| Next changeset 1:1fbb1135da16 (2019-05-10) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e |
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added:
augustus_training.xml extract_features.py macros.xml test-data/annot.gff3 test-data/arabidopsis_augustus.fa test-data/human_augustus.fa test-data/human_augustus_protein_codingseq_introns_cds_codingseq.fasta test-data/human_augustus_protein_codingseq_introns_cds_main.gtf test-data/human_augustus_protein_codingseq_introns_cds_protein.fasta test-data/human_augustus_utr-on.gff test-data/human_augustus_utr-on.gtf |
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| diff -r 000000000000 -r 86c89c3bd99d augustus_training.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/augustus_training.xml Fri Oct 20 03:55:35 2017 -0400 |
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| @@ -0,0 +1,43 @@ +<?xml version="1.0"?> +<tool id="augustus_training" name="Train Augustus" profile="16.04" version="@VERSION@"> + <description>ab-initio gene predictor</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"> + <requirement type="package" version="2.31.9">maker</requirement> + </expand> + <command><![CDATA[ + cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ && + + export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ && + + maker2zff '${maker_gff}' && + + zff2gff3.pl genome.ann | perl -plne 's/\t(\S+)$/\t\.\t$1/' > genome.gff3 && + + autoAugTrain.pl --genome=${genome} --species=local --trainingset=genome.gff3 -v && + + cd 'augustus_dir/species/' && tar cvfz '${output_tar}' 'local' + ]]></command> + <inputs> + <param name="genome" type="data" format="fasta" label="Genome to annotate"/> + <param name="maker_gff" type="data" format="gff" label="Annotation to use for training"/> + </inputs> + <outputs> + <data name="output_tar" format="augustus" label="${tool.name} on ${on_string}: Augustus trained model"/> + </outputs> + <tests> + <test expect_failure="true"> + <param name="genome" value="human_augustus.fa"/> + <param name="maker_gff" value="annot.gff3"/> + <assert_stderr> + <has_text text="Number of training genes is with 2 too low (at least 100 genes required)" /> + </assert_stderr> + </test> + </tests> + <help><![CDATA[ + This tool allows to train Augustus (the ab-initio gene predictor) based on a previous prediction (e.g. made with Maker). + ]]></help> + <expand macro="citations"/> +</tool> |
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| diff -r 000000000000 -r 86c89c3bd99d extract_features.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/extract_features.py Fri Oct 20 03:55:35 2017 -0400 |
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| @@ -0,0 +1,94 @@ +#!/usr/bin/env python + +import argparse +import sys +import textwrap + + +def main( args ): + """ + Extract the protein and coding section from an augustus gff, gtf file + Example file: +HS04636 AUGUSTUS stop_codon 6901 6903 . + 0 Parent=g1.t1 +HS04636 AUGUSTUS transcription_end_site 8857 8857 . + . Parent=g1.t1 +# protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL +# THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD +# PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG +# QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH +# WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE +# KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV +# PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL] +# end gene g1 +### +# +# ----- prediction on sequence number 2 (length = 2344, name = HS08198) ----- +# +# Predicted genes for sequence number 2 on both strands +# start gene g2 +HS08198 AUGUSTUS gene 86 2344 1 + . ID=g2 +HS08198 AUGUSTUS transcript 86 2344 . + . ID=g2.t1;Parent=g2 +HS08198 AUGUSTUS transcription_start_site 86 86 . + . Parent=g2.t1 +HS08198 AUGUSTUS exon 86 582 . + . Parent=g2.t1 +HS08198 AUGUSTUS start_codon 445 447 . + 0 Parent=g2.t1 + """ + protein_seq = '' + coding_seq = '' + if args.protein: + po = open( args.protein, 'w+' ) + if args.codingseq: + co = open( args.codingseq, 'w+' ) + + for line in sys.stdin: + # protein- and coding-sequence are stored as comments + if line.startswith('#'): + line = line[2:].strip() + if line.startswith('start gene'): + gene_name = line[11:].strip() + + if protein_seq: + if line.endswith(']'): + protein_seq += line[:-1] + po.write( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( protein_seq, 80 ) ) ) ) + protein_seq = '' + else: + protein_seq += line + + if coding_seq: + if line.endswith(']'): + coding_seq += line[:-1] + co.write( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( coding_seq, 80 ) ) ) ) + coding_seq = '' + else: + coding_seq += line + + if args.protein and line.startswith('protein sequence = ['): + if line.endswith(']'): + protein_seq = line[20:-1] + po.write( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( protein_seq, 80 ) ) ) ) + protein_seq = '' + else: + line = line[20:] + protein_seq = line + + if args.codingseq and line.startswith('coding sequence = ['): + if line.endswith(']'): + coding_seq = line[19:-1] + co.write( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( coding_seq, 80 ) ) ) ) + coding_seq = '' + else: + line = line[19:] + coding_seq = line + + if args.codingseq: + co.close() + if args.protein: + po.close() + + +if __name__ == '__main__': + parser = argparse.ArgumentParser() + parser.add_argument('-p', '--protein', help='Path to the protein file.') + parser.add_argument('-c', '--codingseq', help='Path to the coding file.') + + args = parser.parse_args() + main( args ) |
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| diff -r 000000000000 -r 86c89c3bd99d macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Oct 20 03:55:35 2017 -0400 |
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| @@ -0,0 +1,20 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">augustus</requirement> + <yield /> + </requirements> + </xml> + + <token name="@VERSION@">3.2.3</token> + + <xml name="citations"> + <citations> + <citation type="doi">10.1093/bioinformatics/btg1080</citation> + <citation type="doi">10.1093/bioinformatics/btr010</citation> + <citation type="doi">10.1093/bioinformatics/btn013</citation> + </citations> + </xml> + +</macros> |
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| diff -r 000000000000 -r 86c89c3bd99d test-data/annot.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annot.gff3 Fri Oct 20 03:55:35 2017 -0400 |
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| @@ -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 +### |
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| diff -r 000000000000 -r 86c89c3bd99d test-data/arabidopsis_augustus.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/arabidopsis_augustus.fa Fri Oct 20 03:55:35 2017 -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 86c89c3bd99d test-data/human_augustus.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/human_augustus.fa Fri Oct 20 03:55:35 2017 -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 86c89c3bd99d 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 Fri Oct 20 03:55:35 2017 -0400 |
| b |
| @@ -0,0 +1,33 @@ +>HS04636.g1 +atgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacagcaaatccttgctgttcccacccatgtca +aaaccgaggtgtatgtatgagtgtgggatttgaccagtataagtgcgattgtacccggacaggattctatggagaaaact +gctcaacaccggaatttttgacaagaataaaattatttctgaaacccactccaaacacagtgcactacatacttacccac +ttcaagggattttggaacgttgtgaataacattcccttccttcgaaatgcaattatgagttatgtcttgacatccagatc +acatttgattgacagtccaccaacttacaatgctgactatggctacaaaagctgggaagccttctctaacctctcctatt +atactagagcccttcctcctgtgcctgatgattgcccgactcccttgggtgtcaaaggtaaaaagcagcttcctgattca +aatgagattgtggaaaaattgcttctaagaagaaagttcatccctgatccccagggctcaaacatgatgtttgcattctt +tgcccagcacttcacgcatcagtttttcaagacagatcataagcgagggccagctttcaccaacgggctgggccatgggg +tggacttaaatcatatttacggtgaaactctggctagacagcgtaaactgcgccttttcaaggatggaaaaatgaaatat +cagataattgatggagagatgtatcctcccacagtcaaagatactcaggcagagatgatctaccctcctcaagtccctga +gcatctacggtttgctgtggggcaggaggtctttggtctggtgcctggtctgatgatgtatgccacaatctggctgcggg +aacacaacagagtatgcgatgtgcttaaacaggagcatcctgaatggggtgatgagcagttgttccagacaagcaggcta +atactgataggagagactattaagattgtgattgaagattatgtgcaacacttgagtggctatcacttcaaactgaaatt +tgacccagaactacttttcaacaaacaattccagtaccaaaatcgtattgctgctgaatttaacaccctctatcactggc +atccccttctgcctgacacctttcaaattcatgaccagaaatacaactatcaacagtttatctacaacaactctatattg +ctggaacatggaattacccagtttgttgaatcattcaccaggcaaattgctggcagggttgctggtggtaggaatgttcc +acccgcagtacagaaagtatcacaggcttccattgaccagagcaggcagatgaaataccagtcttttaatgagtaccgca +aacgctttatgctgaagccctatgaatcatttgaagaacttacaggagaaaaggaaatgtctgcagagttggaagcactc +tatggtgacatcgatgctgtggagctgtatcctgcccttctggtagaaaagcctcggccagatgccatctttggtgaaac +catggtagaagttggagcaccattctccttgaaaggacttatgggtaatgttatatgttctcctgcctactggaagccaa +gcacttttggtggagaagtgggttttcaaatcatcaacactgcctcaattcagtctctcatctgcaataacgtgaagggc +tgtccctttacttcattcagtgttccagatccagagctcattaaaacagtcaccatcaatgcaagttcttcccgctccgg +actagatgatatcaatcccacagtactactaaaagaacgttcgactgaactgtag +>HS08198.g2 +atgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccacg +ccggcccgcatcccccatcagcaccatccagcccaaggccaattttgatgcgcagcaggagcagggccaccgggccgagg +ccaccacactgcatgtggctccccagggcacagccatggctgtcagtaccttccgaaagctggatgggatctgctggcag +gtgcgccagctctatggagacacaggggtcctcggccgcttcctgcttcaagcccgaggcgcccgaggggctgtgcacgt +ggttgtcgctgagaccgactaccagagtttcgctgtcctgtacctggagcgggcggggcagctgtcagtgaagctctacg +cccgctcgctccctgtgagcgactcggtcctgagtgggtttgagcagcgggtccaggaggcccacctgactgaggaccag +atcttctacttccccaagtacggcttctgcgaggctgcagaccagttccacgtcctggacggtgagtgcacagcgggggc +aagcatggcggcgtggtga |
| b |
| diff -r 000000000000 -r 86c89c3bd99d 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 Fri Oct 20 03:55:35 2017 -0400 |
| [ |
| b'@@ -0,0 +1,105 @@\n+# This output was generated with AUGUSTUS (version 3.2.3).\n+# AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de),\n+# O. Keller, S. K\xc3\xb6nig, L. Gerischer and L. Romoth.\n+# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),\n+# Using native and syntenically mapped cDNA alignments to improve de novo gene finding\n+# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013\n+# No extrinsic information on sequences given.\n+# Initialising the parameters using config directory /home/bag/projects/code/galaxy/tool_deps/augustus/3.1/iuc/package_augustus_3_1/820bf3789c44/config/ ...\n+# human version. Using default transition matrix.\n+# Looks like /tmp/tmpboMLLQ/job_working_directory/000/6/task_0/dataset_9.dat is in fasta format.\n+# We have hints for 0 sequences and for 0 of the sequences in the input set.\n+#\n+# ----- prediction on sequence number 1 (length = 9453, name = HS04636) -----\n+#\n+# Constraints/Hints:\n+# (none)\n+# Predicted genes for sequence number 1 on both strands\n+# start gene HS04636.g1\n+HS04636\tAUGUSTUS\tgene\t966\t6903\t1\t+\t.\tHS04636.g1\n+HS04636\tAUGUSTUS\ttranscript\t966\t6903\t.\t+\t.\tHS04636.g1.t1\n+HS04636\tAUGUSTUS\tstart_codon\t966\t968\t.\t+\t0\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tintron\t1018\t1817\t.\t+\t.\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tintron\t1935\t2054\t.\t+\t.\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tintron\t2199\t2851\t.\t+\t.\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tintron\t2996\t3425\t.\t+\t.\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tintron\t3608\t4339\t.\t+\t.\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tintron\t4424\t4542\t.\t+\t.\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tintron\t4790\t5071\t.\t+\t.\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tintron\t5359\t5859\t.\t+\t.\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tintron\t6008\t6493\t.\t+\t.\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tCDS\t966\t1017\t.\t+\t0\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tCDS\t1818\t1934\t.\t+\t2\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tCDS\t2055\t2198\t.\t+\t2\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tCDS\t2852\t2995\t.\t+\t2\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tCDS\t3426\t3607\t.\t+\t2\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tCDS\t4340\t4423\t.\t+\t0\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tCDS\t4543\t4789\t.\t+\t0\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tCDS\t5072\t5358\t.\t+\t2\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tCDS\t5860\t6007\t.\t+\t0\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tCDS\t6494\t6903\t.\t+\t2\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tstop_codon\t6901\t6903\t.\t+\t0\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+# coding sequence = [atgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacagcaaatccttgctgttcccacccatgtc\n+# aaaaccgaggtgtatgtatgagtgtgggatttgaccagtataagtgcgattgtacccggacaggattctatggagaaaactgctcaacaccggaattt\n+# ttgacaagaataaaattatttctgaaacccactccaaacacagtgcactacatacttacccacttcaagggattttggaacgttgtgaataacattcc\n+# cttccttcgaaatgcaattatgagttatgtcttgacatccagatcacatttgattgacagtccaccaacttacaatgctgactatggctacaaaagct\n+# gggaagccttctctaacctctcctattatactagagcccttcctcctgtgcctgatgattgcccgactcccttgggtgtcaaaggtaaaaagcagctt\n+# cctgattcaaatgagattgtggaaaaattgcttctaagaagaaagttcatccctgatccccagggctcaaacatgatgtttgcattctttgcccagca\n+# cttcacgcatcagtttttcaagacagatcataagcgagggccagctttcaccaacgggctgggccatggggtggacttaaatcatatttacggtgaaa\n+# ctctggctagacagcgtaaactgcgccttttcaaggatggaaaaatgaaatatcagataattgatggagagatgtatcctcccacagtcaaagatact\n+# caggcagagatgatctaccctcctcaagt'..b'attacccagtttgttgaatcattcaccaggcaaattgctggca\n+# gggttgctggtggtaggaatgttccacccgcagtacagaaagtatcacaggcttccattgaccagagcaggcagatgaaataccagtcttttaatgag\n+# taccgcaaacgctttatgctgaagccctatgaatcatttgaagaacttacaggagaaaaggaaatgtctgcagagttggaagcactctatggtgacat\n+# cgatgctgtggagctgtatcctgcccttctggtagaaaagcctcggccagatgccatctttggtgaaaccatggtagaagttggagcaccattctcct\n+# tgaaaggacttatgggtaatgttatatgttctcctgcctactggaagccaagcacttttggtggagaagtgggttttcaaatcatcaacactgcctca\n+# attcagtctctcatctgcaataacgtgaagggctgtccctttacttcattcagtgttccagatccagagctcattaaaacagtcaccatcaatgcaag\n+# ttcttcccgctccggactagatgatatcaatcccacagtactactaaaagaacgttcgactgaactgtag]\n+# protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL\n+# THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD\n+# PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG\n+# QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH\n+# WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE\n+# KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV\n+# PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL]\n+# end gene HS04636.g1\n+###\n+#\n+# ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----\n+#\n+# Constraints/Hints:\n+# (none)\n+# Predicted genes for sequence number 2 on both strands\n+# start gene HS08198.g2\n+HS08198\tAUGUSTUS\tgene\t445\t1848\t1\t+\t.\tHS08198.g2\n+HS08198\tAUGUSTUS\ttranscript\t445\t1848\t.\t+\t.\tHS08198.g2.t1\n+HS08198\tAUGUSTUS\tstart_codon\t445\t447\t.\t+\t0\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\tintron\t583\t811\t.\t+\t.\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\tintron\t895\t1052\t.\t+\t.\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\tintron\t1124\t1207\t.\t+\t.\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\tintron\t1316\t1586\t.\t+\t.\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\tintron\t1689\t1771\t.\t+\t.\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\tCDS\t445\t582\t.\t+\t0\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\tCDS\t812\t894\t.\t+\t0\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\tCDS\t1053\t1123\t.\t+\t1\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\tCDS\t1208\t1315\t.\t+\t2\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\tCDS\t1587\t1688\t.\t+\t2\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\tCDS\t1772\t1848\t.\t+\t2\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\tstop_codon\t1846\t1848\t.\t+\t0\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+# coding sequence = [atgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccac\n+# gccggcccgcatcccccatcagcaccatccagcccaaggccaattttgatgcgcagcaggagcagggccaccgggccgaggccaccacactgcatgtg\n+# gctccccagggcacagccatggctgtcagtaccttccgaaagctggatgggatctgctggcaggtgcgccagctctatggagacacaggggtcctcgg\n+# ccgcttcctgcttcaagcccgaggcgcccgaggggctgtgcacgtggttgtcgctgagaccgactaccagagtttcgctgtcctgtacctggagcggg\n+# cggggcagctgtcagtgaagctctacgcccgctcgctccctgtgagcgactcggtcctgagtgggtttgagcagcgggtccaggaggcccacctgact\n+# gaggaccagatcttctacttccccaagtacggcttctgcgaggctgcagaccagttccacgtcctggacggtgagtgcacagcgggggcaagcatggc\n+# ggcgtggtga]\n+# protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC\n+# WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF\n+# HVLDGECTAGASMAAW]\n+# end gene HS08198.g2\n+###\n+# command line:\n+# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=on --codingseq=on --introns=on --start=on --stop=on --cds=on --singlestrand=false /tmp/tmpboMLLQ/job_working_directory/000/6/task_0/dataset_9.dat --UTR=off --genemodel=complete --species=human\n' |
| b |
| diff -r 000000000000 -r 86c89c3bd99d 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 Fri Oct 20 03:55:35 2017 -0400 |
| b |
| @@ -0,0 +1,13 @@ +>HS04636.g1 +MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYILTH +FKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDS +NEIVEKLLLRRKFIPDPQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKY +QIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVGQEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRL +ILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYHWHPLLPDTFQIHDQKYNYQQFIYNNSIL +LEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGEKEMSAELEAL +YGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKG +CPFTSFSVPDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL +>HS08198.g2 +MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGICWQ +VRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQ +IFYFPKYGFCEAADQFHVLDGECTAGASMAAW |
| b |
| diff -r 000000000000 -r 86c89c3bd99d 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 Fri Oct 20 03:55:35 2017 -0400 |
| [ |
| @@ -0,0 +1,106 @@ +##gff-version 3 +# This output was generated with AUGUSTUS (version 3.2.3). +# AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), +# O. Keller, S. König, L. Gerischer and L. Romoth. +# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), +# Using native and syntenically mapped cDNA alignments to improve de novo gene finding +# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 +# No extrinsic information on sequences given. +# Initialising the parameters using config directory /home/bag/projects/code/galaxy/tool_deps/augustus/3.1/iuc/package_augustus_3_1/820bf3789c44/config/ ... +# human version. Using default transition matrix. +# Looks like /tmp/tmpboMLLQ/job_working_directory/000/4/task_0/dataset_5.dat is in fasta format. +# We have hints for 0 sequences and for 0 of the sequences in the input set. +# +# ----- prediction on sequence number 1 (length = 9453, name = HS04636) ----- +# +# Predicted genes for sequence number 1 on both strands +# start gene HS04636.g1 +HS04636 AUGUSTUS gene 836 8857 1 + . ID=HS04636.g1 +HS04636 AUGUSTUS transcript 836 8857 . + . ID=HS04636.g1.t1;Parent=HS04636.g1 +HS04636 AUGUSTUS transcription_start_site 836 836 . + . Parent=HS04636.g1.t1 +HS04636 AUGUSTUS exon 836 1017 . + . Parent=HS04636.g1.t1 +HS04636 AUGUSTUS start_codon 966 968 . + 0 Parent=HS04636.g1.t1 +HS04636 AUGUSTUS CDS 966 1017 . + 0 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1 +HS04636 AUGUSTUS CDS 1818 1934 . + 2 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1 +HS04636 AUGUSTUS exon 1818 1934 . + . Parent=HS04636.g1.t1 +HS04636 AUGUSTUS CDS 2055 2198 . + 2 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1 +HS04636 AUGUSTUS exon 2055 2198 . + . Parent=HS04636.g1.t1 +HS04636 AUGUSTUS CDS 2852 2995 . + 2 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1 +HS04636 AUGUSTUS exon 2852 2995 . + . Parent=HS04636.g1.t1 +HS04636 AUGUSTUS CDS 3426 3607 . + 2 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1 +HS04636 AUGUSTUS exon 3426 3607 . + . Parent=HS04636.g1.t1 +HS04636 AUGUSTUS CDS 4340 4423 . + 0 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1 +HS04636 AUGUSTUS exon 4340 4423 . + . Parent=HS04636.g1.t1 +HS04636 AUGUSTUS CDS 4543 4789 . + 0 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1 +HS04636 AUGUSTUS exon 4543 4789 . + . Parent=HS04636.g1.t1 +HS04636 AUGUSTUS CDS 5072 5358 . + 2 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1 +HS04636 AUGUSTUS exon 5072 5358 . + . Parent=HS04636.g1.t1 +HS04636 AUGUSTUS CDS 5860 6007 . + 0 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1 +HS04636 AUGUSTUS exon 5860 6007 . + . Parent=HS04636.g1.t1 +HS04636 AUGUSTUS CDS 6494 6903 . + 2 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1 +HS04636 AUGUSTUS exon 6494 8857 . + . Parent=HS04636.g1.t1 +HS04636 AUGUSTUS transcription_end_site 8857 8857 . + . Parent=HS04636.g1.t1 +# coding sequence = [atgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacagcaaatccttgctgttcccacccatgtc +# aaaaccgaggtgtatgtatgagtgtgggatttgaccagtataagtgcgattgtacccggacaggattctatggagaaaactgctcaacaccggaattt +# ttgacaagaataaaattatttctgaaacccactccaaacacagtgcactacatacttacccacttcaagggattttggaacgttgtgaataacattcc +# cttccttcgaaatgcaattatgagttatgtcttgacatccagatcacatttgattgacagtccaccaacttacaatgctgactatggctacaaaagct +# gggaagccttctctaacctctcctattatactagagcccttcctcctgtgcctgatgattgcccgactcccttgggtgtcaaaggtaaaaagcagctt +# cctgattcaaatgagattgtggaaaaattgcttctaagaagaaagttcatccctgatccccagggctcaaacatgatgtttgcattctttgcccagca +# cttcacgcatcagtttttcaagacagatcataagcgagggccagctttcaccaacgggctgggccatggggtggacttaaatcatatttacggtgaaa +# ctctggctagacagcgtaaactgcgccttttcaaggatggaaaaatgaaatatcagataattgatggagagatgtatcctcccacagtcaaagatact +# caggcagagatgatctaccctcctcaagtccctgagcatctacggtttgctgtggggcaggaggtctttggtctggtgcctggtctgatgatgtatgc +# cacaatctggctgcgggaacacaacagagtatgcgatgtgcttaaacaggagcatcctgaatggggtgatgagcagttgttccagacaagcaggctaa +# tactgataggagagactattaagattgtgattgaagattatgtgcaacacttgagtggctatcacttcaaactgaaatttgacccagaactacttttc +# aacaaacaattccagtaccaaaatcgtattgctgctgaatttaacaccctctatcactggcatccccttctgcctgacacctttcaaattcatgacca +# gaaatacaactatcaacagtttatctacaacaactctatattgctggaacatggaattacccagtttgttgaatcattcaccaggcaaattgctggca +# gggttgctggtggtaggaatgttccacccgcagtacagaaagtatcacaggcttccattgaccagagcaggcagatgaaataccagtcttttaatgag +# taccgcaaacgctttatgctgaagccctatgaatcatttgaagaacttacaggagaaaaggaaatgtctgcagagttggaagcactctatggtgacat +# cgatgctgtggagctgtatcctgcccttctggtagaaaagcctcggccagatgccatctttggtgaaaccatggtagaagttggagcaccattctcct +# tgaaaggacttatgggtaatgttatatgttctcctgcctactggaagccaagcacttttggtggagaagtgggttttcaaatcatcaacactgcctca +# attcagtctctcatctgcaataacgtgaagggctgtccctttacttcattcagtgttccagatccagagctcattaaaacagtcaccatcaatgcaag +# ttcttcccgctccggactagatgatatcaatcccacagtactactaaaagaacgttcgactgaactgtag] +# protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL +# THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD +# PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG +# QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH +# WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE +# KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV +# PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL] +# end gene HS04636.g1 +### +# +# ----- prediction on sequence number 2 (length = 2344, name = HS08198) ----- +# +# Predicted genes for sequence number 2 on both strands +# start gene HS08198.g2 +HS08198 AUGUSTUS gene 86 2105 1 + . ID=HS08198.g2 +HS08198 AUGUSTUS transcript 86 2105 . + . ID=HS08198.g2.t1;Parent=HS08198.g2 +HS08198 AUGUSTUS transcription_start_site 86 86 . + . Parent=HS08198.g2.t1 +HS08198 AUGUSTUS exon 86 582 . + . Parent=HS08198.g2.t1 +HS08198 AUGUSTUS start_codon 445 447 . + 0 Parent=HS08198.g2.t1 +HS08198 AUGUSTUS CDS 445 582 . + 0 ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1 +HS08198 AUGUSTUS CDS 812 894 . + 0 ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1 +HS08198 AUGUSTUS exon 812 894 . + . Parent=HS08198.g2.t1 +HS08198 AUGUSTUS CDS 1053 1123 . + 1 ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1 +HS08198 AUGUSTUS exon 1053 1123 . + . Parent=HS08198.g2.t1 +HS08198 AUGUSTUS CDS 1208 1315 . + 2 ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1 +HS08198 AUGUSTUS exon 1208 1315 . + . Parent=HS08198.g2.t1 +HS08198 AUGUSTUS CDS 1587 1688 . + 2 ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1 +HS08198 AUGUSTUS exon 1587 1688 . + . Parent=HS08198.g2.t1 +HS08198 AUGUSTUS CDS 1772 1848 . + 2 ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1 +HS08198 AUGUSTUS exon 1772 2105 . + . Parent=HS08198.g2.t1 +HS08198 AUGUSTUS transcription_end_site 2105 2105 . + . Parent=HS08198.g2.t1 +# coding sequence = [atgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccac +# gccggcccgcatcccccatcagcaccatccagcccaaggccaattttgatgcgcagcaggagcagggccaccgggccgaggccaccacactgcatgtg +# gctccccagggcacagccatggctgtcagtaccttccgaaagctggatgggatctgctggcaggtgcgccagctctatggagacacaggggtcctcgg +# ccgcttcctgcttcaagcccgaggcgcccgaggggctgtgcacgtggttgtcgctgagaccgactaccagagtttcgctgtcctgtacctggagcggg +# cggggcagctgtcagtgaagctctacgcccgctcgctccctgtgagcgactcggtcctgagtgggtttgagcagcgggtccaggaggcccacctgact +# gaggaccagatcttctacttccccaagtacggcttctgcgaggctgcagaccagttccacgtcctggacggtgagtgcacagcgggggcaagcatggc +# ggcgtggtga] +# protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC +# WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF +# HVLDGECTAGASMAAW] +# end gene HS08198.g2 +### +# command line: +# augustus --strand=both --noInFrameStop=false --gff3=on --uniqueGeneId=true --protein=on --codingseq=on --introns=off --stop=off --stop=off --cds=on --singlestrand=false /tmp/tmpboMLLQ/job_working_directory/000/4/task_0/dataset_5.dat --UTR=on --genemodel=complete --species=human |
| b |
| diff -r 000000000000 -r 86c89c3bd99d 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 Fri Oct 20 03:55:35 2017 -0400 |
| [ |
| b'@@ -0,0 +1,109 @@\n+# This output was generated with AUGUSTUS (version 3.2.3).\n+# AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de),\n+# O. Keller, S. K\xc3\xb6nig, L. Gerischer and L. Romoth.\n+# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),\n+# Using native and syntenically mapped cDNA alignments to improve de novo gene finding\n+# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013\n+# No extrinsic information on sequences given.\n+# Initialising the parameters using config directory /home/bag/projects/code/galaxy/tool_deps/augustus/3.1/iuc/package_augustus_3_1/820bf3789c44/config/ ...\n+# human version. Using default transition matrix.\n+# Looks like /tmp/tmpboMLLQ/job_working_directory/000/2/task_0/dataset_1.dat is in fasta format.\n+# We have hints for 0 sequences and for 0 of the sequences in the input set.\n+#\n+# ----- prediction on sequence number 1 (length = 9453, name = HS04636) -----\n+#\n+# Constraints/Hints:\n+# (none)\n+# Predicted genes for sequence number 1 on both strands\n+# start gene HS04636.g1\n+HS04636\tAUGUSTUS\tgene\t836\t8857\t1\t+\t.\tHS04636.g1\n+HS04636\tAUGUSTUS\ttranscript\t836\t8857\t.\t+\t.\tHS04636.g1.t1\n+HS04636\tAUGUSTUS\ttss\t836\t836\t.\t+\t.\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\texon\t836\t1017\t.\t+\t.\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tstart_codon\t966\t968\t.\t+\t0\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tCDS\t966\t1017\t.\t+\t0\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tCDS\t1818\t1934\t.\t+\t2\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\texon\t1818\t1934\t.\t+\t.\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tCDS\t2055\t2198\t.\t+\t2\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\texon\t2055\t2198\t.\t+\t.\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tCDS\t2852\t2995\t.\t+\t2\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\texon\t2852\t2995\t.\t+\t.\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tCDS\t3426\t3607\t.\t+\t2\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\texon\t3426\t3607\t.\t+\t.\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tCDS\t4340\t4423\t.\t+\t0\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\texon\t4340\t4423\t.\t+\t.\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tCDS\t4543\t4789\t.\t+\t0\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\texon\t4543\t4789\t.\t+\t.\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tCDS\t5072\t5358\t.\t+\t2\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\texon\t5072\t5358\t.\t+\t.\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tCDS\t5860\t6007\t.\t+\t0\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\texon\t5860\t6007\t.\t+\t.\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\tCDS\t6494\t6903\t.\t+\t2\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\texon\t6494\t8857\t.\t+\t.\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+HS04636\tAUGUSTUS\ttts\t8857\t8857\t.\t+\t.\ttranscript_id "HS04636.g1.t1"; gene_id "HS04636.g1";\n+# coding sequence = [atgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacagcaaatccttgctgttcccacccatgtc\n+# aaaaccgaggtgtatgtatgagtgtgggatttgaccagtataagtgcgattgtacccggacaggattctatggagaaaactgctcaacaccggaattt\n+# ttgacaagaataaaattatttctgaaacccactccaaacacagtgcactacatacttacccacttcaagggattttggaacgttgtgaataacattcc\n+# cttccttcgaaatgcaattatgagttatgtcttgacatccagatcacatttgattgacagtccaccaacttacaatgctgactatggctacaaaagct\n+# gggaagccttctctaacctctcctattatactagagcccttcctcctgtgcctgatgattgcccgactcccttgggtgtcaaaggtaaaaagcagctt\n+# cctgattcaaatgagattgtggaaaaattgcttctaagaagaaagttcatccctgatccccagggctcaaacatgatgtttgcattctttgcccagca\n+# cttcacgcatcagtttttcaagacagatcataagcgagggccagctttcaccaacgggctgggccatggggtggactt'..b'gctttatgctgaagccctatgaatcatttgaagaacttacaggagaaaaggaaatgtctgcagagttggaagcactctatggtgacat\n+# cgatgctgtggagctgtatcctgcccttctggtagaaaagcctcggccagatgccatctttggtgaaaccatggtagaagttggagcaccattctcct\n+# tgaaaggacttatgggtaatgttatatgttctcctgcctactggaagccaagcacttttggtggagaagtgggttttcaaatcatcaacactgcctca\n+# attcagtctctcatctgcaataacgtgaagggctgtccctttacttcattcagtgttccagatccagagctcattaaaacagtcaccatcaatgcaag\n+# ttcttcccgctccggactagatgatatcaatcccacagtactactaaaagaacgttcgactgaactgtag]\n+# protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL\n+# THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD\n+# PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG\n+# QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH\n+# WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE\n+# KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV\n+# PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL]\n+# end gene HS04636.g1\n+###\n+#\n+# ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----\n+#\n+# Constraints/Hints:\n+# (none)\n+# Predicted genes for sequence number 2 on both strands\n+# start gene HS08198.g2\n+HS08198\tAUGUSTUS\tgene\t86\t2105\t1\t+\t.\tHS08198.g2\n+HS08198\tAUGUSTUS\ttranscript\t86\t2105\t.\t+\t.\tHS08198.g2.t1\n+HS08198\tAUGUSTUS\ttss\t86\t86\t.\t+\t.\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\texon\t86\t582\t.\t+\t.\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\tstart_codon\t445\t447\t.\t+\t0\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\tCDS\t445\t582\t.\t+\t0\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\tCDS\t812\t894\t.\t+\t0\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\texon\t812\t894\t.\t+\t.\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\tCDS\t1053\t1123\t.\t+\t1\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\texon\t1053\t1123\t.\t+\t.\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\tCDS\t1208\t1315\t.\t+\t2\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\texon\t1208\t1315\t.\t+\t.\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\tCDS\t1587\t1688\t.\t+\t2\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\texon\t1587\t1688\t.\t+\t.\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\tCDS\t1772\t1848\t.\t+\t2\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\texon\t1772\t2105\t.\t+\t.\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+HS08198\tAUGUSTUS\ttts\t2105\t2105\t.\t+\t.\ttranscript_id "HS08198.g2.t1"; gene_id "HS08198.g2";\n+# coding sequence = [atgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccac\n+# gccggcccgcatcccccatcagcaccatccagcccaaggccaattttgatgcgcagcaggagcagggccaccgggccgaggccaccacactgcatgtg\n+# gctccccagggcacagccatggctgtcagtaccttccgaaagctggatgggatctgctggcaggtgcgccagctctatggagacacaggggtcctcgg\n+# ccgcttcctgcttcaagcccgaggcgcccgaggggctgtgcacgtggttgtcgctgagaccgactaccagagtttcgctgtcctgtacctggagcggg\n+# cggggcagctgtcagtgaagctctacgcccgctcgctccctgtgagcgactcggtcctgagtgggtttgagcagcgggtccaggaggcccacctgact\n+# gaggaccagatcttctacttccccaagtacggcttctgcgaggctgcagaccagttccacgtcctggacggtgagtgcacagcgggggcaagcatggc\n+# ggcgtggtga]\n+# protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC\n+# WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF\n+# HVLDGECTAGASMAAW]\n+# end gene HS08198.g2\n+###\n+# command line:\n+# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=on --codingseq=on --introns=off --stop=off --stop=off --cds=on --singlestrand=false /tmp/tmpboMLLQ/job_working_directory/000/2/task_0/dataset_1.dat --UTR=on --genemodel=complete --species=human\n' |