# HG changeset patch # User bgruening # Date 1373119661 14400 # Node ID af307d3285c506db91038c64a55ef8af5e5c8da9 Uploaded 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 @@ -0,0 +1,246 @@ + + gene prediction for eukaryotic genomes + + augustus + AUGUSTUS_SCRIPT_PATH + + + ## please set export AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config + ## or use the --AUGUSTUS_CONFIG_PATH=path if you are not installing through the toolshed + ## 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 + + augustus + --strand=$strand + $noInFrameStop + $gff + $protein + $introns + $start + $stop + $cds + $codingseq + $singlestrand + $input_genome + $mea + $utr + --genemodel=$genemodel + --species=$organism + ##--outfile=$output + | tee $output + #if $protein or $codingseq: + | python \$AUGUSTUS_SCRIPT_PATH/extract_features.py + #if $protein: + --protein $protein_output + #end if + #if $codingseq: + --codingseq $codingseq_output + #end if + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + protein == True + + + codingseq == True + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +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. + +----- + +**Parameters** + +Gene Model:: + + partial : allow prediction of incomplete genes at the sequence boundaries (default) + intronless : only predict single-exon genes like in prokaryotes and some eukaryotes + complete : only predict complete genes + atleastone : predict at least one complete gene + exactlyone : predict exactly one complete gene + + + +**Example** + +Suppose you have the following DNA formatted sequences:: + + >Seq1 + cccgcggagcgggtaccacatcgctgcgcgatgtgcgagcgaacacccgggctgcgcccg + ggtgttgcgctcccgctccgcgggagcgctggcgggacgctgcgcgtcccgctcaccaag + cccgcttcgcgggcttggtgacgctccgtccgctgcgcttccggagttgcggggcttcgc + cccgctaaccctgggcctcgcttcgctccgccttgggcctgcggcgggtccgctgcgctc + ccccgcctcaagggcccttccggctgcgcctccaggacccaaccgcttgcgcgggcctgg + +Running this tool will produce this:: + + # ----- prediction on sequence number 1 (length = 1992969, name = scaffold1|size1992969) ----- + # + # Constraints/Hints: + # (none) + # Predicted genes for sequence number 1 on both strands + # start gene g1 + scaffold1|size1992969 AUGUSTUS gene 17453 19382 0.11 + . g6 + scaffold1|size1992969 AUGUSTUS transcript 17453 19382 0.11 + . g6.t1 + scaffold1|size1992969 AUGUSTUS start_codon 17453 17455 . + 0 transcript_id "g6.t1"; gene_id "g6"; + scaffold1|size1992969 AUGUSTUS intron 17615 17660 0.38 + . transcript_id "g6.t1"; gene_id "g6"; + scaffold1|size1992969 AUGUSTUS intron 17708 17772 0.54 + . transcript_id "g6.t1"; gene_id "g6"; + scaffold1|size1992969 AUGUSTUS intron 17902 18035 0.58 + . transcript_id "g6.t1"; gene_id "g6"; + scaffold1|size1992969 AUGUSTUS intron 18313 18367 0.99 + . transcript_id "g6.t1"; gene_id "g6"; + scaffold1|size1992969 AUGUSTUS intron 19014 19080 0.44 + . transcript_id "g6.t1"; gene_id "g6"; + scaffold1|size1992969 AUGUSTUS CDS 17453 17614 0.55 + 0 transcript_id "g6.t1"; gene_id "g6"; + scaffold1|size1992969 AUGUSTUS CDS 17661 17707 0.38 + 0 transcript_id "g6.t1"; gene_id "g6"; + scaffold1|size1992969 AUGUSTUS CDS 17773 17901 0.54 + 1 transcript_id "g6.t1"; gene_id "g6"; + scaffold1|size1992969 AUGUSTUS CDS 18036 18312 0.52 + 1 transcript_id "g6.t1"; gene_id "g6"; + scaffold1|size1992969 AUGUSTUS CDS 18368 19013 0.99 + 0 transcript_id "g6.t1"; gene_id "g6"; + scaffold1|size1992969 AUGUSTUS CDS 19081 19379 0.31 + 2 transcript_id "g6.t1"; gene_id "g6"; + scaffold1|size1992969 AUGUSTUS stop_codon 19380 19382 . + 0 transcript_id "g6.t1"; gene_id "g6"; + + +**References** + +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 + + + + 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 ) + 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 @@ -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:: + +

+ +

+ + +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. + 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 @@ -0,0 +1,53 @@ +>arabidopsis +ATATCATTCATGGGCCCCTACGCATTACTCGGTACCAATCTCGCTCTCTCTCTCTAAGTCTTGAAACTCTATCAAGAAT +CTCAAGCCACCATTTTTTCTTCATCTTCATAAAGAGAAAGAGAGAGATCCTCTTGTTTGGCAAGAACCCAATTTGAGTT +CTAAGTCCTGATTTGCTTAGCTCTTTTCTTTCCTTGATTTCATTCTATATAAAGTCAACGGAAAGATATACATATATAG +TTTTCTTCCGATTCTAGGGTTTTCATATTTCCTCTAAATTTTCATGGTCAAAGAAGAAAATCTAAGAAACAATCGAACC +AGCAAGAGAAAGAAGACTTCAATATCAACATCTCTCTCTCCCTCTCTCTCTCTTATATTATAAGGTGAGACCACAAGAA +CTTTTGATTTTCTTTTTCCTTCTTCCCTTCTTTTAATATATTCTTTGAATTTTTTTTCACTAATTCATCTACCCTTTTT +TATAATTGTGGCTAGATTTTTGTTTCGTTTCCTCTTTTTAATATTATCTCTCTAATGTATGTTGAAGATCTCGAGTTGA +GTCATCATCATCGTCAATGGCTTTGAAAAACATCCGCAACAATTCACCAATTGAAGAACAAGAGAAAGGTTTAAACTTC +ATCAAGATTCACTAAGACCCACTAAGAGCCAACTCAAAACTAAACGGAGCAAGGTTTTGCCAAAAACCAAAAAAAAAAA +AAAAAAGATTCAAGAACCATCTCGTAAATCAAGATTTCTCCAAGGAAAATCAGATAAGTCATAATGGATCTATCCCTGG +CTCCGACAACAACAACAAGTTCCGACCAAGAACAAGACAGAGACCAAGAATTAACCTCCAACATCGGAGCAAGCAGCAG +CTCCGGTCCCAGCGGAAACAACAACAACCTTCCGATGATGATGATTCCACCTCCGGAGAAAGAACACATGTTCGACAAA +GTGGTAACACCAAGCGACGTCGGAAAACTCAACAGACTCGTGATCCCTAAACAACACGCTGAGAGGTATTTCCCTCTAG +ACTCCTCAAACAACCAAAACGGCACGCTTTTGAACTTCCAAGACAGAAACGGCAAGATGTGGAGATTCCGTTACTCGTA +TTGGAACTCTAGCCAGAGCTACGTTATGACCAAAGGATGGAGCCGTTTCGTCAAAGAGAAAAAGCTCGATGCAGGAGAC +ATTGTCTCTTTCCAACGAGGCATCGGAGATGAGTCAGAAAGATCCAAACTTTACATAGATTGGAGGCATAGACCCGACA +TGAGCCTCGTTCAAGCACATCAGTTTGGTAATTTTGGTTTCAATTTCAATTTCCCGACCACTTCTCAATATTCCAACAG +ATTTCATCCATTGCCAGAATATAACTCCGTCCCGATTCACCGGGGCTTAAACATCGGAAATCACCAACGTTCCTATTAT +AACACCCAGCGTCAAGAGTTCGTAGGGTATGGTTATGGGAATTTAGCTGGAAGGTGTTACTACACGGGATCACCGTTGG +ATCATAGGAACATTGTTGGATCAGAGCCGTTGGTTATAGACTCAGTCCCTGTGGTTCCCGGGAGATTAACTCCGGTGAT +GTTACCGCCGCTTCCTCCGCCTCCTTCTACGGCGGGAAAGAGACTAAGGCTCTTTGGGGTGAATATGGAATGTGGCAAT +GACTATAATCAACAAGAAGAGTCATGGTTGGTGCCACGTGGCGAAATTGGTGCATCTTCTTCTTCTTCTTCAGCTCTAC +GACTAAATTTATCGACTGATCATGATGATGATAATGATGATGGTGATGATGGCGATGATGATCAATTTGCTAAGAAAGG +GAAGTCTTCACTTTCTCTCAATTTCAATCCATGAGAAGTTTCATCATCTTCTTGTTTTGAATCTCTCTTTATATTGTTT +CATTAGTAATTTTTCTAAGGGTATTAGATTCTAGCTAGTGAGAGGAAGAAAAAACGATCTTCTTCGTTTTTTTGGTTAT +GATTTTTTTTTCCGACATGTTTCTTGATGTTCATCATCATTAGGCTTTTGTCACCATGTTGAAACTCGCATCTTTTCAA +TTTTGTATATAA + +>arabidopsis2 +CTCCTCTGCCTCTCATCTCTTGTTCTCTCCGCCCATCTCTGCTCTCTTTTATTTTCCCAGAAAGTTTTTTTTTTTTTTT +TCCGAATTCCGTTAATCTCATTGGGGTTTCCATTGATAGCAATGGCGACGGCTTTCGCTCCCACTAAGCTCACTGCCAC +GGTTCCTCTGCATGGATCCCATGAGAATCGTCTCTTGCTCCCGATCCGATTGGCTCCTCCTTCTTCTTTCCTCGGATCC +ACCCGTTCCCTCTCCCTTCGCAGACTCAATCACTCCAACGCCACCCGTCGATCTCCCGTCGTCTCTGTCCAGGAAGTTG +TCAAGGAGAAGCAATCCACCAATAATACCAGCCTGGTACGCTTCCTCTCCTCGTCTCCTTCTTTTGGAATTTTACAAGT +TGTGAGATTTGTTGTATTGATTTAAGTAATTTGAAATAGTTGATAACCAAAGAGGAAGGATTGGAGTTGTATGAAGATA +TGATACTAGGTAGATCTTTCGAAGACATGTGTGCTCAAATGTATTACCGAGGCAAGATGTTTGGTTTTGTTCACTTGTA +CAATGGCCAAGAGGCTGTTTCTACTGGCTTTATCAAGCTCCTTACCAAGTCTGACTCTGTCGTTAGTACCTACCGTGAC +CATGTCCATGCCCTCAGCAAAGGTGTCTCTGCTCGTGCTGTTATGAGCGAGCTCTTCGGCAAGGTTACTGGATGCTGCA +GAGGCCAAGGTGGATCCATGCACATGTTCTCCAAAGAACACAACATGCTTGGTGGCTTTGCTTTTATTGGTGAAGGCAT +TCCTGTCGCCACTGGTGCTGCCTTTAGCTCCAAGTACAGGAGGGAAGTCTTGAAACAGGATTGTGATGATGTCACTGTC +GCCTTTTTCGGAGATGGAACTTGTAACAACGGACAGTTCTTCGAGTGTCTCAACATGGCTGCTCTCTATAAACTGCCTA +TTATCTTTGTTGTCGAGAATAACTTGTGGGCCATTGGGATGTCTCACTTGAGAGCCACTTCTGACCCCGAGATTTGGAA +GAAAGGTCCTGCATTTGGGATGCCTGGTGTTCATGTTGACGGTATGGATGTCTTGAAGGTCAGGGAAGTCGCTAAAGAA +GCTGTCACTAGAGCTAGAAGAGGAGAAGGTCCAACCTTGGTTGAATGTGAGACTTATAGATTCAGAGGACACTCCTTGG +CTGATCCCGATGAGCTCCGTGATGCTGGTAAATATCGACTTCCTTCTGCTTCTTGATGCTTGTACTGATTATCTAAGGG +TTGAAACAACCTTCTCTTTAATTTGAATTTTTTTTTGCAGCTGAGAAAGCCAAATACGCGGCTAGAGACCCAATCGCAG +CATTGAAGAAGTATTTGATAGAGAACAAGCTTGCAAAGGAAGCAGAGCTAAAGTCAATAGAGAAAAAGATAGACGAGTT +GGTGGAGGAAGCGGTTGAGTTTGCAGACGCTAGTCCACAGCCCGGTCGCAGTCAGTTGCTAGAGAATGTGTTTGCTGAT +CCAAAAGGATTTGGAATTGGACCTGATGGACGGTACAGATGTGAGGACCCCAAGTTTACCGAAGGCACAGCTCAAGTCT +GAGAAGACAAGTTTAACCATAAGCTGTCTACTGTCTCTTCGATGTTTCTATATATCTTATTAAGTTAAATGCTACAGAG +AATCAGTTTGAATCATTTGCACTTTTTGCTTTTTGTTTGGTGTTACTAAACTATCACAAGGTTCTTCTTGTAGTTCGTT +GGGTTTTCATTGGTTACCACTTACCAGAGAATTGTATTTTTTTTTTTAAAGATAATTATTTTGC diff -r 000000000000 -r 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 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 @@ -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 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+gcaccggctgagtctcgtctctgctgcagaagtgaggaggtgaggccggcacacagctcc +agtgctgagaagtcagtgccccgagagacgaccccaccagtggggtgcccgctgcctgtc +ctccgtgaaaccagcctcagatcagggccctgccacccagggcaggggatcttctgccgg +ctgccccagaggacagtgggtggagtggtacctacttattaaatgtctcagacccctctc +tgactcttctgtccactctggaccggcgccagtaccaccaaggccctctctgcccccacc +ccgcctctttaaaagcccggcgctccctgttggctggagtccacgcagggtcactgggcc +gatttcggctcttgggatttgggaggggagatcctctctggcatatgccatcttgtgccc +tgctggacctgggggcgtccacgtcactccaaggctgctcttgcctgggccatgcctgca +gccc 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 @@ -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 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 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 @@ -0,0 +1,15 @@ +>g1 +MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYILML +ARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYILTHFK +GFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNE +IVEKLLLRRKFIPDPQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQI +IDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVGQEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLIL +IGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYHWHPLLPDTFQIHDQKYNYQQFIYNNSILLE +HGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGEKEMSAELEALYG +DIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCP +FTSFSVPDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL +>g2 +MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGICML +PPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGICWQVR +QLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIF +YFPKYGFCEAADQFHVLDGECTAGASMAAW 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 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 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 @@ -0,0 +1,6 @@ + + +

+ +

+ 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 @@ -0,0 +1,36 @@ + + + + $REPOSITORY_INSTALL_DIR + + + + + http://bioinf.uni-greifswald.de/augustus/binaries/augustus.2.7.tar.gz + make + + bin + $INSTALL_DIR/bin + + + scripts + $INSTALL_DIR/scripts + + + config + $INSTALL_DIR/config + + + $INSTALL_DIR/scripts + $INSTALL_DIR/bin + $INSTALL_DIR/config + + + + 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 + +