Mercurial > repos > sargentl > augustus
changeset 0:7a7d247c7b33 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2f544e337886709995a93d53f394919ce8e4673a-dirty
author | sargentl |
---|---|
date | Wed, 15 May 2019 15:30:45 -0400 |
parents | |
children | fea28b864c14 |
files | augustus.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 |
diffstat | 11 files changed, 1161 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/augustus.xml Wed May 15 15:30:45 2019 -0400 @@ -0,0 +1,387 @@ +<tool id="augustus" name="Augustus" profile="16.04" version="@VERSION@"> + <description>gene prediction for prokaryotic and eukaryotic genomes</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="aggressive"> +<![CDATA[ + #if $model.augustus_mode == 'history' + + ## Using an augustus model from history, we need to unzip it and let augustus find it + + cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ && + + mkdir -p 'augustus_dir/species/' && + + tar -C 'augustus_dir/species/' -xzvf '${model.custom_model}' > /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 + + augustus + --strand=$strand + $noInFrameStop + $gff + --uniqueGeneId=true + + #if 'protein' in str($outputs).split(','): + --protein=on + #else: + --protein=off + #end if + + #if 'codingseq' in str($outputs).split(','): + --codingseq=on + #else: + --codingseq=off + #end if + + #if 'introns' in str($outputs).split(','): + --introns=on + #else: + --introns=off + #end if + + #if 'start' in str($outputs).split(','): + --start=on + #else: + --stop=off + #end if + + #if 'stop' in str($outputs).split(','): + --stop=on + #else: + --stop=off + #end if + + #if 'cds' in str($outputs).split(','): + --cds=on + #else: + --cds=off + #end if + + $singlestrand + $input_genome + $utr + --genemodel=$genemodel + + #if $hints.hinttoggle == 'T' + --hintsfile=$hints.hintsfile --extrinsicCfgFile=$hints.extrinsiccfg + #end if + + #if $range.userange == 'T' + --predictionStart=$range.start --predictionEnd=$range.stop + #end if + + #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(','): + --protein $protein_output + #end if + #if 'codingseq' in str($outputs).split(','): + --codingseq $codingseq_output + #end if + #end if +]]> + </command> + <inputs> + <param name="input_genome" type="data" format="fasta" label="Genome Sequence"/> + <param name="noInFrameStop" argument="--noInFrameStop" type="boolean" + label="Don't report transcripts with in-frame stop codons" + truevalue="--noInFrameStop=true" falsevalue="--noInFrameStop=false" checked="false" + help="Otherwise, intron-spanning stop codons could occur." /> + <param name="singlestrand" type="boolean" argument="--singlestrand" + label="Predict genes independently on each strand" + help="This allows overlapping genes on opposite strands." + truevalue="--singlestrand=true" falsevalue="--singlestrand=false" checked="false" /> + + <param name="utr" type="boolean" argument="--UTR" + label="Predict the untranslated regions in addition to the coding sequence" + truevalue="--UTR=on" falsevalue="--UTR=off" checked="false" + help="This currently works only for human, galdieria, toxoplasma and caenorhabditis." /> + + + <conditional name="model"> + <param name="augustus_mode" type="select" label="Trainingset"> + <option value="builtin">Run Augustus with a predefined trainingset</option> + <option value="history">Run Augustus with a custom trainingset</option> + </param> + <when value="history"> + <param name="custom_model" type="data" format="augustus" label="Augustus model" help="Archive created with the 'Train Augustus' tool"/> + </when> + <when value="builtin"> + <param name="organism" label="Model Organism" type="select" multiple="false" format="text" help="Choose a specialised trainingset."> + <!-- If you update this list, please also update it in maker and busco tools (../maker/maker.xml and ../busco/busco.xml) --> + <option value="human">Homo sapiens</option> + <option value="fly">Drosophila melanogaster</option> + <option value="arabidopsis">Arabidopsis thaliana</option> + <option value="brugia ">Brugia malayi</option> + <option value="aedes">Aedes aegypti</option> + <option value="tribolium2012">Tribolium castaneum</option> + <option value="schistosoma">Schistosoma mansoni</option> + <option value="tetrahymena">Tetrahymena thermophila</option> + <option value="galdieria">Galdieria sulphuraria</option> + <option value="maize">Zea mays</option> + <option value="toxoplasma">Toxoplasma gondii</option> + <option value="caenorhabditis ">Caenorhabditis elegans</option> + <option value="aspergillus_fumigatus">Aspergillus fumigatus</option> + <option value="aspergillus_nidulans ">Aspergillus nidulans</option> + <option value="aspergillus_oryzae ">Aspergillus oryzae</option> + <option value="aspergillus_terreus">Aspergillus terreus</option> + <option value="botrytis_cinerea ">Botrytis cinerea</option> + <option value="candida_albicans ">Candida albicans</option> + <option value="candida_guilliermondii ">Candida guilliermondii</option> + <option value="candida_tropicalis ">Candida tropicalis</option> + <option value="chaetomium_globosum">Chaetomium globosum</option> + <option value="coccidioides_immitis">Coccidioides immitis</option> + <option value="coprinus">Coprinus cinereus</option> + <option value="coprinus_cinereus">Coprinus cinereus</option> + <option value="cryptococcus_neoformans_gattii">Cryptococcus neoformans gattii</option> + <option value="cryptococcus_neoformans_neoformans_B">Cryptococcus neoformans neoformans</option> + <option value="cryptococcus_neoformans_neoformans_JEC21">Cryptococcus neoformans neoformans</option> + <option value="cryptococcus">Cryptococcus neoformans</option> + <option value="debaryomyces_hansenii">Debaryomyces hansenii</option> + <option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi</option> + <option value="eremothecium_gossypii">Eremothecium gossypii</option> + <option value="fusarium_graminearum ">Fusarium graminearum</option> + <option value="histoplasma_capsulatum ">Histoplasma capsulatum</option> + <option value="histoplasma">Histoplasma capsulatum</option> + <option value="kluyveromyces_lactis ">Kluyveromyces lactis</option> + <option value="laccaria_bicolor ">Laccaria bicolor</option> + <option value="lamprey">Petromyzon marinus</option> + <option value="leishmania_tarentolae">Leishmania tarentolae</option> + <option value="lodderomyces_elongisporus">Lodderomyces elongisporus</option> + <option value="magnaporthe_grisea ">Magnaporthe grisea</option> + <option value="neurospora_crassa">Neurospora crassa</option> + <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option> + <option value="pichia_stipitis">Pichia stipitis</option> + <option value="rhizopus_oryzae">Rhizopus oryzae</option> + <option value="saccharomyces_cerevisiae_S288C">Saccharomyces cerevisiae</option> + <option value="saccharomyces_cerevisiae_rm11-1a_1">Saccharomyces cerevisiae</option> + <option value="saccharomyces">Saccharomyces cerevisiae</option> + <option value="schizosaccharomyces_pombe">Schizosaccharomyces pombe</option> + <option value="trichinella">Trichinella spiralis</option> + <option value="ustilago_maydis">Ustilago maydis</option> + <option value="yarrowia_lipolytica">Yarrowia lipolytica</option> + <option value="nasonia">Nasonia vitripennis</option> + <option value="tomato">Solanum lycopersicum</option> + <option value="chlamydomonas">Chlamydomonas reinhardtii</option> + <option value="amphimedon">Amphimedon queenslandica</option> + <option value="pneumocystis">Pneumocystis jirovecii</option> + <option value="chicken">Gallus gallus domesticus (chicken)</option> + <option value="cacao">Theobroma cacao (cacao)</option> + <option value="heliconius_melpomene1">Heliconius melpomene</option> + <option value="xenoturbella">Xenoturbella</option> + <option value="E_coli_K12">E coli K12</option> + <option value="c_elegans_trsk">c elegans trsk</option> + <option value="camponotus_floridanus">Camponotus floridanus</option> + <option value="coyote_tobacco">Coyote tobacco</option> + <option value="s_aureus">Staphylococcus aureus</option> + <option value="thermoanaerobacter_tengcongensis">Thermoanaerobacter tengcongensis</option> + <option value="wheat">wheat</option> + <option value="zebrafish">Danio rerio</option> + <option value="anidulans">Aspergillus nidulans</option> + <option value="bombus_impatiens1">Bombus impatiens1</option> + <option value="bombus_terrestris2">Bombus terrestris2</option> + <option value="botrytis_cinerea">Botrytis cinerea</option> + <option value="brugia_malayi">Brugia malayi</option> + <option value="conidiobolus_coronatus">Conidiobolus coronatus</option> + <option value="cryptococcus_neoformans">Cryptococcus neoformans</option> + <option value="culex_pipiens">Culex pipiens</option> + <option value="elephant_shark">Callorhinchus milii</option> + <option value="honeybee1">Apis mellifera</option> + <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option> + <option value="pea_aphid">Acyrthosiphon pisum</option> + <option value="rhodnius_prolixus">Rhodnius prolixus</option> + <option value="ustilago_maydis">Ustilago maydis</option> + <option value="verticillium_albo_atrum1">Verticillium albo atrum1</option> + <option value="verticillium_longisporum1">Verticillium longisporum1</option> + <option value="Xipophorus_maculatus">Xipophorus_maculatus</option> + <option value="adorsata">adorsata</option> + <option value="ancylostoma_ceylanicum">ancylostoma_ceylanicum</option> + <option value="maker2_athal1">maker2_athal1</option> + <option value="maker2_c_elegans1">maker2_c_elegans1</option> + <option value="maker2_dmel1">maker2_dmel1</option> + <option value="maker2_spomb1">maker2_spomb1</option> + <option value="parasteatoda">parasteatoda</option> + <option value="rice">rice</option> + <option value="schistosoma2">schistosoma2</option> + <option value="sulfolobus_solfataricus">sulfolobus_solfataricus</option> + </param> + </when> + </conditional> + + <param name="strand" type="select" argument="--strand" + label="Predict genes on specific strands"> + <option value="both">both</option> + <option value="forward">forward</option> + <option value="backward">backward</option> + </param> + + <param name="genemodel" label="Gene Model" type="select" + help="Gene Model to predict, for more information please refer to the help."> + <option value="complete">complete</option> + <option value="partial">partial</option> + <option value="intronless">intronless</option> + <option value="atleastone">atleastone</option> + <option value="exactlyone">exactlyone</option> + </param> + + <conditional name="hints"> + <param name="hinttoggle" label="Use hints (extrinsic information)?" type="boolean" + truevalue="T" falsevalue="F" checked="false"> + </param> + <when value="T"> + <param name="hintsfile" label="Select hints file from history" type="data" format="gff" + help="A file containing hints in gff format (--hintsfile)"/> + <param name="extrinsiccfg" label="Select extrinsic configuration file from history" type="data" format="txt" + help="A .cfg file listing hint sources and their boni and mali (--extrinsicCfgFile)"/> + </when> + </conditional> + + <conditional name="range"> + <param name="userange" label="Specify prediction sequence range?" type="boolean" + truevalue="T" falsevalue="F" checked="false"> + </param> + <when value="T"> + <param name="start" label="Starting position" type="integer" value="" + help="The beginning of the search range (--predictionStart)"/> + <param name="stop" label="Ending position" type="integer" value="" + help="The end of the search range (--predictionEnd); must be greater than starting position"/> + </when> + </conditional> + + <param name="gff" type="boolean" label="GFF formated output" + help="Standard output is GTF." + truevalue="--gff3=on" falsevalue="--gff3=off" checked="false" /> + + <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options"> + <option value="protein" selected="True">predicted protein sequences (--protein)</option> + <option value="codingseq" selected="True">coding sequence as comment in the output file (--codingseq)</option> + <option value="introns">predicted intron sequences (--introns)</option> + <option value="start">predicted start codons (--start)</option> + <option value="stop">predicted stop codons (--stop)</option> + <option value="cds" selected="true">CDS region (--cds)</option> + </param> + </inputs> + <outputs> + <data format="gtf" name="output" label="${tool.name} on ${on_string}: GTF/GFF"> + <change_format> + <when input="gff" value="--gff3=on" format="gff3" /> + </change_format> + </data> + <data format="fasta" name="protein_output" label="${tool.name} on ${on_string}: Protein sequence"> + <filter>'protein' in outputs</filter> + </data> + <data format="fasta" name="codingseq_output" label="${tool.name} on ${on_string}: Coding sequence"> + <filter>'codingseq' in outputs</filter> + </data> + </outputs> + <tests> + <test> + <param name="input_genome" value="human_augustus.fa" ftype="fasta" /> + <param name="organism" value="human" /> + <param name="utr" value="True" /> + <output name="output" file="human_augustus_utr-on.gtf" ftype="gtf" lines_diff="6"/> + </test> + <test> + <param name="input_genome" value="human_augustus.fa" ftype="fasta" /> + <param name="organism" value="human" /> + <param name="utr" value="True" /> + <param name="gff" value="True" /> + <output name="output" file="human_augustus_utr-on.gff" ftype="gff3" lines_diff="6"/> + </test> + <test> + <param name="input_genome" value="human_augustus.fa" ftype="fasta" /> + <param name="organism" value="human" /> + <param name="outputs" value="protein,codingseq,introns,cds,start,stop" /> + <output name="output" file="human_augustus_protein_codingseq_introns_cds_main.gtf" ftype="gtf" lines_diff="6"/> + <output name="codingseq_output" file="human_augustus_protein_codingseq_introns_cds_codingseq.fasta" ftype="fasta" /> + <output name="protein_output" file="human_augustus_protein_codingseq_introns_cds_protein.fasta" ftype="fasta" /> + </test> + </tests> + <help> +<![CDATA[ + +**What it does** + +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: + +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 FASTA sequence: + +>Seq1 +cccgcggagcgggtaccacatcgctgcgcgatgtgcgagcgaacacccgggctgcgcccg +ggtgttgcgctcccgctccgcgggagcgctggcgggacgctgcgcgtcccgctcaccaag +cccgcttcgcgggcttggtgacgctccgtccgctgcgcttccggagttgcggggcttcgc +cccgctaaccctgggcctcgcttcgctccgccttgggcctgcggcgggtccgctgcgctc +ccccgcctcaagggcccttccggctgcgcctccaggacccaaccgcttgcgcgggcctgg + + +Running this tool will produce this: + + # ----- prediction on sequence number 1 (length = 1992969, name = scaffold1|size1992969) ----- + # + # Constraints/Hints: + # (none) + # Predicted genes for sequence number 1 on both strands + # start gene g1 + scaffold1|size1992969 AUGUSTUS gene 17453 19382 0.11 + . g6 + scaffold1|size1992969 AUGUSTUS transcript 17453 19382 0.11 + . g6.t1 + scaffold1|size1992969 AUGUSTUS start_codon 17453 17455 . + 0 transcript_id "g6.t1"; gene_id "g6"; + scaffold1|size1992969 AUGUSTUS intron 17615 17660 0.38 + . transcript_id "g6.t1"; gene_id "g6"; + scaffold1|size1992969 AUGUSTUS intron 17708 17772 0.54 + . transcript_id "g6.t1"; gene_id "g6"; + scaffold1|size1992969 AUGUSTUS intron 17902 18035 0.58 + . transcript_id "g6.t1"; gene_id "g6"; + scaffold1|size1992969 AUGUSTUS intron 18313 18367 0.99 + . transcript_id "g6.t1"; gene_id "g6"; + scaffold1|size1992969 AUGUSTUS intron 19014 19080 0.44 + . transcript_id "g6.t1"; gene_id "g6"; + scaffold1|size1992969 AUGUSTUS CDS 17453 17614 0.55 + 0 transcript_id "g6.t1"; gene_id "g6"; + scaffold1|size1992969 AUGUSTUS CDS 17661 17707 0.38 + 0 transcript_id "g6.t1"; gene_id "g6"; + scaffold1|size1992969 AUGUSTUS CDS 17773 17901 0.54 + 1 transcript_id "g6.t1"; gene_id "g6"; + scaffold1|size1992969 AUGUSTUS CDS 18036 18312 0.52 + 1 transcript_id "g6.t1"; gene_id "g6"; + scaffold1|size1992969 AUGUSTUS CDS 18368 19013 0.99 + 0 transcript_id "g6.t1"; gene_id "g6"; + scaffold1|size1992969 AUGUSTUS CDS 19081 19379 0.31 + 2 transcript_id "g6.t1"; gene_id "g6"; + scaffold1|size1992969 AUGUSTUS stop_codon 19380 19382 . + 0 transcript_id "g6.t1"; gene_id "g6"; + + +]]> + </help> + <expand macro="citations"/> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/extract_features.py Wed May 15 15:30:45 2019 -0400 @@ -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 )
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed May 15 15:30:45 2019 -0400 @@ -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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annot.gff3 Wed May 15 15:30:45 2019 -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 +###
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/arabidopsis_augustus.fa Wed May 15 15:30:45 2019 -0400 @@ -0,0 +1,53 @@ +>arabidopsis +ATATCATTCATGGGCCCCTACGCATTACTCGGTACCAATCTCGCTCTCTCTCTCTAAGTCTTGAAACTCTATCAAGAAT +CTCAAGCCACCATTTTTTCTTCATCTTCATAAAGAGAAAGAGAGAGATCCTCTTGTTTGGCAAGAACCCAATTTGAGTT +CTAAGTCCTGATTTGCTTAGCTCTTTTCTTTCCTTGATTTCATTCTATATAAAGTCAACGGAAAGATATACATATATAG +TTTTCTTCCGATTCTAGGGTTTTCATATTTCCTCTAAATTTTCATGGTCAAAGAAGAAAATCTAAGAAACAATCGAACC +AGCAAGAGAAAGAAGACTTCAATATCAACATCTCTCTCTCCCTCTCTCTCTCTTATATTATAAGGTGAGACCACAAGAA +CTTTTGATTTTCTTTTTCCTTCTTCCCTTCTTTTAATATATTCTTTGAATTTTTTTTCACTAATTCATCTACCCTTTTT +TATAATTGTGGCTAGATTTTTGTTTCGTTTCCTCTTTTTAATATTATCTCTCTAATGTATGTTGAAGATCTCGAGTTGA +GTCATCATCATCGTCAATGGCTTTGAAAAACATCCGCAACAATTCACCAATTGAAGAACAAGAGAAAGGTTTAAACTTC +ATCAAGATTCACTAAGACCCACTAAGAGCCAACTCAAAACTAAACGGAGCAAGGTTTTGCCAAAAACCAAAAAAAAAAA +AAAAAAGATTCAAGAACCATCTCGTAAATCAAGATTTCTCCAAGGAAAATCAGATAAGTCATAATGGATCTATCCCTGG +CTCCGACAACAACAACAAGTTCCGACCAAGAACAAGACAGAGACCAAGAATTAACCTCCAACATCGGAGCAAGCAGCAG +CTCCGGTCCCAGCGGAAACAACAACAACCTTCCGATGATGATGATTCCACCTCCGGAGAAAGAACACATGTTCGACAAA +GTGGTAACACCAAGCGACGTCGGAAAACTCAACAGACTCGTGATCCCTAAACAACACGCTGAGAGGTATTTCCCTCTAG +ACTCCTCAAACAACCAAAACGGCACGCTTTTGAACTTCCAAGACAGAAACGGCAAGATGTGGAGATTCCGTTACTCGTA +TTGGAACTCTAGCCAGAGCTACGTTATGACCAAAGGATGGAGCCGTTTCGTCAAAGAGAAAAAGCTCGATGCAGGAGAC +ATTGTCTCTTTCCAACGAGGCATCGGAGATGAGTCAGAAAGATCCAAACTTTACATAGATTGGAGGCATAGACCCGACA +TGAGCCTCGTTCAAGCACATCAGTTTGGTAATTTTGGTTTCAATTTCAATTTCCCGACCACTTCTCAATATTCCAACAG +ATTTCATCCATTGCCAGAATATAACTCCGTCCCGATTCACCGGGGCTTAAACATCGGAAATCACCAACGTTCCTATTAT +AACACCCAGCGTCAAGAGTTCGTAGGGTATGGTTATGGGAATTTAGCTGGAAGGTGTTACTACACGGGATCACCGTTGG +ATCATAGGAACATTGTTGGATCAGAGCCGTTGGTTATAGACTCAGTCCCTGTGGTTCCCGGGAGATTAACTCCGGTGAT +GTTACCGCCGCTTCCTCCGCCTCCTTCTACGGCGGGAAAGAGACTAAGGCTCTTTGGGGTGAATATGGAATGTGGCAAT +GACTATAATCAACAAGAAGAGTCATGGTTGGTGCCACGTGGCGAAATTGGTGCATCTTCTTCTTCTTCTTCAGCTCTAC +GACTAAATTTATCGACTGATCATGATGATGATAATGATGATGGTGATGATGGCGATGATGATCAATTTGCTAAGAAAGG +GAAGTCTTCACTTTCTCTCAATTTCAATCCATGAGAAGTTTCATCATCTTCTTGTTTTGAATCTCTCTTTATATTGTTT +CATTAGTAATTTTTCTAAGGGTATTAGATTCTAGCTAGTGAGAGGAAGAAAAAACGATCTTCTTCGTTTTTTTGGTTAT +GATTTTTTTTTCCGACATGTTTCTTGATGTTCATCATCATTAGGCTTTTGTCACCATGTTGAAACTCGCATCTTTTCAA +TTTTGTATATAA + +>arabidopsis2 +CTCCTCTGCCTCTCATCTCTTGTTCTCTCCGCCCATCTCTGCTCTCTTTTATTTTCCCAGAAAGTTTTTTTTTTTTTTT +TCCGAATTCCGTTAATCTCATTGGGGTTTCCATTGATAGCAATGGCGACGGCTTTCGCTCCCACTAAGCTCACTGCCAC +GGTTCCTCTGCATGGATCCCATGAGAATCGTCTCTTGCTCCCGATCCGATTGGCTCCTCCTTCTTCTTTCCTCGGATCC +ACCCGTTCCCTCTCCCTTCGCAGACTCAATCACTCCAACGCCACCCGTCGATCTCCCGTCGTCTCTGTCCAGGAAGTTG +TCAAGGAGAAGCAATCCACCAATAATACCAGCCTGGTACGCTTCCTCTCCTCGTCTCCTTCTTTTGGAATTTTACAAGT +TGTGAGATTTGTTGTATTGATTTAAGTAATTTGAAATAGTTGATAACCAAAGAGGAAGGATTGGAGTTGTATGAAGATA +TGATACTAGGTAGATCTTTCGAAGACATGTGTGCTCAAATGTATTACCGAGGCAAGATGTTTGGTTTTGTTCACTTGTA +CAATGGCCAAGAGGCTGTTTCTACTGGCTTTATCAAGCTCCTTACCAAGTCTGACTCTGTCGTTAGTACCTACCGTGAC +CATGTCCATGCCCTCAGCAAAGGTGTCTCTGCTCGTGCTGTTATGAGCGAGCTCTTCGGCAAGGTTACTGGATGCTGCA +GAGGCCAAGGTGGATCCATGCACATGTTCTCCAAAGAACACAACATGCTTGGTGGCTTTGCTTTTATTGGTGAAGGCAT +TCCTGTCGCCACTGGTGCTGCCTTTAGCTCCAAGTACAGGAGGGAAGTCTTGAAACAGGATTGTGATGATGTCACTGTC +GCCTTTTTCGGAGATGGAACTTGTAACAACGGACAGTTCTTCGAGTGTCTCAACATGGCTGCTCTCTATAAACTGCCTA +TTATCTTTGTTGTCGAGAATAACTTGTGGGCCATTGGGATGTCTCACTTGAGAGCCACTTCTGACCCCGAGATTTGGAA +GAAAGGTCCTGCATTTGGGATGCCTGGTGTTCATGTTGACGGTATGGATGTCTTGAAGGTCAGGGAAGTCGCTAAAGAA +GCTGTCACTAGAGCTAGAAGAGGAGAAGGTCCAACCTTGGTTGAATGTGAGACTTATAGATTCAGAGGACACTCCTTGG +CTGATCCCGATGAGCTCCGTGATGCTGGTAAATATCGACTTCCTTCTGCTTCTTGATGCTTGTACTGATTATCTAAGGG +TTGAAACAACCTTCTCTTTAATTTGAATTTTTTTTTGCAGCTGAGAAAGCCAAATACGCGGCTAGAGACCCAATCGCAG +CATTGAAGAAGTATTTGATAGAGAACAAGCTTGCAAAGGAAGCAGAGCTAAAGTCAATAGAGAAAAAGATAGACGAGTT +GGTGGAGGAAGCGGTTGAGTTTGCAGACGCTAGTCCACAGCCCGGTCGCAGTCAGTTGCTAGAGAATGTGTTTGCTGAT +CCAAAAGGATTTGGAATTGGACCTGATGGACGGTACAGATGTGAGGACCCCAAGTTTACCGAAGGCACAGCTCAAGTCT +GAGAAGACAAGTTTAACCATAAGCTGTCTACTGTCTCTTCGATGTTTCTATATATCTTATTAAGTTAAATGCTACAGAG +AATCAGTTTGAATCATTTGCACTTTTTGCTTTTTGTTTGGTGTTACTAAACTATCACAAGGTTCTTCTTGTAGTTCGTT +GGGTTTTCATTGGTTACCACTTACCAGAGAATTGTATTTTTTTTTTTAAAGATAATTATTTTGC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/human_augustus.fa Wed May 15 15:30:45 2019 -0400 @@ -0,0 +1,200 @@ +>HS04636 +gagctcacattaactatttacagggtaactgcttaggaccagtattatgaggagaattta +cctttcccgcctctctttccaagaaacaaggagggggtgaaggtacggagaacagtattt +cttctgttgaaagcaacttagctacaaagataaattacagctatgtacactgaaggtagc +tatttcattccacaaaataagagttttttaaaaagctatgtatgtatgtgctgcatatag +agcagatatacagcctattaagcgtcgtcactaaaacataaaacatgtcagcctttctta +accttactcgccccagtctgtcccgacgtgacttcctcgaccctctaaagacgtacagac +cagacacggcggcggcggcgggagaggggattccctgcgcccccggacctcagggccgct +cagattcctggagaggaagccaagtgtccttctgccctcccccggtatcccatccaaggc +gatcagtccagaactggctctcggaagcgctcgggcaaagactgcgaagaagaaaagaca +tctggcggaaacctgtgcgcctggggcggtggaactcggggaggagagggagggatcaga +caggagagtggggactaccccctctgctcccaaattggggcagcttcctgggtttccgat +tttctcatttccgtgggtaaaaaaccctgcccccaccgggcttacgcaatttttttaagg +ggagaggagggaaaaaatttgtgggggggtacgaaaaggcggaaagaaacagtcattcac +atgggcttggttttcagtcttataaaaaggaaggttctctcggttagcgaccaattgtca +tacgacttgcagtgagcgtcaggagcacgtccaggaactcctcagcagcgcctccttcag +ctccacagccagacgccctcagacagcaaagcctacccccgcgccgcgccctgcccgccg +ctcggatgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacaggtg +agtacctggcgccgcgcaccggggactccggttccacgcacccgggcagagtttccgctc +tgacctcctgggtctatcccagtactccgacttctctccgaatagagaagctacgtgact +tgggaaagagcttggaccgctagagtccgaaagaactccgtggatattccagctttccca +caagcactgatcattatgagccagttacttaaccgatctgagacactctcacctcctaaa +tagggatagatgatactaatttgcaggttgtcattatgataagacaggatctgatcaata +tatgtgaattgtttatatttggaacctttttattgagtggaagaagttgttttaaatatt +ctagtcagttctttcctgctcccaggaaagcccggattatgttttaagataagcaaaatg +tcttaaaagtaagctgttttactttgaatttttccctaaatgttgattagtgtactagat +ccattttaatttggaaagtgaagtgctacttatttgaacttcttaaaaatgctaatttta +acatctaaagagttaactaagaaaagcttagtaacatgatgtaccaagttgaatatgctg +ttatccttatttagaatagaaaattggtatttctacgttttatccattctaaggcaggtt +aaaaaattgtatttccatgactacctatatatttcttgaatttattattgtaaagttgat +tcatagtcaaacaattaaatgtttaaattaagattaagacactagagaatgatttatttg +ctgtcctttaattgcagcaaatccttgctgttcccacccatgtcaaaaccgaggtgtatg +tatgagtgtgggatttgaccagtataagtgcgattgtacccggacaggattctatggaga +aaactgctcaacacgtaagtttgtcctttggttgcctcattaggagtggggctggataca +gttatcattgtatagatttgtgtcttataatgagtcccattaatttctccctccctttct +tcgtcttcttgcagcggaatttttgacaagaataaaattatttctgaaacccactccaaa +cacagtgcactacatacttacccacttcaagggattttggaacgttgtgaataacattcc +cttccttcgaaatgcaattatgagttatgtcttgacatgtaagtacaagtgtctttctaa +ggtttttagccttctcaaagaaaaatatgctttataatactgtaagcctaatctaaaaac +atatttccaagcttatcaaaaagactttaagatagcttttaagtttgccttccatcttaa +tcgccaaaaatattgacatttagtcccatccagtttatacagtctgctcacaactctgta +tacctcttctaacctttactgtttggtcagtttgtggaggtagcatggtccagctgttta +ttgaatgcccatgggccacagaattgttctgaacatgtagcacccattaaaataaatttg +gatttggatcagcaagaaaataactttccatgattctaaagtgggtgccatactcagcca +ttcctttcataggcctcttggatagtgagcagatggctacctgaaaaatcaatattgcca +gattataatgtgcagagtatatgtattttattaaagatgtatttcaagtggccattagac +tataaagtgtagttgtttaaaaatagattttttttattttggagttacattcaacctcag +gtgccactttccacattttacaataaaaataatggttgatttacttaacaaatgagaata +aataaaacatttttttctttgaaaatttcagccagatcacatttgattgacagtccacca +acttacaatgctgactatggctacaaaagctgggaagccttctctaacctctcctattat +actagagcccttcctcctgtgcctgatgattgcccgactcccttgggtgtcaaaggtgag +taagaagaatccattagagatgtattaactataagacgggctgcattgctgccaaaaaaa +aaaattgaccttagactaccatttatttattaacaaaagcagtttttacttttagcatgg +ttatctatgggtattttttaaagtatgagtctatataaactattatgtaaaagcaaatga +gcgtcttggtataatgtcttaatattttcaaattatttctttagaaatgaaataattcta +attaaaatagataaaatcattcagtaagaagttgttccaccatatcttagaactgttgtt +tatattatgatcctattcacaattgtaattctcatataaatgaagaattcttggtagatt +gacagtcaccatctcctttcttgaatacatagatggattcttaccttagctttctcattt +ttcaggtaaaaagcagcttcctgattcaaatgagattgtggaaaaattgcttctaagaag +aaagttcatccctgatccccagggctcaaacatgatgtttgcattctttgcccagcactt +cacgcatcagtttttcaagacagatcataagcgagggccagctttcaccaacgggctggg +ccatggggtaagatagagttaatatcttagagttagtaaaattataccaaatcatagtca 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+gcaccggctgagtctcgtctctgctgcagaagtgaggaggtgaggccggcacacagctcc +agtgctgagaagtcagtgccccgagagacgaccccaccagtggggtgcccgctgcctgtc +ctccgtgaaaccagcctcagatcagggccctgccacccagggcaggggatcttctgccgg +ctgccccagaggacagtgggtggagtggtacctacttattaaatgtctcagacccctctc +tgactcttctgtccactctggaccggcgccagtaccaccaaggccctctctgcccccacc +ccgcctctttaaaagcccggcgctccctgttggctggagtccacgcagggtcactgggcc +gatttcggctcttgggatttgggaggggagatcctctctggcatatgccatcttgtgccc +tgctggacctgggggcgtccacgtcactccaaggctgctcttgcctgggccatgcctgca +gccc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/human_augustus_protein_codingseq_introns_cds_codingseq.fasta Wed May 15 15:30:45 2019 -0400 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/human_augustus_protein_codingseq_introns_cds_main.gtf Wed May 15 15:30:45 2019 -0400 @@ -0,0 +1,105 @@ +# 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/000/6/task_0/dataset_9.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 HS04636.g1 +HS04636 AUGUSTUS gene 966 6903 1 + . HS04636.g1 +HS04636 AUGUSTUS transcript 966 6903 . + . HS04636.g1.t1 +HS04636 AUGUSTUS start_codon 966 968 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS intron 1018 1817 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS intron 1935 2054 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS intron 2199 2851 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS intron 2996 3425 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS intron 3608 4339 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS intron 4424 4542 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS intron 4790 5071 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS intron 5359 5859 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS intron 6008 6493 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS CDS 966 1017 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS CDS 1818 1934 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS CDS 2055 2198 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS CDS 2852 2995 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS CDS 3426 3607 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS CDS 4340 4423 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS CDS 4543 4789 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS CDS 5072 5358 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS CDS 5860 6007 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS CDS 6494 6903 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS stop_codon 6901 6903 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.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 HS04636.g1 +### +# +# ----- prediction on sequence number 2 (length = 2344, name = HS08198) ----- +# +# Constraints/Hints: +# (none) +# Predicted genes for sequence number 2 on both strands +# start gene HS08198.g2 +HS08198 AUGUSTUS gene 445 1848 1 + . HS08198.g2 +HS08198 AUGUSTUS transcript 445 1848 . + . HS08198.g2.t1 +HS08198 AUGUSTUS start_codon 445 447 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +HS08198 AUGUSTUS intron 583 811 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +HS08198 AUGUSTUS intron 895 1052 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +HS08198 AUGUSTUS intron 1124 1207 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +HS08198 AUGUSTUS intron 1316 1586 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +HS08198 AUGUSTUS intron 1689 1771 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +HS08198 AUGUSTUS CDS 445 582 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +HS08198 AUGUSTUS CDS 812 894 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +HS08198 AUGUSTUS CDS 1053 1123 . + 1 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +HS08198 AUGUSTUS CDS 1208 1315 . + 2 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +HS08198 AUGUSTUS CDS 1587 1688 . + 2 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +HS08198 AUGUSTUS CDS 1772 1848 . + 2 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +HS08198 AUGUSTUS stop_codon 1846 1848 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +# 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=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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/human_augustus_protein_codingseq_introns_cds_protein.fasta Wed May 15 15:30:45 2019 -0400 @@ -0,0 +1,13 @@ +>HS04636.g1 +MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYILTH +FKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDS +NEIVEKLLLRRKFIPDPQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKY +QIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVGQEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRL +ILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYHWHPLLPDTFQIHDQKYNYQQFIYNNSIL +LEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGEKEMSAELEAL +YGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKG +CPFTSFSVPDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL +>HS08198.g2 +MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGICWQ +VRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQ +IFYFPKYGFCEAADQFHVLDGECTAGASMAAW
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/human_augustus_utr-on.gff Wed May 15 15:30:45 2019 -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/human_augustus_utr-on.gtf Wed May 15 15:30:45 2019 -0400 @@ -0,0 +1,109 @@ +# 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/000/2/task_0/dataset_1.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 HS04636.g1 +HS04636 AUGUSTUS gene 836 8857 1 + . HS04636.g1 +HS04636 AUGUSTUS transcript 836 8857 . + . HS04636.g1.t1 +HS04636 AUGUSTUS tss 836 836 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS exon 836 1017 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS start_codon 966 968 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS CDS 966 1017 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS CDS 1818 1934 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS exon 1818 1934 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS CDS 2055 2198 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS exon 2055 2198 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS CDS 2852 2995 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS exon 2852 2995 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS CDS 3426 3607 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS exon 3426 3607 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS CDS 4340 4423 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS exon 4340 4423 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS CDS 4543 4789 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS exon 4543 4789 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS CDS 5072 5358 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS exon 5072 5358 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS CDS 5860 6007 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS exon 5860 6007 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS CDS 6494 6903 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS exon 6494 8857 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS tts 8857 8857 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.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 HS04636.g1 +### +# +# ----- prediction on sequence number 2 (length = 2344, name = HS08198) ----- +# +# Constraints/Hints: +# (none) +# Predicted genes for sequence number 2 on both strands +# start gene HS08198.g2 +HS08198 AUGUSTUS gene 86 2105 1 + . HS08198.g2 +HS08198 AUGUSTUS transcript 86 2105 . + . HS08198.g2.t1 +HS08198 AUGUSTUS tss 86 86 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +HS08198 AUGUSTUS exon 86 582 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +HS08198 AUGUSTUS start_codon 445 447 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +HS08198 AUGUSTUS CDS 445 582 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +HS08198 AUGUSTUS CDS 812 894 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +HS08198 AUGUSTUS exon 812 894 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +HS08198 AUGUSTUS CDS 1053 1123 . + 1 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +HS08198 AUGUSTUS exon 1053 1123 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +HS08198 AUGUSTUS CDS 1208 1315 . + 2 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +HS08198 AUGUSTUS exon 1208 1315 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +HS08198 AUGUSTUS CDS 1587 1688 . + 2 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +HS08198 AUGUSTUS exon 1587 1688 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +HS08198 AUGUSTUS CDS 1772 1848 . + 2 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +HS08198 AUGUSTUS exon 1772 2105 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +HS08198 AUGUSTUS tts 2105 2105 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +# 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=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