| Previous changeset 2:cf241e076f7b (2023-09-05) |
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Commit message:
planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit d6e73c0417506d93c905b4aeb77d92350b662fbb |
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modified:
README.rst macros.xml test-data/SRR7458692.bam test-data/genome_masked.fa test-data/out_genome/braker.gtf |
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added:
braker.xml |
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removed:
braker3.xml job_conf_braker3.xml |
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| diff -r cf241e076f7b -r ac13de106677 README.rst --- a/README.rst Tue Sep 05 09:40:27 2023 +0000 +++ b/README.rst Wed Sep 06 09:50:12 2023 +0000 |
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| @@ -1,41 +1,24 @@ -Braker3 +Braker ======= -This tool is not in IUC because of the license issues with GeneMark and -ProtHint that makes it impossible to test it using CI. - -GeneMark and ProtHint ---------------------- +This tool is not in IUC because of the license issues with GeneMark and ProtHint that makes it impossible to test it using CI. -Braker requires GeneMark to predict gene, but due to licensing issues, we -are not allowed to distribute GeneMark automatically. +GeneMark +--------- -Braker also requires ProtHint to use protein sequences as hints to predict -genes, but, again, due to licensing issues, we are not allowed to distribute -ProtHint automatically. +Braker can use GeneMark to predict gene, but due to licensing issues, we are not allowed to distribute GeneMark automatically. -To use Braker3, the Galaxy administrator needs to install -GeneMark, and set the ``GENEMARK_PATH`` variable on the job destination. +If you want to use it, the Galaxy administrator needs to install GeneMark, and set the `GENEMARK_PATH` variable on the job destination. -The only working version of GeneMark to install needs to be downloaded from -http://topaz.gatech.edu/GeneMark/etp.for_braker.tar.gz -This archive also contains ProtHint and various other tools in specific versions needed by Braker3. +ProtHint +--------- +Braker can use ProtHint to use protein sequences as hints to predict genes, but due to licensing issues, we are not allowed to distribute ProtHint automatically. -Unzip it, and set the ``GENEMARK_PATH`` variable to point to the extracted ``bin`` -directory. - -Also set the ``PROTHINT_PATH`` variable on the job destination, pointing to the extracted -``bin/gmes/ProtHint/bin/`` directory +If you want to use it, the Galaxy administrator needs to install ProtHint, and set the `PROTHINT_PATH` variable on the job destination. Running tests -------------- - -Tests require working GeneMark and ProtHint installations, which means -both GENEMARK_PATH and PROTHINT_PATH are set in job_conf_braker3.xml. +-------------- -You should then use the ``--job_config_file job_conf_braker3.xml`` -option for planemo commands. +Tests require working GeneMark and ProtHint installations, which means both GENEMARK_PATH and PROTHINT_PATH are set. -You should also copy a valid GeneMark license (from -http://topaz.gatech.edu/GeneMark/license_download.cgi) in -test-data/gm_key_64. +You should also copy a valid GeneMark license (from http://topaz.gatech.edu/GeneMark/license_download.cgi) in test-data/genemark_license.gm_key |
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| diff -r cf241e076f7b -r ac13de106677 braker.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/braker.xml Wed Sep 06 09:50:12 2023 +0000 |
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| @@ -0,0 +1,159 @@ +<tool id="braker" name="Braker genome annotation" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> + <description></description> + <macros> + <import>macros.xml</import> + </macros> + <requirements> + <expand macro="requirements" /> + </requirements> + <version_command><![CDATA[braker.pl --version; $GENEMARK_PATH/gmes_petap.pl | grep version]]></version_command> + <command><![CDATA[ +if [ -z "\$GENEMARK_PATH" ] ; then echo "GeneMark is not installed on this Galaxy server." >&2 ; exit 1 ; fi && +if [ ! -f "\$GENEMARK_PATH/gmes_petap.pl" ] ; then echo "GeneMark is not installed properly on this Galaxy server." >&2 ; exit 1 ; fi && +## GeneMark only search for license in ~/.gm_key +cp '${genemark_license}' ~/.gm_key && + +braker.pl +--genome '${genome}' + +$softmasking + +#if $evidences.bam: + --bam ${evidences.bam} +#end if + +#if $evidences.prot_seq: + --prot_seq ${evidences.prot_seq} +#end if + +## No hints, use esmode +#if not $evidences.bam and not $evidences.prot_seq + --esmode +#end if + +## Both proteins and rnaseq hints, use etpmode +#if $evidences.bam and $evidences.prot_seq + --etpmode +#end if + +#if $output_format == 'gff3' + --gff3 +#end if + +$genemark.fungus + +$augustus.crf +--rounds $augustus.rounds + +$advanced.UTR + +$advanced.filterOutShort + +#if $advanced.eval: + --eval ${advanced.eval} +#end if + +#if $advanced.eval_pseudo: + --eval_pseudo ${advanced.eval_pseudo} +#end if + +--cores \${GALAXY_SLOTS:-2} + ]]></command> + <inputs> + <param name="genemark_license" type="data" format="txt" label="GeneMark license file" help="Braker uses GeneMark, which is not a free software, to use it download and unzip a license from http://topaz.gatech.edu/GeneMark/license_download.cgi (ES/ET/EP version). GeneMark needs to be installed manually by Galaxy administrators." /> + + <param argument="--genome" type="data" format="fasta" label="Assembly to annotate" help="The assembly should be soft-masked (with RepeatMasker for example)" /> + + <param argument="--softmasking" type="boolean" checked="false" truevalue="--softmasking" falsevalue="" label="Genome sequence is soft-masked" /> + + <section name="evidences" expanded="true" title="Evidences"> + <param argument="--bam" type="data" format="bam" optional="true" label="RNA-seq mapped to genome to train Augustus/GeneMark" /> + <param argument="--prot_seq" type="data" format="fasta" optional="true" label="Proteins to map to genome" /> + </section> + + <section name="genemark" expanded="true" title="GeneMark"> + <param argument="--fungus" type="boolean" checked="false" truevalue="--fungus" falsevalue="" label="Fungal genome" help="GeneMark-EX option, run algorithm with branch point model (most useful for fungal genomes)" /> + </section> + + <section name="augustus" expanded="true" title="Augustus"> + <param argument="--crf" type="boolean" checked="false" truevalue="--crf" falsevalue="" label="Use CRF training for Augustus" help="Alternate training method (Conditional Random Field)" /> + <param argument="--rounds" type="integer" value="5" label="Number of optimization rounds used in optimize_augustus.pl" /> + </section> + + <section name="advanced" expanded="false" title="Advanced"> + <param argument="--UTR" type="boolean" checked="false" truevalue="--UTR=on" falsevalue="" label="" help="Experimental, requires RNASeq data (bam) and a softmasked genome" /> + <param argument="--filterOutShort" type="boolean" checked="false" truevalue="--filterOutShort" falsevalue="" label="Filter out too short traingin gene predicted by GeneMark-EX" /> + <param argument="--eval" type="data" format="gtf" optional="true" label="Reference set to evaluate predictions" help="using evaluation scripts from GaTech" /> + <param argument="--eval_pseudo" type="data" format="gff3" optional="true" label="File with pseudogenes that will be excluded from accuracy evaluation" /> + </section> + + <param name="output_format" type="select" label="Output format"> + <option value="gtf" selected="true">GTF</option> + <option value="gff3">GFF3</option> + </param> + </inputs> + <outputs> + <data name='output_gtf' format='gtf' label="${tool.name} on ${on_string}: GTF annotation" from_work_dir="braker/braker.gtf"> + <filter>output_format == 'gtf'</filter> + </data> + <data name='output_gff' format='gff3' label="${tool.name} on ${on_string}: GFF annotation" from_work_dir="braker/braker.gff3"> + <filter>output_format == 'gff3'</filter> + </data> + </outputs> + <tests> + + <test expect_failure="true"> + <param name="genemark_license" value="gm_key_64"/> + <param name="genome" value="genome_masked.fa"/> + <section name="evidences"> + <param name="bam" value="SRR7458692.bam"/> + </section> + <param name="output_format" value="gtf"/> + </test> + + <!-- Disable next 2 for CI (it should pass locally)--> + <!--test> + <param name="genome" value="genome_masked.fa" /> + <param name="softmasking" value="true" /> + <param name="genemark_license" value="genemark_license.gm_key" /> + <output name="output_gtf" file="out_genome/braker.gtf" sort="true" /> + </test> + <test> + <param name="genome" value="genome_masked.fa" /> + <param name="softmasking" value="true" /> + <param name="genemark_license" value="genemark_license.gm_key" /> + <param name="output_format" value="gff3" /> + <output name="output_gff" file="out_genome/braker.gff3" sort="true" /> + </test--> + <!-- following 2 tests throw an error because test dataset is too small --> + <!--test> + <param name="genome" value="genome_masked.fa" /> + <param name="softmasking" value="true" /> + <param name="genemark_license" value="genemark_license.gm_key" /> + <section name="evidences"> + <param name="bam" value="SRR7458692.bam" /> + </section> + <output name="output_gtf" file="out_bam/braker.gtf" sort="true" /> + </test> + <test> + <param name="genome" value="genome_masked.fa" /> + <param name="softmasking" value="true" /> + <param name="genemark_license" value="genemark_license.gm_key" /> + <section name="evidences"> + <param name="prot_seq" value="proteins.fa" /> + </section> + <output name="output_gtf" file="out_prot/braker.gtf" sort="true" /> + </test--> + </tests> + <help><![CDATA[ +Braker_ +------- + +Braker_ allows for fully automated training of the gene prediction tools GeneMark-EX and AUGUSTUS from RNA-Seq and/or protein homology information, and that integrates the extrinsic evidence from RNA-Seq and protein homology information into the prediction. + +In contrast to other available methods that rely on protein homology information, BRAKER reaches high gene prediction accuracy even in the absence of the annotation of very closely related species and in the absence of RNA-Seq data. + +.. _Braker: https://github.com/Gaius-Augustus/BRAKER + ]]></help> + <expand macro="citations" /> +</tool> |
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| diff -r cf241e076f7b -r ac13de106677 braker3.xml --- a/braker3.xml Tue Sep 05 09:40:27 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,203 +0,0 @@\n-<tool id="braker" name="BRAKER3" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">\n- <description>genome annotation</description>\n- <macros>\n- <import>macros.xml</import>\n- </macros>\n- <requirements>\n- <expand macro="requirements" />\n- </requirements>\n- <version_command><![CDATA[braker.pl --version; $GENEMARK_PATH/gmes/gmes_petap.pl | grep version]]></version_command>\n- <command><![CDATA[\n-if [ -z "\\$GENEMARK_PATH" ] ; then echo "GeneMark is not installed on this Galaxy server." >&2 ; exit 1 ; fi &&\n-if [ ! -f "\\$GENEMARK_PATH/gmes/gmes_petap.pl" ] ; then echo "GeneMark is not installed properly on this Galaxy server." >&2 ; exit 1 ; fi &&\n-\n-## This specific GeneMark version has some tools bundled with it, forced to use it.\n-## I feel dirty. Pardon me.\n-\n-export PATH="\\$GENEMARK_PATH/../tools/:\\$PATH" &&\n-\n-## GeneMark only search for license in ~/.gm_key\n-cp \'${genemark_license}\' ~/.gm_key &&\n-\n-braker.pl\n---genome \'${genome}\'\n-\n-$softmasking\n-\n-#if $evidences.bam:\n- --bam ${evidences.bam}\n-#end if\n-\n-#if $evidences.prot_seq:\n- --prot_seq ${evidences.prot_seq}\n-#end if\n-\n-## No hints, use esmode\n-#if not $evidences.bam and not $evidences.prot_seq\n- --esmode\n-#end if\n-\n-#if $output_format == \'gff3\'\n- --gff3\n-#end if\n-\n-$genemark.fungus\n-\n-$augustus.crf\n---rounds $augustus.rounds\n-$augustus.AUGUSTUS_ab_initio\n-$augustus.keepCrf\n-\n-$advanced.UTR\n-\n-$advanced.filterOutShort\n-\n-#if $advanced.eval:\n- --eval ${advanced.eval}\n-#end if\n-\n-#if $advanced.eval_pseudo:\n- --eval_pseudo ${advanced.eval_pseudo}\n-#end if\n-\n-#if $species:\n- --species \'$species\'\n-#end if\n-\n-$advanced.alternatives_from_evidence\n-\n-#if $dev.splice_sites:\n- --splice_sites \'$dev.splice_sites\'\n-#end if\n-\n-#if $dev.min_contig:\n- --min_contig $dev.min_contig\n-#end if\n-\n---gc_probability $dev.gc_probability\n---downsampling_lambda $dev.downsampling_lambda\n-\n-#if $dev.gm_max_intergenic:\n---gm_max_intergenic $dev.gm_max_intergenic\n-#end if\n-\n---threads \\${GALAXY_SLOTS:-2}\n-]]></command>\n- <inputs>\n- <param name="genemark_license" type="data" format="txt" label="GeneMark license file" help="Braker uses GeneMark, which is not a free software, to use it download and unzip a license from http://topaz.gatech.edu/GeneMark/license_download.cgi (ES/ET/EP version). GeneMark needs to be installed manually by Galaxy administrators." />\n-\n- <param argument="--genome" type="data" format="fasta" label="Assembly to annotate" help="The assembly should preferably be soft-masked (with RepeatMasker for example)" />\n-\n- <param argument="--softmasking" type="boolean" checked="true" truevalue="" falsevalue="--softmasking_off" label="Genome sequence is soft-masked" />\n-\n- <param argument="--species" type="text" label="Species name" optional="true" help="Using Sp_1, if no species is assigned"/>\n-\n- <section name="evidences" expanded="true" title="Evidences">\n- <param argument="--bam" type="data" format="bam" optional="true" label="RNA-seq mapped to genome to train Augustus/GeneMark" />\n- <param argument="--prot_seq" type="data" format="fasta" optional="true" label="Proteins to map to genome" />\n- </section>\n-\n- <section name="genemark" expanded="true" title="GeneMark">\n- <param argument="--fungus" type="boolean" checked="false" truevalue="--fungus" falsevalue="" label="Fungal genome" help="GeneMark-EX option, run algorithm with branch point model (most useful for fungal genomes)" />\n- </section>\n-\n- <section name="augustus" expanded="true" title="Augustus">\n- <param argument="--crf" type="boolean" checked="false" truevalue="--crf" falsevalue="" label="Use CRF training for Augustus" help="Alternate training method (Conditional Random Field)" />\n- <param argument="--rounds" type="integer" value="5" label="Number of optimization rounds used in optimize_augustus.pl" />\n- <'..b'ility" type="float" min="0" max="1" value="0.001" label="Probablity for donor splice site pattern GC for gene prediction with GeneMark-EX"/>\n- <param argument="--gm_max_intergenic" type="integer" optional="true" label="Maximum allowed size of intergenic regions in GeneMark-EX" help="If not set, the value is automatically determined by GeneMark-EX"/>\n- <param argument="--downsampling_lambda" type="integer" min="0" value="2" label="Lambda parameter of the Poisson distribution" help="for downsampling of training gene structures according to their number of introns distribution"/>\n- </section>\n-\n- <param name="output_format" type="select" label="Output format">\n- <option value="gtf" selected="true">GTF</option>\n- <option value="gff3">GFF3</option>\n- </param>\n- </inputs>\n-\n- <outputs>\n- <data name=\'output_gtf\' format=\'gtf\' label="GTF Annotation" from_work_dir="braker/braker.gtf">\n- <filter>output_format == \'gtf\'</filter>\n- </data>\n- <data name=\'output_gff\' format=\'gff3\' label="GFF Annotation" from_work_dir="braker/braker.gff3">\n- <filter>output_format == \'gff3\'</filter>\n- </data>\n- </outputs>\n- \n- <tests>\n- <test expect_failure="true">\n- <param name="genemark_license" value="gm_key_64"/>\n- <param name="genome" value="genome_masked.fa"/>\n- <section name="evidences">\n- <param name="bam" value="SRR7458692.bam"/>\n- </section>\n- <param name="output_format" value="gtf" />\n- </test>\n- </tests>\n-\n- <!-- <test expect_num_outputs="1">\n- <param name="genemark_license" value="gm_key_64" />\n- <param name="genome" value="genome_masked.fa" />\n- <section name="augustus">\n- <param name="rounds" value="2" />\n- </section>\n- <section name="evidences">\n- <param name="bam" value="SRR7458692.bam" />\n- </section>\n- <param name="output_format" value="gtf" />\n- <output name="output_gtf" file="out_genome/braker.gtf" sort="true"/>\n- </test>\n-\n- <test expect_num_outputs="1">\n- <param name="genemark_license" value="gm_key_64" />\n- <param name="genome" value="genome_masked.fa" />\n- <section name="augustus">\n- <param name="rounds" value="2" />\n- </section>\n- <section name="evidences">\n- <param name="bam" value="SRR7458692.bam" />\n- <param name="prot_seq" value="proteins.fa" />\n- </section>\n- <param name="output_format" value="gff3" />\n- <output name="output_gff" file="out_genome/braker.gff3"/>\n- </test>\n-\n- <test expect_num_outputs="1">\n- <param name="genemark_license" value="gm_key_64" />\n- <param name="genome" value="genome_masked.fa" />\n- <section name="augustus">\n- <param name="rounds" value="2" />\n- </section>\n- <section name="evidences">\n- <param name="prot_seq" value="proteins.fa" />\n- </section>\n- <param name="output_format" value="gff3" />\n- <output name="output_gff" file="out_genome/braker.gff3"/>\n- </test> -->\n-\n- \n- <help><![CDATA[\n-\n-Braker_ allows for fully automated training of the gene prediction tools GeneMark-EX and AUGUSTUS from RNA-Seq and/or protein homology information, and that integrates the extrinsic evidence from RNA-Seq and protein homology information into the prediction.\n-\n-In contrast to other available methods that rely on protein homology information, BRAKER reaches high gene prediction accuracy even in the absence of the annotation of very closely related species and in the absence of RNA-Seq data.\n-\n-.. _Braker: https://github.com/Gaius-Augustus/BRAKER\n- ]]></help>\n- <expand macro="citations" />\n-</tool>\n' |
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| diff -r cf241e076f7b -r ac13de106677 job_conf_braker3.xml --- a/job_conf_braker3.xml Tue Sep 05 09:40:27 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,20 +0,0 @@ -<!-- Adapt the paths to your install of GeneMark and ProtHint, then run planemo with the job_config_file option --> -<job_conf> - <plugins> - <plugin id="planemo_runner" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> - </plugins> - <handlers> - </handlers> - <destinations default="planemo_dest"> - <destination id="planemo_dest" runner="planemo_runner"> - <env id="GENEMARK_PATH">/home/abretaud/softs/etp.for_braker/bin/</env> - <env id="PROTHINT_PATH">/home/abretaud/softs/etp.for_braker/bin/gmes/ProtHint/bin/</env> - </destination> - <destination id="upload_dest" runner="planemo_runner"> - <param id="docker_enabled">false</param> - </destination> - </destinations> - <tools> - <tool id="upload1" destination="upload_dest" /> - </tools> -</job_conf> |
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| diff -r cf241e076f7b -r ac13de106677 macros.xml --- a/macros.xml Tue Sep 05 09:40:27 2023 +0000 +++ b/macros.xml Wed Sep 06 09:50:12 2023 +0000 |
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| @@ -1,10 +1,10 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">3.0.3</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@TOOL_VERSION@">2.1.6</token> + <token name="@VERSION_SUFFIX@">1</token> <xml name="requirements"> - <requirement type="package" version="@TOOL_VERSION@">braker3</requirement> + <requirement type="package" version="@TOOL_VERSION@">braker2</requirement> </xml> <xml name="citations"> |
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| diff -r cf241e076f7b -r ac13de106677 test-data/SRR7458692.bam |
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| Binary file test-data/SRR7458692.bam has changed |
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| diff -r cf241e076f7b -r ac13de106677 test-data/genome_masked.fa --- a/test-data/genome_masked.fa Tue Sep 05 09:40:27 2023 +0000 +++ b/test-data/genome_masked.fa Wed Sep 06 09:50:12 2023 +0000 |
| b |
| b'@@ -4313,10104 +4313,7 @@\n CATGTCAAGTATTATTATCGAGCAACTACAAACGAAATACAAACATACAT\n TTAATTGCCAAGAATGTTCCTAGCCAAACAAATGTCGAAATAATGTCGGG\n CCACGGCCAAAGATTTATCATATTCACTCGACTGTCATAAAAAGCAATTA\n-GGCCCGGGCGAAAGATACACGACCGGCAGTCCCGAAATGTAATAAAAAaa\n-taacaaaatACACCGAAGGGGCGCAGCGAAAGAAGAAAGAAACGATGTGT\n-GATTTGAAGTTGTTTCTGGTTTTCGGTTTCGCTTAATGAGTTTGCCGCAC\n-AAAAAGTCGCTTCGAGGGAAGCGATTAAAGATTCCACATCCAGTGCGGCA\n-CGTCGGGGTTGTTGCTTCTGTAGCGGATGGTCCTGCACCCGAAAAAATAA\n-TTTCACTCGAGGCTATCAGAAAATGGTGTAGCGGTGTGGTCCAGATATGC\n-CTCCAGATATTGAGTACGCCGTGTCAGTGAATTTGAATTCAAAAAATGTT\n-TGAAAACTTTAATTGTTTTCCTCTCTCCTGATGATAACTACTTTGAACGA\n-CGGAAAAACGTACTATAAACAAAGTATAATTAAATCTTTTCCATTTGTTA\n-TAGAGTACTCTTTACTTAAATAGTTTGAATTTGGCCTAAAAGTTATCAGT\n-GATAACTGAGCGTTATTCATCACGTTATTCTTTGGTCGACTTCTTAGATT\n-TTTTGGATGGAGTCTAAGTCTGCCTAATTTCAGATTTCAGATAATTTAAT\n-TTAAATGAGTGGGACAATTTCTTTAAGTGCAGCGTGTCTCTTGTAATTAG\n-TATGCCTGCACACTCGCCGTGCCctgtgccctgtgccctTCGAAATAAAA\n-GCGGAAGCGGAGGTCCCCGCGAACAGTTGGCCCTTTGGGACAGAGAAAGG\n-CAGGTTCGGTTTGAAGGGCACTCGTCAGCAGAAACGAAAGGTGGGGAGGG\n-GCGGCGATACTATCCACGTTCCGATCCGAAAACAAGCGACCTGCCGATTC\n-GGATTGGTGTGAAAAGTCCGCCCCATGGCAACTGGCCTTGTTTTTTCCGT\n-CTGTTGCATATTTTCACAAGTAATTAACATGTGCCCGACGTTGTCCTTGT\n-CCGTAGCCAGGGATCCGGGAAGCCAGCCTGTTCCCGCGCAACTGTCCAAA\n-CAGGCTGCCCCGTTGTTGTTCGTCAGCGGGGTAACAAAGCGCTGCCTCCG\n-CATTAATTTGCATTATTTTCACATTTAACTTTCAAGCGAGTGCGCCTGCC\n-GAAGTTGCACTCTGCCGGCGAGCGGACAGGTGGAGCAGGTGGAACTGAAG\n-TGCCACTTCTAATTGTGCGGTGATTGGGGCACGGCTTTGAAAGATTCCGT\n-TCGAATGGCTTCCATCGGCAAACACCAACTATCGTCCCTGCCTTGATTGA\n-GTTAATAAGGGTTTAGGAATAATTTGATTGGCGTTAATAAAATATTGgta\n-aaacatcggtaaaacgTTATGTTGTATGCAAGTTTCACAATGAAGCTACA\n-ATAATATGATAATTTGCTTTAGCGAAGATTAGTACCAATAATTTGATTta\n-ATTTGAGTCGAAACTTTAAATATCAATTAATTCATTAACCGGGAGGGTAT\n-GATTAAAATATGCACCCTGTTGCTAAAATTAAATTTATGGTTTCTGTTGC\n-AAAGAATTTTACAGTGATGACAGAATGACGAGAGACACATTTCTGATCAA\n-CCTCTCCACCTCAGAAAAGATCTCAAATTTTAAGCAGCAGTTGCATCCAC\n-TTACTTTAAAACGACAACTTATAATTTGATCAGTGCTCTCAACATATATC\n-CAATTTATTAGATTTCCATGGCACCAATTCGATTTTTACTTTTAAATGGA\n-AAATCAAAAAGGGGAGAGAATCCCGGAAAGAGGAGCACTGATTTCTAGAA\n-TATTTATTTAGGAACATTTTAATATTGAATTCTTCAAGCCGGAGGAACAT\n-GCCACTTACAGTTCAATAGTTTTTACTTAGAAATTACATATCATTGCTAT\n-CATTACTTTTCGATCGCTATTCAGTGTTTATTTTATGGCTTTCGATCCCC\n-AAACTGTGTTAGGCTTAAGTTTAAATAATATTCCTTCGATTCTAGAACGC\n-TGTGCCCTGTTTCATAAACTTACATAGTTCATGGGCGGAAAACTTactta\n-ctgactgGCGATGATGCTGCCCCATTGCCCCATTTGGGCCATTTAGTTCG\n-CCGTTGATGATAAATTCTGCACTATGGCCCCGGGCGAATGTGCAATAAAA\n-TGCTCCCCGCGCTCCGCACAGCAACAAACCTTGCAACATAAATTAAGGCG\n-CAAAATGTTTATTTACGCTGCGGGAGGGAGTCGGAGGGAAGTCGGGAGAA\n-AGGGGCAAACACGCCGGCTGTTTCCTGCGCAACATTTGCATTTTGACGCC\n-GCATTACGCGTGATGTGAGGAGCCCCGGCCACTCGGCTTATCAGCCCAGA\n-GAAATCAAACGGCGCAGAAGTCGGCGGAGATTGTGGAGTTGCACGTCCAC\n-TGCCCGCAGCATCTTGCAACATTTTGTTTTAATTTCGCACTCTTGAAAAG\n-TGGCAGCCGCCACTCGGACGGTTTTTGAATTGGCCAAGTGAATTGCCACG\n-GACCACAGCGGCAGGGAATGTAGTAGAGTCCAAGACAGGGAATGGAGCCA\n-GCTGCTGGTCGATCTCACCTAGGGAATGGAGTCCATCGCTTTCCTTTCCC\n-CTTTGCAATGCTGCAATACCTTAAGATATTTCCTATACTTCGGCTTTAAT\n-ttggaaaaaaaaGTAACACTTACTAAGGTAAAATGAAATCTCGTATCTCT\n-GCTTAAGTAAAATTAGAATCAGTAGGGAACATTCCAAGTGCTTTGGAATA\n-TTAAACTTCATATCATACCAAGAATGATATTTCTCTGCCCTGAATTTATC\n-ACTCATTGTCGGTTCATTCAAGTGATTCCTTTTTTAAATATGATTATTGA\n-TTATCAATTTCTTTCATGTTGAGTCCCATTCCCCTTGCAACAGAAAACTT\n-CACACTCGGCTGTTTTTTCAGGCATTTTTAAAATCAAGGGGCCCACATCA\n-AAGGGCATTGCCTAAGAAACGAAGCCAATTGTATCTGCGTCCCAGTGCGT\n-GTATACACGTATCTGcatctgtatctgtaGTATATCAGtataTCAATGGC\n-CGTATCTGAAGGTGCGAGTTTTGATTGCGTTCGCTCTGTCAGGCAGAGGG\n-ACAGAAGGGCGCTTTATTTGATTTCAAGTTATGTTGTTTTTAGTGAGTTC\n-CTCTGGCACTCCCCTCCAGGTTTTTTGGCTTTTGTTTGTTGAACTTTGGC\n-TGACTAATAGCTGGTGAAGGGGGACCTCCAGGGGAGTGGGGCAGTTATGA\n-CGATGCCATAGTTTTTCGAACACATCCGAACATGTGTATTTATTACCGCC\n-TGATGCGGGCTGTTTGTTCCCAGCGCCCTGCACCGTGATTTGATTTATTT\n-GTACACAGTTTTATGATATTTACATGTCTGCAACTGAGGGTCCATGGTGT\n-GGCAAGGAGGGGTTGGTGGCCAGCGGTGCGGCAGGAGCAGCAAATGCAAT\n-CTACACCAGTGATTCAATTCTAGGTTCATCGAGTTCGCCTTGCACTTCTT\n-CGTTTTGTTCAAGGGTTATACAATAGTAGGTTAAGTTATTATATAAAAAT\n-ATGTTATGCGGCTCATAGTACGCCAGTACATAGAAAGCGCTGAGTTTAAA\n-ATTTGATTGCCGCTCCGGATTAATTTGTATTTTATTCGATCATAGTAAAT\n-GACGTTTTCAAATTAAAGTATAAATTGTGTGTTTTTTGATTGCATTGATG\n-GCGTTCTTTCTAAACTATAT'..b'TATACTTTGGATTC\n-GGAAACGCATTCTTGTGCCTGTTACGTGTTGTTCTAAAGACTTACCTCTT\n-CTCTTCCTGCTCCTCGTCTTTTCCGTGGCACATTGCGAACACCCTTAGCT\n-TGGAGTTCTGCCAGTGGGAGCGCATGGAGATTATGTAGGGCAGGAGAATT\n-GTGAGACCTACATGTATTCCCAATGACTTGTGGATTAGTTGCAAAGTGGC\n-TGATTACGACCAAGTACCCACCTCCGTCGTCGTACAGCCAGAAGACATCG\n-ATTGTGCCCTTGGGCTGTTTGCGCGTGAATATGGTCATGGCGTCCAGCAA\n-GTTTTGGGGTATGTCCGATCCGCCCTTGGTGTGGTAGGTGACGGCGGGCT\n-CATCCGAGCTGGTCACCTTGTAGCTGCGGGAGTTGCGCTGCATGTTGGGC\n-ATCGGTGCTGGCTGGGGCATTGTGAAAGAGGAGTTGGGGCTGTCCATGCT\n-GGCTAGGTTCAGGTTGGAGTCAATGTGCAGCAGCTCCGAGGCTGCATTGG\n-CCGCCGGCATCAGTTCGTTGGTGAATCCATGCGCATTGGCGGTATGCATG\n-TGACCCATTCCGTTGGCCGGCAGAGTGACCTCGGAACTCAGCTCAGAGAA\n-ATCCAATCCGTTGGGCAGTCGGAGCAGGGCCACGCCCATACGCTGAGAAA\n-AAGCATTGCTATGGAAGAGGTGGACTTGGTAAGGCATCCAATAACATAGT\n-TTGGGGAAATAACTTACTACAAAATGGAAAAGTAACTCTCCACCTCCTCC\n-TTGCGACAGCGATTCCAGTCCGGCTTGTAGCCCACCAGCACAATGTTCGG\n-AGACATTTTGCCGAAGCCCGTTGACTTTGTCAACGCATTTATTCCGTCCT\n-CCAGGCTGAACCCATCAATCACATTGTAGAAGGCCTTGATCTTGCGGGCA\n-TCCAGGTACTTTTGTCCATCCTTCACCAGGTGCTGCCGGTTCTTGTAGCC\n-CACCCGCACCTGAAAGGATATAACAAGTATTTTAGTAAGAATCACCATTC\n-CGCTTTTCTTGATGTCCAACAAAATGGGTGAGTTTTCCCTTATCAAGAAA\n-TCCATTCACGTACCGGTATTATATTTGCCACGAACATGAGGGAGTTGTTC\n-TTGGTCAGCAGGTAGCCAAAGTCCACGAGTGGCGGTCTGGTCTTGGGATC\n-GCCGGAGAGCACCAGCACCTGGGGATGGTAGTTCTTGACGTGATCCGAGA\n-CGTTCTGCAGTCGGTGGACGGCCATTAGAGCAGCCTTGTACTGCTGAGCC\n-TGCGTGGTGGATCCCCAGTTGGCCTCCGGCTTGCGGTACATGACCACCAG\n-ATAGAGGGCGAAGATGATGCCAAAGGTGATGATGGCGGCCACGTAGTTGA\n-TCAGGAACATGATGGCCACGCACATGGCGAACCCGAAGAGGCTGAGCCAG\n-GCGTTGTAGTACTTAAAGGTGGGTCGCCATCCCAATGGCTTCACGAAGGC\n-CGCGTGGAATGTGCAAAAGTTGATGAGGGCGTAGGAGGCCAGGTAGAAGG\n-TGGAGATCAGAGGAGCGATCAGGTTAAGCTCTCCGATCAGCAGGAAGCCG\n-GTggtgatgaagaagGTGAGCACGTAGCCGCGATACGGTTCGCCGTGCTT\n-GCCGTACGGCTTCGAGAAGAAGATTAGACCCGGGTAGATCTGGTCAATGC\n-CCAGGGCCTGCACCAGCCTGGGAACGGAAAGCAAGTTGGTCAGGGCCGTG\n-CTTAACGTGGCTGCAAAGCAGCCGGCGTAGATGAGTGGTCCCCACAGCGA\n-CATCTCCTGCATCATTTCGTACGAGTTGAAGAGACCCCAGGTGCAGTTGC\n-CCGTGGCCATGCACGGCAGCTCCGAGGAAACAATGGTGCCATTGACGAGG\n-TCAGCTGGTATACCGGAGGCATCTCTTACAGCAGCGCCACCGGCGAAGAG\n-GACAAAGAGAGCGTATGAGGACATCGAGATGAGCAGGGACCAGAAGGTGC\n-CCTTCGGTATAGCAGCTCCGGCATCCTTGAGGTCTCCGCAGATATTTGCT\n-CCTGCCTGGATGCCCGTCACGCTGGGAAAGAAGATAGCGAACACGCTGAA\n-AAAGTCGTGGTTTACGCCCTCCGCATAGCGATAGTCCGATCCGAAGTTCT\n-CCTTCAAAGTAGCCCCTAATTTAGGTAACCAGTTATGAGGTTATTACTTT\n-CTTAAGTTCTCTTATGAACTCACATGAAAAGCCGACGAAACCCCTAGAGA\n-TTTGCTCCTCATTACCCTGGGGTCCAATGGCAGCTCCGATCAGGAAATTG\n-AAGATGGCCAGGACAATCGTGACGATCAGGAAGTTCTGCGCCTTCGTCTC\n-CCACTCCATACCCACGCAGCAGATTAGGATGAGCACCAGCACGGTTATCG\n-ATCCCACGATCCGGATGTCATTGATCCCGTTGTCGACAATCTTCAGGTCG\n-TTGTTCTCTGGAAATGAGATTAATGATTACTCCGGAACTAAGTTAAGGAT\n-ATCCTCAAACTTAATTAAACCAGACTGGATCCATGAAATATAGTGAAAGT\n-CGTTTCTATTTCAACCTTTATTTTTTATCCTATTTATTTAGGACATTTAA\n-AGCTGCCCCATTTGTGGCCACCCTATTCAAGTTAATCGAATGGCCTCTGT\n-GTGCACAAGTCAATTGATACTCACTGAGTAAAACATTTAGCGATTCGCAG\n-AAGCCGATGGTGTTCATCGAGGCTGAgacggcgttggcgaaggcgaagac\n-cacgcccacCGACGCCCCAAACTCGGGGCCCAGCGAACGGGATATGAtga\n-agtagacgccgccgccCTTGACCTCGCCGTTGGTGCTAATGGCCGACAGC\n-GAGAGCGTCGTGATGACGCAGACCACCGCGGAGATCGTAATTATAATCAG\n-GGACTGCAGGATGCCCGACTCGGCCACCACCCAGCTGAGGCGCAGGAAGA\n-GCATTACGCCCCAGATGTTGAGAAGGCAAGGTATCAGCACGCCCACGATC\n-CATCCTAGCTTGATGTGTCCGCCAGTTGCCTCCGGTTCGGgttcgGGAAT\n-AGTGATGCTCTGCAATGGAGAAACGATCTTATGGATAATAAaaatatata\n-tgtatgtaGtatgtaGGTCGTCCTTATAAGTAATACCTTTCTTAAGTAAG\n-ACACATTAGTATTAACTTTTCACATAGGTTATGTTCAATCTAGCCGGCTA\n-ATGATTTGGGCAAACGGGAAAAGGCCGTCATCGGATTGTTATTTGCCTGA\n-TAATGGGATCTTGACATAAGTGGCATTCAATCGAATGTGTGCTAACTGTG\n-TGAGATTGAATTGAGTTCGGCTtttttttttAACTGTATACGACTCGAAC\n-AGCTGCTTGGGTGAGTTTTTATCCGGAATTACTCATACGACATGTGTGCA\n-ATTTAGTACTCGGATTCAATTAACGACCCGttaacgacccCCAAAATACG\n-AAAGCAGCAGCAAGCGAAGGCACAGCCACAACCAGATTATGAGCAGCAGC\n-TCACATTGCTTTCCATTCTAATTAAAGTTCACTTTTATTAGCCGCACTTA\n-AACTGGAAACATTATGAAAATGTTCACATAAAAGCTGAAACCCACCCAAT\n-GAGATGCCACCAAGTCAACTATTTAACGTATGCCCCAAAGTATTTCCTTT\n-GTTCGGTTCGGATATAGTTCGTCCAATAGGGCGGCAAGTGCAAAAACAAA\n-GACGAAATCCACTTTAACTGCGGCGAGGAA\n+GGCCCGGGCGAAAGATACACGACCGGCAGTCCCGAAATGT\n >sample2\n GAAAATCATTCATTTGGAATTGTAATCACCTATGCACTTTGGTATAAGCT\n TTTCTGTGCACATTTTCCTGGAAAATGAATGAGACTCCTCGGCAGCCATT\n' |
| b |
| diff -r cf241e076f7b -r ac13de106677 test-data/out_genome/braker.gtf --- a/test-data/out_genome/braker.gtf Tue Sep 05 09:40:27 2023 +0000 +++ b/test-data/out_genome/braker.gtf Wed Sep 06 09:50:12 2023 +0000 |
| b |
| b'@@ -1,1484 +1,465 @@\n-sample\tAUGUSTUS\tgene\t2126\t3863\t.\t+\t.\tg1\n-sample\tAUGUSTUS\ttranscript\t2126\t3863\t0.33\t+\t.\tg1.t1\n-sample\tAUGUSTUS\tstart_codon\t2126\t2128\t.\t+\t0\ttranscript_id "g1.t1"; gene_id "g1";\n-sample\tAUGUSTUS\tCDS\t2126\t2199\t1\t+\t0\ttranscript_id "g1.t1"; gene_id "g1";\n-sample\tAUGUSTUS\texon\t2126\t2199\t.\t+\t.\ttranscript_id "g1.t1"; gene_id "g1";\n-sample\tAUGUSTUS\tintron\t2200\t2257\t1\t+\t.\ttranscript_id "g1.t1"; gene_id "g1";\n-sample\tAUGUSTUS\tCDS\t2258\t3224\t1\t+\t1\ttranscript_id "g1.t1"; gene_id "g1";\n-sample\tAUGUSTUS\texon\t2258\t3224\t.\t+\t.\ttranscript_id "g1.t1"; gene_id "g1";\n-sample\tAUGUSTUS\tintron\t3225\t3283\t1\t+\t.\ttranscript_id "g1.t1"; gene_id "g1";\n-sample\tAUGUSTUS\tCDS\t3284\t3490\t0.62\t+\t0\ttranscript_id "g1.t1"; gene_id "g1";\n-sample\tAUGUSTUS\texon\t3284\t3490\t.\t+\t.\ttranscript_id "g1.t1"; gene_id "g1";\n-sample\tAUGUSTUS\tintron\t3491\t3548\t0.53\t+\t.\ttranscript_id "g1.t1"; gene_id "g1";\n-sample\tAUGUSTUS\tCDS\t3549\t3603\t0.44\t+\t0\ttranscript_id "g1.t1"; gene_id "g1";\n-sample\tAUGUSTUS\texon\t3549\t3603\t.\t+\t.\ttranscript_id "g1.t1"; gene_id "g1";\n-sample\tAUGUSTUS\tintron\t3604\t3768\t0.43\t+\t.\ttranscript_id "g1.t1"; gene_id "g1";\n-sample\tAUGUSTUS\tCDS\t3769\t3863\t0.42\t+\t2\ttranscript_id "g1.t1"; gene_id "g1";\n-sample\tAUGUSTUS\texon\t3769\t3863\t.\t+\t.\ttranscript_id "g1.t1"; gene_id "g1";\n-sample\tAUGUSTUS\tstop_codon\t3861\t3863\t.\t+\t0\ttranscript_id "g1.t1"; gene_id "g1";\n-sample\tAUGUSTUS\tgene\t4248\t6494\t.\t-\t.\tg2\n-sample\tAUGUSTUS\ttranscript\t4248\t6494\t1\t-\t.\tg2.t1\n-sample\tAUGUSTUS\tstop_codon\t4248\t4250\t.\t-\t0\ttranscript_id "g2.t1"; gene_id "g2";\n-sample\tAUGUSTUS\tCDS\t4248\t4759\t1\t-\t2\ttranscript_id "g2.t1"; gene_id "g2";\n-sample\tAUGUSTUS\texon\t4248\t4759\t.\t-\t.\ttranscript_id "g2.t1"; gene_id "g2";\n-sample\tAUGUSTUS\tintron\t4760\t4929\t1\t-\t.\ttranscript_id "g2.t1"; gene_id "g2";\n-sample\tAUGUSTUS\tCDS\t4930\t5539\t1\t-\t0\ttranscript_id "g2.t1"; gene_id "g2";\n-sample\tAUGUSTUS\texon\t4930\t5539\t.\t-\t.\ttranscript_id "g2.t1"; gene_id "g2";\n-sample\tAUGUSTUS\tintron\t5540\t6038\t1\t-\t.\ttranscript_id "g2.t1"; gene_id "g2";\n-sample\tAUGUSTUS\tCDS\t6039\t6494\t1\t-\t0\ttranscript_id "g2.t1"; gene_id "g2";\n-sample\tAUGUSTUS\texon\t6039\t6494\t.\t-\t.\ttranscript_id "g2.t1"; gene_id "g2";\n-sample\tAUGUSTUS\tstart_codon\t6492\t6494\t.\t-\t0\ttranscript_id "g2.t1"; gene_id "g2";\n-sample\tAUGUSTUS\tgene\t7691\t11104\t.\t-\t.\tg3\n-sample\tAUGUSTUS\ttranscript\t7691\t11104\t0.91\t-\t.\tg3.t1\n-sample\tAUGUSTUS\tstop_codon\t7691\t7693\t.\t-\t0\ttranscript_id "g3.t1"; gene_id "g3";\n-sample\tAUGUSTUS\tCDS\t7691\t8385\t0.99\t-\t2\ttranscript_id "g3.t1"; gene_id "g3";\n-sample\tAUGUSTUS\texon\t7691\t8385\t.\t-\t.\ttranscript_id "g3.t1"; gene_id "g3";\n-sample\tAUGUSTUS\tintron\t8386\t8706\t0.98\t-\t.\ttranscript_id "g3.t1"; gene_id "g3";\n-sample\tAUGUSTUS\tCDS\t8707\t10515\t0.95\t-\t2\ttranscript_id "g3.t1"; gene_id "g3";\n-sample\tAUGUSTUS\texon\t8707\t10515\t.\t-\t.\ttranscript_id "g3.t1"; gene_id "g3";\n-sample\tAUGUSTUS\tintron\t10516\t10646\t0.96\t-\t.\ttranscript_id "g3.t1"; gene_id "g3";\n-sample\tAUGUSTUS\tCDS\t10647\t10794\t1\t-\t0\ttranscript_id "g3.t1"; gene_id "g3";\n-sample\tAUGUSTUS\texon\t10647\t10794\t.\t-\t.\ttranscript_id "g3.t1"; gene_id "g3";\n-sample\tAUGUSTUS\tintron\t10795\t10852\t1\t-\t.\ttranscript_id "g3.t1"; gene_id "g3";\n-sample\tAUGUSTUS\tCDS\t10853\t11104\t0.97\t-\t0\ttranscript_id "g3.t1"; gene_id "g3";\n-sample\tAUGUSTUS\texon\t10853\t11104\t.\t-\t.\ttranscript_id "g3.t1"; gene_id "g3";\n-sample\tAUGUSTUS\tstart_codon\t11102\t11104\t.\t-\t0\ttranscript_id "g3.t1"; gene_id "g3";\n-sample\tAUGUSTUS\tgene\t14247\t28143\t.\t-\t.\tg4\n-sample\tAUGUSTUS\ttranscript\t14247\t28143\t0.88\t-\t.\tg4.t1\n-sample\tAUGUSTUS\tstop_codon\t14247\t14249\t.\t-\t0\ttranscript_id "g4.t1"; gene_id "g4";\n-sample\tAUGUSTUS\tCDS\t14247\t14707\t1\t-\t2\ttranscript_id "g4.t1"; gene_id "g4";\n-sample\tAUGUSTUS\texon\t14247\t14707\t.\t-\t.\ttranscript_id "g4.t1"; gene_id "g4";\n-sample\tAUGUSTUS\tintron\t14708\t14793\t1\t-\t.\ttranscript_id "g4.t1"; gene_id "g4";\n-sample\tAUGUSTUS\tCDS\t14794\t14995\t1\t-\t0\ttranscript_id "g4.t1"; gene_id "g4";\n-sample\tAUGUSTUS\texon\t14794\t14995\t.\t-\t.\ttranscript_id "g4.t1"; gene_id "g4";\n-sample\tAUGUSTUS\tintron\t14996\t15100\t1\t-\t.\ttranscript_id "g4.t1"; gene_id "g4";\n-sample\tAUGUSTUS\tCDS\t15101\t15289\t1\t-'..b'e_2_13_g"; transcript_id "file_2_13_t";\n+sample\tGeneMark.hmm3\tCDS\t102521\t103151\t.\t-\t0\tgene_id "file_2_13_g"; transcript_id "file_2_13_t"; cds_type "file_2_Internal"; count "file_2_4_5";\n+sample\tGeneMark.hmm3\tintron\t103152\t103222\t.\t-\t0\tgene_id "file_2_13_g"; transcript_id "file_2_13_t";\n+sample\tGeneMark.hmm3\tCDS\t103223\t103812\t.\t-\t2\tgene_id "file_2_13_g"; transcript_id "file_2_13_t"; cds_type "file_2_Internal"; count "file_2_3_5";\n+sample\tGeneMark.hmm3\tintron\t103813\t111230\t.\t-\t1\tgene_id "file_2_13_g"; transcript_id "file_2_13_t";\n+sample\tGeneMark.hmm3\tCDS\t111231\t111342\t.\t-\t0\tgene_id "file_2_13_g"; transcript_id "file_2_13_t"; cds_type "file_2_Internal"; count "file_2_2_5";\n+sample\tGeneMark.hmm3\tintron\t111343\t113595\t.\t-\t0\tgene_id "file_2_13_g"; transcript_id "file_2_13_t";\n+sample\tGeneMark.hmm3\tgene\t97476\t113919\t.\t-\t.\tgene_id "file_2_13_g"; transcript_id "file_2_13_t";\n+sample\tGeneMark.hmm3\tmRNA\t97476\t113919\t.\t-\t.\tgene_id "file_2_13_g"; transcript_id "file_2_13_t";\n+sample\tGeneMark.hmm3\tCDS\t113596\t113919\t.\t-\t0\tgene_id "file_2_13_g"; transcript_id "file_2_13_t"; cds_type "file_2_Initial"; count "file_2_1_5";\n+sample\tGeneMark.hmm3\tstart_codon\t113917\t113919\t.\t-\t0\tgene_id "file_2_13_g"; transcript_id "file_2_13_t";\n+sample4\tAUGUSTUS\tstop_codon\t1092\t1094\t.\t-\t0\ttranscript_id "file_1_g26.t1"; gene_id "file_1_g26";\n+sample4\tAUGUSTUS\tCDS\t1092\t1364\t0.76\t-\t0\ttranscript_id "file_1_g26.t1"; gene_id "file_1_g26";\n+sample4\tAUGUSTUS\texon\t1092\t1364\t.\t-\t.\ttranscript_id "file_1_g26.t1"; gene_id "file_1_g26";\n+sample4\tAUGUSTUS\tstart_codon\t1362\t1364\t.\t-\t0\ttranscript_id "file_1_g26.t1"; gene_id "file_1_g26";\n+sample4\tAUGUSTUS\tgene\t1092\t1364\t0.76\t-\t.\tg26\n+sample4\tAUGUSTUS\ttranscript\t1092\t1364\t0.76\t-\t.\tg26.t1\n+sample\tAUGUSTUS\tstop_codon\t34843\t34845\t.\t-\t0\ttranscript_id "file_1_g7.t1"; gene_id "file_1_g7";\n+sample\tAUGUSTUS\tCDS\t34843\t35679\t0.35\t-\t0\ttranscript_id "file_1_g7.t1"; gene_id "file_1_g7";\n+sample\tAUGUSTUS\texon\t34843\t35679\t.\t-\t.\ttranscript_id "file_1_g7.t1"; gene_id "file_1_g7";\n+sample\tAUGUSTUS\tstart_codon\t35677\t35679\t.\t-\t0\ttranscript_id "file_1_g7.t1"; gene_id "file_1_g7";\n+sample\tAUGUSTUS\tgene\t34843\t35679\t0.35\t-\t.\tg7\n+sample\tAUGUSTUS\ttranscript\t34843\t35679\t0.35\t-\t.\tg7.t1\n+sample\tAUGUSTUS\tstop_codon\t40166\t40168\t.\t-\t0\ttranscript_id "file_1_g8.t1"; gene_id "file_1_g8";\n+sample\tAUGUSTUS\tCDS\t40166\t40531\t0.99\t-\t0\ttranscript_id "file_1_g8.t1"; gene_id "file_1_g8";\n+sample\tAUGUSTUS\texon\t40166\t40531\t.\t-\t.\ttranscript_id "file_1_g8.t1"; gene_id "file_1_g8";\n+sample\tAUGUSTUS\tstart_codon\t40529\t40531\t.\t-\t0\ttranscript_id "file_1_g8.t1"; gene_id "file_1_g8";\n+sample\tAUGUSTUS\tgene\t40166\t40531\t0.99\t-\t.\tg8\n+sample\tAUGUSTUS\ttranscript\t40166\t40531\t0.99\t-\t.\tg8.t1\n+sample4\tAUGUSTUS\tstart_codon\t2126\t2128\t.\t+\t0\ttranscript_id "file_1_g27.t1"; gene_id "file_1_g27";\n+sample4\tAUGUSTUS\tCDS\t2126\t2199\t1\t+\t0\ttranscript_id "file_1_g27.t1"; gene_id "file_1_g27";\n+sample4\tAUGUSTUS\texon\t2126\t2199\t.\t+\t.\ttranscript_id "file_1_g27.t1"; gene_id "file_1_g27";\n+sample4\tAUGUSTUS\tintron\t2200\t2257\t1\t+\t.\ttranscript_id "file_1_g27.t1"; gene_id "file_1_g27";\n+sample4\tAUGUSTUS\tCDS\t2258\t3224\t0.45\t+\t1\ttranscript_id "file_1_g27.t1"; gene_id "file_1_g27";\n+sample4\tAUGUSTUS\texon\t2258\t3224\t.\t+\t.\ttranscript_id "file_1_g27.t1"; gene_id "file_1_g27";\n+sample4\tAUGUSTUS\tintron\t3225\t3283\t0.33\t+\t.\ttranscript_id "file_1_g27.t1"; gene_id "file_1_g27";\n+sample4\tAUGUSTUS\tCDS\t3284\t3512\t0.14\t+\t0\ttranscript_id "file_1_g27.t1"; gene_id "file_1_g27";\n+sample4\tAUGUSTUS\texon\t3284\t3512\t.\t+\t.\ttranscript_id "file_1_g27.t1"; gene_id "file_1_g27";\n+sample4\tAUGUSTUS\tintron\t3513\t3807\t0.22\t+\t.\ttranscript_id "file_1_g27.t1"; gene_id "file_1_g27";\n+sample4\tAUGUSTUS\tCDS\t3808\t3863\t0.59\t+\t2\ttranscript_id "file_1_g27.t1"; gene_id "file_1_g27";\n+sample4\tAUGUSTUS\tgene\t2126\t3863\t0.07\t+\t.\tg27\n+sample4\tAUGUSTUS\ttranscript\t2126\t3863\t0.07\t+\t.\tg27.t1\n+sample4\tAUGUSTUS\texon\t3808\t3863\t.\t+\t.\ttranscript_id "file_1_g27.t1"; gene_id "file_1_g27";\n+sample4\tAUGUSTUS\tstop_codon\t3861\t3863\t.\t+\t0\ttranscript_id "file_1_g27.t1"; gene_id "file_1_g27";\n' |