| Next changeset 1:e2b822d7408f (2013-12-05) |
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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 |
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| 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 |
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| 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' |
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| 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 |
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| @@ -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 ) + |
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| 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 |
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| @@ -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. + |
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| 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 |
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| @@ -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 |
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| 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 |
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| 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> |
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| 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> |