Mercurial > repos > greg > plant_tribes_gene_family_integrator
changeset 3:276f0f31ddb0 draft
Uploaded
| author | greg |
|---|---|
| date | Mon, 30 Oct 2017 09:53:09 -0400 |
| parents | a322e5e668a3 |
| children | 8ef8997aaa0c |
| files | .shed.yml gene_family_integrator.py gene_family_integrator.xml macros.xml test-data/3722.faa test-data/3722.fna test-data/3722_integrated.faa test-data/3722_integrated.fna test-data/38889.faa test-data/38889.fna test-data/38889_integrated.faa test-data/38889_integrated.fna test-data/39614.faa test-data/39614.fna test-data/39614_integrated.faa test-data/39614_integrated.fna test-data/tool-data/plant_tribes/scaffolds/README.txt utils.py |
| diffstat | 18 files changed, 725 insertions(+), 220 deletions(-) [+] |
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--- a/.shed.yml Thu Aug 24 13:32:01 2017 -0400 +++ b/.shed.yml Mon Oct 30 09:53:09 2017 -0400 @@ -8,7 +8,7 @@ utilize objective classifications of complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. This tool integrates classified post processed de novo transcriptome assembly sequences with the scaffold gene family sequences. -remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/plant_tribes/gene_family_integrator +remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/phylogenetics/plant_tribes/gene_family_integrator type: unrestricted categories: - Phylogenetics
--- a/gene_family_integrator.py Thu Aug 24 13:32:01 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,32 +0,0 @@ -#!/usr/bin/env python -import argparse -import os - -import utils - -OUTPUT_DIR = 'integratedGeneFamilies_dir' - -parser = argparse.ArgumentParser() -parser.add_argument('--orthogroup_faa', dest='orthogroup_faa', help='Directory of input fasta datasets') -parser.add_argument('--scaffold', dest='scaffold', help='Orthogroups or gene families proteins scaffold') -parser.add_argument('--method', dest='method', help='Protein clustering method') -parser.add_argument('--orthogroup_fna', dest='orthogroup_fna', default=None, help='Use correspong coding sequences') -parser.add_argument('--output', dest='output', help='Output dataset') -parser.add_argument('--output_dir', dest='output_dir', help='Output dataset file_path directory') - -args = parser.parse_args() - -# Build the command line. -cmd = 'GeneFamilyIntegrator' -cmd += ' --orthogroup_faa %s' % args.orthogroup_faa -cmd += ' --scaffold %s' % args.scaffold -cmd += ' --method %s' % args.method -if args.orthogroup_fna is not None: - cmd += ' --orthogroup_fna' - -# Run the command. -utils.run_command(cmd) - -# Handle outputs. -utils.move_directory_files(os.path.join(OUTPUT_DIR, 'orthogroups_fasta'), args.output_dir) -utils.write_html_output(args.output, 'Integrated gene family sequences', args.output_dir)
--- a/gene_family_integrator.xml Thu Aug 24 13:32:01 2017 -0400 +++ b/gene_family_integrator.xml Mon Oct 30 09:53:09 2017 -0400 @@ -1,70 +1,58 @@ -<tool id="plant_tribes_gene_family_integrator" name="GeneFamilyIntegrator" version="@WRAPPER_VERSION@.2"> +<tool id="plant_tribes_gene_family_integrator" name="GeneFamilyIntegrator" version="@WRAPPER_VERSION@.3.0"> <description>integrates gene models in pre-computed orthologous gene family clusters with classified gene coding sequences</description> <macros> <import>macros.xml</import> </macros> - <expand macro="requirements_gene_family_integrator" /> + <requirements> + <requirement type="package" version="1.0.3">plant_tribes_gene_family_integrator</requirement> + </requirements> <command detect_errors="exit_code"><![CDATA[ -#set input_format = $input_format_cond.input_format -#set scaffold = $input_format_cond.scaffold -#set method = $input_format_cond.method - -python '$__tool_directory__/gene_family_integrator.py' +#set input_dir = 'input_dir' +mkdir $input_dir && +#for $i in $input: + #set filename = $i.file_name + #set name = $i.name + ln -s $filename $input_dir/$name && +#end for +GeneFamilyIntegrator +--orthogroup_fasta '$input_dir' --scaffold '$scaffold.fields.path' --method $method -#if str($input_format) == 'ptortho': - --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path' - --output '$output_ptortho' - --output_dir '$output_ptortho.files_path' -#else: - ## str($input_format) == 'ptorthocs' - --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path' - #if str($input_format_cond.orthogroup_fna) == 'yes': - --orthogroup_fna true - --output '$output_ptorthocs' - --output_dir '$output_ptorthocs.files_path' - #else: - --output '$output_ptortho' - --output_dir '$output_ptortho.files_path' - #end if -#end if +&>proc.log ]]></command> <inputs> - <conditional name="input_format_cond"> - <param name="input_format" type="select" label="Classified orthogroup fasta files"> - <option value="ptortho">Proteins orthogroup fasta files</option> - <option value="ptorthocs">Protein and coding sequences orthogroup fasta files</option> - </param> - <when value="ptortho"> - <param name="input_ptortho" format="ptortho" type="data" label="Proteins orthogroup fasta files"> - <validator type="empty_extra_files_path" /> - </param> - <expand macro="param_scaffold" /> - <expand macro="param_method" /> - </when> - <when value="ptorthocs"> - <param name="input_ptorthocs" format="ptorthocs" type="data" label="Protein and coding sequences orthogroup fasta files"> - <validator type="empty_extra_files_path" /> - </param> - <expand macro="param_scaffold" /> - <expand macro="param_method" /> - <expand macro="param_orthogroup_fna" /> - </when> - </conditional> + <param name="input" format="fasta" type="data_collection" collection_type="list" label="Classified orthogroup fasta files" /> + <expand macro="param_scaffold" /> + <expand macro="param_method" /> </inputs> <outputs> - <data name="output_ptortho" format="ptortho" label="${tool.name} (integrated gene family clusters) on ${on_string}"> - <filter>input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['orthogroup_fna'] == 'no')</filter> - </data> - <data name="output_ptorthocs" format="ptorthocs" label="${tool.name} (integrated gene family clusters) on ${on_string}"> - <filter>input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['orthogroup_fna'] == 'yes'</filter> - </data> + <collection name="output" type="list" label="${tool.name} (integrated gene family clusters) on ${on_string}"> + <discover_datasets pattern="__name__" directory="integratedGeneFamilies_dir" format="fasta" /> + </collection> </outputs> <tests> - <!-- Test framework does not currently support inputs whose associated extra_files_path contains files to be analyzed. <test> + <param name="input"> + <collection type="list"> + <element name="3722.faa" value="3722.faa"/> + <element name="3722.fna" value="3722.fna"/> + <element name="38889.faa" value="38889.faa"/> + <element name="38889.fna" value="38889.fna"/> + <element name="39614.faa" value="39614.faa"/> + <element name="39614.fna" value="39614.fna"/> + </collection> + </param> + <param name="scaffold" value="22Gv1.1"/> + <param name="method" value="orthomcl"/> + <output_collection name="output" type="list"> + <element name="3722.faa" file="3722_integrated.faa" ftype="fasta"/> + <element name="3722.fna" file="3722_integrated.fna" ftype="fasta"/> + <element name="38889.faa" file="38889_integrated.faa" ftype="fasta"/> + <element name="38889.fna" file="38889_integrated.fna" ftype="fasta"/> + <element name="39614.faa" file="39614_integrated.faa" ftype="fasta"/> + <element name="39614.fna" file="39614_integrated.fna" ftype="fasta"/> + </output_collection> </test> - --> </tests> <help> This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary @@ -79,11 +67,6 @@ * **Gene family scaffold** - one of the PlantTribes gene family scaffolds installed into Galaxy by the PlantTribes Scaffold Data Manager tool. * **Protein clustering method** - gene family scaffold protein clustering method as described in the AssemblyPostProcessor tool. - -**Other options** - - * **Orthogroups coding sequences** - Select 'Yes' to create corresponding coding sequences orthogroup fasta files for the classified protein sequences. - </help> <citations> <expand macro="citation1" />
--- a/macros.xml Thu Aug 24 13:32:01 2017 -0400 +++ b/macros.xml Mon Oct 30 09:53:09 2017 -0400 @@ -1,47 +1,6 @@ <?xml version='1.0' encoding='UTF-8'?> <macros> <token name="@WRAPPER_VERSION@">1.0</token> - <xml name="requirements_assembly_post_processor"> - <requirements> - <requirement type="package" version="1.0.2">plant_tribes_assembly_post_processor</requirement> - </requirements> - </xml> - <xml name="requirements_gene_family_aligner"> - <requirements> - <requirement type="package" version="1.0.2">plant_tribes_gene_family_aligner</requirement> - </requirements> - </xml> - <xml name="requirements_gene_family_classifier"> - <requirements> - <requirement type="package" version="1.0.2">plant_tribes_gene_family_classifier</requirement> - </requirements> - </xml> - <xml name="requirements_gene_family_integrator"> - <requirements> - <requirement type="package" version="1.0.2">plant_tribes_gene_family_integrator</requirement> - </requirements> - </xml> - <xml name="requirements_kaks_analysis"> - <requirements> - <requirement type="package" version="1.0.2">plant_tribes_kaks_analysis</requirement> - </requirements> - </xml> - <xml name="requirements_ks_distribution"> - <requirements> - <requirement type="package" version="1.3.2">r-optparse</requirement> - </requirements> - </xml> - <xml name="requirements_gene_family_phylogeny_builder"> - <requirements> - <requirement type="package" version="1.0.2">plant_tribes_gene_family_phylogeny_builder</requirement> - </requirements> - </xml> - <xml name="param_codon_alignments"> - <param name="codon_alignments" type="select" label="Codon alignments"> - <option value="yes" selected="true">Yes</option> - <option value="no">No</option> - </param> - </xml> <xml name="param_method"> <param name="method" type="select" label="Protein clustering method"> <option value="gfam" selected="true">GFam</option> @@ -49,74 +8,12 @@ <option value="orthomcl">OrthoMCL</option> </param> </xml> - <xml name="param_options_type"> - <param name="options_type" type="select" label="Options Configuration"> - <option value="basic" selected="true">Basic</option> - <option value="advanced">Advanced</option> - </param> - </xml> - <xml name="param_orthogroup_fna"> - <param name="orthogroup_fna" type="select" label="Orthogroups coding sequences"> - <option value="yes" selected="true">Yes</option> - <option value="no">No</option> - </param> - </xml> <xml name="param_scaffold"> <param name="scaffold" type="select" label="Gene family scaffold"> <options from_data_table="plant_tribes_scaffolds" /> <validator type="no_options" message="No PlantTribes scaffolds are available. Use the PlantTribes Scaffolds Download Data Manager tool in Galaxy to install and populate the PlantTribes scaffolds data table." /> </param> </xml> - <xml name="param_sequence_type"> - <param name="sequence_type" type="select" label="Sequence type used in the phylogenetic inference (dna)"> - <option value="protein" selected="true">Amino acid based</option> - <option value="dna">Nucleotide based</option> - </param> - </xml> - <xml name="cond_alignment_method"> - <conditional name="alignment_method_cond"> - <param name="alignment_method" type="select" force_select="true" label="Multiple sequence alignment method"> - <option value="mafft" selected="true">MAFFT</option> - <option value="pasta">PASTA</option> - </param> - <when value="mafft" /> - <when value="pasta"> - <param name="pasta_iter_limit" type="integer" value="3" min="1" label="PASTA iteration limit" /> - </when> - </conditional> - </xml> - <xml name="cond_remove_gappy_sequences"> - <conditional name="remove_gappy_sequences_cond"> - <param name="remove_gappy_sequences" type="select" label="Alignment post-processing configuration"> - <option value="no" selected="true">No</option> - <option value="yes">Yes</option> - </param> - <when value="no" /> - <when value="yes"> - <conditional name="trim_type_cond"> - <param name="trim_type" type="select" label="Trimming method"> - <option value="gap_trimming" selected="true">Gap score based trimming</option> - <option value="automated_trimming">Automated heuristic trimming</option> - </param> - <when value="gap_trimming"> - <param name="gap_trimming" type="float" optional="true" min="0" max="1.0" label="Gap score" /> - </when> - <when value="automated_trimming" /> - </conditional> - <conditional name="remove_sequences_with_gaps_cond"> - <param name="remove_sequences_with_gaps" type="select" label="Remove sequences"> - <option value="no" selected="true">No</option> - <option value="yes">Yes</option> - </param> - <when value="no" /> - <when value="yes"> - <param name="remove_sequences_with_gaps_of" type="float" optional="true" min="0" max="1" label="Coverage score" /> - <param name="iterative_realignment" type="integer" optional="true" min="0" label="Realignment iteration limit" /> - </when> - </conditional> - </when> - </conditional> - </xml> <xml name="citation1"> <citation type="bibtex"> @misc{None,
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3722.faa Mon Oct 30 09:53:09 2017 -0400 @@ -0,0 +1,3 @@ +>contig_7 +ENEWSGAEFLNEMAAMMTQNKSNENGTGTFEELQQLFDEMFQSDIESFNGCSSSSNETCSNSNKRNSIESSSANFRPENG +NESGEISGKKNTRKGKGDX
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3722.fna Mon Oct 30 09:53:09 2017 -0400 @@ -0,0 +1,5 @@ +>contig_7 +GAGAATGAGTGGTCTGGGGCTGAGTTTTTGAATGAAATGGCGGCAATGATGACTCAAAATAAATCCAATGAAAACGGAAC +CGGAACTTTTGAAGAACTGCAACAATTGTTCGATGAAATGTTTCAGAGCGACATCGAGTCCTTCAATGGTTGTTCTTCAT +CATCCAATGAAACATGTAGCAACTCGAACAAGAGGAATTCCATTGAGTCGAGCTCGGCTAATTTCAGACCCGAAAATGGA +AACGAAAGCGGCGAGATTAGCGGGAAGAAGAATACTAGGAAAGGTAAAGGTGACGNN
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3722_integrated.faa Mon Oct 30 09:53:09 2017 -0400 @@ -0,0 +1,161 @@ +>gnl_Glyma1.01_PACid_16266208 +MANEGKKSNNFYSILGLSKECTELELKNAYRKLAKKWHPDRCSATGNLELVEEAKKKFQEIREAYSVLSDANKRLMYDVG +VYDSDDDENGMGDFLDEMLTMMSHTKSNENGEESFEELQQLFEDMFQADIGLDGGPSLASSDSSTSSAYMTYSESSSSNK +RNSSEMNFGKAENSSVFDASYQNFCFGVNQLQDIKKGKGGILGGGGRSRHRSGRKQKMFYGHDV +>gnl_Glyma1.01_PACid_16266209 +MANEGKKSNNFYSILGLSKECTELELKNAYRKLAKKWHPDRCSATGNLELVEEAKKKFQEIREAYSVLSDANKRLMYDVG +VYDSDDDENGMGDFLDEMLTMMSHTKSNENGEESFEELQQLFEDMFQADIGLDGGPSLASSDSSTSSAYMTYSESSSSNK +RNSSEMNFGKAENSSVFDASYQNFCFGTGEPTPRYKEGKGGNSRRRR +>gnl_Glyma1.01_PACid_16266210 +MANEGKKSNNFYSILGLSKECTELELKNAYRKLAKKWHPDRCSATGNLELVEEAKKKFQEIREAYSVLSDANKRLMYDVG +VYDSDDDENGMGDFLDEMLTMMSHTKSNENGEESFEELQQLFEDMFQADIGLDGGPSLASSDSSTSSAYMTYSESSSSNK +RNSSEMNFGKAENSSVFDASYQNFCFGVGHVNYHYQ +>gnl_Glyma1.01_PACid_16301083 +MADEGNKSNNFYSILGLKKECTELELKNAYRKLAKKWHPDRCSATGNSELVEEAKKKFQEIREAYSVLSDANKRLMYDVG 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+MANGGEDKWKSNDLYQVLGLNKECTDTELRSAYKKLALRWHPDRCSASGNSKFVEEAKKKFQAIQQAYSVLSDTNKRFLY +DVGVDDSDDDENGMGDFLNEMAVMMSQTKPSENMEESLEELQELFDEMFQEDLHSFGIDSQAAPSCPPSYVSYSESSNSN +NKRVSADMNLGKTKVDDSSSFNSHFEKFCLGTGGTAATFQEGEGGSKRRNSRRSQRQTKARQETKSFFGL +>gnl_Poptr2.2_PACid_18234651 +MENGGEEKGKSNDFYQVLGLNKDCTATELRNAYKKLALKWHPDRCSASENSRFVDEAKKKFQTIQQAYSVLSDTNKRFLY +DVGVYDSEDDENGMGGFMNEMAAMMSQTKPHENVEESFEELQGLFEEMFQEDLDSFGIACQATTCVSYSESSNSNDKRVS +VDMNLKKTKVDDSSGFNSHVEKFCLGVSGTPAIFQEGEGSKRRSSRRNRR +>gnl_Poptr2.2_PACid_18234649 +MLRMENGGEEKGKSNDFYQVLGLNKDCTATELRNAYKKLALKWHPDRCSASENSRFVDEAKKKFQTIQQAYSVLSDTNKR +FLYDVGVYDSEDDENGMGGFMNEMAAMMSQTKPHENVEESFEELQGLFEEMFQEDLDSFGIACQATTCVSYSESSNSNDK +RVSVDMNLKKTKVDDSSGFNSHVEKFCLGVEHQQSFKKGKGVRGGVQGGTGGRERKGRKQEVSSGYDVSSHDHGISAS +>gnl_Poptr2.2_PACid_18234650 +MENGGEEKGKSNDFYQVLGLNKDCTATELRNAYKKLALKWHPDRCSASENSRFVDEAKKKFQTIQQAYSVLSDTNKRFLY +DVGVYDSEDDENGMGGFMNEMAAMMSQTKPHENVEESFEELQGLFEEMFQEDLDSFGIACQATTCVSYSESSNSNDKRVS +VDMNLKKTKVDDSSGFNSHVEKFCLGVEHQQSFKKGKGVRGGVQGGTGGRERKGRKQEVSSGYDVSSHDHGISAS +>gnl_Soltu3.4_PGSC0003DMP400016105 +MGNDYYAVLGLKKECTETELRNAYKKLALKWHPDRCSASGNSKFVDEAKKKFQAIQEAYSVLSDANKRFLYDVGVYDSGD +DDDENGMGDFLNEMAAMMSQNKSNENQEETFEELQDMFDEIFNSDNGMSSSSSSSSRTGTPSMCSTTSSTSSSETFFTFS +NKRSSGEMKSGKGDSCQFQGFCEGTGGASGKSNERERSRRKNSKSGRKQ +>gnl_Soltu3.4_PGSC0003DMP400016106 +MGNDYYAVLGLKKECTETELRNAYKKLALKWHPDRCSASGNSKFVDEAKKKFQAIQEAYSVLSDANKRFLYDVGVYDSGD +DDDENGMGDFLNEMAAMMSQNKSNENQEETFEELQDMFDEIFNSDNGMSSSSSSSSRTGTPSMCSTTSSTSSSETFFTFS +NKRSSGEMKSGKGDSCQFQGFCEGVEHLEKAMKENGVGGKIPRVDGSNRMDAKRQKVLS +>gnl_Ambtr1.0.27_AmTr_v1.0_scaffold00007.329 +MAPRGEKDSDFYAILGLKKECSASDLRNAYKRLALRWHPDRCSASGNTKFVEECKKKFQAIQQAYSVLSDANKRFLYDVG +AYGSDDDDQGMGEFLGEMAVMMSQTKPSEKGPESFEDLQNLFQEMFERDLDMFKSSTSHNNNNDNNNNNHRSSDNNNCSS +VHCFSNTNKRNCSDMNAGEASEVGRFAFSCYATEFLHKQTFSVGADDVRSESSNKRRNGRKQKSTSSSRKS +>gnl_Aquco1.0_PACid_18141277 +MASEEEASDFYKVLGLKNNCSSLELRNAYKKLALKWHPDRCAASGNSKFVEEAKKNFQAIQEAYSVLSDEQKRFMYDVGV +YDKDDDDENEDMGDFLGEMMSMMKQENTSADGQQSFEDLQNLFQEMVQNDKEFYNPASQNSSIYNASNNMFSFSNNENLN +NASNNTFSSFYNENLNSSNKKSCSSMSAENTKVDFNMESLDFRSFSIGLEGGTSFQNSKGRGVTGRRTGRKQKGSSCNDM +SSHDSKILA +>gnl_Arath10_AT3G14200.1 +MASSNSEKINENLYAVLGLKKECSKTELRSAYKKLALRWHPDRCSSMEFVEEAKKKFQAIQEAYSVLSDSNKRFLYDVGA +YNTDDDDDQNGMGDFLNEMATMMNQSKPSDNNTGDSFEQLQDLFNEMFQGDAAAFPSSSSCSTSNFTSSRSFVFDTNSQR +SSSFATSSMGMNNDPFGYDPRAHSFSLGVDHQQEFKKGKNNGGRRNRRKNNVPSAGHETSSSNNYGVPTS +>gnl_Bradi1.2_Bradi3g60090.1 +MATGGDKCGGKPAAAGVGGGDLYSVLGVNKECSDADLKVAYRKLAMRWHPDRCSSSSSTKHMEEAKEKFQEIQGAYSVLS +DANKRFLYDVGVYEEHEEEDDDTLQGMGDFLGEMAHMMSQTQPARQESFEELQQLFVDMFQSDIESGFCNGPAKDHDPVQ +RQTRTFSTPPSPSPSPPPPLATVDEAASCNGINKRGSSAMGSGKPPRAGEVSGGHGQSEFCFGMSDAKQAPKARGGNASR +RRNGQKQKLSSKHDVSSGDEMPRPHAAV +>gnl_Carpa1.181_PACid_16420351 +MADGEDKNNSDLYAVLGLNKECTPAELRNAYKKLAMRWHPDRCSASGNSMFVEEAKKKFQAIQEAYSVLSDANKRFLYDV +GAYESDDDENGMGDFLNEMAAMMSQTKPNENGNAQESFEELQELFQEMFQGDMGFNTFGSSSQPTTSSCSASSAYATCSE +TSNPNNNKRNSSEMNYGKKKVDDSSGFHAHFQTFCLGVEQQQDFKKGKEARGGIRGKPGGSRRQGRKQKVSSRHNVSSND +LGISAS +>gnl_Frave2.0_gene05408 +MAGGKWVPPPLSQFHLHIKRFRRRQKVSGSSGNTEPSGYTDCKNISNRRMEEKGNDFYAVMGLKKECSDSELRNAYKKLA +LIWHPDRCSASGNSKFVEEAKKKFQDIQQAYSVLSDANKRFLYDVGAYESDDDENGMGDFLNEMAVMMSQTKPNENGGES +FEQLQELFEEMFQGDIEGFSSCSQPPTSCSTSSSSYALYCENSTPSNKRNSSAMNYGNATLDSSGFDAHFHNFCVGTGGK +PAKDREGDARKRKDSRRSNR +>gnl_Mimgu1.0_PACid_17694730 +MAADEEKSSDFYGVLGLRKECTAAELRVAYKKLAMKWHPDRCSASGNLKYVEEAKNKFQAVQQAYSVLSDANKRFLYDVG +IYDSEDDADENGMGDFLNEMVAMMGQSKPNENKNESFQELQDLFEEIFNNDAEEVFKIPPPHFPYQDSCSETRTASNKRN +AREMGSVNFSNIEATPFEGFCIGENVIFGGERIQTRPGGGSRRTKPKISTSIDGLIS +>gnl_Nelnu1.0_NNU_010544-RA +MNLLLQKWHPDRCSSSGNSKFVEDSKKKFQAIQEAYSVLSDENKRFLYDVGVYDCDDDDDDENGMGEFLGEMATMMSQIK +PSENGPESLEKLQELFEEMFQRDMDDGFFSPSPQCASFSSSCSSSSSSTTYFSYNNNKHDNKRNCSDISSMDDFYTFGTD +SIQFSNFCIGVEGGEDSKVRGGKSRRKSNRRQKVSSSKHDPSCR +>gnl_Solly2.3_Solyc03g123560.2.1 +MEDKSNDYYAVLGLKKECTDTELRNAYKKLALKWHPDRCSASGNLKFVDEAKKQFQAIQEAYSVLSDANKKFLYDVGVYD +SGDDDDENGMGDFLNEMAAMMSQNKSNENQGEETFEELQDMFNEMFNSDNGTFSSSSSSSSSWTGTPSMCSTTSSTSSSE +TFLTFPNKRSSGEMKSGSSVRGDSCQFQGFCVGAGGTSGKCNERERSWRKNSKSGRKH +>gnl_Sorbi1.4_PACid_1968370 +MDAGGEKFSDAAAAEGGEGGGDLYAVLGLKKECSDADLKVAYRKLAKKWHPDKCSSSSSVKHMEEAKEKFQEIQGAYSVL +SDANKRLLYDVGVYDDEDDEDSMQGMGDFIGEMAQMMSQVRPTRQESFEELQQLFVDMFQSDIDSGFCNGSAKDQVQGQA +KSRTCSTSPSSSPSPPPPPTIVKEAEVSSCNGFNKRGSSAMDSGKPPRPVEGGAGQAGFCFGVSDTKQTPKPRGPNTSRR +RNGRKQKLSSKHDVSSEDETAGS +>gnl_Thepa2.0_Tp3g12470 +MASNNSEKGNDDLYGVLGLKKECTTTELRTAYKKLALRWHPDRCSSMGTPEFVDEAKKKFQAIQEAYSVLSDSNKRFLYD +VGAYNSDDEDQNGMGDFLNEMAAMMNQSKPSENNSGDSFEQLQDLFNEMFQGDAAAFSSSSSSSCSASTFTSSCSFVFDT +NSQRSPFETSSMGTNDLFGFDHSAHTFSLGVEHQQDFKKGKNSGGRRNRRKNNAQSAAHETASSNNYGVPTS +>gnl_Theca1.0_Tc06_g010450 +MANGEEKNNDFYAVLGLNKECTPTELRTAYKKLALRWHPDRCSASGNSKFVEEAKKKFQAIQQAYSVLSDSNKRFLYDVG +AYDSDDDENGMGDFLNEMAGMMSQTKSNENGGESFEELQELFEEMFQADIDSFESTGQSTPSCSASSSFGSYGESSSSNK +RNSSEMSSVETRLESSSSFDAQFHSFCLGVEHRQDIKQHRGARGGMRGAAGGSRRRNGRKQKVSSGHDVTSNDCGISAS +>gnl_Vitvi12X_PACid_17827068 +MAAGEEKSNDFYAVLGLKKECTASELRNAYKRLALMWHPDRCSSSGNSKFVEEAKKKFQAIQEAYSVLSDANKRFLYDVG +AYDSDDDENGMGDFLNEMAVMMSQTKSNENGKESFEELQELFEDMFQRDVDAFNSASHHPMNSFPSSTSTSSYCESSNAN +NKRNSAEMGSGRMMSAGESSAFDAHFQSFCFGTGGTPGRFQEGERSKRRNSRRSQR +>gnl_Selmo1.0_PACid_15401289 +MEKRKEDPYTVLGVQKSSSSSEIRSAYRKLAMKWHPDKQHSLEDQAKAKFQGIQEAYSVLSDDKKRVLYDSGLYDEGDDE +VS +>gnl_Orysa6.0_PACid_16864430 +MARGGGGGGGADADLYAVLGLSRECTDADLRLAYRKLAMIWHPDRCSVAGGSASAAGVDEAKERFQEIQGAYSVLSDSNK +RFLYDVGVYDGNDGDDDDDEADLSGMGDFLGEMAQMMSQATPAESFEELQQLFVDMFQDDIDAGLCQSTPPPPSWPSPPA +AANARSPAAAATSRKGVNKRCSPAAMDMDSGLSSLLGISGFCFEAPWTSQDASTAAGGGGGKRRKQRPPPASHNV +>gnl_Sorbi1.4_PACid_1982925 +MAATSHCGNIQDQDEEASAPGAADLYAVLGLNRECTDAELRVAYRRLAMIWHPDRCSASGSSPARMEEAKERFQEIQGAY +SVLSDSNKRLLYDVGVYDSDDDEADLSGMGDFLGEMADMMSQATPTETFEELQQVFVDMFQDDLDDAGFFGGLPTTGRRA +QAPSTSLPPSVSSSPLRPTPAAGRSKGPQATPSSSFKGVERRGSTSTAKRPRPNGSAGLESDLGLSGFCFMVSKEMSKSK +ERQAVWASDDGDRSTDGKQRLSTSRDVSGGGMSRSLQGQSSKNLLQCMASKS +>gnl_Medtr3.5_Medtr8g022310.3 +MANEGNKSNDFYAVLGLNKECSDSELRNAYKKLALKWHPDRCSASGNVKFVEEAKKKFQAIQEAYSVLSDSNKRLMYDVG +VYDSDDDENVRHLFHTIHELGTLFCVMFCFFISLRGEKRSNLNLTFSLSH +>gnl_Nelnu1.0_NNU_000115-RA +MEVDSHRSSPSYYTILGVDQNSSASEIRNAYRKLAMQWHPDKWTKTPSLLEKAKSKFQQIQEAYSGGLLVFMLSDQGKRT +LYDVGLYDPDDETNDEVGLRRFHAGDDISHERCEETGEEIQLGGTTGDVSGNVTRAGVEDGECWWCVVVRWSCSLKEELK +EGQMGIISESDDAGHDTPSLPHLHGSELELLGRTGCCN +>contig_7 +ENEWSGAEFLNEMAAMMTQNKSNENGTGTFEELQQLFDEMFQSDIESFNGCSSSSNETCSNSNKRNSIESSSANFRPENG +NESGEISGKKNTRKGKGDX
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3722_integrated.fna Mon Oct 30 09:53:09 2017 -0400 @@ -0,0 +1,378 @@ +>gnl_Glyma1.01_PACid_16266208 +ATGGCTAATGAAGGAAAGAAAAGCAATAACTTCTATTCGATCTTGGGCTTGAGCAAGGAGTGCACTGAATTGGAGCTAAA +GAATGCTTATAGGAAACTTGCAAAGAAATGGCACCCAGATCGTTGTTCAGCCACCGGGAATTTAGAGTTAGTGGAAGAAG +CTAAGAAAAAATTTCAGGAAATTCGGGAAGCCTATTCTGTTTTATCTGACGCCAACAAAAGGTTAATGTACGACGTGGGA +GTCTACGACAGTGATGACGACGAAAACGGCATGGGGGACTTCTTGGACGAAATGTTAACAATGATGAGTCATACCAAATC +AAATGAAAATGGAGAGGAGAGCTTTGAGGAGTTGCAACAGCTTTTTGAAGACATGTTTCAAGCGGATATTGGATTGGATG +GAGGCCCTTCTCTTGCTTCTTCTGATTCCTCAACTTCATCTGCTTACATGACTTACAGTGAAAGTTCTAGTTCAAATAAA +CGCAATTCCTCTGAGATGAATTTCGGGAAGGCAGAGAATTCTTCTGTCTTTGATGCCAGTTACCAGAATTTCTGTTTTGG +GGTGAACCAACTCCAAGATATAAAGAAGGGAAAGGGGGGAATTCTAGGAGGAGGAGGTAGAAGTAGACACAGAAGTGGCA +GAAAGCAAAAAATGTTCTATGGCCATGATGTT +>gnl_Glyma1.01_PACid_16266209 +ATGGCTAATGAAGGAAAGAAAAGCAATAACTTCTATTCGATCTTGGGCTTGAGCAAGGAGTGCACTGAATTGGAGCTAAA +GAATGCTTATAGGAAACTTGCAAAGAAATGGCACCCAGATCGTTGTTCAGCCACCGGGAATTTAGAGTTAGTGGAAGAAG +CTAAGAAAAAATTTCAGGAAATTCGGGAAGCCTATTCTGTTTTATCTGACGCCAACAAAAGGTTAATGTACGACGTGGGA +GTCTACGACAGTGATGACGACGAAAACGGCATGGGGGACTTCTTGGACGAAATGTTAACAATGATGAGTCATACCAAATC +AAATGAAAATGGAGAGGAGAGCTTTGAGGAGTTGCAACAGCTTTTTGAAGACATGTTTCAAGCGGATATTGGATTGGATG +GAGGCCCTTCTCTTGCTTCTTCTGATTCCTCAACTTCATCTGCTTACATGACTTACAGTGAAAGTTCTAGTTCAAATAAA +CGCAATTCCTCTGAGATGAATTTCGGGAAGGCAGAGAATTCTTCTGTCTTTGATGCCAGTTACCAGAATTTCTGTTTTGG +GACAGGTGAACCAACTCCAAGATATAAAGAAGGGAAAGGGGGGAATTCTAGGAGGAGGAGG +>gnl_Glyma1.01_PACid_16266210 +ATGGCTAATGAAGGAAAGAAAAGCAATAACTTCTATTCGATCTTGGGCTTGAGCAAGGAGTGCACTGAATTGGAGCTAAA +GAATGCTTATAGGAAACTTGCAAAGAAATGGCACCCAGATCGTTGTTCAGCCACCGGGAATTTAGAGTTAGTGGAAGAAG +CTAAGAAAAAATTTCAGGAAATTCGGGAAGCCTATTCTGTTTTATCTGACGCCAACAAAAGGTTAATGTACGACGTGGGA +GTCTACGACAGTGATGACGACGAAAACGGCATGGGGGACTTCTTGGACGAAATGTTAACAATGATGAGTCATACCAAATC +AAATGAAAATGGAGAGGAGAGCTTTGAGGAGTTGCAACAGCTTTTTGAAGACATGTTTCAAGCGGATATTGGATTGGATG +GAGGCCCTTCTCTTGCTTCTTCTGATTCCTCAACTTCATCTGCTTACATGACTTACAGTGAAAGTTCTAGTTCAAATAAA +CGCAATTCCTCTGAGATGAATTTCGGGAAGGCAGAGAATTCTTCTGTCTTTGATGCCAGTTACCAGAATTTCTGTTTTGG +GGTCGGTCATGTAAACTATCATTACCAA +>gnl_Glyma1.01_PACid_16301083 +ATGGCCGATGAAGGAAACAAAAGCAATAACTTCTATTCGATCTTGGGGTTGAAGAAGGAGTGCACTGAATTGGAGCTAAA +GAATGCTTATAGGAAACTTGCAAAGAAATGGCACCCAGATCGTTGTTCAGCGACCGGGAATTCAGAGTTAGTGGAAGAAG +CTAAGAAAAAATTTCAGGAAATTCGGGAAGCCTATTCAGTTTTATCTGACGCCAACAAAAGGTTAATGTACGACGTGGGA +GTCTACGACAGTGATGACGACGAGAACGGCATGGGGGACTTCTTGGACGAAATGCTAACAATGATGAGTCAGACCAAATC +GAATGAAAACGGAGAGGAGAGCTTTGAGGAGTTGCAACAGTTGTTTGAAGACATGTTTGAAGCAGATATTGGATTGGACG +GAGGCCCTTCTCTTGCTTCTTCTGATTGCTCAACTTCATCTGCTTACATGACTTATAGTGAAAGTTCTAGTTCAAATAAA +CACAATTCCTCTGAGATGAATTTCGGGAAGGCAGAGAATTCTTCTGTCTTTGATGCTGGTTACCAGAATTTCTGTTTTGG +GGTGAACCAACTCCAAGATATAAAGAAGAAAAAGGGGGGAATTCTAGGAGGAGGTAGAAGTAGACACAGAAATGGCAGAA +AGCAAAATATGTCCTATGGCCATGATGTTTCATCGAATGACTACCCTGGAATTTCCACAAAG +>gnl_Glyma1.01_PACid_16301085 +ATGGCCGATGAAGGAAACAAAAGCAATAACTTCTATTCGATCTTGGGGTTGAAGAAGGAGTGCACTGAATTGGAGCTAAA +GAATGCTTATAGGAAACTTGCAAAGAAATGGCACCCAGATCGTTGTTCAGCGACCGGGAATTCAGAGTTAGTGGAAGAAG +CTAAGAAAAAATTTCAGGAAATTCGGGAAGCCTATTCAGTTTTATCTGACGCCAACAAAAGGTTAATGTACGACGTGGGA +GTCTACGACAGTGATGACGACGAGAACGGCATGGGGGACTTCTTGGACGAAATGCTAACAATGATGAGTCAGACCAAATC +GAATGAAAACGGAGAGGAGAGCTTTGAGGAGTTGCAACAGTTGTTTGAAGACATGTTTGAAGCAGATATTGGATTGGACG +GAGGCCCTTCTCTTGCTTCTTCTGATTGCTCAACTTCATCTGCTTACATGACTTATAGTGAAAGTTCTAGTTCAAATAAA +CACAATTCCTCTGAGATGAATTTCGGGAAGGCAGAGAATTCTTCTGTCTTTGATGCTGGTTACCAGAATTTCTGTTTTGG +GGTAGGTCATGTAAACTATCATTACCAA +>gnl_Glyma1.01_PACid_16301084 +ATGGCCGATGAAGGAAACAAAAGCAATAACTTCTATTCGATCTTGGGGTTGAAGAAGGAGTGCACTGAATTGGAGCTAAA +GAATGCTTATAGGAAACTTGCAAAGAAATGGCACCCAGATCGTTGTTCAGCGACCGGGAATTCAGAGTTAGTGGAAGAAG +CTAAGAAAAAATTTCAGGAAATTCGGGAAGCCTATTCAGTTTTATCTGACGCCAACAAAAGGTTAATGTACGACGTGGGA +GTCTACGACAGTGATGACGACGAGAACGGCATGGGGGACTTCTTGGACGAAATGCTAACAATGATGAGTCAGACCAAATC +GAATGAAAACGGAGAGGAGAGCTTTGAGGAGTTGCAACAGTTGTTTGAAGACATGTTTGAAGCAGATATTGGATTGGACG +GAGGCCCTTCTCTTGCTTCTTCTGATTGCTCAACTTCATCTGCTTACATGACTTATAGTGAAAGTTCTAGTTCAAATAAA +CACAATTCCTCTGAGATGAATTTCGGGAAGGCAGAGAATTCTTCTGTCTTTGATGCTGGTTACCAGAATTTCTGTTTTGG +GACAGGTGAACCAACTCCAAGATATAAAGAAGAAAAAGGGGGGAATTCTAGGAGGAGG +>gnl_Medtr3.5_Medtr8g022310.1 +ATGGCTAACGAAGGAAACAAAAGCAATGATTTCTATGCAGTTTTGGGATTGAATAAGGAATGCTCTGATTCAGAGCTAAG +GAATGCTTATAAGAAACTTGCACTGAAATGGCATCCAGATCGTTGTTCAGCTTCAGGGAATGTGAAGTTTGTGGAAGAAG +CTAAGAAGAAATTTCAGGCAATTCAAGAAGCCTATTCTGTTTTATCTGACTCGAACAAGAGATTAATGTACGACGTTGGA +GTTTACGACAGTGATGATGACGAAAATGGTATGGGAGACTTTCTGAATGAAATGGTTACAATGATGAGCCAAACTAAATC +AAATGAAAATGGAGAGGAGAGCTTCGAGGAGTTACAACAGTTGTTTGATGATATGTTTCAAGCGGATATCGGATTAAATG +GAAGCACCTCTCTTAATGCTTCGGGTTGCTCCACTTCATCGACTTTCATGACGTTCAGTGAAAGCTCGAATTCAAATAAG +CGCAATTCCACTCAAATGAATTTTGGGAAGGCAGAGGATTCTTCTAGTTTTGGTGCAAATTACCAGAACTTCTGTTTTGG +GATGAAGCACCTTCAAGAAGATGTGGAGAAGGAAAAAGGGGGAATTCTAGAAGGAGGAGGTAGCAAAAAACAAAGAAAAG +GAAGAAAACAAAAAATTTCATGTGGACATGTTTCCTCTAATGACCATCCTGGTATTTCTGCTAAT +>gnl_Medtr3.5_Medtr8g022310.2 +ATGGCTAACGAAGGAAACAAAAGCAATGATTTCTATGCAGTTTTGGGATTGAATAAGGAATGCTCTGATTCAGAGCTAAG +GAATGCTTATAAGAAACTTGCACTGAAATGGCATCCAGATCGTTGTTCAGCTTCAGGGAATGTGAAGTTTGTGGAAGAAG +CTAAGAAGAAATTTCAGGCAATTCAAGAAGCCTATTCTGTTTTATCTGACTCGAACAAGAGATTAATGTACGACGTTGGA +GTTTACGACAGTGATGATGACGAAAATGGTATGGGAGACTTTCTGAATGAAATGGTTACAATGATGAGCCAAACTAAATC +AAATGAAAATGGAGAGGAGAGCTTCGAGGAGTTACAACAGTTGTTTGATGATATGTTTCAAGCGGATATCGGATTAAATG +GAAGCACCTCTCTTAATGCTTCGGGTTGCTCCACTTCATCGACTTTCATGACGTTCAGTGAAAGCTCGAATTCAAATAAG +CGCAATTCCACTCAAATGAATTTTGGGAAGGCAGAGGATTCTTCTAGTTTTGGTGCAAATTACCAGAACTTCTGTTTTGG +GGTCAATCTTGTAAATTATCATTACCAA +>gnl_Musac1.0_GSMUA_Achr6T31040_001 +ATGGCGGCCGAAGAGGACAAAAGCGGCGACTTCTACGCCGTGTTGGGGCTCAGGAAGGAGTGCTCCGAAACCGAGCTGAG +GAATGCGTACAAGAAGCTTGCCATGAGGTGGCATCCGGATAAGTGCTTGGCTTCGGGAAATGCTCAAATCGTGGGGGAAG +CCAAGGAGAAGTTTCAGGAGATCCAGAAAGCCTACTCTGTTCTCTCAGACTCCAATAAGAGATTCCTGTACGATGTGGGA +GTCTACGACAACGATGATGACAATGACGAAAACGGTATGGGAGACTTTATAGGGGAGATGTTGGAGATGATGAGCCAAAC +GAAACCCAATGAGAACAGCCAAGATAGCTTCCAGGAGCTGCAGGAGCTGTTTGTGGAGATGTTCCAGGACGACCTGGATG +CCGGATTTGGTGGTTCCATCTTCCACGATTGCCCCTGGGCTCAACCGACCAATGGCCAAGATTGCTGGACTTCATCGGGA +CTGCACTTTGCTAATGGAAGGAGTAAGTGTGGCAACAAGCGGGGCAACTCAGCTGTGAACTTGGGAAAGGTCAATCTTGA +AGAGTTGGAACATGGTACCAGCGACTTCTATTTTGGGCTAAATGATGCAGCACAGCCATCACAAGGGAAAGGAGGCAGTA +ATAACAAGAGAAGGAATGGAAGAAAGCAAAAGGTTTCATCCAATCATGATGTCTCATCC +>gnl_Musac1.0_GSMUA_Achr9T18140_001 +ATGGCCGCCGGGGAGGAAAAGATCGGCGATTTCTACACGGTGCTGGGGCTCAGGAAGGAGTGCTCGGAGGCGGAGCTGAG +GATCGCGTACAAGAAGCTGGCTATGAGATGGCATCCGGATAAGTGCTCGGCTTCGGGAAACCATCGAAGGATGGAGGAAG +CGAAGGAGAAGTTCCAGGAAATCCAAAAAGCCTACTCTGTTCTCTCGGACTCCAGCAAGAGATTTCTGTATGATGTGGGA +ATCTACGATAACGAGGATGATAATGACGAAAAAGGAATGGGGGATTTTATTGGGGAGATAGCTCAGATGATGAGCCAAAC +GAAATCTGGGGAGAATGGTCATGATAGCTTTGAGGAGCTGCAGCGGATGTTCCTGGATATGTTCCAGGACGACCTGGACG +CCGGATTCGGTGATTCTTCCATCCACAGTGGCCCCCAAGCTCGGCCAACCGACGGTCTCAATTGCTCGATGCCATCAGGA +CTGCAGTTTGCTGATGGAGGGAACAATGGCAGCAACAAGAGAGGCAACTCGGAGAAGGCAAAGCTGGATGGGTTGGAAAA +CAGTTCCACTGGCTTCTGCTTCGGGTTGAATGATGCAGGGCAGTCATCAAAAGGAAAAGGAAGCGCTAATAGCAAGAGAA +GGAATGGAAGAAAGCAGAAGGTCTCATCCAAACATGATGTCTCATCCAGTGATGCTGAGGTCTCATTT +>gnl_Musac1.0_GSMUA_Achr8T23700_001 +ATGGCGAGCGACATGGATGCAAGCGGCGATTTCTACTCGGTGCTGGGGCTGAAGAAGGAGTGCTCCGAGGCGGAGCTCAG +GAATGCGTACAAGAAGCTCGCTTTGAAGTGGCATCCCGATAAGTGCTCGGCGTCGGGTAATGAGATTCGCATGAAGGAAG +CGAAGCAGCAGTTCCAGGAGATCCAGAAAGCCTACTCTGTTCTCTCCGACTCCAACAAGAGATTTCTGTACGATGTTGGA +GCCTACGACAAAGACGACGACAAAGACGAAGAGGGGATGGTGGAGTTTCTTGGGGAGATGGCGCAAATGATGAGGCAAAC +CAAATGCTGTGGGAGCGGCCAGGAGAGCTTCGAGCAGCTGCAGCAGATGTTCGTGGAGATGTTCCACGACGATCTGGACG +CGGGATTCTGCGGCCACTCCTCGGCCACCTCGGGCGCGGCGTCCTGCGGCAACAAACGGGACAACTCGGCGATGGACTCG +GGCAAGCGGAAGCCGGACGAGTTGGACCCGGCCGCCATTGGGTTCTGCCTCGGGACAAAGGATGCAGGGCAATCCTCAAA +AGGAAGAGGTAGCAACAGCAAGAGAAGGAACAGAAGAAAGCAAAAGGCATCATCCAAGCATGACAACTCATCTCACAATG +CTAAGGTCTCAGCT +>gnl_Musac1.0_GSMUA_AchrUn_randomT02210_001 +ATGGAGGGGGACGAGGAGAAGAGCGGGGATTTCTACGCGGTGCTGGGGCTGAAGAAAGAGGGCTCCATGGCGGAGCTCAA +GAATGCGTACAAGAAGCTGGCGATGAAGTGGCATCCCGATAAGTGTCCTGCGTCAGGCAATAAGATACGCATGGATAAAG +CGAAGGAGAAGTTCCAGGAGATCCAAAAAGCCTACTCTGTTCTCTCCGACTCCAACAAGCGATTCCTGTACGATGTCGGA +GTTTACGACAAAGACGATGAGGAAGATGAAGAGGGGATGGGGGACTTCATTGGGGAGATCGCGCAAATGATGAGCCAGTC +CAAACCCAGCGGGAGCGGCCACGAGAGCTTGGAGGAGCTGCATCGGCAGGTCGTGGAGATGTTCCTCGACGAACTGGACG +CCGGAGATCGCTTCTCCTCGGCCAACCAAGGCGCGTCGTCCTGCGACGGCAGGGACGACGGCGGCGGTAACAAGCGTGGC +AACTGGGCGGTGGACTGGGGCAAGGAGAAGCTGAACGAGTTGGGCCCGGGCACCGGCGGGTTCTGCTTCGGGGTGAGTCG +CCGAGTCCACTCCTTTGATCTTATGATAGACGTAGTCCACCTCATCCATTCTGATCTGACTCTGGAA +>gnl_Orysa6.0_PACid_16843526 +ATGGCCGACGGGGGAGAGAAGTGCCGGGACGCGGCCGGCGAGGGCGGCGGCGGCGGCGACCTGTACGCCGTGCTCGGGCT +CAAGAAGGAGTGCTCCGACGCCGACCTCAAGCTCGCGTACCGGAAGCTCGCCATGAGATGGCATCCGGACAAATGCTCAT +CCTCCAGCAGTGCAAAGCACATGGAGGAAGCCAAGGAGAAGTTCCAGGAGATCCAGGGCGCCTATTCCGTCCTCTCAGAC +TCAAACAAGCGGTTCCTCTACGACGTGGGGGTATATGATGATGACGACAATGACGATGACAACCTGCAGGGGATGGGGGA +CTTCATTGGTGAGATGGCCCAGATGATGAGCCAGGCACGGCCAACGAGGCAGGAGAGCTTTAAAGAACTGCAGCAGCTAT +TCGTAGACATGTTCCAAGCTGATCTTGATTCGGGTTTCTGCAATGGACCCTCAAAGTGCTACCATACCCAGGCCCAAAGC +CAGACTCGAACATCCTCAACCTCCCCTTCGATGTCACCGTCTCCACCGCCTCCAGTAGCTACTGAGGCAGAATCGCCATC +ATGTAATGGTATTAATAAGCGTGGTTCATCAGCAATGGACTCTGGGAAGCCTCCAAGAGCCAGCGAAGTCGGTTCTGGAC +AGAGTCAATCAGGGTTTTGTTTCGGGAAGAGTGATGCTAAACAAGCGGCGAAGACGCGAAGCGGGAACACGGCCAGCCGG +AGGAGGAACGGCCGGAAGCAGAAGGTGTCGTCGAAGCACGACGTCTCGTCTGAGGACGAGATGCCAGGTTCGCAGTGGCA +CGGCGTGGCC +>gnl_Orysa6.0_PACid_16843528 +ATGGCCGACGGGGGAGAGAAGTGCCGGGACGCGGCCGGCGAGGGCGGCGGCGGCGGCGACCTGTACGCCGTGCTCGGGCT +CAAGAAGGAGTGCTCCGACGCCGACCTCAAGCTCGCGTACCGGAAGCTCGCCATGAGATGGCATCCGGACAAATGCTCAT +CCTCCAGCAGTGCAAAGCACATGGAGGAAGCCAAGGAGAAGTTCCAGGAGATCCAGGGCGCCTATTCCGTCCTCTCAGAC +TCAAACAAGCGGTTCCTCTACGACGTGGGGGTATATGATGATGACGACAATGACGATGACAACCTGCAGGGGATGGGGGA +CTTCATTGGTGAGATGGCCCAGATGATGAGCCAGGCACGGCCAACGAGGCAGGAGAGCTTTAAAGAACTGCAGCAGCTAT +TCGTAGACATGTTCCAAGCTGATCTTGATTCGGGTTTCTGCAATGGACCCTCAAAGTGCTACCATACCCAGGCCCAAAGC +CAGACTCGAACATCCTCAACCTCCCCTTCGATGTCACCGTCTCCACCGCCTCCAGTAGCTACTGAGGCAGAATCGCCATC +ATGTAATGGTATTAATAAGCGTGGTTCATCAGCAATGGACTCTGGGAAGCCTCCAAGAGCCAGCGAAGTCGGTTCTGGAC +AGAGTCAATCAGGGTTTTGTTTCGGGCAGAAGAGTGATGCTAAACAAGCGGCGAAGACGCGAAGCGGGAACACGGCCAGC +CGGAGGAGGAACGGCCGGAAGCAGAAGGTGTCGTCGAAGCACGACGTCTCGTCTGAGGACGAGATGCCAGGTTCGCAGTG +GCACGGCGTGGCC +>gnl_Poptr2.2_PACid_18217800 +ATGGCAAACGGAGGAGAAGATAAATGGAAAAGCAATGACTTATATCAAGTCTTGGGGTTGAATAAGGAATGCACTGATAC +AGAGCTCAGGAGTGCTTATAAGAAACTTGCACTGAGATGGCATCCAGATCGATGTTCAGCTTCAGGAAATTCTAAGTTCG +TTGAAGAAGCCAAAAAGAAGTTTCAGGCAATTCAACAGGCCTATTCTGTTCTTTCTGACACCAACAAGAGGTTTCTTTAC +GACGTTGGTGTTGATGACAGTGATGACGACGAAAATGGAATGGGTGATTTTCTGAATGAAATGGCTGTCATGATGAGCCA +AACGAAGCCTAGCGAAAACATGGAGGAGAGCCTAGAGGAACTGCAAGAATTATTTGACGAGATGTTCCAAGAGGATCTGC +ATTCGTTTGGGATTGACAGTCAGGCTGCTCCTTCATGTCCTCCTTCTTATGTATCCTACAGCGAAAGTTCCAACTCAAAT +AACAAACGTGTTTCTGCTGATATGAACTTGGGGAAGACTAAAGTGGATGATTCTTCTAGCTTCAACTCTCACTTTGAGAA +ATTCTGTTTAGGGACAGGTGGAACAGCAGCAACCTTTCAAGAAGGTGAAGGTGGGAGTAAGAGGAGGAATTCAAGGAGGA +GCCAGCGGCAGACGAAGGCAAGACAAGAAACAAAGAGTTTCTTCGGGCTA +>gnl_Poptr2.2_PACid_18234651 +ATGGAAAATGGAGGAGAAGAGAAAGGGAAAAGCAATGACTTTTATCAGGTTTTGGGGTTGAATAAGGATTGCACTGCCAC +AGAGCTGAGGAATGCTTATAAGAAACTTGCACTGAAATGGCATCCAGATCGATGTTCAGCTTCGGAAAATTCCAGGTTCG +TTGACGAAGCCAAAAAGAAGTTTCAGACAATTCAACAGGCCTATTCTGTTCTTTCTGACACCAACAAGAGGTTTCTTTAC +GACGTTGGTGTTTATGACAGTGAAGACGACGAAAATGGAATGGGCGGATTTATGAATGAAATGGCTGCTATGATGAGCCA +AACAAAGCCCCACGAAAACGTGGAGGAGAGCTTTGAGGAATTGCAAGGATTGTTTGAGGAGATGTTCCAAGAGGATTTGG +ATTCGTTTGGGATTGCCTGTCAGGCTACTACCTGTGTGTCATACAGCGAAAGCTCCAACTCAAATGATAAACGTGTTTCT +GTCGATATGAACTTGAAGAAGACAAAGGTGGATGATTCTTCTGGCTTCAATTCTCACGTCGAGAAGTTCTGTTTAGGGGT +AAGTGGAACACCAGCAATCTTTCAAGAAGGGGAAGGGAGTAAGAGGAGGAGTTCAAGGAGGAACCGGCGG +>gnl_Poptr2.2_PACid_18234649 +ATGCTAAGAATGGAAAATGGAGGAGAAGAGAAAGGGAAAAGCAATGACTTTTATCAGGTTTTGGGGTTGAATAAGGATTG +CACTGCCACAGAGCTGAGGAATGCTTATAAGAAACTTGCACTGAAATGGCATCCAGATCGATGTTCAGCTTCGGAAAATT +CCAGGTTCGTTGACGAAGCCAAAAAGAAGTTTCAGACAATTCAACAGGCCTATTCTGTTCTTTCTGACACCAACAAGAGG +TTTCTTTACGACGTTGGTGTTTATGACAGTGAAGACGACGAAAATGGAATGGGCGGATTTATGAATGAAATGGCTGCTAT +GATGAGCCAAACAAAGCCCCACGAAAACGTGGAGGAGAGCTTTGAGGAATTGCAAGGATTGTTTGAGGAGATGTTCCAAG +AGGATTTGGATTCGTTTGGGATTGCCTGTCAGGCTACTACCTGTGTGTCATACAGCGAAAGCTCCAACTCAAATGATAAA +CGTGTTTCTGTCGATATGAACTTGAAGAAGACAAAGGTGGATGATTCTTCTGGCTTCAATTCTCACGTCGAGAAGTTCTG +TTTAGGGGTGGAACACCAGCAATCTTTCAAGAAGGGGAAGGGAGTAAGAGGAGGAGTTCAAGGAGGAACCGGCGGTAGAG +AGAGGAAAGGCAGGAAACAAGAAGTTTCATCTGGCTATGATGTCTCCTCCCATGACCATGGTATTTCTGCTTCA +>gnl_Poptr2.2_PACid_18234650 +ATGGAAAATGGAGGAGAAGAGAAAGGGAAAAGCAATGACTTTTATCAGGTTTTGGGGTTGAATAAGGATTGCACTGCCAC +AGAGCTGAGGAATGCTTATAAGAAACTTGCACTGAAATGGCATCCAGATCGATGTTCAGCTTCGGAAAATTCCAGGTTCG +TTGACGAAGCCAAAAAGAAGTTTCAGACAATTCAACAGGCCTATTCTGTTCTTTCTGACACCAACAAGAGGTTTCTTTAC +GACGTTGGTGTTTATGACAGTGAAGACGACGAAAATGGAATGGGCGGATTTATGAATGAAATGGCTGCTATGATGAGCCA +AACAAAGCCCCACGAAAACGTGGAGGAGAGCTTTGAGGAATTGCAAGGATTGTTTGAGGAGATGTTCCAAGAGGATTTGG +ATTCGTTTGGGATTGCCTGTCAGGCTACTACCTGTGTGTCATACAGCGAAAGCTCCAACTCAAATGATAAACGTGTTTCT +GTCGATATGAACTTGAAGAAGACAAAGGTGGATGATTCTTCTGGCTTCAATTCTCACGTCGAGAAGTTCTGTTTAGGGGT +GGAACACCAGCAATCTTTCAAGAAGGGGAAGGGAGTAAGAGGAGGAGTTCAAGGAGGAACCGGCGGTAGAGAGAGGAAAG +GCAGGAAACAAGAAGTTTCATCTGGCTATGATGTCTCCTCCCATGACCATGGTATTTCTGCTTCA +>gnl_Soltu3.4_PGSC0003DMP400016105 +ATGGGCAATGATTATTATGCAGTTTTGGGATTGAAAAAGGAATGCACTGAAACAGAGCTTAGGAATGCTTATAAGAAGCT +TGCACTGAAATGGCACCCAGATCGCTGTTCAGCATCGGGGAATTCGAAGTTTGTAGATGAAGCAAAGAAGAAATTTCAGG +CAATTCAAGAAGCATATTCTGTGTTATCGGATGCAAACAAAAGGTTTCTGTACGATGTAGGAGTTTATGACTCTGGTGAT +GATGACGACGAAAATGGCATGGGTGATTTCCTGAATGAAATGGCAGCTATGATGAGCCAAAATAAGTCCAATGAAAATCA +GGAAGAAACCTTTGAGGAATTGCAGGATATGTTTGACGAAATTTTCAATAGTGATAATGGGATGTCTTCTTCTTCTTCTT +CTTCTTCTCGGACTGGAACTCCTTCAATGTGTTCTACTACATCGTCTACATCTTCCAGTGAGACCTTTTTTACCTTTTCC +AACAAAAGAAGTTCAGGTGAAATGAAGTCGGGTAAAGGCGATTCTTGCCAATTCCAAGGATTTTGTGAAGGGACAGGTGG +AGCATCTGGAAAAAGCAATGAAAGAGAACGGAGTCGGAGGAAAAATTCCAAGAGTGGACGGAAGCAA +>gnl_Soltu3.4_PGSC0003DMP400016106 +ATGGGCAATGATTATTATGCAGTTTTGGGATTGAAAAAGGAATGCACTGAAACAGAGCTTAGGAATGCTTATAAGAAGCT +TGCACTGAAATGGCACCCAGATCGCTGTTCAGCATCGGGGAATTCGAAGTTTGTAGATGAAGCAAAGAAGAAATTTCAGG +CAATTCAAGAAGCATATTCTGTGTTATCGGATGCAAACAAAAGGTTTCTGTACGATGTAGGAGTTTATGACTCTGGTGAT +GATGACGACGAAAATGGCATGGGTGATTTCCTGAATGAAATGGCAGCTATGATGAGCCAAAATAAGTCCAATGAAAATCA +GGAAGAAACCTTTGAGGAATTGCAGGATATGTTTGACGAAATTTTCAATAGTGATAATGGGATGTCTTCTTCTTCTTCTT +CTTCTTCTCGGACTGGAACTCCTTCAATGTGTTCTACTACATCGTCTACATCTTCCAGTGAGACCTTTTTTACCTTTTCC +AACAAAAGAAGTTCAGGTGAAATGAAGTCGGGTAAAGGCGATTCTTGCCAATTCCAAGGATTTTGTGAAGGGGTGGAGCA +TCTGGAAAAAGCAATGAAAGAGAACGGAGTCGGAGGAAAAATTCCAAGAGTGGACGGAAGCAATAGGATGGATGCTAAAA +GGCAAAAGGTTCTATCA +>gnl_Ambtr1.0.27_AmTr_v1.0_scaffold00007.329 +ATGGCACCCCGAGGAGAGAAAGACAGTGATTTTTATGCAATTTTAGGGTTGAAGAAGGAGTGCTCTGCTTCAGATCTCAG +AAATGCGTACAAAAGGCTCGCACTTCGGTGGCATCCAGATAGGTGCTCTGCCTCAGGGAACACAAAGTTTGTGGAGGAAT +GCAAGAAAAAGTTCCAGGCCATTCAGCAGGCTTATTCCGTGCTCTCGGATGCAAATAAGAGGTTTTTGTACGATGTTGGA +GCATATGGAAGTGACGATGACGATCAGGGAATGGGTGAATTTCTTGGGGAGATGGCGGTAATGATGAGCCAGACAAAGCC +CAGTGAAAAAGGGCCGGAGAGCTTTGAGGATCTACAGAACTTGTTTCAGGAGATGTTCGAAAGGGATCTGGACATGTTTA +AGTCATCGACCTCCCACAACAACAACAATGATAACAACAATAATAATCATAGGAGTAGTGACAATAATAATTGTAGTAGT +GTTCATTGTTTTAGTAACACCAACAAGAGGAATTGCTCGGATATGAATGCCGGAGAAGCCTCGGAGGTCGGGCGCTTTGC +TTTCTCATGCTATGCGACAGAGTTCCTGCACAAGCAAACTTTCTCCGTCGGGGCGGATGATGTGCGATCGGAGTCGAGCA +ACAAGAGACGAAACGGGAGGAAACAGAAATCCACCTCCTCTTCAAGGAAAAGT +>gnl_Aquco1.0_PACid_18141277 +ATGGCTAGTGAAGAAGAAGCAAGTGATTTCTATAAAGTTTTGGGATTGAAAAATAACTGTTCTTCCTTGGAGCTCAGGAA +CGCTTATAAGAAGCTTGCACTGAAATGGCATCCGGATCGTTGTGCTGCTTCAGGAAACTCAAAGTTTGTTGAAGAAGCAA +AGAAGAATTTTCAAGCAATACAAGAAGCTTATTCTGTTCTTTCAGATGAGCAGAAACGATTTATGTATGACGTTGGTGTC +TACGATAAAGATGATGATGACGAAAATGAAGATATGGGCGATTTTTTAGGTGAAATGATGTCTATGATGAAGCAAGAAAA +TACTAGTGCGGATGGACAACAAAGTTTTGAAGACCTTCAAAACCTATTCCAGGAAATGGTTCAAAATGACAAAGAATTTT +ATAATCCAGCCTCTCAAAACTCGTCGATATATAATGCTAGTAACAACATGTTCTCCTTCTCTAATAACGAGAACTTAAAC +AATGCTAGCAACAACACATTCTCCTCTTTTTATAATGAGAACCTAAACAGCAGCAACAAGAAAAGTTGCTCAAGTATGAG +CGCAGAAAATACCAAGGTGGACTTTAACATGGAATCATTGGACTTCCGCAGCTTTTCTATTGGGTTAGAAGGCGGTACAT +CATTTCAAAACTCCAAAGGGAGAGGAGTAACGGGTAGGCGGACAGGAAGGAAACAGAAGGGGTCGTCCTGTAATGATATG +TCTTCCCATGATTCTAAGATTTTGGCG +>gnl_Arath10_AT3G14200.1 +ATGGCGTCCAGTAATAGCGAGAAGATCAACGAGAATCTGTACGCTGTTCTGGGTTTGAAGAAGGAATGTTCTAAGACGGA +GCTCCGTTCTGCTTATAAGAAGCTTGCTCTCAGATGGCATCCAGATCGTTGTTCGTCAATGGAGTTTGTAGAAGAAGCAA +AGAAGAAATTTCAGGCAATCCAAGAAGCCTACTCTGTTCTGTCTGACTCCAACAAGAGGTTCCTGTATGATGTTGGTGCT +TATAATACTGATGATGATGATGACCAAAACGGAATGGGAGATTTCTTGAACGAAATGGCGACTATGATGAATCAATCCAA +GCCTAGTGATAATAACACAGGGGACAGTTTTGAACAACTACAAGATCTGTTTAATGAGATGTTTCAAGGAGACGCTGCAG +CATTCCCATCATCATCGTCCTGCTCCACTTCAAATTTCACTTCATCTCGTAGTTTTGTATTCGATACAAATTCTCAGCGG +TCATCTTCGTTTGCGACAAGTTCGATGGGGATGAATAATGATCCTTTCGGATATGACCCGAGAGCTCATTCCTTCTCTTT +AGGGGTGGACCATCAGCAAGAGTTCAAGAAAGGGAAAAACAATGGCGGAAGAAGAAACAGGAGAAAGAACAATGTTCCAT +CGGCTGGTCACGAAACGTCGTCGTCAAACAACTATGGAGTCCCCACCTCA +>gnl_Bradi1.2_Bradi3g60090.1 +ATGGCCACCGGGGGCGACAAGTGCGGCGGAAAGCCGGCGGCCGCGGGGGTGGGCGGCGGTGACCTGTACTCTGTGCTGGG +CGTCAACAAGGAGTGCTCCGACGCCGACCTCAAGGTCGCCTACCGGAAGCTCGCCATGAGATGGCATCCGGATAGATGCT +CCTCCTCCAGCAGCACCAAGCACATGGAGGAAGCAAAAGAGAAGTTCCAGGAGATCCAGGGCGCCTATTCCGTCCTCTCC +GATGCCAACAAGCGCTTCCTCTATGACGTGGGGGTATATGAAGAACATGAAGAAGAAGATGATGACACTCTGCAGGGGAT +GGGGGACTTCCTTGGTGAGATGGCCCATATGATGAGCCAGACGCAGCCAGCGAGACAGGAAAGCTTTGAGGAGCTCCAGC +AGCTCTTCGTGGACATGTTCCAGTCTGATATTGAATCGGGATTCTGCAACGGACCTGCCAAGGACCATGACCCAGTCCAA +AGACAGACGCGAACATTCTCGACCCCTCCTTCGCCATCGCCATCTCCACCGCCTCCACTAGCTACAGTGGACGAAGCGGC +ATCATGTAATGGCATCAATAAGCGTGGCTCATCAGCAATGGGCTCTGGGAAGCCTCCAAGAGCTGGTGAAGTGAGTGGGG +GTCACGGCCAGTCTGAGTTCTGTTTCGGGATGAGCGACGCCAAGCAAGCGCCGAAGGCGCGAGGCGGGAACGCTAGCAGG +AGAAGGAACGGCCAGAAGCAGAAACTGTCGTCGAAGCACGACGTCTCCTCCGGCGATGAGATGCCGAGACCACATGCAGC +AGTA +>gnl_Carpa1.181_PACid_16420351 +ATGGCGGATGGAGAAGACAAGAACAACAGTGATTTGTATGCGGTTCTTGGATTGAATAAGGAATGTACTCCAGCAGAGCT +CAGGAACGCTTATAAGAAACTTGCAATGAGATGGCATCCAGATCGCTGTTCCGCGTCGGGGAATTCAATGTTTGTGGAAG +AAGCAAAGAAGAAATTTCAGGCAATCCAAGAAGCCTACTCTGTTCTTTCTGACGCAAACAAGAGGTTTCTGTACGACGTC +GGAGCTTACGAAAGTGATGACGACGAAAATGGAATGGGTGATTTTTTAAACGAAATGGCAGCCATGATGAGCCAAACAAA +GCCTAATGAGAATGGGAATGCACAAGAGAGCTTTGAAGAATTGCAAGAGTTGTTTCAAGAGATGTTTCAAGGGGATATGG +GATTCAACACATTTGGATCTAGTTCTCAGCCTACTACTTCTTCGTGTTCTGCTTCCTCTGCATATGCAACCTGTAGCGAA +ACCTCCAATCCTAACAACAACAAGCGCAATTCATCAGAAATGAATTATGGCAAGAAAAAGGTAGATGATTCTTCAGGGTT +TCATGCTCATTTCCAAACCTTTTGTTTAGGGGTGGAACAGCAGCAAGATTTCAAGAAGGGGAAGGAAGCAAGAGGAGGAA +TTCGAGGAAAACCCGGAGGTAGTAGGAGGCAGGGAAGGAAACAGAAGGTTTCATCTCGCCACAATGTCTCATCCAATGAC +TTGGGCATTTCTGCTTCC +>gnl_Frave2.0_gene05408 +ATGGCGGGGGGAAAGTGGGTCCCCCCACCCCTGTCCCAGTTTCATCTTCACATAAAGAGGTTCCGTCGACGTCAGAAAGT +CTCTGGATCCAGTGGAAACACAGAACCTTCTGGATACACAGACTGCAAAAATATCTCCAATCGAAGAATGGAAGAGAAAG +GCAATGACTTTTATGCTGTTATGGGGTTGAAGAAGGAATGCTCTGACTCGGAGCTCAGGAATGCTTATAAGAAACTTGCA +CTGATATGGCACCCAGATCGTTGCTCTGCCTCAGGAAATTCAAAGTTCGTGGAAGAAGCCAAGAAGAAGTTTCAGGACAT +TCAACAAGCCTATTCTGTTCTGTCCGACGCCAACAAGAGGTTTCTGTACGATGTAGGAGCTTATGAAAGTGATGATGACG +AAAATGGAATGGGTGATTTTTTAAACGAGATGGCGGTGATGATGAGCCAGACTAAGCCGAATGAAAATGGAGGAGAGAGC +TTCGAACAATTGCAGGAGCTCTTTGAAGAAATGTTTCAGGGGGATATTGAGGGCTTTAGCTCCTGCTCTCAGCCTCCTAC +TTCCTGTTCTACTTCCTCATCTTCATACGCATTGTACTGTGAAAATTCTACTCCCAGTAACAAACGTAATTCCTCCGCAA +TGAATTATGGCAACGCAACCCTGGACAGTTCTGGTTTTGATGCTCATTTTCACAATTTCTGTGTAGGGACAGGCGGGAAG +CCAGCAAAGGATCGGGAAGGGGATGCCAGGAAGAGAAAGGATTCCAGGAGGAGTAACCGG +>gnl_Mimgu1.0_PACid_17694730 +ATGGCTGCTGATGAAGAGAAAAGCAGCGATTTTTACGGCGTTCTGGGGCTGAGGAAAGAATGTACGGCGGCGGAGCTCAG +GGTTGCCTACAAGAAACTTGCAATGAAATGGCATCCAGATCGTTGCTCTGCTTCTGGGAATTTAAAGTATGTGGAGGAAG +CAAAGAACAAGTTTCAAGCTGTCCAACAGGCCTATTCTGTGCTTTCCGATGCCAACAAAAGGTTTCTCTACGACGTAGGA +ATCTACGATTCTGAAGACGATGCTGACGAAAACGGTATGGGTGATTTCTTGAATGAAATGGTAGCAATGATGGGCCAAAG +TAAACCAAATGAAAATAAAAACGAGAGCTTCCAAGAATTGCAAGATCTATTCGAGGAAATATTCAACAATGACGCGGAAG +AGGTTTTCAAGATTCCTCCTCCGCACTTTCCGTACCAAGATTCTTGCAGCGAGACCCGCACCGCATCGAACAAGAGGAAC +GCCCGCGAAATGGGCTCCGTAAATTTCAGTAATATCGAAGCCACACCATTTGAAGGGTTCTGCATAGGGGAAAATGTAAT +TTTTGGGGGAGAGAGAATACAAACGAGGCCCGGAGGAGGTAGTAGGAGGACGAAGCCGAAGATTTCGACATCGATCGATG +GTTTAATTAGT +>gnl_Nelnu1.0_NNU_010544-RA +ATGAACCTGTTGTTGCAGAAATGGCATCCGGATCGATGCTCCTCGTCGGGAAACTCTAAGTTCGTGGAAGATTCAAAGAA +GAAATTTCAGGCAATTCAAGAGGCTTATTCTGTTCTATCCGACGAGAATAAGCGATTTCTTTACGACGTTGGAGTTTACG +ACTGCGACGACGATGACGATGACGAAAACGGAATGGGAGAATTTTTGGGGGAAATGGCGACTATGATGAGCCAAATTAAA +CCCAGCGAGAACGGGCCGGAGAGTTTGGAGAAGCTGCAGGAACTGTTCGAGGAAATGTTCCAAAGGGACATGGATGATGG +TTTCTTCTCCCCCTCCCCCCAATGCGCTTCTTTTTCTTCGTCTTGCTCATCTTCTTCGTCGTCGACGACTTATTTTTCAT +ATAATAACAACAAGCACGACAATAAAAGGAATTGCTCCGACATCAGTTCTATGGACGATTTCTACACATTTGGCACGGAT +TCTATACAATTCAGCAATTTCTGCATTGGGGTGGAAGGAGGAGAAGATTCAAAAGTAAGAGGAGGAAAGTCAAGGCGGAA +GAGCAACAGGAGACAAAAAGTTTCATCGTCTAAACACGATCCGTCGTGCCGT +>gnl_Solly2.3_Solyc03g123560.2.1 +ATGGAAGACAAAAGCAATGATTATTATGCAGTTTTGGGGTTGAAGAAGGAATGCACTGACACAGAACTTAGGAATGCCTA +TAAGAAGCTTGCACTGAAATGGCACCCAGATCGCTGTTCAGCATCGGGGAATTTGAAGTTTGTAGATGAAGCAAAGAAGC +AATTTCAGGCAATTCAAGAAGCATATTCTGTGTTATCGGATGCAAACAAAAAGTTTTTGTACGATGTAGGAGTTTATGAC +TCTGGTGATGATGACGACGAAAATGGCATGGGTGATTTCCTGAATGAAATGGCAGCTATGATGAGCCAAAATAAGTCCAA +TGAAAATCAGGGAGAAGAAACCTTTGAGGAATTGCAGGATATGTTTAATGAAATGTTCAACAGTGATAATGGAACGTTTT +CTTCTTCTTCTTCTTCTTCTTCTTCTTGGACTGGAACTCCTTCAATGTGCTCTACTACATCATCTACATCTTCAAGTGAG +ACTTTTTTAACCTTTCCCAACAAGAGAAGTTCAGGTGAAATGAAGTCGGGTAGTAGTGTAAGAGGCGATTCTTGCCAATT +CCAAGGATTTTGTGTAGGGGCAGGTGGAACTTCTGGAAAATGCAATGAAAGAGAACGAAGTTGGAGGAAAAATTCCAAGA +GTGGACGGAAGCAT +>gnl_Sorbi1.4_PACid_1968370 +ATGGACGCCGGGGGAGAGAAGTTCAGCGACGCGGCGGCGGCGGAGGGCGGTGAGGGCGGCGGCGACCTCTACGCCGTCCT +CGGGCTCAAGAAGGAGTGCTCCGACGCCGACCTCAAGGTCGCTTACCGGAAGCTCGCCAAGAAATGGCACCCGGACAAAT +GCTCCTCCTCCAGCAGCGTGAAACACATGGAGGAAGCCAAGGAGAAGTTCCAAGAGATCCAGGGCGCCTATTCCGTACTC +TCTGACGCCAATAAACGGCTCCTCTACGATGTTGGAGTATACGACGATGAGGACGACGAGGATAGCATGCAGGGGATGGG +TGACTTCATTGGTGAGATGGCCCAGATGATGAGCCAGGTGCGGCCGACGAGGCAGGAAAGCTTTGAGGAGCTGCAGCAGC +TTTTTGTGGACATGTTCCAGTCTGATATTGATTCAGGATTCTGCAACGGGTCTGCTAAGGATCAAGTTCAGGGGCAAGCC +AAAAGTAGAACATGCTCGACCTCACCTTCATCATCACCGTCCCCACCTCCTCCTCCTACTATAGTAAAGGAGGCAGAGGT +GTCATCATGTAATGGCTTCAATAAGCGGGGTTCATCAGCAATGGACTCAGGGAAGCCTCCAAGGCCTGTTGAAGGCGGTG +CTGGTCAGGCTGGATTTTGTTTTGGGGTGAGCGATACGAAGCAAACGCCGAAGCCGAGAGGTCCGAACACCAGCCGGAGG +AGGAACGGCCGGAAACAGAAGCTGTCATCCAAGCACGATGTTTCATCTGAAGATGAAACGGCCGGTTCC +>gnl_Thepa2.0_Tp3g12470 +ATGGCGTCGAACAATAGCGAGAAAGGAAACGATGATTTGTATGGTGTTCTGGGCTTGAAGAAGGAATGTACGACGACGGA +GCTCCGTACTGCTTATAAGAAGCTTGCTCTAAGATGGCATCCAGATCGTTGTTCGTCAATGGGGACTCCAGAGTTTGTAG +ACGAAGCAAAGAAGAAGTTTCAGGCAATCCAAGAGGCCTATTCTGTTCTGTCTGACTCCAACAAGAGGTTCCTCTATGAT +GTTGGAGCTTATAACAGTGATGATGAAGACCAAAACGGTATGGGAGATTTCTTGAACGAAATGGCGGCAATGATGAATCA +GTCCAAGCCTAGTGAGAATAACTCAGGGGACAGTTTTGAGCAGCTACAAGATCTGTTTAATGAGATGTTTCAAGGAGACG +CTGCAGCATTCTCATCATCATCATCATCATCTTGCTCTGCTTCGACTTTTACTTCCTCTTGTAGCTTTGTCTTTGACACA +AATAGTCAGCGGTCACCGTTTGAGACAAGCTCAATGGGGACTAATGATCTTTTTGGATTCGATCACAGTGCTCACACCTT +CTCTTTAGGGGTGGAACATCAGCAGGATTTCAAGAAGGGGAAGAACAGTGGTGGAAGAAGAAACAGAAGGAAGAACAATG +CTCAATCGGCTGCTCACGAGACGGCGTCGTCCAACAACTATGGAGTCCCCACTTCA +>gnl_Theca1.0_Tc06_g010450 +ATGGCAAATGGAGAAGAGAAAAACAATGATTTTTATGCAGTTTTGGGGTTGAATAAAGAATGCACTCCGACAGAGCTCAG +GACTGCTTATAAGAAACTTGCCCTGAGATGGCACCCTGATCGTTGCTCAGCTTCGGGAAATTCAAAGTTCGTGGAAGAAG +CCAAGAAGAAATTTCAGGCCATTCAACAAGCCTATTCTGTTCTGTCTGACTCAAACAAGAGGTTTCTGTACGACGTAGGA +GCTTATGACAGTGATGATGACGAAAATGGAATGGGAGATTTTTTGAACGAAATGGCAGGGATGATGAGCCAGACAAAATC +TAATGAAAATGGAGGGGAAAGCTTCGAGGAACTACAGGAATTGTTTGAAGAAATGTTCCAAGCGGACATTGATTCATTTG +AGTCTACTGGTCAGTCCACTCCTTCCTGCTCTGCTTCATCTTCGTTTGGGTCATATGGTGAAAGTTCCAGCTCCAACAAG +CGGAATTCCTCTGAAATGAGTTCTGTGGAGACTAGGCTGGAGAGTTCTTCTAGCTTCGATGCACAATTTCACAGTTTTTG +TCTCGGGGTGGAACACAGGCAAGATATCAAGCAACACAGAGGAGCCAGAGGAGGAATGCGAGGAGCAGCCGGCGGTAGTA +GACGGAGAAATGGCAGGAAACAAAAGGTTTCATCTGGCCATGATGTTACTTCCAACGACTGTGGCATTTCTGCTTCA +>gnl_Vitvi12X_PACid_17827068 +ATGGCCGCCGGAGAAGAGAAGAGCAATGATTTTTATGCCGTTCTAGGGTTGAAAAAGGAATGCACCGCCTCCGAGCTCAG +AAATGCGTACAAGAGACTTGCCCTGATGTGGCACCCAGATCGTTGCTCCTCGTCGGGAAACTCGAAATTCGTGGAAGAAG +CGAAGAAGAAATTTCAGGCCATACAAGAAGCCTATTCAGTTCTCTCTGATGCGAATAAAAGGTTTCTGTACGACGTTGGA +GCCTACGACAGCGATGATGACGAAAACGGAATGGGGGATTTTTTGAATGAGATGGCGGTTATGATGAGCCAAACCAAGTC +CAATGAAAATGGGAAGGAGAGCTTTGAGGAGTTGCAGGAGCTCTTTGAGGATATGTTCCAAAGGGATGTCGACGCATTCA +ACTCTGCCTCTCATCACCCCATGAACTCTTTCCCCAGTTCTACTTCCACTTCTTCCTACTGCGAAAGCTCCAATGCCAAC +AACAAGCGGAATTCGGCTGAAATGGGCTCTGGAAGGATGATGAGTGCAGGGGAGTCCTCTGCTTTTGATGCCCACTTTCA +GAGCTTCTGCTTTGGGACAGGCGGCACGCCAGGGAGATTTCAGGAGGGGGAAAGGAGCAAGAGGAGGAATTCCAGGAGGA +GCCAACGG +>gnl_Selmo1.0_PACid_15401289 +ATGGAGAAGAGGAAAGAGGATCCCTACACTGTTCTTGGTGTCCAAAAGTCGAGTTCTAGCTCGGAAATTCGCTCCGCTTA +TCGGAAGCTCGCCATGAAATGGCATCCAGATAAGCAACACTCTTTAGAGGATCAAGCAAAAGCGAAGTTCCAGGGCATTC +AAGAAGCTTATTCAGTGCTATCCGACGACAAAAAAAGAGTTCTTTATGATTCGGGACTTTATGACGAGGGAGATGACGAG +GTGAGT +>gnl_Orysa6.0_PACid_16864430 +ATGGCCCGCGGCGGCGGCGGCGGCGGCGGCGCGGACGCCGACCTGTACGCCGTCCTCGGCCTCAGCAGGGAGTGCACCGA +CGCCGACCTCAGGCTCGCCTACCGCAAGCTCGCCATGATATGGCATCCGGACAGGTGCTCGGTGGCCGGCGGCAGCGCGA +GCGCGGCGGGCGTCGACGAGGCCAAGGAGCGATTCCAGGAGATCCAGGGCGCCTACTCCGTGCTCTCCGACTCCAACAAG +CGCTTCCTCTACGACGTCGGCGTCTACGACGGCAACGACGGCGACGACGACGACGACGAAGCAGATCTGTCGGGGATGGG +CGATTTCCTCGGCGAGATGGCGCAGATGATGAGCCAGGCGACGCCTGCGGAGAGCTTCGAGGAGTTGCAGCAGCTGTTCG +TGGACATGTTCCAGGACGACATCGACGCCGGCCTCTGCCAGTCGACGCCGCCGCCGCCGTCATGGCCGTCGCCTCCGGCG +GCCGCCAATGCACGATCGCCGGCGGCGGCGGCGACTTCACGCAAGGGCGTGAACAAGCGGTGCTCACCGGCGGCGATGGA +CATGGACTCCGGTTTGAGCAGCCTGCTGGGCATTTCGGGCTTCTGTTTCGAGGCGCCATGGACGTCGCAGGACGCGAGCA +CTGCCGCCGGCGGTGGCGGCGGCAAGAGGAGAAAGCAGAGGCCGCCGCCGGCGAGCCACAACGTG +>gnl_Sorbi1.4_PACid_1982925 +ATGGCTGCTACAAGTCACTGCGGCAACATCCAGGACCAGGACGAAGAAGCTTCGGCTCCTGGCGCCGCCGACCTCTACGC +CGTGCTCGGGCTCAACAGGGAGTGCACCGACGCCGAGCTCAGGGTCGCGTACCGGCGGCTCGCCATGATATGGCATCCGG +ACAGGTGCTCGGCGTCCGGCAGCTCGCCGGCGCGCATGGAGGAGGCCAAGGAGCGGTTCCAGGAGATCCAGGGCGCCTAC +TCCGTGCTCTCCGACTCCAACAAGCGGCTCCTCTACGACGTCGGCGTCTACGACAGCGACGACGACGAGGCTGACCTGTC +GGGGATGGGCGACTTCCTCGGAGAGATGGCCGACATGATGAGCCAGGCCACGCCAACGGAGACCTTCGAGGAGCTGCAGC +AGGTGTTCGTGGACATGTTCCAGGACGACCTGGACGACGCCGGCTTCTTCGGCGGGCTTCCGACGACGGGCCGCAGGGCC +CAGGCACCCAGCACCTCGCTGCCGCCGTCGGTGTCGTCGTCGCCGTTGCGGCCGACGCCTGCCGCTGGAAGAAGCAAGGG +TCCGCAAGCGACGCCGTCGTCGTCGTTTAAAGGCGTCGAGAGGCGGGGTTCGACGTCGACGGCGAAACGGCCGAGGCCCA +ACGGGTCGGCGGGCCTGGAATCGGACCTGGGCCTCTCCGGATTCTGCTTCATGGTGAGTAAGGAGATGAGCAAGTCGAAG +GAGAGGCAAGCGGTATGGGCCAGTGACGACGGTGACAGGAGCACCGATGGCAAGCAGAGGTTGTCGACGAGCCGCGATGT +CTCCGGTGGTGGGATGTCACGCTCACTGCAGGGCCAAAGCAGCAAAAACTTGTTGCAGTGTATGGCCTCTAAGTCT +>gnl_Medtr3.5_Medtr8g022310.3 +ATGGCTAACGAAGGAAACAAAAGCAATGATTTCTATGCAGTTTTGGGATTGAATAAGGAATGCTCTGATTCAGAGCTAAG +GAATGCTTATAAGAAACTTGCACTGAAATGGCATCCAGATCGTTGTTCAGCTTCAGGGAATGTGAAGTTTGTGGAAGAAG +CTAAGAAGAAATTTCAGGCAATTCAAGAAGCCTATTCTGTTTTATCTGACTCGAACAAGAGATTAATGTACGACGTTGGA +GTTTACGACAGTGATGATGACGAAAATGTAAGGCACTTGTTTCACACCATTCATGAGTTGGGGACCCTCTTTTGCGTTAT +GTTTTGTTTCTTCATTTCCTTGAGGGGAGAGAAGAGAAGCAACCTTAATTTAACCTTTTCACTTTCACAT +>gnl_Nelnu1.0_NNU_000115-RA +ATGGAGGTGGACTCCCATCGATCATCTCCATCTTACTACACCATCCTTGGTGTAGATCAGAATTCCTCCGCTTCCGAGAT +ACGCAATGCTTACAGGAAGCTCGCGATGCAATGGCATCCAGACAAATGGACGAAAACTCCGTCGCTCTTAGAGAAAGCCA +AGAGTAAATTCCAGCAAATCCAGGAGGCTTATTCGGGTGGGTTACTCGTTTTCATGTTATCGGATCAGGGGAAGAGAACA +CTGTATGATGTCGGTCTGTATGACCCGGACGATGAAACGAATGACGAGGTGGGGCTTCGCAGATTTCATGCAGGAGATGA +TATCTCTCATGAACGATGTGAAGAAACAGGAGAAGAAATACAGCTTGGAGGAACTACAGGAGATGTTAGTGGAAATGTCA +CAAGGGCTGGAGTTGAAGATGGAGAGTGCTGGTGGTGTGTGGTTGTTAGATGGAGCTGCAGCCTCAAGGAGGAGCTCAAA +GAGGGCCAGATGGGAATCATCAGCGAGTCCGACGACGCTGGACACGACACACCTTCTCTCCCCCACTTGCACGGTTCAGA +GCTGGAATTGTTAGGAAGAACCGGCTGTTGCAAT +>contig_7 +GAGAATGAGTGGTCTGGGGCTGAGTTTTTGAATGAAATGGCGGCAATGATGACTCAAAATAAATCCAATGAAAACGGAAC +CGGAACTTTTGAAGAACTGCAACAATTGTTCGATGAAATGTTTCAGAGCGACATCGAGTCCTTCAATGGTTGTTCTTCAT +CATCCAATGAAACATGTAGCAACTCGAACAAGAGGAATTCCATTGAGTCGAGCTCGGCTAATTTCAGACCCGAAAATGGA +AACGAAAGCGGCGAGATTAGCGGGAAGAAGAATACTAGGAAAGGTAAAGGTGACGNN
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/38889.faa Mon Oct 30 09:53:09 2017 -0400 @@ -0,0 +1,4 @@ +>contig_2 +XLSKVPIPSNNIYAINDKKSPEDAADDYENRLKELVSEKIIPVSTISGFPKFDLMLLGMGPDGHVASLFPSHMQRYEKEK +WVTFITDSPKPPPSRITFTFPMINSASEIAMVVTGADLAGTTKIALGTTGNVKPGETPLPCTEVSAEGEVTWFLDKDAAS +QLLNYVRFDD
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/38889.fna Mon Oct 30 09:53:09 2017 -0400 @@ -0,0 +1,8 @@ +>contig_2 +NNCCTTTCCAAGGTACCCATCCCATCCAACAACATATATGCTATAAATGATAAGAAGTCCCCGGAAGATGCAGCAGACGA +CTACGAAAACCGCCTCAAGGAACTCGTCTCCGAAAAAATCATACCCGTTTCAACCATTAGCGGGTTCCCGAAGTTCGACC +TCATGTTGCTTGGAATGGGGCCCGACGGCCATGTGGCCTCTCTTTTCCCTTCTCACATGCAACGCTATGAGAAGGAGAAA +TGGGTCACTTTCATAACTGACTCTCCCAAACCGCCTCCGTCGAGAATCACTTTTACGTTTCCGATGATCAACTCGGCTTC +GGAGATCGCTATGGTGGTTACCGGGGCTGATTTGGCTGGTACAACTAAGATAGCATTGGGTACTACGGGCAATGTTAAGC +CGGGTGAGACTCCTTTGCCTTGTACTGAAGTTTCGGCTGAGGGAGAGGTTACTTGGTTCTTGGACAAAGATGCTGCTTCA +CAACTGTTAAATTATGTGCGCTTTGATGAT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/38889_integrated.faa Mon Oct 30 09:53:09 2017 -0400 @@ -0,0 +1,14 @@ +>gnl_Mimgu1.0_PACid_17675619 +MAETKTKVLKFDAEEDVAVALAKYTAYLSEKYIKEKNSFSVVLSGGTLIDTLRKLVEFPYKDSVDWSKWLIFWVDERVVP +LDHEDSNYLLAYRGFLSKVPIPPSNIYAINDKKSPEGAADDYEERIKNLVEEKTLPISDSGFPKFDLMLLGMGPDGHVAS +LFPSHNQRYEKKRWVTFITDSPKPPPPRITFTFPVINSASDIAMVVTGAELADTTKKALGNEKHTLPPLPCTEVSAEREL +TWFLDKDAASKL +>gnl_Solly2.3_Solyc06g053200.2.1 +MATQKGKKTVLKFDSEEDVSKALAKYTAELSEKFIKQKGSFTVVLSGGSLIDTMRKLVEPPYKDSIDWSKWWIFWVDERV +VPLGHDDSNYKLASDGFLSKVPIPSSNIYAINDKESPEGAAADYEARLKQLIESKVLPLSAITGFPKFDLMLLGMGPDGH +VASLFPLHPHRHEKERLVTFITDSPKPPPPRITFTFPVINSASEIAMVVTGAELAHMVDVALGNAPPPDGIPPPCTEVSA +EEELTWFLDKDAASELQTSR +>contig_2 +XLSKVPIPSNNIYAINDKKSPEDAADDYENRLKELVSEKIIPVSTISGFPKFDLMLLGMGPDGHVASLFPSHMQRYEKEK +WVTFITDSPKPPPSRITFTFPMINSASEIAMVVTGADLAGTTKIALGTTGNVKPGETPLPCTEVSAEGEVTWFLDKDAAS +QLLNYVRFDD
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/38889_integrated.fna Mon Oct 30 09:53:09 2017 -0400 @@ -0,0 +1,30 @@ +>gnl_Mimgu1.0_PACid_17675619 +ATGGCCGAAACCAAAACAAAAGTACTGAAATTCGACGCGGAGGAAGATGTGGCCGTCGCTCTAGCAAAGTACACCGCCTA +TCTCTCCGAAAAGTACATCAAGGAAAAGAATTCTTTCTCGGTGGTTCTCTCCGGCGGCACCCTAATAGATACACTCAGGA +AACTAGTAGAGTTTCCATACAAGGATTCTGTGGATTGGTCGAAATGGCTGATATTTTGGGTTGACGAGAGAGTGGTTCCT +CTTGATCATGAAGACAGCAACTACTTACTTGCATACCGTGGTTTTCTTTCAAAGGTACCTATTCCTCCAAGCAACATTTA +CGCAATCAACGACAAGAAGTCTCCGGAAGGTGCAGCCGATGATTACGAGGAGCGTATCAAGAATCTGGTCGAGGAAAAAA +CCCTACCTATTTCAGACAGTGGCTTCCCTAAATTCGACCTTATGCTTCTCGGAATGGGGCCCGATGGCCACGTGGCGTCT +CTTTTCCCCTCTCACAATCAACGGTACGAAAAGAAACGGTGGGTGACATTCATAACTGACTCTCCCAAACCGCCGCCACC +TAGGATCACTTTCACATTCCCAGTCATCAACTCTGCTTCGGACATTGCAATGGTGGTCACTGGTGCTGAGCTGGCGGATA +CTACGAAGAAAGCATTGGGAAACGAGAAGCATACTCTTCCTCCTCTTCCTTGTACTGAAGTTTCGGCTGAGAGAGAGCTC +ACTTGGTTCTTGGACAAAGATGCTGCTTCTAAACTG +>gnl_Solly2.3_Solyc06g053200.2.1 +ATGGCAACCCAGAAAGGGAAGAAGACGGTGCTAAAATTCGACTCCGAAGAAGATGTATCAAAGGCACTTGCTAAATACAC +TGCTGAGCTATCGGAAAAATTCATCAAACAAAAAGGTTCTTTCACTGTTGTGCTCTCTGGTGGTTCTCTTATCGATACCA +TGAGGAAATTGGTAGAGCCGCCGTACAAAGACTCAATTGATTGGTCGAAATGGTGGATTTTTTGGGTAGACGAAAGAGTG +GTTCCTCTAGGTCACGATGATAGCAATTATAAACTTGCTTCGGATGGGTTTCTTTCTAAGGTTCCGATCCCCTCTTCTAA +CATTTATGCGATTAATGACAAGGAGTCACCTGAGGGTGCAGCTGCTGATTACGAAGCTCGTCTGAAACAATTGATTGAGA +GCAAAGTTCTTCCGTTATCAGCAATTACTGGATTCCCCAAATTTGATCTTATGCTATTAGGTATGGGGCCAGATGGACAT +GTAGCGTCTTTGTTTCCTTTGCATCCTCACCGCCACGAGAAGGAGCGGCTGGTCACCTTCATTACAGACTCACCAAAACC +TCCTCCACCAAGGATTACTTTCACCTTTCCGGTAATTAATTCGGCTTCAGAGATAGCAATGGTGGTCACAGGAGCAGAGT +TAGCTCATATGGTTGATGTCGCTTTGGGTAATGCGCCTCCTCCTGATGGAATTCCTCCCCCTTGTACTGAGGTTTCAGCT +GAAGAGGAACTGACCTGGTTTTTAGACAAGGATGCTGCATCAGAACTACAGACCTCTAGA +>contig_2 +NNCCTTTCCAAGGTACCCATCCCATCCAACAACATATATGCTATAAATGATAAGAAGTCCCCGGAAGATGCAGCAGACGA +CTACGAAAACCGCCTCAAGGAACTCGTCTCCGAAAAAATCATACCCGTTTCAACCATTAGCGGGTTCCCGAAGTTCGACC +TCATGTTGCTTGGAATGGGGCCCGACGGCCATGTGGCCTCTCTTTTCCCTTCTCACATGCAACGCTATGAGAAGGAGAAA +TGGGTCACTTTCATAACTGACTCTCCCAAACCGCCTCCGTCGAGAATCACTTTTACGTTTCCGATGATCAACTCGGCTTC +GGAGATCGCTATGGTGGTTACCGGGGCTGATTTGGCTGGTACAACTAAGATAGCATTGGGTACTACGGGCAATGTTAAGC +CGGGTGAGACTCCTTTGCCTTGTACTGAAGTTTCGGCTGAGGGAGAGGTTACTTGGTTCTTGGACAAAGATGCTGCTTCA +CAACTGTTAAATTATGTGCGCTTTGATGAT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/39614.faa Mon Oct 30 09:53:09 2017 -0400 @@ -0,0 +1,3 @@ +>contig_3 +XVDEGVVVAGLSEQEKASVSEILTTARAHSETIENLKRDHSQQVSCIEQHTNDTFRQKYMDYEPTGSTPVRSEPDIPSKG +TIESLRAMPIDALEEEFRENHSYESAVTGKELMPSVTTRAPFSQIN
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/39614.fna Mon Oct 30 09:53:09 2017 -0400 @@ -0,0 +1,6 @@ +>contig_3 +NNTGTGGATGAAGGAGTTGTTGTTGCTGGCTTGTCAGAGCAGGAGAAGGCATCTGTTTCTGAAATTCTGACAACTGCTAG +AGCTCATTCAGAAACAATTGAGAACCTTAAGAGAGATCATTCCCAGCAGGTATCCTGTATCGAACAGCACACGAATGATA +CTTTCAGGCAAAAATACATGGATTACGAGCCTACAGGGTCCACGCCAGTTAGGAGCGAGCCGGATATTCCCAGCAAAGGC +ACAATAGAGTCACTTCGTGCCATGCCTATAGATGCACTTGAAGAAGAATTTCGAGAAAACCATTCATACGAATCTGCTGT +TACAGGAAAGGAACTAATGCCGTCTGTTACGACTCGTGCACCATTTTCACAGATCAAC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/39614_integrated.faa Mon Oct 30 09:53:09 2017 -0400 @@ -0,0 +1,19 @@ +>gnl_Orysa6.0_PACid_16878968 +MSHMEAFQNVVLLHKANSNSTLEDISSLSAASCCSLDQLLACVEGEAQKIFGDIQNLLADHRSEVAHFTQELRESFRISL +DRTKDMSSFILGLFDKYVEETSKLQSHSNHTHEAQVKSLEDFQKAYEEQSKSEEQKLLADITSLVSKHVTRQRELVGGRL +NSLGDAARGNKAFLDEHTSAMEVVTKDAKRKWEMFAEQAENDCKVGSNFSAAKHCRMETILQECACTVDTAAQQWKASHA +TVNDLCRKQIAEVEALVRSAIETNEQHEAEIASSRATAEEHASNSSKDLLQDVDNMLQEARNSSSRVVSTVEAHLGESQH +LQESHSSHTAGINTHADNAFQSSYKDYEPTGETPVRSEPEVPSKDAIESLRAMPMESLMDEFRENHPYEPSKDRRPSLIP +RSPLATINN +>gnl_Phoda3.0_PDK_30s1023721g001 +VNQKMMKCTLIKDLYGEIERLKAEVYAAREKVGVYIPKERYHQEESERKAMAEQIEQMGVLLENNQKQIEDLQERYNTQL +QQSDDLSKKLDATEILCVSLSKKLDATEKSLEHTSKLLAAAREDLKQAQYTLKEKDFVISEQRKAAREDKLNTANRSIVN +NFRADLATRVGTLCNTVVASLDRQNEHLQSVEKLCQSSLDFHDKAVSELKRKVSASRALYTSHMEALQNVVRLHKASSNA +SLEEMSSMISANTCSLDQLLALGQSEADLIFSDLQSILSIHRGEIANFTRELREKFQVNLDRTKEMSNFILELLEKIGKG +TKEFQNDSTLVHEAQVKSIGDFQKAYEVEVRLTGLGDAARDSKAIMDNHASSMDIVTTDAKRKWEEYSKQAEQDSEDGSN +FSAAKHCRMELMLQQCVNSVDATSQQWKKTHASVSEMSSKHVAEIEALVRSAIESNDQHDAEVASARMAAEEDVAKNSKD +VLQHFDTVIDHERNSAAGVMAAVEAHSATLHKLQEEQSSQATEINSHAEDTFQNTYMDYEPTGETPTRSEPDIPSRGTIE +SLRAMPIEALLEEFRENHPYESKEPKPSLIPRSPLVQLN +>contig_3 +XVDEGVVVAGLSEQEKASVSEILTTARAHSETIENLKRDHSQQVSCIEQHTNDTFRQKYMDYEPTGSTPVRSEPDIPSKG +TIESLRAMPIDALEEEFRENHSYESAVTGKELMPSVTTRAPFSQIN
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/39614_integrated.fna Mon Oct 30 09:53:09 2017 -0400 @@ -0,0 +1,47 @@ +>gnl_Orysa6.0_PACid_16878968 +ATGTCACATATGGAAGCCTTCCAAAATGTTGTGCTCCTGCATAAAGCAAATTCAAATTCTACACTAGAGGATATATCATC +CCTATCTGCTGCAAGCTGTTGCAGCCTTGATCAGCTTCTAGCTTGTGTCGAGGGAGAGGCACAGAAGATATTTGGTGATA +TCCAGAATTTGCTAGCTGATCATCGAAGCGAAGTGGCACATTTCACTCAAGAGTTGCGGGAGAGTTTCCGCATTAGCTTG +GATAGGACGAAGGACATGTCTAGTTTCATCCTTGGGTTGTTCGATAAGTATGTGGAGGAAACTTCGAAGTTGCAGAGCCA +CTCCAATCACACACATGAAGCACAAGTCAAAAGCCTTGAAGATTTCCAGAAGGCTTATGAGGAGCAATCAAAATCAGAAG +AACAAAAGCTTCTGGCGGACATCACCAGTTTGGTTTCTAAACACGTTACTCGACAACGAGAACTGGTGGGTGGTAGACTA +AACTCTCTTGGTGACGCCGCTCGTGGAAACAAAGCATTTTTGGATGAGCACACGTCCGCCATGGAGGTGGTCACGAAGGA +CGCCAAGAGAAAGTGGGAAATGTTTGCAGAGCAGGCAGAGAATGACTGCAAAGTTGGGTCCAACTTCTCTGCAGCTAAGC +ATTGTCGCATGGAAACCATTCTGCAGGAATGTGCATGCACCGTCGACACTGCTGCTCAACAATGGAAAGCATCACATGCA +ACTGTTAACGATCTATGCAGAAAACAAATAGCTGAAGTTGAAGCACTCGTCAGGAGTGCAATCGAAACCAACGAGCAGCA +CGAAGCAGAGATTGCATCTTCCCGTGCCACGGCCGAGGAGCATGCGTCCAACAGCAGCAAGGACCTACTCCAAGATGTTG +ACAATATGCTGCAGGAGGCGCGCAATTCGTCGTCGAGAGTGGTGTCGACGGTGGAAGCTCATTTGGGAGAGAGCCAGCAT +CTACAGGAGAGCCACTCCAGCCATACCGCCGGCATCAACACCCACGCCGACAACGCTTTCCAGAGCAGCTACAAGGACTA +CGAGCCGACCGGCGAAACTCCGGTGAGGTCGGAGCCGGAGGTGCCGAGCAAAGACGCGATCGAGTCGCTGCGAGCGATGC +CGATGGAGTCCCTGATGGACGAGTTCCGCGAGAACCACCCCTACGAGCCGAGCAAGGACCGCAGGCCATCGCTCATCCCT +CGCTCGCCGCTCGCCACCATCAACAAC +>gnl_Phoda3.0_PDK_30s1023721g001 +GTAAACCAAAAAATGATGAAATGTACATTAATCAAAGATCTCTATGGAGAAATTGAGCGTCTAAAAGCAGAGGTGTATGC +TGCTCGTGAGAAAGTTGGAGTTTACATACCAAAAGAACGCTACCATCAAGAAGAGAGCGAACGGAAGGCAATGGCAGAAC +AAATTGAACAAATGGGGGTCTTGCTCGAAAACAATCAAAAGCAAATTGAGGATCTACAAGAAAGGTATAATACTCAACTT +CAACAGTCTGATGACCTGAGCAAAAAGCTTGATGCCACCGAGATTCTCTGTGTTTCTCTGAGCAAAAAGCTTGATGCCAC +CGAGAAAAGTTTGGAGCACACTAGCAAGTTATTGGCTGCTGCCAGAGAAGATCTGAAGCAAGCTCAGTATACTCTGAAGG +AGAAAGATTTTGTTATATCAGAGCAGAGGAAAGCAGCTAGAGAAGACAAACTGAATACTGCCAACAGATCTATTGTGAAC +AATTTTCGGGCTGATCTTGCAACAAGGGTTGGAACACTTTGTAATACTGTTGTTGCATCCTTGGATCGGCAAAATGAACA +CCTTCAGTCTGTTGAGAAACTATGTCAATCTAGCCTTGATTTCCATGACAAGGCAGTATCAGAGCTGAAAAGGAAAGTGT +CAGCTTCAAGAGCTTTGTATACTTCCCATATGGAAGCACTACAAAATGTAGTGCGTTTGCATAAGGCAAGCAGCAATGCC +AGCTTAGAAGAGATGTCATCCATGATTTCTGCCAATACCTGCTCTCTTGATCAGTTACTTGCCTTGGGGCAAAGCGAAGC +AGATCTGATTTTTAGTGATCTGCAAAGCATATTGTCAATTCACCGAGGAGAGATTGCAAATTTCACCCGTGAACTTCGTG +AGAAATTTCAAGTTAATTTGGATCGGACAAAGGAGATGTCCAATTTTATTCTTGAGCTGCTTGAAAAGATAGGGAAGGGA +ACAAAAGAATTTCAGAATGACTCAACTTTGGTACATGAGGCTCAGGTGAAGAGCATTGGTGATTTCCAAAAGGCATATGA +GGTGGAAGTGAGGCTCACTGGACTGGGAGATGCTGCTCGAGATAGCAAAGCAATTATGGATAACCATGCATCATCAATGG +ACATCGTCACAACTGATGCTAAGAGGAAGTGGGAAGAATATTCCAAGCAGGCAGAGCAAGATTCAGAGGACGGTTCTAAC +TTTTCAGCAGCAAAACATTGTCGCATGGAACTCATGCTCCAACAGTGTGTAAACTCTGTTGATGCTACTTCTCAACAGTG +GAAGAAGACACATGCATCTGTTAGTGAGATGAGCAGCAAACACGTTGCTGAAATTGAAGCACTTGTAAGGAGTGCCATTG +AGAGCAATGATCAGCATGATGCTGAGGTTGCTTCAGCAAGAATGGCAGCAGAAGAGGATGTAGCGAAAAATAGCAAAGAT +GTTCTTCAGCATTTTGATACTGTGATTGATCATGAGCGCAACTCAGCCGCTGGAGTGATGGCAGCAGTCGAAGCTCACTC +AGCAACCCTGCATAAACTGCAAGAGGAACAATCAAGCCAGGCAACAGAGATTAATAGCCATGCGGAGGACACATTCCAAA +ACACCTACATGGACTATGAACCAACGGGAGAAACCCCAACAAGGTCGGAACCAGATATACCAAGCAGGGGAACAATCGAA +TCTCTTCGAGCCATGCCGATAGAAGCCCTCCTTGAAGAGTTCCGGGAGAACCATCCATACGAGTCCAAGGAGCCCAAACC +GTCTCTCATACCACGCTCTCCACTCGTCCAGCTCAAC +>contig_3 +NNTGTGGATGAAGGAGTTGTTGTTGCTGGCTTGTCAGAGCAGGAGAAGGCATCTGTTTCTGAAATTCTGACAACTGCTAG +AGCTCATTCAGAAACAATTGAGAACCTTAAGAGAGATCATTCCCAGCAGGTATCCTGTATCGAACAGCACACGAATGATA +CTTTCAGGCAAAAATACATGGATTACGAGCCTACAGGGTCCACGCCAGTTAGGAGCGAGCCGGATATTCCCAGCAAAGGC +ACAATAGAGTCACTTCGTGCCATGCCTATAGATGCACTTGAAGAAGAATTTCGAGAAAACCATTCATACGAATCTGCTGT +TACAGGAAAGGAACTAATGCCGTCTGTTACGACTCGTGCACCATTTTCACAGATCAAC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tool-data/plant_tribes/scaffolds/README.txt Mon Oct 30 09:53:09 2017 -0400 @@ -0,0 +1,3 @@ +For functional tests to work, this directory must contain symlinks to the scaffolds data +installed into the Galaxy instance to which planemo points via the --galaxy_root parameter. +This would typically be something like ~/galaxy/tool-data/plant_tribes/scaffolds/22Gv1.1.
--- a/utils.py Thu Aug 24 13:32:01 2017 -0400 +++ b/utils.py Mon Oct 30 09:53:09 2017 -0400 @@ -27,7 +27,7 @@ return fstderr, fherr, fstdout, fhout -def move_directory_files(source_dir, destination_dir, copy=False): +def move_directory_files(source_dir, destination_dir, copy=False, remove_source_dir=False): source_directory = os.path.abspath(source_dir) destination_directory = os.path.abspath(destination_dir) if not os.path.isdir(destination_directory): @@ -38,6 +38,8 @@ shutil.copy(source_entry, destination_directory) else: shutil.move(source_entry, destination_directory) + if remove_source_dir: + os.rmdir(source_directory) def run_command(cmd): @@ -52,29 +54,3 @@ def stop_err(msg): sys.exit(msg) - - -def write_html_output(output, title, dir): - with open(output, 'w') as fh: - dir_items = sorted(os.listdir(dir)) - # Directories can only contain either files or directories, - # but not both. - if len(dir_items) > 0: - item_path = os.path.join(dir, dir_items[0]) - if os.path.isdir(item_path): - header = 'Directories' - else: - header = 'Datasets' - else: - header = '' - fh.write('<html><head><h3>%s: %d items</h3></head>\n' % (title, len(dir_items))) - fh.write('<body><p/><table cellpadding="2">\n') - fh.write('<tr><b>%s</th></b>\n' % header) - for index, fname in enumerate(dir_items): - if index % 2 == 0: - bgcolor = '#D8D8D8' - else: - bgcolor = '#FFFFFF' - link = '<a href="%s" type="text/plain">%s</a>\n' % (fname, fname) - fh.write('<tr bgcolor="%s"><td>%s</td></tr>\n' % (bgcolor, link)) - fh.write('</table></body></html>\n')