# HG changeset patch # User iuc # Date 1508485737 14400 # Node ID 4de31938431bb44e70dbd2789ad5538bcae55cdc # Parent f5075dee9d6b4e250f0894579082c341173bbf4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e diff -r f5075dee9d6b -r 4de31938431b augustus.xml --- a/augustus.xml Fri May 22 04:55:25 2015 -0400 +++ b/augustus.xml Fri Oct 20 03:48:57 2017 -0400 @@ -1,17 +1,24 @@ - - gene prediction for eukaryotic genomes - - - augustus - - - - - - - - + + gene prediction for prokaryotic and eukaryotic genomes + + macros.xml + + + /dev/null && + + export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ && + #end if + ## 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 @@ -61,9 +68,15 @@ $input_genome $utr --genemodel=$genemodel - --species=$organism + - | tee $output + #if $model.augustus_mode == 'history' + --species=local + #else + --species=$model.organism + #end if + + | tee '$output' #if 'protein' in str($outputs).split(',') or 'codingseq' in str($outputs).split(','): | python $__tool_directory__/extract_features.py #if 'protein' in str($outputs).split(','): @@ -78,126 +91,139 @@ + help="Otherwise, intron-spanning stop codons could occur." /> + help="This currently works only for human, galdieria, toxoplasma and caenorhabditis." /> + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + label="Predict genes on specific strands"> + help="Gene Model to predict, for more information please refere to the help."> @@ -206,7 +232,7 @@ @@ -216,10 +242,7 @@ - - - @@ -262,37 +285,47 @@ **What it does** -AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller. +AUGUSTUS is a gene prediction program for prokaryotes and 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. ------ + +**Input** + +Input data for the gene prediction tool Augustus is a FASTA file with a genomic nucleotide sequence. + + +**Output** + +Augustus produces three output files: a FASTA file with predicted coding sequences, a FASTA file with predicted protein sequences and a gtf/GFF output file if selected. + **Parameters** -Gene Model:: +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 +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:: +Suppose you have the following DNA FASTA sequence: - >Seq1 - cccgcggagcgggtaccacatcgctgcgcgatgtgcgagcgaacacccgggctgcgcccg - ggtgttgcgctcccgctccgcgggagcgctggcgggacgctgcgcgtcccgctcaccaag - cccgcttcgcgggcttggtgacgctccgtccgctgcgcttccggagttgcggggcttcgc - cccgctaaccctgggcctcgcttcgctccgccttgggcctgcggcgggtccgctgcgctc - ccccgcctcaagggcccttccggctgcgcctccaggacccaaccgcttgcgcgggcctgg +>Seq1 +cccgcggagcgggtaccacatcgctgcgcgatgtgcgagcgaacacccgggctgcgcccg +ggtgttgcgctcccgctccgcgggagcgctggcgggacgctgcgcgtcccgctcaccaag +cccgcttcgcgggcttggtgacgctccgtccgctgcgcttccggagttgcggggcttcgc +cccgctaaccctgggcctcgcttcgctccgccttgggcctgcggcgggtccgctgcgctc +ccccgcctcaagggcccttccggctgcgcctccaggacccaaccgcttgcgcgggcctgg -Running this tool will produce this:: + +Running this tool will produce this: # ----- prediction on sequence number 1 (length = 1992969, name = scaffold1|size1992969) ----- # @@ -319,7 +352,5 @@ ]]> - - 10.1093/bioinformatics/btg1080 - + diff -r f5075dee9d6b -r 4de31938431b extract_features.py --- a/extract_features.py Fri May 22 04:55:25 2015 -0400 +++ b/extract_features.py Fri Oct 20 03:48:57 2017 -0400 @@ -1,10 +1,10 @@ #!/usr/bin/env python -import os +import argparse import sys -import argparse import textwrap + def main( args ): """ Extract the protein and coding section from an augustus gff, gtf file @@ -45,6 +45,22 @@ if line.startswith('start gene'): gene_name = line[11:].strip() + if protein_seq: + if line.endswith(']'): + protein_seq += line[:-1] + po.write( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( protein_seq, 80 ) ) ) ) + protein_seq = '' + else: + protein_seq += line + + if coding_seq: + if line.endswith(']'): + coding_seq += line[:-1] + co.write( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( coding_seq, 80 ) ) ) ) + coding_seq = '' + else: + coding_seq += line + if args.protein and line.startswith('protein sequence = ['): if line.endswith(']'): protein_seq = line[20:-1] @@ -63,26 +79,12 @@ 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.') @@ -90,4 +92,3 @@ args = parser.parse_args() main( args ) - diff -r f5075dee9d6b -r 4de31938431b macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Oct 20 03:48:57 2017 -0400 @@ -0,0 +1,20 @@ + + + + + augustus + + + + + 3.2.3 + + + + 10.1093/bioinformatics/btg1080 + 10.1093/bioinformatics/btr010 + 10.1093/bioinformatics/btn013 + + + + diff -r f5075dee9d6b -r 4de31938431b readme.rst --- a/readme.rst Fri May 22 04:55:25 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,84 +0,0 @@ -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/bgruening/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 -- v0.3.1: added parallelism and changed the output parameters from boolean to a select box - -Licence (MIT) -============= - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in -all copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN -THE SOFTWARE. - diff -r f5075dee9d6b -r 4de31938431b test-data/annot.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annot.gff3 Fri Oct 20 03:48:57 2017 -0400 @@ -0,0 +1,41 @@ +##gff-version 3 +HS08198 maker gene 352 1848 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0;Name=maker-HS08198-exonerate_est2genome-gene-0.0 +HS08198 maker mRNA 352 1848 2869 + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1;Parent=maker-HS08198-exonerate_est2genome-gene-0.0;Name=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1;_AED=0.00;_eAED=0.00;_QI=70|1|1|1|0|0|7|0|192 +HS08198 maker exon 352 397 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:9;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker exon 421 582 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:10;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker exon 812 894 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:11;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker exon 1053 1123 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:12;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker exon 1208 1315 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:13;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker exon 1587 1688 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:14;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker exon 1772 1848 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:15;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker five_prime_UTR 352 397 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker five_prime_UTR 421 444 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker CDS 445 582 . + 0 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker CDS 812 894 . + 0 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker CDS 1053 1123 . + 1 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker CDS 1208 1315 . + 2 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker CDS 1587 1688 . + 2 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker CDS 1772 1848 . + 2 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +### +HS04636 maker gene 1813 6903 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0;Name=maker-HS04636-exonerate_est2genome-gene-0.0 +HS04636 maker mRNA 1813 6903 8728 + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1;Parent=maker-HS04636-exonerate_est2genome-gene-0.0;Name=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1;_AED=0.00;_eAED=0.00;_QI=49|1|1|1|0|0|9|0|572 +HS04636 maker exon 1813 1934 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:0;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 2055 2198 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:1;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 2852 2995 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:2;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 3426 3607 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:3;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 4340 4423 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:4;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 4543 4789 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:5;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 5072 5358 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:6;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 5860 6007 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:7;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 6494 6903 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:8;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker five_prime_UTR 1813 1861 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 1862 1934 . + 0 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 2055 2198 . + 2 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 2852 2995 . + 2 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 3426 3607 . + 2 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 4340 4423 . + 0 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 4543 4789 . + 0 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 5072 5358 . + 2 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 5860 6007 . + 0 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 6494 6903 . + 2 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +### diff -r f5075dee9d6b -r 4de31938431b test-data/human_augustus_protein_codingseq_introns_cds_codingseq.fasta --- a/test-data/human_augustus_protein_codingseq_introns_cds_codingseq.fasta Fri May 22 04:55:25 2015 -0400 +++ b/test-data/human_augustus_protein_codingseq_introns_cds_codingseq.fasta Fri Oct 20 03:48:57 2017 -0400 @@ -1,35 +1,33 @@ >HS04636.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 +aaaccgaggtgtatgtatgagtgtgggatttgaccagtataagtgcgattgtacccggacaggattctatggagaaaact +gctcaacaccggaatttttgacaagaataaaattatttctgaaacccactccaaacacagtgcactacatacttacccac +ttcaagggattttggaacgttgtgaataacattcccttccttcgaaatgcaattatgagttatgtcttgacatccagatc +acatttgattgacagtccaccaacttacaatgctgactatggctacaaaagctgggaagccttctctaacctctcctatt +atactagagcccttcctcctgtgcctgatgattgcccgactcccttgggtgtcaaaggtaaaaagcagcttcctgattca +aatgagattgtggaaaaattgcttctaagaagaaagttcatccctgatccccagggctcaaacatgatgtttgcattctt +tgcccagcacttcacgcatcagtttttcaagacagatcataagcgagggccagctttcaccaacgggctgggccatgggg +tggacttaaatcatatttacggtgaaactctggctagacagcgtaaactgcgccttttcaaggatggaaaaatgaaatat +cagataattgatggagagatgtatcctcccacagtcaaagatactcaggcagagatgatctaccctcctcaagtccctga +gcatctacggtttgctgtggggcaggaggtctttggtctggtgcctggtctgatgatgtatgccacaatctggctgcggg +aacacaacagagtatgcgatgtgcttaaacaggagcatcctgaatggggtgatgagcagttgttccagacaagcaggcta +atactgataggagagactattaagattgtgattgaagattatgtgcaacacttgagtggctatcacttcaaactgaaatt +tgacccagaactacttttcaacaaacaattccagtaccaaaatcgtattgctgctgaatttaacaccctctatcactggc +atccccttctgcctgacacctttcaaattcatgaccagaaatacaactatcaacagtttatctacaacaactctatattg +ctggaacatggaattacccagtttgttgaatcattcaccaggcaaattgctggcagggttgctggtggtaggaatgttcc +acccgcagtacagaaagtatcacaggcttccattgaccagagcaggcagatgaaataccagtcttttaatgagtaccgca +aacgctttatgctgaagccctatgaatcatttgaagaacttacaggagaaaaggaaatgtctgcagagttggaagcactc +tatggtgacatcgatgctgtggagctgtatcctgcccttctggtagaaaagcctcggccagatgccatctttggtgaaac +catggtagaagttggagcaccattctccttgaaaggacttatgggtaatgttatatgttctcctgcctactggaagccaa +gcacttttggtggagaagtgggttttcaaatcatcaacactgcctcaattcagtctctcatctgcaataacgtgaagggc +tgtccctttacttcattcagtgttccagatccagagctcattaaaacagtcaccatcaatgcaagttcttcccgctccgg +actagatgatatcaatcccacagtactactaaaagaacgttcgactgaactgtag >HS08198.g2 -atgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccaca -tgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccacgc -cggcccgcatcccccatcagcaccatccagcccaaggccaattttgatgcgcagcaggagcagggccaccgggccgaggc -caccacactgcatgtggctccccagggcacagccatggctgtcagtaccttccgaaagctggatgggatctgctggcagg -tgcgccagctctatggagacacaggggtcctcggccgcttcctgcttcaagcccgaggcgcccgaggggctgtgcacgtg -gttgtcgctgagaccgactaccagagtttcgctgtcctgtacctggagcgggcggggcagctgtcagtgaagctctacgc -ccgctcgctccctgtgagcgactcggtcctgagtgggtttgagcagcgggtccaggaggcccacctgactgaggaccaga -tcttctacttccccaagtacggcttctgcgaggctgcagaccagttccacgtcctggacggtgagtgcacagcgggggca -agcatggcggcgtggtga +atgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccacg +ccggcccgcatcccccatcagcaccatccagcccaaggccaattttgatgcgcagcaggagcagggccaccgggccgagg +ccaccacactgcatgtggctccccagggcacagccatggctgtcagtaccttccgaaagctggatgggatctgctggcag +gtgcgccagctctatggagacacaggggtcctcggccgcttcctgcttcaagcccgaggcgcccgaggggctgtgcacgt +ggttgtcgctgagaccgactaccagagtttcgctgtcctgtacctggagcgggcggggcagctgtcagtgaagctctacg +cccgctcgctccctgtgagcgactcggtcctgagtgggtttgagcagcgggtccaggaggcccacctgactgaggaccag +atcttctacttccccaagtacggcttctgcgaggctgcagaccagttccacgtcctggacggtgagtgcacagcgggggc +aagcatggcggcgtggtga diff -r f5075dee9d6b -r 4de31938431b test-data/human_augustus_protein_codingseq_introns_cds_main.gtf --- a/test-data/human_augustus_protein_codingseq_introns_cds_main.gtf Fri May 22 04:55:25 2015 -0400 +++ b/test-data/human_augustus_protein_codingseq_introns_cds_main.gtf Fri Oct 20 03:48:57 2017 -0400 @@ -1,6 +1,6 @@ -# This output was generated with AUGUSTUS (version 3.1.0). -# AUGUSTUS is a gene prediction tool written by Mario Stanke (mario.stanke@uni-greifswald.de), -# Oliver Keller, Stefanie König and Lizzy Gerischer. +# This output was generated with AUGUSTUS (version 3.2.3). +# AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), +# O. Keller, S. König, L. Gerischer and L. Romoth. # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), # Using native and syntenically mapped cDNA alignments to improve de novo gene finding # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 diff -r f5075dee9d6b -r 4de31938431b test-data/human_augustus_protein_codingseq_introns_cds_protein.fasta --- a/test-data/human_augustus_protein_codingseq_introns_cds_protein.fasta Fri May 22 04:55:25 2015 -0400 +++ b/test-data/human_augustus_protein_codingseq_introns_cds_protein.fasta Fri Oct 20 03:48:57 2017 -0400 @@ -1,15 +1,13 @@ >HS04636.g1 -MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYILML -ARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYILTHFK -GFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNE -IVEKLLLRRKFIPDPQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQI -IDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVGQEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLIL -IGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYHWHPLLPDTFQIHDQKYNYQQFIYNNSILLE -HGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGEKEMSAELEALYG -DIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCP -FTSFSVPDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL +MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYILTH +FKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDS +NEIVEKLLLRRKFIPDPQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKY +QIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVGQEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRL +ILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYHWHPLLPDTFQIHDQKYNYQQFIYNNSIL +LEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGEKEMSAELEAL +YGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKG +CPFTSFSVPDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL >HS08198.g2 -MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGICML -PPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGICWQVR -QLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIF -YFPKYGFCEAADQFHVLDGECTAGASMAAW +MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGICWQ +VRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQ +IFYFPKYGFCEAADQFHVLDGECTAGASMAAW diff -r f5075dee9d6b -r 4de31938431b test-data/human_augustus_utr-on.gff --- a/test-data/human_augustus_utr-on.gff Fri May 22 04:55:25 2015 -0400 +++ b/test-data/human_augustus_utr-on.gff Fri Oct 20 03:48:57 2017 -0400 @@ -1,7 +1,7 @@ ##gff-version 3 -# This output was generated with AUGUSTUS (version 3.1.0). -# AUGUSTUS is a gene prediction tool written by Mario Stanke (mario.stanke@uni-greifswald.de), -# Oliver Keller, Stefanie König and Lizzy Gerischer. +# This output was generated with AUGUSTUS (version 3.2.3). +# AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), +# O. Keller, S. König, L. Gerischer and L. Romoth. # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), # Using native and syntenically mapped cDNA alignments to improve de novo gene finding # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 diff -r f5075dee9d6b -r 4de31938431b test-data/human_augustus_utr-on.gtf --- a/test-data/human_augustus_utr-on.gtf Fri May 22 04:55:25 2015 -0400 +++ b/test-data/human_augustus_utr-on.gtf Fri Oct 20 03:48:57 2017 -0400 @@ -1,6 +1,6 @@ -# This output was generated with AUGUSTUS (version 3.1.0). -# AUGUSTUS is a gene prediction tool written by Mario Stanke (mario.stanke@uni-greifswald.de), -# Oliver Keller, Stefanie König and Lizzy Gerischer. +# This output was generated with AUGUSTUS (version 3.2.3). +# AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), +# O. Keller, S. König, L. Gerischer and L. Romoth. # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), # Using native and syntenically mapped cDNA alignments to improve de novo gene finding # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 diff -r f5075dee9d6b -r 4de31938431b tool_dependencies.xml --- a/tool_dependencies.xml Fri May 22 04:55:25 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ - - - - - -