Galaxy |

Changeset 0:e50ea151f221 (2021-10-05)

Next changeset 1:ca7c12566894 (2021-10-21)

Commit message:
"planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/braker commit aa4a7f87d556b5af582d1ab8fe9a986922a59a1d"

added:
README.md
braker.xml
macros.xml
test-data/SRR7458692.bam
test-data/genemark_license.gm_key
test-data/genome_masked.fa
test-data/out_bam/braker.gtf
test-data/out_genome/braker.gff3
test-data/out_genome/braker.gtf
test-data/out_prot/braker.gtf
test-data/proteins.fa

diff -r 000000000000 -r e50ea151f221 README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md Tue Oct 05 12:35:42 2021 +0000

@@ -0,0 +1,21 @@
+# 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
+
+Braker can use GeneMark to predict gene, but due to licensing issues, we are not allowed to distribute GeneMark automatically.
+
+If you want to use it, the Galaxy administrator needs to install GeneMark, and set the `GENEMARK_PATH` variable on the job destination.
+
+## 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.
+
+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.
+
+You should also copy a valid GeneMark license (from http://topaz.gatech.edu/GeneMark/license_download.cgi) in test-data/genemark_license.gm_key

diff -r 000000000000 -r e50ea151f221 braker.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/braker.xml Tue Oct 05 12:35:42 2021 +0000

[

@@ -0,0 +1,144 @@
+<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
+
+#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 ${on_string}: annotation" from_work_dir="braker/braker.gtf">
+            <filter>output_format == 'gtf'</filter>
+        </data>
+        <data name='output_gff' format='gff3' label="${tool.name} on ${on_string}: annotation" from_work_dir="braker/braker.gff3">
+            <filter>output_format == 'gff3'</filter>
+        </data>
+    </outputs>
+    <tests>
+        
+        
+        
+        
+    </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>

diff -r 000000000000 -r e50ea151f221 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Tue Oct 05 12:35:42 2021 +0000

@@ -0,0 +1,131 @@
+<?xml version="1.0"?>
+<macros>
+    <token name="@TOOL_VERSION@">2.1.6</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+
+    <xml name="requirements">
+        <requirement type="package" version="@TOOL_VERSION@">braker2</requirement>
+    </xml>
+
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1093/nargab/lqaa108</citation>
+            <citation type="doi">10.1007/978-1-4939-9173-0_5</citation>
+            <citation type="doi">10.1093/bioinformatics/btv661</citation>
+            <citation type="doi">10.1093/bioinformatics/btn013</citation>
+            <citation type="doi">10.1186/1471-2105-7-62</citation>
+        </citations>
+    </xml>
+
+    <xml name="augustus_species">
+        
+        <option value="adorsata">adorsata</option>
+        <option value="aedes">aedes</option>
+        <option value="amphimedon">amphimedon</option>
+        <option value="ancylostoma_ceylanicum">ancylostoma_ceylanicum</option>
+        <option value="anidulans">anidulans</option>
+        <option value="arabidopsis">arabidopsis</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="bombus_impatiens1">bombus_impatiens1</option>
+        <option value="bombus_terrestris2">bombus_terrestris2</option>
+        <option value="botrytis_cinerea">botrytis_cinerea</option>
+        <option value="b_pseudomallei">b_pseudomallei</option>
+        <option value="brugia">brugia</option>
+        <option value="cacao">cacao</option>
+        <option value="caenorhabditis">caenorhabditis</option>
+        <option value="camponotus_floridanus">camponotus_floridanus</option>
+        <option value="candida_albicans">candida_albicans</option>
+        <option value="candida_guilliermondii">candida_guilliermondii</option>
+        <option value="candida_tropicalis">candida_tropicalis</option>
+        <option value="c_elegans_trsk">c_elegans_trsk</option>
+        <option value="chaetomium_globosum">chaetomium_globosum</option>
+        <option value="chicken">chicken</option>
+        <option value="chiloscyllium">chiloscyllium</option>
+        <option value="chlamy2011">chlamy2011</option>
+        <option value="chlamydomonas">chlamydomonas</option>
+        <option value="chlorella">chlorella</option>
+        <option value="ciona">ciona</option>
+        <option value="coccidioides_immitis">coccidioides_immitis</option>
+        <option value="Conidiobolus_coronatus">Conidiobolus_coronatus</option>
+        <option value="coprinus">coprinus</option>
+        <option value="coprinus_cinereus">coprinus_cinereus</option>
+        <option value="coyote_tobacco">coyote_tobacco</option>
+        <option value="cryptococcus">cryptococcus</option>
+        <option value="cryptococcus_neoformans_gattii">cryptococcus_neoformans_gattii</option>
+        <option value="cryptococcus_neoformans_neoformans_B">cryptococcus_neoformans_neoformans_B</option>
+        <option value="cryptococcus_neoformans_neoformans_JEC21">cryptococcus_neoformans_neoformans_JEC21</option>
+        <option value="culex">culex</option>
+        <option value="debaryomyces_hansenii">debaryomyces_hansenii</option>
+        <option value="E_coli_K12">E_coli_K12</option>
+        <option value="elephant_shark">elephant_shark</option>
+        <option value="encephalitozoon_cuniculi_GB">encephalitozoon_cuniculi_GB</option>
+        <option value="eremothecium_gossypii">eremothecium_gossypii</option>
+        <option value="fly">fly</option>
+        <option value="fly_exp">fly_exp</option>
+        <option value="fusarium">fusarium</option>
+        <option value="fusarium_graminearum">fusarium_graminearum</option>
+        <option value="galdieria">galdieria</option>
+        <option value="generic">generic</option>
+        <option value="heliconius_melpomene1">heliconius_melpomene1</option>
+        <option value="histoplasma">histoplasma</option>
+        <option value="histoplasma_capsulatum">histoplasma_capsulatum</option>
+        <option value="honeybee1">honeybee1</option>
+        <option value="human">human</option>
+        <option value="japaneselamprey">japaneselamprey</option>
+        <option value="kluyveromyces_lactis">kluyveromyces_lactis</option>
+        <option value="laccaria_bicolor">laccaria_bicolor</option>
+        <option value="leishmania_tarentolae">leishmania_tarentolae</option>
+        <option value="lodderomyces_elongisporus">lodderomyces_elongisporus</option>
+        <option value="magnaporthe_grisea">magnaporthe_grisea</option>
+        <option value="maize">maize</option>
+        <option value="maize5">maize5</option>
+        <option value="mnemiopsis_leidyi">mnemiopsis_leidyi</option>
+        <option value="nasonia">nasonia</option>
+        <option value="nematostella_vectensis">nematostella_vectensis</option>
+        <option value="neurospora">neurospora</option>
+        <option value="neurospora_crassa">neurospora_crassa</option>
+        <option value="parasteatoda">parasteatoda</option>
+        <option value="pchrysosporium">pchrysosporium</option>
+        <option value="pea_aphid">pea_aphid</option>
+        <option value="pfalciparum">pfalciparum</option>
+        <option value="phanerochaete_chrysosporium">phanerochaete_chrysosporium</option>
+        <option value="pichia_stipitis">pichia_stipitis</option>
+        <option value="pisaster">pisaster</option>
+        <option value="pneumocystis">pneumocystis</option>
+        <option value="rhincodon">rhincodon</option>
+        <option value="rhizopus_oryzae">rhizopus_oryzae</option>
+        <option value="rhodnius">rhodnius</option>
+        <option value="rice">rice</option>
+        <option value="saccharomyces">saccharomyces</option>
+        <option value="saccharomyces_cerevisiae_rm11-1a_1">saccharomyces_cerevisiae_rm11-1a_1</option>
+        <option value="saccharomyces_cerevisiae_S288C">saccharomyces_cerevisiae_S288C</option>
+        <option value="s_aureus">s_aureus</option>
+        <option value="schistosoma">schistosoma</option>
+        <option value="schistosoma2">schistosoma2</option>
+        <option value="schizosaccharomyces_pombe">schizosaccharomyces_pombe</option>
+        <option value="scyliorhinus">scyliorhinus</option>
+        <option value="sealamprey">sealamprey</option>
+        <option value="s_pneumoniae">s_pneumoniae</option>
+        <option value="strongylocentrotus_purpuratus">strongylocentrotus_purpuratus</option>
+        <option value="sulfolobus_solfataricus">sulfolobus_solfataricus</option>
+        <option value="template_prokaryotic">template_prokaryotic</option>
+        <option value="tetrahymena">tetrahymena</option>
+        <option value="thermoanaerobacter_tengcongensis">thermoanaerobacter_tengcongensis</option>
+        <option value="tomato">tomato</option>
+        <option value="toxoplasma">toxoplasma</option>
+        <option value="tribolium2012">tribolium2012</option>
+        <option value="trichinella">trichinella</option>
+        <option value="ustilago">ustilago</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="volvox">volvox</option>
+        <option value="wheat">wheat</option>
+        <option value="Xipophorus_maculatus">Xipophorus_maculatus</option>
+        <option value="yarrowia_lipolytica">yarrowia_lipolytica</option>
+        <option value="zebrafish">zebrafish</option>
+    </xml>
+</macros>

diff -r 000000000000 -r e50ea151f221 test-data/SRR7458692.bam

Binary file test-data/SRR7458692.bam has changed

diff -r 000000000000 -r e50ea151f221 test-data/genome_masked.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome_masked.fa Tue Oct 05 12:35:42 2021 +0000

b'@@ -0,0 +1,4554 @@\n+>sample\n+GTGGCCGGCTGATTTCACGTCCTAACTTTGGGCTTAACTGGTTCGCCAGT\n+TGACTTTCTTCGCCATCATGTGATGCATTAATTAAACAATAATTACTAAT\n+TGacagtaattaataattgTGGCAAAAAGCGCGACACGTTTTTTCGGCAA\n+ACTCCTCGGAAGACCGATTGTTTAAAGACGTAGGGAAAAGTAGTTCCCAA\n+GCATTTTAAAAAGATACCTATGACATGTGACACCTTTAAAGTGCAATACA\n+AGTTTTCATCTCTTTATATCCTTTTACTCCCTAATTTGAATATAAAAGGA\n+ATCGCATTGAGAGTATAAAGGCTTTAGTTCTTATCGATagatagttagtG\n+ATGAAATAAAATTATAACCGTGGTTTTAGTTTGAAATGTTGTAAAGACTT\n+TCTTTAAATTTAACCAAATTTATGTGATAAAATGGATATTCCATAGATAA\n+GACATTTAAGTTAAATGTTTTTATACATCAAAAAGGAAACATTGTGCACG\n+CTATCAAATGGTATTCTTAAAATCGAGTCAgttaggtaagttattaatta\n+aATGGTAACTTTTTAACGTGCGTCAAATAATCTAGAAATTCTTCTTCAAC\n+TCATCCAAAACATTCTCAACACCACAATATCTATGCTCAGCGATGACAAA\n+TTTCTCCTGATTTCTTAATTTTCTATCTATGctatgcGATCAATCAACGA\n+ATGTGTGCTAATTTCTTGTGACGATTATTTTGCAAAGTCGTCTCCGCGTT\n+AATATCCGATGTAAATAAACCTATGAAAATCGCAAAGATCTATTCCTTTG\n+CGCTTAACCTTGTTATTGAACTCCCTCCCGCCCGGATTTTCGCAGCTTCC\n+AACTAAGTGATACCTTTTAAACAAACGCCACAACAAAACAGGTGACAATC\n+ATATTTTATCAACAAAAGAAAAGAGAGATAATATCTGCTGCTAATTCAAT\n+TTATTGGGCTTTGTGTTTATTTGCATTGGGAATCCGTGGAGCTGATATTG\n+TTTACTTTGGCAATTTCCCAGTCATTATGGTCGCCGTATAATGTGAATGG\n+CCAACAGGAAAATTTCACAGATTCCACTGGTTATTCACTGTTCATGCTGG\n+CGGTTGATCCGCTCCAAATCCCGGATGAGGCGGCGGAAGATCCTTATACC\n+GCTTACTTACGTATTCACTGCTTAACATCTTATCATAGAATTCGTTAGCT\n+TTCACATAGTTTGGATTCCGAATGAATCTCTTCTGTCGACCTCGCGTTTT\n+TGGCAATTTTCGGAGCTCTTCGCTACTGCTAGTTGATTTAAGGCCTACAT\n+CTTTCTGATCCTTAATCATCCTTTTAGGTGATTCTCCTGCTACCATGGGA\n+TCCACCAGTTTCATATATAATGGATCGGGCTCGTTTGCAAGTGGGTTTCC\n+AGTTTCAGAAGACTCTGACGTTCTAAGCGCCAATAAAATGAAAATAACCA\n+AAAGGAAACTAGACATGTTTCGTTACAGACAGATATAGATTGGATATTAT\n+TGAAAGAAAATgaaaataAACAGCGATAATGATCTGTGACTTATTGGAAA\n+TTAGATGGCTTATGGATGATGGGGCGATAAATTCGAACAAACACTGAGAG\n+CATTTTTGGGAGCATTGTGGGAGCTTTTCTATTATCCAGTACTTTATATA\n+CATATATCATTTATATACTAATCATTTCTGGTAGCCGTTCGTAATCAGGA\n+TCGGATCCTTTTTTACCCGTTAGTCAGCTAGAAGAAACGAAAAATTAAAA\n+TAGTAAAatctaaaagtatacaaaaattcaaatagtaaaaccaaaaagta\n+ttaaaaaaAATATCAATCGTTTTTAAACGTTGATTTTTCAGCTTGTGGGG\n+TGATTTATCGCTAACTTGGAAAATGATAATAAAGCATTATCCATAATATT\n+AGTTGTGGAAATGAAATTCAAATAGATGTTGTGTTATATACGATGAGGAT\n+GTTGCATTTGAGTCCCCGGAAATATAGTATTTTTTTTACCGAAGGTATTA\n+TCGTACCGGTCAAGTACGGTCACACTGCCAAGCGCAGATTTGAGGATTTC\n+TAGATTTGGCCTCTTGATGGACTAGAAGCGCTACCAAAACTGGGGCTTGA\n+GTTGAATTACCTGTTGGAAGACACAATGCCACCCACGATCAACAATTCGG\n+CGGTAAACAGTGCCGCCGAAAAGCGACCCCAGCGGCAAACGGAGCGCAAG\n+TAAGTGAACAGATCCCTAAACAGACGCCAGATACTCAGACTGATGTGTAC\n+CTTGCAGATCCGAGATCATTTGCCGCGTGAAGTATGGAAACAACCTGCCG\n+GATATACCATTTGATCTGAAGTTTCTGCAGTACCCCTTCGACAGCCACCG\n+CTTCGTGCAGTACAACCCAACGTCGCTAGAGCGTAACTTCAAGTATGACG\n+TGCTGACGGAACACGATTTGGGTGTCACGGTGGACCTGATTAACCGGGAG\n+CTCTATCAGGCCGACTCCATGACGCTGCTGGACCCCGCCGATGAAAAACT\n+GCTGGAGGAGGAGACTCTGACGCCCACAGACTCTGTGCGTTCGCGCCAGC\n+ATTCGAGGACGGTGTCATGGTTGCGCAAATCCGAGTACATCTCCACCGAG\n+CAGACGCGCTTCCAGCCCCAGAACCTGGAGAACATCGAGGCCAAGGTCGG\n+TTACAACGTCAAGAAGTCGCTTCGGGAGGAGACTCTCTACCTGGACCGCG\n+AAGCCCAGATCAAAGCCATCGAGAAGACCTTCAGCGACACCAAGAGCGAA\n+ATTACCAAGCACTATTCCAAGCCCAATGTGGTGCCAGTGGAGGTACTGCC\n+TATCTTCCCCGACTTCACCAACTGGAAGTTCCCGTGCGCCCAGGTCATAT\n+TTGACAGTGATCCCGCTCCTGCGGGCAAGAACGTGCCCGCCCAGCTGGAG\n+GAGATGTCGCAGGCCATGATTCGTGGTGTGATGGACGAGAGCGGCGAACA\n+GTTTGTCGCCTACTTCCTGCCCACAGAGCAGACGCTGGAGAAACGCCGTA\n+CAGACTTCATCAATGGCGAGCTGTACAAGGAGGaggaggagtacgagtac\n+aagATCGCTCGAGAGTACAACTGGAACGTGAAGACCAAAGCTTCCAAGGG\n+CTACGAAGAAAACTACTTCTTCGTGATGCGTCAGGACGGCATCTACTACA\n+ACGAGCTAGAAACCCGTGTGCGCCTTAACAAGCGTCGCGTTAAGGTTGGC\n+CAGCAACCCAACAACACCAAGCTGGTAAGTATATTTATGCGCATACATCT\n+ATAGCGAGCTTTACTTTGTATTATTTCTACCAGGTTGTCAAGCATCGTCC\n+ATTGGACAGCATGGAGCATCGTATGCAGCGCTATCGCGAGCGCCAGCTAG\n+AAGTTCCTGGCGAGGaggaggaGATCGTGGAAGAAGTGAGGGAAGAGGAG\n+CAAATGCAAATCATTGGCGAGACGGAGAAGACGAGCGAGGACGCAGCTGT\n+TGGCGCACAGGCAGCATCTGGAGCGGACTCACCCGCCCAGGTAGCCCGCG\n+ATCGACAGTCTCGTTCTCGGAGTCGAACTCGCAGCGGGTCCAgttcagga\n+tctggatctggctccggctcTCGGGCCAgcagccgctcaaagtctggttc\n+tcggtctggtagcggctcCAGATCACGCACAAATTCGCCGGCAGGATCCC\n+AGAAATCCGGatccagatcgagatcggtatcacgttcccgatcccgttcc\n+aagtcCGGCTCTCGGtcgcgttctaggtcgagatccaagtccggttcccg\n+atcacgttcgggctccagatctggctctgggtcgcgatcgCCCAGCCGGT\n+CTCGCAGTGGCTCGCCTT'..b'cgcgttctaggtcgagatccaagtccggttcccg\n+atcacgttcgggctccagatctggctctgggtcgcgatcgCCCAGCCGGT\n+CTCGCAGTGGCTCGCCTTCTGGTTCAGGATCCAGCTCTGGAAGCGCCTCA\n+GATGAATGATTAATTACAAAAAACGGCGTTCATAATAAATAAGTTTATAA\n+TCAACCAAGTACATTTGAAAACTGAACTAACTCGATTTAATATCATTTTC\n+GCCTCAACTCAGCGCTCGGGTTCGTTGCCCAGAATAGTTTTAAATAAAAT\n+CGGCAGTTTAACATAATTTATATTAGATGTtgttgttgtATTGCAAACAA\n+GTCGGGTCCTAGTCGATTTACACTTGGCTGAGATAAAACAACTAAGATTC\n+AAATAATATCCTCATAAGAAGATGTAATTAAGACGTTTTTCTTAGGGGGT\n+GCTTAGGAATTGATTAGATCGCCTTTGGGGAAGTGCAAACAATGTAAaat\n+gatataaaagggtataaaTTAAGTGGATATATGCATCTTCGTTCCAACTA\n+CGTGGCGTCCATCAAAAAGCGCTGGAAGACTTCGCCATCGGAACTAGGTA\n+GCTCTGTTTGTTGCGGTGAGTAGATTCTCAAGTTCTGGAGTTGCTGCAGC\n+GGAGAGCCATTCCCGCTGAAGTGTACCACCGCAACCGGCTGTAGGGATAT\n+GAGCTGTCCCTCCTCCCGCGGCTCCACACCACAGATGCCCAGCTTTTGGC\n+ACTGCTCAACGACAATGTCGTCGATTGACTGCGAAAGCAGTGCCTCCTGC\n+TCAGGATCCACAATGGAGCTGCTGTTGATGGCAGCTATTTCGGCGCTCGC\n+TGGTGAAGGCTGAGTATGCGAGTCGTTGCCCTCCAGGAACGCCTTTATCA\n+GCTGCTCCGGTGTCTGGGCCTCCTCGGTGGGACATCGATGGGTCCTTTGA\n+CTGACCTTGTACCTGAACGTCTTTTGGCAGAGCTCGCACTTGTAGGGCAT\n+CACTCCCGTGTGGATGCGCGTGTGGACAAGGAAAGAGACTCGCTGCCGGA\n+AACACTTGCCTGTGGACGAGTCCGAAATACGAAAAGGTTAGACATGGAGT\n+GACCCGGAAAAGAAGGTATACCTCTCCTTCATTTAAAGTAAATAGGGCAA\n+ATCGCAATGGAGTATGCTCATTTATAAGCTGGCTAACAAAATAAGGGGCG\n+GCTAATTAAGGGGTTTGATCGATACTCACCGCAGACTTCGCACTTGAAGG\n+GCTTTTCGCCGCTGTGAATCCTCTGGTGGTTATGCAGCGTAGACAGTTCC\n+TTGAAGGCGCGTCCACAAACCCCGCAGACATGGGGCTTTACCTCGCTGTG\n+GTAGAGCAAATGCTTGTGGTACGACTGCTGGAAGGTGAAGGTCCTGGCGC\n+AGATCTCGCATGTGTACGGCATCTCGCCGGTGTGGAGCCGCTTGTGCTTC\n+TTCAGAAAGTACTTGGTGGTGAAGGACTTGCTGCACACATCGCACTCCCA\n+CAGCTTCGGGGTGGCCGTGCCCGACTCCGGCGAACTGGGGGACTGCTGGA\n+GCATGCTCAGCGCCCCACTCAGCGCGTATGGCTGGGATGCGGTGCACGTG\n+GAGTTATTTCCGTTGCCAAGGGCTCCAGGCTCTGTGTGTCGAATGCGATC\n+GCAAATGCTCAGCTTGGGCGTGGCAGTAACTGCACTGGTGGTAGAAGCGG\n+GTGTAGGACtgggattaggatttggattgggattggAGCAGGGCACGCCC\n+ATCATGTGCACTACTTTCAGGTGGATTCGAAGGGAGCCCTTCATTCGGAA\n+CGTCTTGGAGCAGAGATGGCACTTGTAGGGCTCCTGGTCCTGTATAAAGC\n+AATAATCGGAATTTCACTTATATTTATCAATTCATCAATATGCCCTCATG\n+GCCAAATATTCCATTACATTACCGTCTGTCTCTCAGTTTCAAATTTATGC\n+ACAAAAATCATTCACTTTCATTCACTATATCACAAAGTTGCCATGGTTTT\n+AAATTGATCAAAAACAAATTAATATCTATCATATATaTACATAGTCATAT\n+GAACAGTTGAAAAATTAATTGAAAATAATGGGAACGATATACGTACATAC\n+ATCAGTTGTTTTTAAAATATAAGGGTATATAGATTTCTTTCttgttgttg\n+ttgatTTTAATTACGTCAAACTTTTGTTTCAGATTCAATGTAAATGGTCT\n+AGCTTTTTAAGTATGATTTTTTTTTGCTGCCAGTGAGCATAGAAaaaaaa\n+aatCaaaATCGATATAAGAATATGCGAAAGTGCATTACGAAACTCTTTAG\n+ATAATAGCACTTAATATATGTACATAGCCAATAGTTACCGGTTCCTTCTG\n+TTGGggttccttttgcttgggttcTCCCTCCGCATTTTCGTGGACTAAGC\n+GGACGTGCATGTCCCTCAGCTCGGTATTCCGGAAACTGAACTCGCAAATG\n+TCGCAGTGGGCGGGCGGGGTGGTCCGCACAGGCGGTGGGGTTGGGACGAC\n+GGGCTTGGACCTGGTTCGCTTGGCCCTCCGTTTGGGAGGAGCTGCGGCAA\n+GGAAGCCCCGGGACGAGGCGGGTTGGCCATTCGCTGGACTCTCGTTTCCC\n+TCCTGAGCCATCAGACTTGTGTGCGAGAACAGGTGGATGGTGAGCTTGTC\n+CAGCCCCAGGAAGAGCTCCTTGCAGTTGGCAAAGGGACAGGCCAGTGGGC\n+CGTTGGCCGCCTTGATCAGCCTCTGCTGCAGTGCGTCAATACTGCCGAAA\n+CTGGGCACCGCGCAGAGCGGACACAGCACCGAGGTGGAACACATTTCGCC\n+AGTGCACTCAATCGAATCTTATGCAAATGCTTCACCTCCTATTGGGATTA\n+TCCTCCTGTTCGGTCTGTGATCATCTATTCAGGAGTCCATTCCCAGACTG\n+CCTAGTCTTTCTGCTTTCAAAATTTTCTAAAAATATCAGCAAGTGAAGAT\n+TTTTGAAAACTTTGGGCCCAGCAATCTGACTTCTCGGCACCGATGCCAGC\n+TAACGAAATAATGAAaaataatgaaaTGCCCGGCGCGGATCGTCGAATCG\n+TCAAGAAGACTTTCGGAAACACTCGCAGCACCGAAATCCCATCTCTCGAA\n+CAAGGCAGTCTCTTTTCTCCGTGTCTCTGGGTAGCTCATTTCGAAATATA\n+GCTCTGAGCACGGCTATATACTATATGTATGTAGAATTATTTCTGGCCGA\n+TATATGTTGCACTGGCGGCCATATAGCCTTCGTTCTAGTCTTTGTAACGC\n+ACGATGCGCAGGAGCAATTCGCTGAGATGACCACATGCGATTTGCGGGAC\n+TTATCTAGAGATCTATCATTATCGCCAGATTGGTTTAATAATTGGCTTTT\n+CCGCCAATATCCAATTGGAATATGGTTGGTTACTGCAATTGTCGCTCCAT\n+TTTTTAAGCACTCCATAAAAAGTAAACACATTAATATGTACTCTTATTGG\n+AGATTTCTTCTTTCGATTTTAGTTTCGGACCAGTGAAAATCATTCGTTTC\n+ATTTTCGTAAATAAGAACTGAGAAAATATtattattatATATATTTCTTT\n+ATTAGGAAAATACGAAGATTGAGTATTTCAGATTGAATTAGCATATCCGT\n+CTAAATCTTAATGCTGTAATGAGCTTACTTGAGATCTGATCAAAACCAAT\n+ACaaaacccacacCAAAGGTGGTAGCTAATATACATATTTTGTGTAATAC\n+TTTTGTAGAGTATTTACTATTCAGCGATTTAAACAAGCAATCGCCTAGAC\n+ACACACATTTGTCCGCCTATGTGTATGTGCACCGAGCTATACCCCCACTG\n+AATCGCTGTGTGCTATTTTTATGGCCGCGATGCTCTCTTGTTTTGACCCG\n+CTTGGGCAAC\n'

diff -r 000000000000 -r e50ea151f221 test-data/out_bam/braker.gtf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out_bam/braker.gtf Tue Oct 05 12:35:42 2021 +0000

b'@@ -0,0 +1,465 @@\n+sample\tAUGUSTUS\tstart_codon\t79526\t79528\t.\t+\t0\ttranscript_id "file_1_g14.t1"; gene_id "file_1_g14";\n+sample\tAUGUSTUS\tCDS\t79526\t80474\t0.4\t+\t0\ttranscript_id "file_1_g14.t1"; gene_id "file_1_g14";\n+sample\tAUGUSTUS\texon\t79526\t80474\t.\t+\t.\ttranscript_id "file_1_g14.t1"; gene_id "file_1_g14";\n+sample\tAUGUSTUS\tintron\t80475\t87860\t0.49\t+\t.\ttranscript_id "file_1_g14.t1"; gene_id "file_1_g14";\n+sample\tAUGUSTUS\tCDS\t87861\t88125\t0.39\t+\t2\ttranscript_id "file_1_g14.t1"; gene_id "file_1_g14";\n+sample\tAUGUSTUS\texon\t87861\t88125\t.\t+\t.\ttranscript_id "file_1_g14.t1"; gene_id "file_1_g14";\n+sample\tAUGUSTUS\tintron\t88126\t92148\t0.19\t+\t.\ttranscript_id "file_1_g14.t1"; gene_id "file_1_g14";\n+sample\tAUGUSTUS\tCDS\t92149\t92252\t0.17\t+\t1\ttranscript_id "file_1_g14.t1"; gene_id "file_1_g14";\n+sample\tAUGUSTUS\texon\t92149\t92252\t.\t+\t.\ttranscript_id "file_1_g14.t1"; gene_id "file_1_g14";\n+sample\tAUGUSTUS\tintron\t92253\t94562\t0.19\t+\t.\ttranscript_id "file_1_g14.t1"; gene_id "file_1_g14";\n+sample\tAUGUSTUS\tCDS\t94563\t94732\t0.96\t+\t2\ttranscript_id "file_1_g14.t1"; gene_id "file_1_g14";\n+sample\tAUGUSTUS\texon\t94563\t94732\t.\t+\t.\ttranscript_id "file_1_g14.t1"; gene_id "file_1_g14";\n+sample\tAUGUSTUS\tintron\t94733\t94872\t0.91\t+\t.\ttranscript_id "file_1_g14.t1"; gene_id "file_1_g14";\n+sample\tAUGUSTUS\tCDS\t94873\t95333\t0.79\t+\t0\ttranscript_id "file_1_g14.t1"; gene_id "file_1_g14";\n+sample\tAUGUSTUS\texon\t94873\t95333\t.\t+\t.\ttranscript_id "file_1_g14.t1"; gene_id "file_1_g14";\n+sample\tAUGUSTUS\tintron\t95334\t95584\t0.51\t+\t.\ttranscript_id "file_1_g14.t1"; gene_id "file_1_g14";\n+sample\tAUGUSTUS\tCDS\t95585\t95762\t0.35\t+\t1\ttranscript_id "file_1_g14.t1"; gene_id "file_1_g14";\n+sample\tAUGUSTUS\tgene\t79526\t95762\t0.01\t+\t.\tg14\n+sample\tAUGUSTUS\ttranscript\t79526\t95762\t0.01\t+\t.\tg14.t1\n+sample\tAUGUSTUS\texon\t95585\t95762\t.\t+\t.\ttranscript_id "file_1_g14.t1"; gene_id "file_1_g14";\n+sample\tAUGUSTUS\tstop_codon\t95760\t95762\t.\t+\t0\ttranscript_id "file_1_g14.t1"; gene_id "file_1_g14";\n+sample4\tAUGUSTUS\tstop_codon\t4248\t4250\t.\t-\t0\ttranscript_id "file_1_g28.t1"; gene_id "file_1_g28";\n+sample4\tAUGUSTUS\tCDS\t4248\t4738\t0.42\t-\t2\ttranscript_id "file_1_g28.t1"; gene_id "file_1_g28";\n+sample4\tAUGUSTUS\texon\t4248\t4738\t.\t-\t.\ttranscript_id "file_1_g28.t1"; gene_id "file_1_g28";\n+sample4\tAUGUSTUS\tintron\t4739\t4929\t0.42\t-\t.\ttranscript_id "file_1_g28.t1"; gene_id "file_1_g28";\n+sample4\tAUGUSTUS\tCDS\t4930\t5539\t0.37\t-\t0\ttranscript_id "file_1_g28.t1"; gene_id "file_1_g28";\n+sample4\tAUGUSTUS\texon\t4930\t5539\t.\t-\t.\ttranscript_id "file_1_g28.t1"; gene_id "file_1_g28";\n+sample4\tAUGUSTUS\tintron\t5540\t6038\t0.29\t-\t.\ttranscript_id "file_1_g28.t1"; gene_id "file_1_g28";\n+sample4\tAUGUSTUS\tCDS\t6039\t6494\t0.47\t-\t0\ttranscript_id "file_1_g28.t1"; gene_id "file_1_g28";\n+sample4\tAUGUSTUS\tgene\t4248\t6494\t0.12\t-\t.\tg28\n+sample4\tAUGUSTUS\ttranscript\t4248\t6494\t0.12\t-\t.\tg28.t1\n+sample4\tAUGUSTUS\texon\t6039\t6494\t.\t-\t.\ttranscript_id "file_1_g28.t1"; gene_id "file_1_g28";\n+sample4\tAUGUSTUS\tstart_codon\t6492\t6494\t.\t-\t0\ttranscript_id "file_1_g28.t1"; gene_id "file_1_g28";\n+sample\tAUGUSTUS\tstop_codon\t209044\t209046\t.\t-\t0\ttranscript_id "file_1_g24.t1"; gene_id "file_1_g24";\n+sample\tAUGUSTUS\tCDS\t209044\t210483\t0.38\t-\t0\ttranscript_id "file_1_g24.t1"; gene_id "file_1_g24";\n+sample\tAUGUSTUS\texon\t209044\t210483\t.\t-\t.\ttranscript_id "file_1_g24.t1"; gene_id "file_1_g24";\n+sample\tAUGUSTUS\tstart_codon\t210481\t210483\t.\t-\t0\ttranscript_id "file_1_g24.t1"; gene_id "file_1_g24";\n+sample\tAUGUSTUS\tgene\t209044\t210483\t0.38\t-\t.\tg24\n+sample\tAUGUSTUS\ttranscript\t209044\t210483\t0.38\t-\t.\tg24.t1\n+sample\tAUGUSTUS\tstart_codon\t2126\t2128\t.\t+\t0\ttranscript_id "file_1_g2.t1"; gene_id "file_1_g2";\n+sample\tAUGUSTUS\tCDS\t2126\t2199\t1\t+\t0\ttranscript_id "file_1_g2.t1"; gene_id "file_1_g2";\n+sample\tAUGUSTUS\texon\t2126\t2199\t.\t+\t.\ttranscript_id "file_1_g2.t1"; gene_id "file_1_g2";\n+sample\tAUGUSTUS\tintron\t2200\t2257\t1\t+\t.\ttranscript_id "file_1_g2.t1"; gene_id "file_1_g2";\n+sample\tAUGUSTUS\tCDS\t2258\t3224\t0.49\t+\t1\ttranscript_id "file_1_g2.t1"; gene_id "file_1_g2";\n+sample\tAUGUSTUS\texon\t2258\t3224\t.\t+\t.\ttranscript_id "fi'..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'

diff -r 000000000000 -r e50ea151f221 test-data/out_genome/braker.gff3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out_genome/braker.gff3 Tue Oct 05 12:35:42 2021 +0000

b'@@ -0,0 +1,280 @@\n+sample\tAUGUSTUS\tstart_codon\t40692\t40694\t.\t+\t0\tID=file_1_g9.t1.start1;Parent=file_1_g9.t1;\n+sample\tAUGUSTUS\tCDS\t40692\t41193\t0.54\t+\t0\tID=file_1_g9.t1.CDS1;Parent=file_1_g9.t1;\n+sample\tAUGUSTUS\texon\t40692\t41193\t.\t+\t.\tID=file_1_g9.t1.exon1;Parent=file_1_g9.t1;\n+sample\tAUGUSTUS\tintron\t41194\t41706\t0.54\t+\t.\tID=file_1_g9.t1.intron1;Parent=file_1_g9.t1;\n+sample\tAUGUSTUS\tCDS\t41707\t42103\t0.64\t+\t2\tID=file_1_g9.t1.CDS2;Parent=file_1_g9.t1;\n+sample\tAUGUSTUS\texon\t41707\t42103\t.\t+\t.\tID=file_1_g9.t1.exon2;Parent=file_1_g9.t1;\n+sample\tAUGUSTUS\tintron\t42104\t43371\t0.21\t+\t.\tID=file_1_g9.t1.intron2;Parent=file_1_g9.t1;\n+sample\tAUGUSTUS\tCDS\t43372\t43609\t0.14\t+\t1\tID=file_1_g9.t1.CDS3;Parent=file_1_g9.t1;\n+sample\tAUGUSTUS\texon\t43372\t43609\t.\t+\t.\tID=file_1_g9.t1.exon3;Parent=file_1_g9.t1;\n+sample\tAUGUSTUS\tintron\t43610\t43677\t0.46\t+\t.\tID=file_1_g9.t1.intron3;Parent=file_1_g9.t1;\n+sample\tAUGUSTUS\tCDS\t43678\t44130\t0.46\t+\t0\tID=file_1_g9.t1.CDS4;Parent=file_1_g9.t1;\n+sample\tAUGUSTUS\texon\t43678\t44130\t.\t+\t.\tID=file_1_g9.t1.exon4;Parent=file_1_g9.t1;\n+sample\tAUGUSTUS\tstop_codon\t44128\t44130\t.\t+\t0\tID=file_1_g9.t1.stop1;Parent=file_1_g9.t1;\n+sample4\tAUGUSTUS\tstop_codon\t1092\t1094\t.\t-\t0\tID=file_1_g26.t1.stop1;Parent=file_1_g26.t1;\n+sample4\tAUGUSTUS\tCDS\t1092\t1364\t0.76\t-\t0\tID=file_1_g26.t1.CDS1;Parent=file_1_g26.t1;\n+sample4\tAUGUSTUS\texon\t1092\t1364\t.\t-\t.\tID=file_1_g26.t1.exon1;Parent=file_1_g26.t1;\n+sample4\tAUGUSTUS\tstart_codon\t1362\t1364\t.\t-\t0\tID=file_1_g26.t1.start1;Parent=file_1_g26.t1;\n+sample\tAUGUSTUS\tstart_codon\t167121\t167123\t.\t+\t0\tID=file_1_g21.t1.start1;Parent=file_1_g21.t1;\n+sample\tAUGUSTUS\tCDS\t167121\t168360\t1\t+\t0\tID=file_1_g21.t1.CDS1;Parent=file_1_g21.t1;\n+sample\tAUGUSTUS\texon\t167121\t168360\t.\t+\t.\tID=file_1_g21.t1.exon1;Parent=file_1_g21.t1;\n+sample\tAUGUSTUS\tintron\t168361\t168721\t1\t+\t.\tID=file_1_g21.t1.intron1;Parent=file_1_g21.t1;\n+sample\tAUGUSTUS\tCDS\t168722\t169167\t1\t+\t2\tID=file_1_g21.t1.CDS2;Parent=file_1_g21.t1;\n+sample\tAUGUSTUS\texon\t168722\t169167\t.\t+\t.\tID=file_1_g21.t1.exon2;Parent=file_1_g21.t1;\n+sample\tAUGUSTUS\tintron\t169168\t172584\t0.87\t+\t.\tID=file_1_g21.t1.intron2;Parent=file_1_g21.t1;\n+sample\tAUGUSTUS\tCDS\t172585\t172957\t0.81\t+\t0\tID=file_1_g21.t1.CDS3;Parent=file_1_g21.t1;\n+sample\tAUGUSTUS\texon\t172585\t172957\t.\t+\t.\tID=file_1_g21.t1.exon3;Parent=file_1_g21.t1;\n+sample\tAUGUSTUS\tintron\t172958\t180019\t0.41\t+\t.\tID=file_1_g21.t1.intron3;Parent=file_1_g21.t1;\n+sample\tAUGUSTUS\tCDS\t180020\t180579\t0.57\t+\t2\tID=file_1_g21.t1.CDS4;Parent=file_1_g21.t1;\n+sample\tAUGUSTUS\texon\t180020\t180579\t.\t+\t.\tID=file_1_g21.t1.exon4;Parent=file_1_g21.t1;\n+sample\tAUGUSTUS\tstop_codon\t180577\t180579\t.\t+\t0\tID=file_1_g21.t1.stop1;Parent=file_1_g21.t1;\n+sample\tAUGUSTUS\tstart_codon\t119778\t119780\t.\t+\t0\tID=file_1_g18.t1.start1;Parent=file_1_g18.t1;\n+sample\tAUGUSTUS\tCDS\t119778\t120378\t1\t+\t0\tID=file_1_g18.t1.CDS1;Parent=file_1_g18.t1;\n+sample\tAUGUSTUS\texon\t119778\t120378\t.\t+\t.\tID=file_1_g18.t1.exon1;Parent=file_1_g18.t1;\n+sample\tAUGUSTUS\tintron\t120379\t123327\t0.98\t+\t.\tID=file_1_g18.t1.intron1;Parent=file_1_g18.t1;\n+sample\tAUGUSTUS\tCDS\t123328\t123512\t0.99\t+\t2\tID=file_1_g18.t1.CDS2;Parent=file_1_g18.t1;\n+sample\tAUGUSTUS\texon\t123328\t123512\t.\t+\t.\tID=file_1_g18.t1.exon2;Parent=file_1_g18.t1;\n+sample\tAUGUSTUS\tintron\t123513\t133208\t0.5\t+\t.\tID=file_1_g18.t1.intron2;Parent=file_1_g18.t1;\n+sample\tAUGUSTUS\tCDS\t133209\t134539\t1\t+\t0\tID=file_1_g18.t1.CDS3;Parent=file_1_g18.t1;\n+sample\tAUGUSTUS\texon\t133209\t134539\t.\t+\t.\tID=file_1_g18.t1.exon3;Parent=file_1_g18.t1;\n+sample\tAUGUSTUS\tintron\t134540\t134667\t1\t+\t.\tID=file_1_g18.t1.intron3;Parent=file_1_g18.t1;\n+sample\tAUGUSTUS\tCDS\t134668\t135510\t1\t+\t1\tID=file_1_g18.t1.CDS4;Parent=file_1_g18.t1;\n+sample\tAUGUSTUS\texon\t134668\t135510\t.\t+\t.\tID=file_1_g18.t1.exon4;Parent=file_1_g18.t1;\n+sample\tAUGUSTUS\tintron\t135511\t135568\t1\t+\t.\tID=file_1_g18.t1.intron4;Parent=file_1_g18.t1;\n+sample\tAUGUSTUS\tCDS\t135569\t136346\t0.99\t+\t1\tID=file_1_g18.t1.CDS5;Parent=file_1_g18.t1;\n+sample\tAUGUSTUS\texon\t135569\t136346\t.\t+\t.\tID=file_1_g18.t1.exon5;Parent=file_1_g18.t1;\n+sample\tAUGUSTUS\tstop'..b't_codon\t115274\t115276\t.\t+\t0\tID=file_1_g16.t1.start1;Parent=file_1_g16.t1;\n+sample\tAUGUSTUS\tCDS\t115274\t116488\t0.87\t+\t0\tID=file_1_g16.t1.CDS1;Parent=file_1_g16.t1;\n+sample\tAUGUSTUS\texon\t115274\t116488\t.\t+\t.\tID=file_1_g16.t1.exon1;Parent=file_1_g16.t1;\n+sample\tAUGUSTUS\tstop_codon\t116486\t116488\t.\t+\t0\tID=file_1_g16.t1.stop1;Parent=file_1_g16.t1;\n+sample\tAUGUSTUS\tstop_codon\t209044\t209046\t.\t-\t0\tID=file_1_g24.t1.stop1;Parent=file_1_g24.t1;\n+sample\tAUGUSTUS\tCDS\t209044\t210483\t0.38\t-\t0\tID=file_1_g24.t1.CDS1;Parent=file_1_g24.t1;\n+sample\tAUGUSTUS\texon\t209044\t210483\t.\t-\t.\tID=file_1_g24.t1.exon1;Parent=file_1_g24.t1;\n+sample\tAUGUSTUS\tstart_codon\t210481\t210483\t.\t-\t0\tID=file_1_g24.t1.start1;Parent=file_1_g24.t1;\n+sample\tAUGUSTUS\tstop_codon\t100542\t100544\t.\t-\t0\tID=file_1_g15.t1.stop1;Parent=file_1_g15.t1;\n+sample\tAUGUSTUS\tCDS\t100542\t100756\t0.3\t-\t2\tID=file_1_g15.t1.CDS1;Parent=file_1_g15.t1;\n+sample\tAUGUSTUS\texon\t100542\t100756\t.\t-\t.\tID=file_1_g15.t1.exon1;Parent=file_1_g15.t1;\n+sample\tAUGUSTUS\tintron\t100757\t102520\t0.32\t-\t.\tID=file_1_g15.t1.intron1;Parent=file_1_g15.t1;\n+sample\tAUGUSTUS\tCDS\t102521\t103133\t0.26\t-\t0\tID=file_1_g15.t1.CDS2;Parent=file_1_g15.t1;\n+sample\tAUGUSTUS\texon\t102521\t103133\t.\t-\t.\tID=file_1_g15.t1.exon2;Parent=file_1_g15.t1;\n+sample\tAUGUSTUS\tintron\t103134\t103264\t0.25\t-\t.\tID=file_1_g15.t1.intron2;Parent=file_1_g15.t1;\n+sample\tAUGUSTUS\tCDS\t103265\t104819\t0.09\t-\t1\tID=file_1_g15.t1.CDS3;Parent=file_1_g15.t1;\n+sample\tAUGUSTUS\texon\t103265\t104819\t.\t-\t.\tID=file_1_g15.t1.exon3;Parent=file_1_g15.t1;\n+sample\tAUGUSTUS\tintron\t104820\t108228\t0.15\t-\t.\tID=file_1_g15.t1.intron3;Parent=file_1_g15.t1;\n+sample\tAUGUSTUS\tCDS\t108229\t108299\t0.42\t-\t0\tID=file_1_g15.t1.CDS4;Parent=file_1_g15.t1;\n+sample\tAUGUSTUS\texon\t108229\t108299\t.\t-\t.\tID=file_1_g15.t1.exon4;Parent=file_1_g15.t1;\n+sample\tAUGUSTUS\tstart_codon\t108297\t108299\t.\t-\t0\tID=file_1_g15.t1.start1;Parent=file_1_g15.t1;\n+sample\tAUGUSTUS\tstop_codon\t214566\t214568\t.\t-\t0\tID=file_1_g25.t1.stop1;Parent=file_1_g25.t1;\n+sample\tAUGUSTUS\tCDS\t214566\t214811\t0.19\t-\t0\tID=file_1_g25.t1.CDS1;Parent=file_1_g25.t1;\n+sample\tAUGUSTUS\texon\t214566\t214811\t.\t-\t.\tID=file_1_g25.t1.exon1;Parent=file_1_g25.t1;\n+sample\tAUGUSTUS\tstart_codon\t214809\t214811\t.\t-\t0\tID=file_1_g25.t1.start1;Parent=file_1_g25.t1;\n+sample\tAUGUSTUS\tstart_codon\t58640\t58642\t.\t+\t0\tID=file_1_g12.t1.start1;Parent=file_1_g12.t1;\n+sample\tAUGUSTUS\tCDS\t58640\t58677\t0.01\t+\t0\tID=file_1_g12.t1.CDS1;Parent=file_1_g12.t1;\n+sample\tAUGUSTUS\texon\t58640\t58677\t.\t+\t.\tID=file_1_g12.t1.exon1;Parent=file_1_g12.t1;\n+sample\tAUGUSTUS\tintron\t58678\t59091\t0.01\t+\t.\tID=file_1_g12.t1.intron1;Parent=file_1_g12.t1;\n+sample\tAUGUSTUS\tCDS\t59092\t59204\t0.01\t+\t1\tID=file_1_g12.t1.CDS2;Parent=file_1_g12.t1;\n+sample\tAUGUSTUS\texon\t59092\t59204\t.\t+\t.\tID=file_1_g12.t1.exon2;Parent=file_1_g12.t1;\n+sample\tAUGUSTUS\tintron\t59205\t69536\t0.01\t+\t.\tID=file_1_g12.t1.intron2;Parent=file_1_g12.t1;\n+sample\tAUGUSTUS\tCDS\t69537\t69745\t0.01\t+\t2\tID=file_1_g12.t1.CDS3;Parent=file_1_g12.t1;\n+sample\tAUGUSTUS\texon\t69537\t69745\t.\t+\t.\tID=file_1_g12.t1.exon3;Parent=file_1_g12.t1;\n+sample\tAUGUSTUS\tstop_codon\t69743\t69745\t.\t+\t0\tID=file_1_g12.t1.stop1;Parent=file_1_g12.t1;\n+sample\tAUGUSTUS\tstop_codon\t45527\t45529\t.\t-\t0\tID=file_1_g10.t1.stop1;Parent=file_1_g10.t1;\n+sample\tAUGUSTUS\tCDS\t45527\t46157\t0.51\t-\t1\tID=file_1_g10.t1.CDS1;Parent=file_1_g10.t1;\n+sample\tAUGUSTUS\texon\t45527\t46157\t.\t-\t.\tID=file_1_g10.t1.exon1;Parent=file_1_g10.t1;\n+sample\tAUGUSTUS\tintron\t46158\t46752\t0.42\t-\t.\tID=file_1_g10.t1.intron1;Parent=file_1_g10.t1;\n+sample\tAUGUSTUS\tCDS\t46753\t47379\t0.43\t-\t1\tID=file_1_g10.t1.CDS2;Parent=file_1_g10.t1;\n+sample\tAUGUSTUS\texon\t46753\t47379\t.\t-\t.\tID=file_1_g10.t1.exon2;Parent=file_1_g10.t1;\n+sample\tAUGUSTUS\tintron\t47380\t49616\t0.44\t-\t.\tID=file_1_g10.t1.intron2;Parent=file_1_g10.t1;\n+sample\tAUGUSTUS\tCDS\t49617\t49792\t0.45\t-\t0\tID=file_1_g10.t1.CDS3;Parent=file_1_g10.t1;\n+sample\tAUGUSTUS\texon\t49617\t49792\t.\t-\t.\tID=file_1_g10.t1.exon3;Parent=file_1_g10.t1;\n+sample\tAUGUSTUS\tstart_codon\t49790\t49792\t.\t-\t0\tID=file_1_g10.t1.start1;Parent=file_1_g10.t1;\n'

diff -r 000000000000 -r e50ea151f221 test-data/out_genome/braker.gtf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out_genome/braker.gtf Tue Oct 05 12:35:42 2021 +0000

diff -r 000000000000 -r e50ea151f221 test-data/out_prot/braker.gtf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out_prot/braker.gtf Tue Oct 05 12:35:42 2021 +0000

diff -r 000000000000 -r e50ea151f221 test-data/proteins.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/proteins.fa Tue Oct 05 12:35:42 2021 +0000

@@ -0,0 +1,96 @@
+>FUN_000001-T1 FUN_000001
+MSSFLLVIFILLALRTSESSETGNPLANEPDPLYMKLVDPMVAGESPKRMIKDQKDVGLKSTSSSEELRKLPKTRGRQKR
+FIRNPNYVKANEFYDKMLSSEYVSKRYKDLPPPHPGFGADQPPA
+>FUN_000002-T1 FUN_000002
+MPLYGVSPASALWAGSRRQTVRRSRPSHHESWPATSPPAGRAQSLLPKRLLDVVTDLGLDVLQVLGLEARLLGGDVLGFA
+QP
+>FUN_000003-T1 FUN_000003
+MYDQEPYKCHLCSKTFRMKGSLRIHLKVVHMMGVPCSNPNPNPNPSPTPASTTSAVTATPKLSICDRIRHTEPGALGNGN
+NSTCTASQPYALSGALSMLQQSPSSPESGTATPKLWECDVCSKSFTTKYFLKKHKRLHTGEMPYTCEICARTFTFQQSYH
+KHLLYHSEVKPHVCGVCGRAFKELSTLHNHQRIHSGEKPFKCERVSFLVHTRIHTGVMPYKCELCQKTFRYKVSQRTHRC
+PTEEAQTPEQLIKAFLEGNDSHTQPSPASAEIAAINSSSIVDPEQEALLSQSIDDIVVEQCQKLGICGVEPREEGQLISL
+QPVAVVHFSGNGSPLQQLQNLRIYSPQQTELPSSDGEVFQRFLMDAT
+>FUN_000004-T1 FUN_000004
+MSNKREIDELTSRIKSAKTTLVEWTEAMEDGNKGYQLIEKYYLDDQQKARELNIKRQLLQADIDKRRKQVVLLYDEQMTL
+EKNLERTACLYRSAHAERRQMVETWKSAVNQMTQREHDIQRSEIECAELAQKAQQTAQTYKEYDNQLTEVIENNRQVELA
+IESLNEESSDMKNQIQILIDATLLKEREIDGLRRELENLSNRVHLQRMDNRSQMKKRDEKAKELENFASVMEKVNARLKS
+VQNKALNAEQRLQILEEMMQAEETALRNLDKEQEKVNEMLYRTQRQVIELQDEEKVLKVQNDSLNSNLAAINRNQQQVNN
+ELKRQTEIHYSLSFKCLEAERRLAEIKGLADDPEVEATNMARLNTLEQEYEKLQRLIATTEAQNKKLNYNMNNLVVQYNA
+DEKELEMVRFKIKEAQVYCEGTVKRLRQIRYENSELIVDLNMVKMRCSDLEVGIGGCEQGTYDLEQHRLAFRRAIKDRTV
+ELRSQEDVLLLKKKHLNEELSTLRADLGERKKQIEAMKARFELTAQLLGKNEDGSIMTSTQLKVVSAQERQMLADEGDAL
+NKKVLKAEKEVVALENTLRQFDKSNDNYRKTFRSVDENSKDRERAELELKELEAAYCRELEKLKVLRCKAQHYQQKHAAQ
+RAEEEDLISKIEKAKASRAEHSAVLEKIERELDDQRMKLDRANREIRTQLREIKARPFSEEYLAQFERDLSLQELEARNT
+KALNMITDLANSDESGTDIIGILLRKGIKLPMHLKRTCSRVSWNSSSSGKSSQGQDTASYLNVKGKKFSCDGASARSSVS
+DMSSLKDDTSSTTSHSGLSIISLELPLPKKK
+>FUN_000005-T1 FUN_000005
+MRCVFCGSGSEQQHSRWEIKMLQESCRTDHGFHQDSQAIQYLYEILASYNRDEQRAFLQFVTGSPRLPTGGFKALTPPLT
+IVRKTLDENQNPNDYLPSVMTCVNYLKLPDYSSREVMRQKLKVAANEGSMSFHLS
+>FUN_000006-T1 FUN_000006
+MLILIGAGARGAVLHRLLASSATQDVRTTARACGRMLVLLCGCCCSGGAAAHKRRSCYCWSVLVRGGCLKSILDVQHSAV
+GLDYVYNGHRVLFASCTVTTSAGRELLRKGFRAEITTGAIPSCHSSVFLRMNLLLDL
+>FUN_000007-T1 FUN_000007
+MSFCDFLRDAALGANSANLSIVAAALSAARDVGGGSDGGGSAGGATPATGASASSVGNTSAVGASSSSNSSAGQAASSNS
+NNVTATGSGSAPGGGPTSTGTTSGTQHGSGSGAAAAVDSESDDSEVGRLQALLEARGLPPHLFGALGPRVTHILHRTIGN
+SSSSKANQLLQGLQSHDESQQLQAAIEMCQMLVMGNEDTLAGFPIKQVVPALIQLLRMEHNFDIMNNACRALAYMLEALP
+RSSGTVVEAVPVFLEKLQVIQCMDVAEQSLSALEILSRRHNKAILQANGISACLTYLDFFSIVAQRAALAIAANCCLNMH
+PEEFHFVAESLPLLARLLSQQDKKCIESVCSAFCRLVESFQHDGQRLQQIASPDLLKNCQQLLLVTPAILNTGTFTAVVR
+MLSLMCCSCPDLAISLLRNDIAATLLYLLTGNAEPAAASATHVELISRSPSELYELTCLIGELMPRLPLDGIFAVDSLLD
+RPTLNTQDQVHWQWRDDRGSWHNYSTIDSRLIEAANQSSEDEISLSTFGRTYTVDFHAMQQINEDTGTTRPVQRRLNHNY
+VAPMSAGQDLTTTSAGSAAAGGASTSAAAAAASSNNNNNNNNNPPGNSVNLNQVKRRPSLDARIACLKEERGLAADFIKH
+IFNVLYEVYSSSAGPNVRYKCLRALLRMVYYATPELLRQVLKYQLVSSHIAGMLGSNDLRIVVGALQMAEILMRQLPDVF
+GTHFRREGVIYQFTQLTDPNNPICANPSPKPLSATATPTANAGGSQSAPASANSLQVNPFFMDSAPGLSSASTTPSSSKH
+QSYSVKSFSHAMNALTASAKGTPSGALDATSSSTTAGGYNYSSSAPSSSSGAPAAYFVTQQGDPRQYVHFQQPAVPAPPP
+QQELLPSGVQQQGQQVPQVIYQPHHQQPAHLVLASTSSGAASSSSSSSSSSSASALQHKMTDMLKRKAPPKRKSQSGGRA
+KSRQEDAAVAPAGSGPGGAPPSSSGSAMHELLSRATSKYIFQ
+>FUN_000008-T1 FUN_000008
+MKFRALMQDPLYMKEFQAIVATLTKLAKDCVMILGSRQMHFIVNEDQSSAASPLVWAGITAEEYFPEYRMEAAHPDQEYI
+VLGVSSANLGRALSVLRGGGVNSCKLKLQRIQFPCISVIASVLTSSSTEAREVVHDVPVTIIPGSDWSAYVVPRVPNSQL
+ALGLPSLRLLKSLIDKLKNISPSLEFQVNVDGELNVIATSEMSTVTSRFQKLLIRTVSGSQQEASCSVDSRKASAFFGAL
+QLPNEELTIGIDREHSIHLQIDVRQDVVLHSILPAVCM
+>FUN_000009-T1 FUN_000009
+MCGNPAVGNGTRALILVGGYGTRLRPLTLSTPKPLVEFANKPILLHQLEALVDAGCRQVILAVSYRAEQMEKELKVEAKK
+LGVELIFSHETEPLGTAGPLALAKTILAASSEPFFVLNSDVICDFPFKQLVQFHCNHGKEGTIVVTKVEEPSKYGVVLYD
+ENGCIKNFIEKPQEFVSNKINAGIYIFNPSVLDRIEVKPTSIEKEVFPEMTQQQELYAMDLTGFWMDIGQPKDFLTGMCL
+YLSSLRQKQSPKLYTGPGVVGNVLVDPTAKIGEGCRIGPNVTIGPDVVIEDGVCIKRSTILKGAIVRSHSWLDSCIVGWR
+STVGRWVRIEGITVLGEDVIVKDELYINGGQVLPHKSIAASLRGAIVQAGQLVILPDEEVFSHVQGVWNLSSDQGNLGSF
+VVTNIRLVWFADANETFNISLPYLQIESSKYGPALVIQTAETGGGYVLGFRVDPAERLNELFKELSSLHTVYGEHPNFGI
+QYNANDARRRLEAASEEAAQASQIKVDNFEELDERQEREINTKLNSYLAEGCLGKVPSQGERAPVYCKELGFAMEPIGDG
+YKLQDLWNVMPTKMETME
+>FUN_000010-T1 FUN_000010
+MDFIHEAVGTSAAPSANPGPMPLCQPVRLELPFSPRHSFALGHFPFQLCPCLYAVWVQTMGLVLLLLIVFAPFLFRVLFK
+PCNPKRYLTT
+>FUN_000011-T1 FUN_000011
+MCHSKDNLHSGNEDGGMPKDTEYISSDHDDSPSWSQQSLLSSDRSKSYSQICSEILEESKERQEKAECAFRVYNINRSKL
+RRSHQQSLSRGPGSGSYGSSMASEYSSKSEAGYQDYDSPSTDPSREHTAEVTFLQLRHRNRAHKEIIFRAAAHAIVIILI
+IIARGVCQRHIKIVEIVPLTSRRGARRATTRNLTSHFAPRKWRRRFSSADQGDRQFKGHDGDCLRSTEKKRSISNEQSPI
+TLRNTNAKDVDIPDCFGSFAMNKHLSVITEDASQHHKDPDEDMIDSQLSNSVLLETYDEGEKYAYSYQYSYKPEICNNNQ
+FVSDESDLKVSSKEGYQMDQEDYVMDKQELVHEGGSDASLSEVAKSKSFLSLKIYDADEALMEIPEDFEGPAIVLDDDAD
+FLDITLTDDEEKIRAKLMAAALTTRKTTSSISPNISLRTRSPIEPSSLSYKPNVIFTRRSEVIKDNYTPRPDDRVALLAE
+KFLQSFSESAPNDYGWKPSKQEVTSAVSISHLFNENGVTRRGGDTPLCGDRQLLSVEFNRKLQRQLKVIVESFQ
+>FUN_000012-T1 FUN_000012
+MSLDRRGEITTPPTRYDLTLGSDKSSSLSRSEAGTYDVIQAEIQHAKRQELATGVATASHQNGNGNGNGHTLSTQHDIEA
+EVKKRKWPTEPSYFLAKELLMTERTYKKDLDVLNTTFRQVLSLGDVEQLQPLFELLDSLAQHHNLFLRDIEHRMVQWEGR
+GGHEAHRIGDVMMKHMAALPIYDEYVQTHLDILHCMNDMYEGDERFRQVYKEFEQQKVCYLPIGELLLKPLNRLLHYQLI
+LERLCDYYGEEHIDYADAMAVHHLLVRSTKGIRSQLPDSANFVELCELQRDINFEQLVQPHRRLIRQGCLLKHSKRGSSE
+EGLDLFGLSNGNNSSLNSSVNGGGPLTTQQQKLQLQQQQQNRTQPSRSNTALHVCWHRGATVGLGDHLIAAEHQLSGYLL
+RKFKNSSGWQKLWVVFTSFCLYFYKSYQDEFALASLPLLGYTVGPPGHQDAVQKEFVFKLSFKNHVYFFRAESAHTYNR
+>FUN_000013-T1 FUN_000013
+MQPIAMEMGQNQLEVKASVLGGSPQLGDLKVGGAQDVQLLGFYREPGGSIQNAQISNVEGL
+>FUN_000014-T1 FUN_000014
+MASKSFDLVIEEKTKKPERLYQPRRMRWLKYIILPAVFSFALLLILVNVDFSDNSEDSTHLGNDTSLIISGYGFENNTLR
+RGFFSGGIALHSLVIENCTIVHINDAAFNQESTVNITSLQLINVQLENLTESALEGLQKLQNFTLVNENNHFRPFGFLSA
+VAESLVSAEIHQSLAAAISYSVCDFLGSRNFPQLKYLDLSGTHLDKSLIKESFDNLPALEQLLLRNCGLGNIEWEIVRPR
+LKLLHYLDLGGAQKTGNYEHQLDVSAFSPETTTNAEEISTILAKRAMAPEVVGTTTLGPTTSIEISPPSTQSTTTPKEES
+TSMTETTILTTPSPKCEEELCQDLECSRITTDTVASADLGKSSCQDGLLVEICESTCTTPTFFCVILGENFTSASNCCSH
+HTMRCVVSAQVSWFEDHSGLVIGLGVGLLFIGSFLGMLIVFGTLRLNPSWLRGNKRRESNTIGLIQGRFEKDPYEQELQR
+IREL
+>FUN_000015-T1 FUN_000015
+MSSFLLVIFILLALRTSESSETGNPLANEPDPLYMKLVDPMVAGESPKRMIKDQKDVGLKSTSSSEELRKLPKTRGRQKR
+FIRNPNYVKANEFYDKMLSSEYVSKRYKDLPPPHPGFGADQPPA
+>FUN_000016-T1 FUN_000016
+MPPTINNSAVNSAAEKRPQRQTERKSEIICRVKYGNNLPDIPFDLKFLQYPFDSHRFVQYNPTSLERNFKYDVLTEHDLG
+VTVDLINRELYQADSMTLLDPADEKLLEEETLTPTDSVRSRQHSRTVSWLRKSEYISTEQTRFQPQNLENIEAKVGYNVK
+KSLREETLYLDREAQIKAIEKTFSDTKSEITKHYSKPNVVPVEVLPIFPDFTNWKFPCAQVIFDSDPAPAGKNVPAQLEE
+MSQAMIRGVMDESGEQFVAYFLPTEQTLEKRRTDFINGELYKEEEEYEYKIAREYNWNVKTKASKGYEENYFFVMRQDGI
+YYNELETRVRLNKRRVKVGQQPNNTKLVVKHRPLDSMEHRMQRYRERQLEVPGEEEEIVEEVREEEQMQIIGETEKTSED
+AAVGAQAASGADSPAQVARDRQSRSRSRTRS