CDS 1326 1415 0.05 - 1 transcript_id "g2.t1"; gene_id "g2";
+arabidopsis AUGUSTUS CDS 1513 1661 0.35 - 0 transcript_id "g2.t1"; gene_id "g2";
+# protein sequence = [SLPHSIFTPKSLSLFPAVEGGGGSGGNITGVNLPGTTGTESITNGSDPTMNVGDFRCLSPGESGRSYILAMDEICWNI
+# EKDNVSCIELFLFDETAPSFGHNVALARVPIRREIPLSVLFRDHESVEFSDVAWCYHFVEHVFFLRRWNHHHRKVVVVSAGTGAAACSDVGG]
+# end gene g2
+###
+#
+# ----- prediction on sequence number 2 (length = 1802, name = arabidopsis2) -----
+#
+# Constraints/Hints:
+# (none)
+# Predicted genes for sequence number 2 on both strands
+# start gene g3
+arabidopsis2 AUGUSTUS gene 97 1600 . - . g3
+arabidopsis2 AUGUSTUS transcript 97 1600 . - . g3.t1
+arabidopsis2 AUGUSTUS stop_codon 97 99 . - 0 transcript_id "g3.t1"; gene_id "g3";
+arabidopsis2 AUGUSTUS intron 349 521 0.73 - . transcript_id "g3.t1"; gene_id "g3";
+arabidopsis2 AUGUSTUS intron 1210 1333 0.36 - . transcript_id "g3.t1"; gene_id "g3";
+arabidopsis2 AUGUSTUS intron 1452 1560 0.54 - . transcript_id "g3.t1"; gene_id "g3";
+arabidopsis2 AUGUSTUS CDS 97 348 0.73 - 0 transcript_id "g3.t1"; gene_id "g3";
+arabidopsis2 AUGUSTUS CDS 522 1209 0.6 - 1 transcript_id "g3.t1"; gene_id "g3";
+arabidopsis2 AUGUSTUS CDS 1334 1451 0.44 - 2 transcript_id "g3.t1"; gene_id "g3";
+arabidopsis2 AUGUSTUS CDS 1561 1600 0.42 - 0 transcript_id "g3.t1"; gene_id "g3";
+arabidopsis2 AUGUSTUS start_codon 1598 1600 . - 0 transcript_id "g3.t1"; gene_id "g3";
+# protein sequence = [MVKLVFSDLSCAFASANSTASSTNSSIFFSIDFSSASFASLFSIKYFFNAAIGITELIGISQGVSSESISLTFNQGWT
+# FSSSSSSDSFFSDFPDLQDIHTVNMNTRHPKCRTFLPNLGVRSGSQVRHPNGPQVILDNKDNRQFIESSHVETLEELSVVTSSISEKGDSDIITILFQ
+# DFPPVLGAKGSTSGDRNAFTNKSKATKHVVFFGEHVHGSTLASAASSNLAEELAHNSTSRDTFAEGMDMVTVGTNDRVRLGKELDKASRNSLLAIVQV
+# NKTKHLASAGIIGGLLLLDNFLDRDDGRSTGGVGVIESAKGEGTGGSEERRRRSQSDREQETILMGSMQRNRGSELSGSESRRHCYQWKPQ]
+# end gene g3
+###
+# start gene g4
+arabidopsis2 AUGUSTUS gene 121 1582 0 + . g4
+arabidopsis2 AUGUSTUS transcript 121 1582 . + . g4.t1
+arabidopsis2 AUGUSTUS start_codon 121 123 . + 0 transcript_id "g4.t1"; gene_id "g4";
+arabidopsis2 AUGUSTUS intron 352 434 0.97 + . transcript_id "g4.t1"; gene_id "g4";
+arabidopsis2 AUGUSTUS intron 1213 1304 1 + . transcript_id "g4.t1"; gene_id "g4";
+arabidopsis2 AUGUSTUS CDS 121 351 0.72 + 0 transcript_id "g4.t1"; gene_id "g4";
+arabidopsis2 AUGUSTUS CDS 435 1212 0.97 + 0 transcript_id "g4.t1"; gene_id "g4";
+arabidopsis2 AUGUSTUS CDS 1305 1582 1 + 2 transcript_id "g4.t1"; gene_id "g4";
+arabidopsis2 AUGUSTUS stop_codon 1580 1582 . + 0 transcript_id "g4.t1"; gene_id "g4";
+# protein sequence = [MATAFAPTKLTATVPLHGSHENRLLLPIRLAPPSSFLGSTRSLSLRRLNHSNATRRSPVVSVQEVVKEKQSTNNTSLL
+# ITKEEGLELYEDMILGRSFEDMCAQMYYRGKMFGFVHLYNGQEAVSTGFIKLLTKSDSVVSTYRDHVHALSKGVSARAVMSELFGKVTGCCRGQGGSM
+# HMFSKEHNMLGGFAFIGEGIPVATGAAFSSKYRREVLKQDCDDVTVAFFGDGTCNNGQFFECLNMAALYKLPIIFVVENNLWAIGMSHLRATSDPEIW
+# KKGPAFGMPGVHVDGMDVLKVREVAKEAVTRARRGEGPTLVECETYRFRGHSLADPDELRDAAEKAKYAARDPIAALKKYLIENKLAKEAELKSIEKK
+# IDELVEEAVEFADASPQPGRSQLLENVFADPKGFGIGPDGRYRCEDPKFTEGTAQV]
+# end gene g4
+###
+# command line:
+# ./bin/augustus --species=arabidopsis --UTR=off --singlestrand=true --mea=1 /home/bag/projects/github/galaxytools/augustus/test-data/arabidopsis_augustus.fa
b
diff -r 000000000000 -r af307d3285c5 test-data/human_augustus.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/human_augustus.fa Sat Jul 06 10:07:41 2013 -0400
b
b'@@ -0,0 +1,200 @@\n+>HS04636\n+gagctcacattaactatttacagggtaactgcttaggaccagtattatgaggagaattta\n+cctttcccgcctctctttccaagaaacaaggagggggtgaaggtacggagaacagtattt\n+cttctgttgaaagcaacttagctacaaagataaattacagctatgtacactgaaggtagc\n+tatttcattccacaaaataagagttttttaaaaagctatgtatgtatgtgctgcatatag\n+agcagatatacagcctattaagcgtcgtcactaaaacataaaacatgtcagcctttctta\n+accttactcgccccagtctgtcccgacgtgacttcctcgaccctctaaagacgtacagac\n+cagacacggcggcggcggcgggagaggggattccctgcgcccccggacctcagggccgct\n+cagattcctggagaggaagccaagtgtccttctgccctcccccggtatcccatccaaggc\n+gatcagtccagaactggctctcggaagcgctcgggcaaagactgcgaagaagaaaagaca\n+tctggcggaaacctgtgcgcctggggcggtggaactcggggaggagagggagggatcaga\n+caggagagtggggactaccccctctgctcccaaattggggcagcttcctgggtttccgat\n+tttctcatttccgtgggtaaaaaaccctgcccccaccgggcttacgcaatttttttaagg\n+ggagaggagggaaaaaatttgtgggggggtacgaaaaggcggaaagaaacagtcattcac\n+atgggcttggttttcagtcttataaaaaggaaggttctctcggttagcgaccaattgtca\n+tacgacttgcagtgagcgtcaggagcacgtccaggaactcctcagcagcgcctccttcag\n+ctccacagccagacgccctcagacagcaaagcctacccccgcgccgcgccctgcccgccg\n+ctcggatgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacaggtg\n+agtacctggcgccgcgcaccggggactccggttccacgcacccgggcagagtttccgctc\n+tgacctcctgggtctatcccagtactccgacttctctccgaatagagaagctacgtgact\n+tgggaaagagcttggaccgctagagtccgaaagaactccgtggatattccagctttccca\n+caagcactgatcattatgagccagttacttaaccgatctgagacactctcacctcctaaa\n+tagggatagatgatactaatttgcaggttgtcattatgataagacaggatctgatcaata\n+tatgtgaattgtttatatttggaacctttttattgagtggaagaagttgttttaaatatt\n+ctagtcagttctttcctgctcccaggaaagcccggattatgttttaagataagcaaaatg\n+tcttaaaagtaagctgttttactttgaatttttccctaaatgttgattagtgtactagat\n+ccattttaatttggaaagtgaagtgctacttatttgaacttcttaaaaatgctaatttta\n+acatctaaagagttaactaagaaaagcttagtaacatgatgtaccaagttgaatatgctg\n+ttatccttatttagaatagaaaattggtatttctacgttttatccattctaaggcaggtt\n+aaaaaattgtatttccatgactacctatatatttcttgaatttattattgtaaagttgat\n+tcatagtcaaacaattaaatgtttaaattaagattaagacactagagaatgatttatttg\n+ctgtcctttaattgcagcaaatccttgctgttcccacccatgtcaaaaccgaggtgtatg\n+tatgagtgtgggatttgaccagtataagtgcgattgtacccggacaggattctatggaga\n+aaactgctcaacacgtaagtttgtcctttggttgcctcattaggagtggggctggataca\n+gttatcattgtatagatttgtgtcttataatgagtcccattaatttctccctccctttct\n+tcgtcttcttgcagcggaatttttgacaagaataaaattatttctgaaacccactccaaa\n+cacagtgcactacatacttacccacttcaagggattttggaacgttgtgaataacattcc\n+cttccttcgaaatgcaattatgagttatgtcttgacatgtaagtacaagtgtctttctaa\n+ggtttttagccttctcaaagaaaaatatgctttataatactgtaagcctaatctaaaaac\n+atatttccaagcttatcaaaaagactttaagatagcttttaagtttgccttccatcttaa\n+tcgccaaaaatattgacatttagtcccatccagtttatacagtctgctcacaactctgta\n+tacctcttctaacctttactgtttggtcagtttgtggaggtagcatggtccagctgttta\n+ttgaatgcccatgggccacagaattgttctgaacatgtagcacccattaaaataaatttg\n+gatttggatcagcaagaaaataactttccatgattctaaagtgggtgccatactcagcca\n+ttcctttcataggcctcttggatagtgagcagatggctacctgaaaaatcaatattgcca\n+gattataatgtgcagagtatatgtattttattaaagatgtatttcaagtggccattagac\n+tataaagtgtagttgtttaaaaatagattttttttattttggagttacattcaacctcag\n+gtgccactttccacattttacaataaaaataatggttgatttacttaacaaatgagaata\n+aataaaacatttttttctttgaaaatttcagccagatcacatttgattgacagtccacca\n+acttacaatgctgactatggctacaaaagctgggaagccttctctaacctctcctattat\n+actagagcccttcctcctgtgcctgatgattgcccgactcccttgggtgtcaaaggtgag\n+taagaagaatccattagagatgtattaactataagacgggctgcattgctgccaaaaaaa\n+aaaattgaccttagactaccatttatttattaacaaaagcagtttttacttttagcatgg\n+ttatctatgggtattttttaaagtatgagtctatataaactattatgtaaaagcaaatga\n+gcgtcttggtataatgtcttaatattttcaaattatttctttagaaatgaaataattcta\n+attaaaatagataaaatcattcagtaagaagttgttccaccatatcttagaactgttgtt\n+tatattatgatcctattcacaattgtaattctcatataaatgaagaattcttggtagatt\n+gacagtcaccatctcctttcttgaatacatagatggattcttaccttagctttctcattt\n+ttcaggtaaaaagcagcttcctgattcaaatgagattgtggaaaaattgcttctaagaag\n+aaagttcatccctgatccccagggctcaaacatgatgtttgcattctttgcccagcactt\n+cacgcatcagtttttcaagacagatcataagcgagggccagctttcaccaacgggctggg\n+ccatggggtaagatagagttaatatcttagagttagtaaaattataccaaatcatagtca\n+agggctaacattaaaggagatatacagatagatagatccaaataacttatccactttttt\n+taaaaagaagtcttatctataaaaaccttaaaggaattttccatttacttcactggtcta\n+gtaaaattatacacacacacagacatgcacacacatatataaacattcacacacatacat\n+at'..b'ccaagctgtgcttgaataacgatatgttttctcagattttc\n+tgttgtacagtttaatttagcagtccatatcacattgcaaaagtagcaatgacctcataa\n+aatacctcttcaaaatgcttaaattcatttcacacattaattttatctcagtcttgaagc\n+caattcagtaggtgcattggaatcaagcctggctacctgcatgctgttccttttcttttc\n+ttcttttagccattttgctaagagacacagtcttctcatcacttcgtttctcctattttg\n+ttttactagttttaagatcagagttcactttctttggactctgcctatattttcttacct\n+gaacttttgcaagttttcaggtaaacctcagctcaggactgctatttagctcctcttaag\n+aagattaaaagagaaaaaaaaaggcccttttaaaaatagtatacacttattttaagtgaa\n+aagcagagaattttatttatagctaattttagctatctgtaaccaagatggatgcaaaga\n+ggctagtgcctcagagagaactgtacggggtttgtgactggaaaaagttacgttcccatt\n+ctaattaatgccctttcttatttaaaaacaaaaccaaatgatatctaagtagttctcagc\n+aataataataatgacgataatacttcttttccacatctcattgtcactgacatttaatgg\n+tactgtatattacttaatttattgaagattattatttatgtcttattaggacactatggt\n+tataaactgtgtttaagcctacaatcattgatttttttttgttatgtcacaatcagtata\n+ttttctttggggttacctctctgaatattatgtaaacaatccaaagaaatgattgtatta\n+agatttgtgaataaatttttagaaatctgattggcatattgagatatttaaggttgaatg\n+tttgtccttaggataggcctatgtgctagcccacaaagaatattgtctcattagcctgaa\n+tgtgccataagactgaccttttaaaatgttttgagggatctgtggatgcttcgttaattt\n+gttcagccacaatttattgagaaaatattctgtgtcaagcactgtgggttttaatatttt\n+taaatcaaacgctgattacagataatagtatttatataaataattgaaaaaaattttctt\n+ttgggaagagggagaaaatgaaataaatatcattaaagataactcaggagaatcttcttt\n+acaattttacgtttagaatgtttaaggttaagaaagaaatagtcaatatgcttgtataaa\n+acactgttcactgttttttttaaaaaaaaaacttgatttgttattaacattgatctgctg\n+acaaaacctgggaatttgggttgtgtatgcgaatgtttcagtgcctcagacaaatgtgta\n+tttaacttatgtaaaagataagtctggaaataaatgtctgtttatttttgtactatttaa\n+aaaaaaaaaaaaaaatcgatgtcgactcgagtc\n+>HS08198\n+agcgggcggcggtcgtgggcggggttgcaggcgaggctcaacgaacgctggtctgaccgt\n+cggcgctccctgttgccgggccctgagcaagtggcttcatgaaccccgtgacgttggcca\n+tggagataagaccactgggtgatggtttaaggaagataacgtgtaaagggctaaggactg\n+tcggtggaaatcaggggtgcaggagaaatggataaacagccagaggtcaactcggacttt\n+gtacataggacatggtgccaggccctgccaggaagtgcagatcgaagctaggctcacgag\n+gaggctggaggtggggggtggggaggcaacggatggacatggacttcctgggctgggctc\n+tgtgacagcagagtagactctgtcctgggacttggtggtgctacccttggcctcccacag\n+tcctgccaccctgctgccgccaccatgctgccccctgggactgcgaccctcttgactctg\n+ctcctggcagctggctcgctgggccagaagcctcagaggccacgccggcccgcatccccc\n+atcagcaccatccagcccaaggccaattttgatgcgcagcaggtagaagttggggggggt\n+agagggaggcaggtagaagttgtgggaggggtagagggagacaggtagaagttgttgcgg\n+gggagagggaagcaggtgaagttgtggggggtgtagagggaagcaggtgaggggccctcc\n+cacagtgccctcgagttctcccatggtctgcccccagtttgcagggacctggctccttgt\n+ggctgtgggctccgcttgccgtttcctgcaggagcagggccaccgggccgaggccaccac\n+actgcatgtggctccccagggcacagccatggctgtcagtaccttccgaaagctgtgagt\n+cccagagcagccctgcaccctaaccccaaccctcctctcagcccccggacttcagccctg\n+ctctggcccctgaccccaccccggctgtggcctggactaggattcctggttggggtctcc\n+cagcctgtggtgcctcctccccgcccccccagggatgggatctgctggcaggtgcgccag\n+ctctatggagacacaggggtcctcggccgcttcctgcttcaaggtgaggcaggggctgca\n+ggtcatgtgggtgggggatgacgcagccactgtggctctctgacatggctactgtggctc\n+tgcccagcccgaggcgcccgaggggctgtgcacgtggttgtcgctgagaccgactaccag\n+agtttcgctgtcctgtacctggagcgggcggggcagctgtcagtgaagctctacggtatg\n+tgggggccagcctctgtgaccaggcaggcgctcaagctctgcacactcactgggccaccc\n+cgaggggctgggtgagccatggggacacacttcctttctcccatcctgatcctcctgcta\n+agcaggggcccagggagtagtgacagacaggcctggtgtgggagcagggaggagggcccc\n+gaggggcaggggacacacagaccccgttcccagagccctccacgccgcctggtgccagga\n+ccccaggaaccctgtctgccctgcagcccgctcgctccctgtgagcgactcggtcctgag\n+tgggtttgagcagcgggtccaggaggcccacctgactgaggaccagatcttctacttccc\n+caagtacggtgagtgtccccagcaggtccccagctcagccacccccactctctggctgat\n+gtccagcctgacccctgccttggcgccccaggcttctgcgaggctgcagaccagttccac\n+gtcctggacggtgagtgcacagcgggggcaagcatggcggcgtggtgaggggggccactc\n+gcaccggctgagtctcgtctctgctgcagaagtgaggaggtgaggccggcacacagctcc\n+agtgctgagaagtcagtgccccgagagacgaccccaccagtggggtgcccgctgcctgtc\n+ctccgtgaaaccagcctcagatcagggccctgccacccagggcaggggatcttctgccgg\n+ctgccccagaggacagtgggtggagtggtacctacttattaaatgtctcagacccctctc\n+tgactcttctgtccactctggaccggcgccagtaccaccaaggccctctctgcccccacc\n+ccgcctctttaaaagcccggcgctccctgttggctggagtccacgcagggtcactgggcc\n+gatttcggctcttgggatttgggaggggagatcctctctggcatatgccatcttgtgccc\n+tgctggacctgggggcgtccacgtcactccaaggctgctcttgcctgggccatgcctgca\n+gccc\n'
b
diff -r 000000000000 -r af307d3285c5 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 Sat Jul 06 10:07:41 2013 -0400
b
@@ -0,0 +1,35 @@
+>g1
+atgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacagcaaatccttgctgttcccacccatgtca
+tgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacagcaaatccttgctgttcccacccatgtcaa
+aaccgaggtgtatgtatgagtgtgggatttgaccagtataagtgcgattgtacccggacaggattctatggagaaaactg
+ctcaacaccggaatttttgacaagaataaaattatttctgaaacccactccaaacacagtgcactacatacttacccact
+tcaagggattttggaacgttgtgaataacattcccttccttcgaaatgcaattatgagttatgtcttgacatccagatca
+catttgattgacagtccaccaacttacaatgctgactatggctacaaaagctgggaagccttctctaacctctcctatta
+tactagagcccttcctcctgtgcctgatgattgcccgactcccttgggtgtcaaaggtaaaaagcagcttcctgattcaa
+atgagattgtggaaaaattgcttctaagaagaaagttcatccctgatccccagggctcaaacatgatgtttgcattcttt
+gcccagcacttcacgcatcagtttttcaagacagatcataagcgagggccagctttcaccaacgggctgggccatggggt
+ggacttaaatcatatttacggtgaaactctggctagacagcgtaaactgcgccttttcaaggatggaaaaatgaaatatc
+agataattgatggagagatgtatcctcccacagtcaaagatactcaggcagagatgatctaccctcctcaagtccctgag
+catctacggtttgctgtggggcaggaggtctttggtctggtgcctggtctgatgatgtatgccacaatctggctgcggga
+acacaacagagtatgcgatgtgcttaaacaggagcatcctgaatggggtgatgagcagttgttccagacaagcaggctaa
+tactgataggagagactattaagattgtgattgaagattatgtgcaacacttgagtggctatcacttcaaactgaaattt
+gacccagaactacttttcaacaaacaattccagtaccaaaatcgtattgctgctgaatttaacaccctctatcactggca
+tccccttctgcctgacacctttcaaattcatgaccagaaatacaactatcaacagtttatctacaacaactctatattgc
+tggaacatggaattacccagtttgttgaatcattcaccaggcaaattgctggcagggttgctggtggtaggaatgttcca
+cccgcagtacagaaagtatcacaggcttccattgaccagagcaggcagatgaaataccagtcttttaatgagtaccgcaa
+acgctttatgctgaagccctatgaatcatttgaagaacttacaggagaaaaggaaatgtctgcagagttggaagcactct
+atggtgacatcgatgctgtggagctgtatcctgcccttctggtagaaaagcctcggccagatgccatctttggtgaaacc
+atggtagaagttggagcaccattctccttgaaaggacttatgggtaatgttatatgttctcctgcctactggaagccaag
+cacttttggtggagaagtgggttttcaaatcatcaacactgcctcaattcagtctctcatctgcaataacgtgaagggct
+gtccctttacttcattcagtgttccagatccagagctcattaaaacagtcaccatcaatgcaagttcttcccgctccgga
+ctagatgatatcaatcccacagtactactaaaagaacgttcgactgaactgtag
+>g2
+atgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccaca
+tgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccacgc
+cggcccgcatcccccatcagcaccatccagcccaaggccaattttgatgcgcagcaggagcagggccaccgggccgaggc
+caccacactgcatgtggctccccagggcacagccatggctgtcagtaccttccgaaagctggatgggatctgctggcagg
+tgcgccagctctatggagacacaggggtcctcggccgcttcctgcttcaagcccgaggcgcccgaggggctgtgcacgtg
+gttgtcgctgagaccgactaccagagtttcgctgtcctgtacctggagcgggcggggcagctgtcagtgaagctctacgc
+ccgctcgctccctgtgagcgactcggtcctgagtgggtttgagcagcgggtccaggaggcccacctgactgaggaccaga
+tcttctacttccccaagtacggcttctgcgaggctgcagaccagttccacgtcctggacggtgagtgcacagcgggggca
+agcatggcggcgtggtga
b
diff -r 000000000000 -r af307d3285c5 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 Sat Jul 06 10:07:41 2013 -0400
[
@@ -0,0 +1,101 @@
+# This output was generated with AUGUSTUS (version 2.7).
+# AUGUSTUS is a gene prediction tool for eukaryotes written by Mario Stanke (mario.stanke@uni-greifswald.de)
+# and Oliver Keller (keller@cs.uni-goettingen.de).
+# 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 ...
+# human version. Using default transition matrix.
+# Looks like /home/bag/projects/galaxy/galaxy-central/database/files/001/dataset_1149.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 g1
+HS04636 AUGUSTUS gene 966 6903 1 + . g1
+HS04636 AUGUSTUS transcript 966 6903 . + . g1.t1
+HS04636 AUGUSTUS intron 1018 1817 . + . transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS intron 1935 2054 . + . transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS intron 2199 2851 . + . transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS intron 2996 3425 . + . transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS intron 3608 4339 . + . transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS intron 4424 4542 . + . transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS intron 4790 5071 . + . transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS intron 5359 5859 . + . transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS intron 6008 6493 . + . transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS CDS 966 1017 . + 0 transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS CDS 1818 1934 . + 2 transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS CDS 2055 2198 . + 2 transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS CDS 2852 2995 . + 2 transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS CDS 3426 3607 . + 2 transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS CDS 4340 4423 . + 0 transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS CDS 4543 4789 . + 0 transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS CDS 5072 5358 . + 2 transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS CDS 5860 6007 . + 0 transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS CDS 6494 6903 . + 2 transcript_id "g1.t1"; gene_id "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 g1
+###
+#
+# ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----
+#
+# Constraints/Hints:
+# (none)
+# Predicted genes for sequence number 2 on both strands
+# start gene g2
+HS08198 AUGUSTUS gene 445 1848 1 + . g2
+HS08198 AUGUSTUS transcript 445 1848 . + . g2.t1
+HS08198 AUGUSTUS intron 583 811 . + . transcript_id "g2.t1"; gene_id "g2";
+HS08198 AUGUSTUS intron 895 1052 . + . transcript_id "g2.t1"; gene_id "g2";
+HS08198 AUGUSTUS intron 1124 1207 . + . transcript_id "g2.t1"; gene_id "g2";
+HS08198 AUGUSTUS intron 1316 1586 . + . transcript_id "g2.t1"; gene_id "g2";
+HS08198 AUGUSTUS intron 1689 1771 . + . transcript_id "g2.t1"; gene_id "g2";
+HS08198 AUGUSTUS CDS 445 582 . + 0 transcript_id "g2.t1"; gene_id "g2";
+HS08198 AUGUSTUS CDS 812 894 . + 0 transcript_id "g2.t1"; gene_id "g2";
+HS08198 AUGUSTUS CDS 1053 1123 . + 1 transcript_id "g2.t1"; gene_id "g2";
+HS08198 AUGUSTUS CDS 1208 1315 . + 2 transcript_id "g2.t1"; gene_id "g2";
+HS08198 AUGUSTUS CDS 1587 1688 . + 2 transcript_id "g2.t1"; gene_id "g2";
+HS08198 AUGUSTUS CDS 1772 1848 . + 2 transcript_id "g2.t1"; gene_id "g2";
+# coding sequence = [atgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccac
+# gccggcccgcatcccccatcagcaccatccagcccaaggccaattttgatgcgcagcaggagcagggccaccgggccgaggccaccacactgcatgtg
+# gctccccagggcacagccatggctgtcagtaccttccgaaagctggatgggatctgctggcaggtgcgccagctctatggagacacaggggtcctcgg
+# ccgcttcctgcttcaagcccgaggcgcccgaggggctgtgcacgtggttgtcgctgagaccgactaccagagtttcgctgtcctgtacctggagcggg
+# cggggcagctgtcagtgaagctctacgcccgctcgctccctgtgagcgactcggtcctgagtgggtttgagcagcgggtccaggaggcccacctgact
+# gaggaccagatcttctacttccccaagtacggcttctgcgaggctgcagaccagttccacgtcctggacggtgagtgcacagcgggggcaagcatggc
+# ggcgtggtga]
+# protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC
+# WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF
+# HVLDGECTAGASMAAW]
+# end gene g2
+###
+# command line:
+# augustus --strand=both --noInFrameStop=false --gff3=off --protein=on --introns=on --start=off --stop=off --cds=on --codingseq=on --singlestrand=false /home/bag/projects/galaxy/galaxy-central/database/files/001/dataset_1149.dat --UTR=off --genemodel=complete --species=human
b
diff -r 000000000000 -r af307d3285c5 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 Sat Jul 06 10:07:41 2013 -0400
b
@@ -0,0 +1,15 @@
+>g1
+MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYILML
+ARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYILTHFK
+GFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNE
+IVEKLLLRRKFIPDPQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQI
+IDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVGQEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLIL
+IGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYHWHPLLPDTFQIHDQKYNYQQFIYNNSILLE
+HGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGEKEMSAELEALYG
+DIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCP
+FTSFSVPDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL
+>g2
+MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGICML
+PPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGICWQVR
+QLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIF
+YFPKYGFCEAADQFHVLDGECTAGASMAAW
b
diff -r 000000000000 -r af307d3285c5 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 Sat Jul 06 10:07:41 2013 -0400
[
@@ -0,0 +1,77 @@
+##gff-version 3
+# This output was generated with AUGUSTUS (version 2.7).
+# AUGUSTUS is a gene prediction tool for eukaryotes written by Mario Stanke (mario.stanke@uni-greifswald.de)
+# and Oliver Keller (keller@cs.uni-goettingen.de).
+# 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 ...
+# human version. Using species specific transition matrix: /home/bag/Downloads/augustus.2.7/config/species/human/human_trans_shadow_partial_utr.pbl
+# Looks like ./examples/example.fa 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 g1
+HS04636 AUGUSTUS gene 836 8857 1 + . ID=g1
+HS04636 AUGUSTUS transcript 836 8857 . + . ID=g1.t1;Parent=g1
+HS04636 AUGUSTUS transcription_start_site 836 836 . + . Parent=g1.t1
+HS04636 AUGUSTUS exon 836 1017 . + . Parent=g1.t1
+HS04636 AUGUSTUS start_codon 966 968 . + 0 Parent=g1.t1
+HS04636 AUGUSTUS CDS 966 1017 . + 0 ID=g1.t1.cds;Parent=g1.t1
+HS04636 AUGUSTUS CDS 1818 1934 . + 2 ID=g1.t1.cds;Parent=g1.t1
+HS04636 AUGUSTUS exon 1818 1934 . + . Parent=g1.t1
+HS04636 AUGUSTUS CDS 2055 2198 . + 2 ID=g1.t1.cds;Parent=g1.t1
+HS04636 AUGUSTUS exon 2055 2198 . + . Parent=g1.t1
+HS04636 AUGUSTUS CDS 2852 2995 . + 2 ID=g1.t1.cds;Parent=g1.t1
+HS04636 AUGUSTUS exon 2852 2995 . + . Parent=g1.t1
+HS04636 AUGUSTUS CDS 3426 3607 . + 2 ID=g1.t1.cds;Parent=g1.t1
+HS04636 AUGUSTUS exon 3426 3607 . + . Parent=g1.t1
+HS04636 AUGUSTUS CDS 4340 4423 . + 0 ID=g1.t1.cds;Parent=g1.t1
+HS04636 AUGUSTUS exon 4340 4423 . + . Parent=g1.t1
+HS04636 AUGUSTUS CDS 4543 4789 . + 0 ID=g1.t1.cds;Parent=g1.t1
+HS04636 AUGUSTUS exon 4543 4789 . + . Parent=g1.t1
+HS04636 AUGUSTUS CDS 5072 5358 . + 2 ID=g1.t1.cds;Parent=g1.t1
+HS04636 AUGUSTUS exon 5072 5358 . + . Parent=g1.t1
+HS04636 AUGUSTUS CDS 5860 6007 . + 0 ID=g1.t1.cds;Parent=g1.t1
+HS04636 AUGUSTUS exon 5860 6007 . + . Parent=g1.t1
+HS04636 AUGUSTUS CDS 6494 6903 . + 2 ID=g1.t1.cds;Parent=g1.t1
+HS04636 AUGUSTUS exon 6494 8857 . + . Parent=g1.t1
+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
+HS08198 AUGUSTUS CDS 445 582 . + 0 ID=g2.t1.cds;Parent=g2.t1
+HS08198 AUGUSTUS CDS 812 894 . + 0 ID=g2.t1.cds;Parent=g2.t1
+HS08198 AUGUSTUS exon 812 894 . + . Parent=g2.t1
+HS08198 AUGUSTUS CDS 1053 1123 . + 1 ID=g2.t1.cds;Parent=g2.t1
+HS08198 AUGUSTUS exon 1053 1123 . + . Parent=g2.t1
+HS08198 AUGUSTUS CDS 1208 1315 . + 2 ID=g2.t1.cds;Parent=g2.t1
+HS08198 AUGUSTUS exon 1208 1315 . + . Parent=g2.t1
+HS08198 AUGUSTUS CDS 1587 1688 . + 2 ID=g2.t1.cds;Parent=g2.t1
+HS08198 AUGUSTUS exon 1587 1688 . + . Parent=g2.t1
+# protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC
+# WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKY]
+# end gene g2
+###
+# command line:
+# ./bin/augustus --species=human --UTR=on --gff3=on ./examples/example.fa
b
diff -r 000000000000 -r af307d3285c5 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 Sat Jul 06 10:07:41 2013 -0400
[
@@ -0,0 +1,80 @@
+# This output was generated with AUGUSTUS (version 2.7).
+# AUGUSTUS is a gene prediction tool for eukaryotes written by Mario Stanke (mario.stanke@uni-greifswald.de)
+# and Oliver Keller (keller@cs.uni-goettingen.de).
+# 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 ...
+# human version. Using species specific transition matrix: /home/bag/Downloads/augustus.2.7/config/species/human/human_trans_shadow_partial_utr.pbl
+# Looks like ./examples/example.fa 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 g1
+HS04636 AUGUSTUS gene 836 8857 1 + . g1
+HS04636 AUGUSTUS transcript 836 8857 . + . g1.t1
+HS04636 AUGUSTUS tss 836 836 . + . transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS exon 836 1017 . + . transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS start_codon 966 968 . + 0 transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS CDS 966 1017 . + 0 transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS CDS 1818 1934 . + 2 transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS exon 1818 1934 . + . transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS CDS 2055 2198 . + 2 transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS exon 2055 2198 . + . transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS CDS 2852 2995 . + 2 transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS exon 2852 2995 . + . transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS CDS 3426 3607 . + 2 transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS exon 3426 3607 . + . transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS CDS 4340 4423 . + 0 transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS exon 4340 4423 . + . transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS CDS 4543 4789 . + 0 transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS exon 4543 4789 . + . transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS CDS 5072 5358 . + 2 transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS exon 5072 5358 . + . transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS CDS 5860 6007 . + 0 transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS exon 5860 6007 . + . transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS CDS 6494 6903 . + 2 transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS exon 6494 8857 . + . transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS stop_codon 6901 6903 . + 0 transcript_id "g1.t1"; gene_id "g1";
+HS04636 AUGUSTUS tts 8857 8857 . + . transcript_id "g1.t1"; gene_id "g1";
+# protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL
+# THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD
+# PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG
+# QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH
+# WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE
+# KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV
+# PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL]
+# end gene g1
+###
+#
+# ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----
+#
+# Constraints/Hints:
+# (none)
+# Predicted genes for sequence number 2 on both strands
+# start gene g2
+HS08198 AUGUSTUS gene 86 2344 1 + . g2
+HS08198 AUGUSTUS transcript 86 2344 . + . g2.t1
+HS08198 AUGUSTUS tss 86 86 . + . transcript_id "g2.t1"; gene_id "g2";
+HS08198 AUGUSTUS exon 86 582 . + . transcript_id "g2.t1"; gene_id "g2";
+HS08198 AUGUSTUS start_codon 445 447 . + 0 transcript_id "g2.t1"; gene_id "g2";
+HS08198 AUGUSTUS CDS 445 582 . + 0 transcript_id "g2.t1"; gene_id "g2";
+HS08198 AUGUSTUS CDS 812 894 . + 0 transcript_id "g2.t1"; gene_id "g2";
+HS08198 AUGUSTUS exon 812 894 . + . transcript_id "g2.t1"; gene_id "g2";
+HS08198 AUGUSTUS CDS 1053 1123 . + 1 transcript_id "g2.t1"; gene_id "g2";
+HS08198 AUGUSTUS exon 1053 1123 . + . transcript_id "g2.t1"; gene_id "g2";
+HS08198 AUGUSTUS CDS 1208 1315 . + 2 transcript_id "g2.t1"; gene_id "g2";
+HS08198 AUGUSTUS exon 1208 1315 . + . transcript_id "g2.t1"; gene_id "g2";
+HS08198 AUGUSTUS CDS 1587 1688 . + 2 transcript_id "g2.t1"; gene_id "g2";
+HS08198 AUGUSTUS exon 1587 1688 . + . transcript_id "g2.t1"; gene_id "g2";
+# protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC
+# WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKY]
+# end gene g2
+###
+# command line:
+# ./bin/augustus --species=human --UTR=on ./examples/example.fa
b
diff -r 000000000000 -r af307d3285c5 tool_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_conf.xml Sat Jul 06 10:07:41 2013 -0400
b
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<toolbox>
+  <section name="Gene Prediction" id="gene_prediction">
+        <tool file="gene_prediction/tools/augustus/augustus.xml" />
+  </section>
+</toolbox>
b
diff -r 000000000000 -r af307d3285c5 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Sat Jul 06 10:07:41 2013 -0400
b
@@ -0,0 +1,36 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <set_environment version="1.0">
+        <environment_variable name="AUGUSTUS_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
+    </set_environment>
+    <package name="augustus" version="2.7">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://bioinf.uni-greifswald.de/augustus/binaries/augustus.2.7.tar.gz</action>
+                <action type="shell_command">make</action>
+                <action type="move_directory_files">
+                    <source_directory>bin</source_directory>
+                    <destination_directory>$INSTALL_DIR/bin</destination_directory>
+                </action>
+                <action type="move_directory_files">
+                    <source_directory>scripts</source_directory>
+                    <destination_directory>$INSTALL_DIR/scripts</destination_directory>
+                </action>
+                <action type="move_directory_files">
+                    <source_directory>config</source_directory>
+                    <destination_directory>$INSTALL_DIR/config</destination_directory>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/scripts</environment_variable>
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable name="AUGUSTUS_CONFIG_PATH" action="set_to">$INSTALL_DIR/config</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller.
+It can be used as an ab initio program, which means it bases its prediction purely on the
+sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources
+such as EST, MS/MS, protein alignments and synthenic genomic alignments.
+http://augustus.gobics.de/binaries/README.TXT</readme>
+    </package>
+</tool_dependency>