| Previous changeset 2:a322e5e668a3 (2017-08-24) Next changeset 4:8ef8997aaa0c (2017-12-21) |
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Commit message:
Uploaded |
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modified:
.shed.yml gene_family_integrator.xml macros.xml utils.py |
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added:
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 |
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removed:
gene_family_integrator.py |
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| diff -r a322e5e668a3 -r 276f0f31ddb0 .shed.yml --- a/.shed.yml Thu Aug 24 13:32:01 2017 -0400 +++ b/.shed.yml Mon Oct 30 09:53:09 2017 -0400 |
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| @@ -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 |
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| diff -r a322e5e668a3 -r 276f0f31ddb0 gene_family_integrator.py --- a/gene_family_integrator.py Thu Aug 24 13:32:01 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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) |
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| diff -r a322e5e668a3 -r 276f0f31ddb0 gene_family_integrator.xml --- 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 |
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| @@ -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" /> |
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| diff -r a322e5e668a3 -r 276f0f31ddb0 macros.xml --- a/macros.xml Thu Aug 24 13:32:01 2017 -0400 +++ b/macros.xml Mon Oct 30 09:53:09 2017 -0400 |
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| @@ -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, |
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| diff -r a322e5e668a3 -r 276f0f31ddb0 test-data/3722.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3722.faa Mon Oct 30 09:53:09 2017 -0400 |
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| @@ -0,0 +1,3 @@ +>contig_7 +ENEWSGAEFLNEMAAMMTQNKSNENGTGTFEELQQLFDEMFQSDIESFNGCSSSSNETCSNSNKRNSIESSSANFRPENG +NESGEISGKKNTRKGKGDX |
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| diff -r a322e5e668a3 -r 276f0f31ddb0 test-data/3722.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3722.fna Mon Oct 30 09:53:09 2017 -0400 |
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| @@ -0,0 +1,5 @@ +>contig_7 +GAGAATGAGTGGTCTGGGGCTGAGTTTTTGAATGAAATGGCGGCAATGATGACTCAAAATAAATCCAATGAAAACGGAAC +CGGAACTTTTGAAGAACTGCAACAATTGTTCGATGAAATGTTTCAGAGCGACATCGAGTCCTTCAATGGTTGTTCTTCAT +CATCCAATGAAACATGTAGCAACTCGAACAAGAGGAATTCCATTGAGTCGAGCTCGGCTAATTTCAGACCCGAAAATGGA +AACGAAAGCGGCGAGATTAGCGGGAAGAAGAATACTAGGAAAGGTAAAGGTGACGNN |
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| diff -r a322e5e668a3 -r 276f0f31ddb0 test-data/3722_integrated.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3722_integrated.faa Mon Oct 30 09:53:09 2017 -0400 |
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| b'@@ -0,0 +1,161 @@\n+>gnl_Glyma1.01_PACid_16266208\n+MANEGKKSNNFYSILGLSKECTELELKNAYRKLAKKWHPDRCSATGNLELVEEAKKKFQEIREAYSVLSDANKRLMYDVG\n+VYDSDDDENGMGDFLDEMLTMMSHTKSNENGEESFEELQQLFEDMFQADIGLDGGPSLASSDSSTSSAYMTYSESSSSNK\n+RNSSEMNFGKAENSSVFDASYQNFCFGVNQLQDIKKGKGGILGGGGRSRHRSGRKQKMFYGHDV\n+>gnl_Glyma1.01_PACid_16266209\n+MANEGKKSNNFYSILGLSKECTELELKNAYRKLAKKWHPDRCSATGNLELVEEAKKKFQEIREAYSVLSDANKRLMYDVG\n+VYDSDDDENGMGDFLDEMLTMMSHTKSNENGEESFEELQQLFEDMFQADIGLDGGPSLASSDSSTSSAYMTYSESSSSNK\n+RNSSEMNFGKAENSSVFDASYQNFCFGTGEPTPRYKEGKGGNSRRRR\n+>gnl_Glyma1.01_PACid_16266210\n+MANEGKKSNNFYSILGLSKECTELELKNAYRKLAKKWHPDRCSATGNLELVEEAKKKFQEIREAYSVLSDANKRLMYDVG\n+VYDSDDDENGMGDFLDEMLTMMSHTKSNENGEESFEELQQLFEDMFQADIGLDGGPSLASSDSSTSSAYMTYSESSSSNK\n+RNSSEMNFGKAENSSVFDASYQNFCFGVGHVNYHYQ\n+>gnl_Glyma1.01_PACid_16301083\n+MADEGNKSNNFYSILGLKKECTELELKNAYRKLAKKWHPDRCSATGNSELVEEAKKKFQEIREAYSVLSDANKRLMYDVG\n+VYDSDDDENGMGDFLDEMLTMMSQTKSNENGEESFEELQQLFEDMFEADIGLDGGPSLASSDCSTSSAYMTYSESSSSNK\n+HNSSEMNFGKAENSSVFDAGYQNFCFGVNQLQDIKKKKGGILGGGRSRHRNGRKQNMSYGHDVSSNDYPGISTK\n+>gnl_Glyma1.01_PACid_16301085\n+MADEGNKSNNFYSILGLKKECTELELKNAYRKLAKKWHPDRCSATGNSELVEEAKKKFQEIREAYSVLSDANKRLMYDVG\n+VYDSDDDENGMGDFLDEMLTMMSQTKSNENGEESFEELQQLFEDMFEADIGLDGGPSLASSDCSTSSAYMTYSESSSSNK\n+HNSSEMNFGKAENSSVFDAGYQNFCFGVGHVNYHYQ\n+>gnl_Glyma1.01_PACid_16301084\n+MADEGNKSNNFYSILGLKKECTELELKNAYRKLAKKWHPDRCSATGNSELVEEAKKKFQEIREAYSVLSDANKRLMYDVG\n+VYDSDDDENGMGDFLDEMLTMMSQTKSNENGEESFEELQQLFEDMFEADIGLDGGPSLASSDCSTSSAYMTYSESSSSNK\n+HNSSEMNFGKAENSSVFDAGYQNFCFGTGEPTPRYKEEKGGNSRRR\n+>gnl_Medtr3.5_Medtr8g022310.1\n+MANEGNKSNDFYAVLGLNKECSDSELRNAYKKLALKWHPDRCSASGNVKFVEEAKKKFQAIQEAYSVLSDSNKRLMYDVG\n+VYDSDDDENGMGDFLNEMVTMMSQTKSNENGEESFEELQQLFDDMFQADIGLNGSTSLNASGCSTSSTFMTFSESSNSNK\n+RNSTQMNFGKAEDSSSFGANYQNFCFGMKHLQEDVEKEKGGILEGGGSKKQRKGRKQKISCGHVSSNDHPGISAN\n+>gnl_Medtr3.5_Medtr8g022310.2\n+MANEGNKSNDFYAVLGLNKECSDSELRNAYKKLALKWHPDRCSASGNVKFVEEAKKKFQAIQEAYSVLSDSNKRLMYDVG\n+VYDSDDDENGMGDFLNEMVTMMSQTKSNENGEESFEELQQLFDDMFQADIGLNGSTSLNASGCSTSSTFMTFSESSNSNK\n+RNSTQMNFGKAEDSSSFGANYQNFCFGVNLVNYHYQ\n+>gnl_Musac1.0_GSMUA_Achr6T31040_001\n+MAAEEDKSGDFYAVLGLRKECSETELRNAYKKLAMRWHPDKCLASGNAQIVGEAKEKFQEIQKAYSVLSDSNKRFLYDVG\n+VYDNDDDNDENGMGDFIGEMLEMMSQTKPNENSQDSFQELQELFVEMFQDDLDAGFGGSIFHDCPWAQPTNGQDCWTSSG\n+LHFANGRSKCGNKRGNSAVNLGKVNLEELEHGTSDFYFGLNDAAQPSQGKGGSNNKRRNGRKQKVSSNHDVSS\n+>gnl_Musac1.0_GSMUA_Achr9T18140_001\n+MAAGEEKIGDFYTVLGLRKECSEAELRIAYKKLAMRWHPDKCSASGNHRRMEEAKEKFQEIQKAYSVLSDSSKRFLYDVG\n+IYDNEDDNDEKGMGDFIGEIAQMMSQTKSGENGHDSFEELQRMFLDMFQDDLDAGFGDSSIHSGPQARPTDGLNCSMPSG\n+LQFADGGNNGSNKRGNSEKAKLDGLENSSTGFCFGLNDAGQSSKGKGSANSKRRNGRKQKVSSKHDVSSSDAEVSF\n+>gnl_Musac1.0_GSMUA_Achr8T23700_001\n+MASDMDASGDFYSVLGLKKECSEAELRNAYKKLALKWHPDKCSASGNEIRMKEAKQQFQEIQKAYSVLSDSNKRFLYDVG\n+AYDKDDDKDEEGMVEFLGEMAQMMRQTKCCGSGQESFEQLQQMFVEMFHDDLDAGFCGHSSATSGAASCGNKRDNSAMDS\n+GKRKPDELDPAAIGFCLGTKDAGQSSKGRGSNSKRRNRRKQKASSKHDNSSHNAKVSA\n+>gnl_Musac1.0_GSMUA_AchrUn_randomT02210_001\n+MEGDEEKSGDFYAVLGLKKEGSMAELKNAYKKLAMKWHPDKCPASGNKIRMDKAKEKFQEIQKAYSVLSDSNKRFLYDVG\n+VYDKDDEEDEEGMGDFIGEIAQMMSQSKPSGSGHESLEELHRQVVEMFLDELDAGDRFSSANQGASSCDGRDDGGGNKRG\n+NWAVDWGKEKLNELGPGTGGFCFGVSRRVHSFDLMIDVVHLIHSDLTLE\n+>gnl_Orysa6.0_PACid_16843526\n+MADGGEKCRDAAGEGGGGGDLYAVLGLKKECSDADLKLAYRKLAMRWHPDKCSSSSSAKHMEEAKEKFQEIQGAYSVLSD\n+SNKRFLYDVGVYDDDDNDDDNLQGMGDFIGEMAQMMSQARPTRQESFKELQQLFVDMFQADLDSGFCNGPSKCYHTQAQS\n+QTRTSSTSPSMSPSPPPPVATEAESPSCNGINKRGSSAMDSGKPPRASEVGSGQSQSGFCFGKSDAKQAAKTRSGNTASR\n+RRNGRKQKVSSKHDVSSEDEMPGSQWHGVA\n+>gnl_Orysa6.0_PACid_16843528\n+MADGGEKCRDAAGEGGGGGDLYAVLGLKKECSDADLKLAYRKLAMRWHPDKCSSSSSAKHMEEAKEKFQEIQGAYSVLSD\n+SNKRFLYDVGVYDDDDNDDDNLQGMGDFIGEMAQMMSQARPTRQESFKELQQLFVDMFQADLDSGFCNGPSKCYHTQAQS\n+QTRTSSTSPSMSPSPPPPVATEAESPSCNGINKRGSSAMDSGKPPRASEVGSGQSQSGFCFGQKSDAKQAAKTRSGNTAS\n+RRRNGRKQKVSSKHDVSSEDEMPGSQWHGVA\n+>gnl_Poptr2.2_PACid_18217800\n+MANGGEDKWKSNDLYQVLGLNKECTDTELRSAYKKLALRWHPDRCSASGNSKFVEEAKKKFQAIQQAYSVLSDTNKRFLY\n+DVGVDDSDDDENGMGDFLNEMAVMMSQTKPSENMEESLEELQELFDEMFQEDLHSFGIDSQAAPSCPPSYVSYSESSNSN\n+NKRVSADMNLGKTKVDDSSSFNSHFEKFCLGTGGTAATFQEGEGGSKRRNSRRSQRQTKARQETKSFFGL\n+>gnl_Poptr2.2_PACid_18234651\n+M'..b'SFSLGVDHQQEFKKGKNNGGRRNRRKNNVPSAGHETSSSNNYGVPTS\n+>gnl_Bradi1.2_Bradi3g60090.1\n+MATGGDKCGGKPAAAGVGGGDLYSVLGVNKECSDADLKVAYRKLAMRWHPDRCSSSSSTKHMEEAKEKFQEIQGAYSVLS\n+DANKRFLYDVGVYEEHEEEDDDTLQGMGDFLGEMAHMMSQTQPARQESFEELQQLFVDMFQSDIESGFCNGPAKDHDPVQ\n+RQTRTFSTPPSPSPSPPPPLATVDEAASCNGINKRGSSAMGSGKPPRAGEVSGGHGQSEFCFGMSDAKQAPKARGGNASR\n+RRNGQKQKLSSKHDVSSGDEMPRPHAAV\n+>gnl_Carpa1.181_PACid_16420351\n+MADGEDKNNSDLYAVLGLNKECTPAELRNAYKKLAMRWHPDRCSASGNSMFVEEAKKKFQAIQEAYSVLSDANKRFLYDV\n+GAYESDDDENGMGDFLNEMAAMMSQTKPNENGNAQESFEELQELFQEMFQGDMGFNTFGSSSQPTTSSCSASSAYATCSE\n+TSNPNNNKRNSSEMNYGKKKVDDSSGFHAHFQTFCLGVEQQQDFKKGKEARGGIRGKPGGSRRQGRKQKVSSRHNVSSND\n+LGISAS\n+>gnl_Frave2.0_gene05408\n+MAGGKWVPPPLSQFHLHIKRFRRRQKVSGSSGNTEPSGYTDCKNISNRRMEEKGNDFYAVMGLKKECSDSELRNAYKKLA\n+LIWHPDRCSASGNSKFVEEAKKKFQDIQQAYSVLSDANKRFLYDVGAYESDDDENGMGDFLNEMAVMMSQTKPNENGGES\n+FEQLQELFEEMFQGDIEGFSSCSQPPTSCSTSSSSYALYCENSTPSNKRNSSAMNYGNATLDSSGFDAHFHNFCVGTGGK\n+PAKDREGDARKRKDSRRSNR\n+>gnl_Mimgu1.0_PACid_17694730\n+MAADEEKSSDFYGVLGLRKECTAAELRVAYKKLAMKWHPDRCSASGNLKYVEEAKNKFQAVQQAYSVLSDANKRFLYDVG\n+IYDSEDDADENGMGDFLNEMVAMMGQSKPNENKNESFQELQDLFEEIFNNDAEEVFKIPPPHFPYQDSCSETRTASNKRN\n+AREMGSVNFSNIEATPFEGFCIGENVIFGGERIQTRPGGGSRRTKPKISTSIDGLIS\n+>gnl_Nelnu1.0_NNU_010544-RA\n+MNLLLQKWHPDRCSSSGNSKFVEDSKKKFQAIQEAYSVLSDENKRFLYDVGVYDCDDDDDDENGMGEFLGEMATMMSQIK\n+PSENGPESLEKLQELFEEMFQRDMDDGFFSPSPQCASFSSSCSSSSSSTTYFSYNNNKHDNKRNCSDISSMDDFYTFGTD\n+SIQFSNFCIGVEGGEDSKVRGGKSRRKSNRRQKVSSSKHDPSCR\n+>gnl_Solly2.3_Solyc03g123560.2.1\n+MEDKSNDYYAVLGLKKECTDTELRNAYKKLALKWHPDRCSASGNLKFVDEAKKQFQAIQEAYSVLSDANKKFLYDVGVYD\n+SGDDDDENGMGDFLNEMAAMMSQNKSNENQGEETFEELQDMFNEMFNSDNGTFSSSSSSSSSWTGTPSMCSTTSSTSSSE\n+TFLTFPNKRSSGEMKSGSSVRGDSCQFQGFCVGAGGTSGKCNERERSWRKNSKSGRKH\n+>gnl_Sorbi1.4_PACid_1968370\n+MDAGGEKFSDAAAAEGGEGGGDLYAVLGLKKECSDADLKVAYRKLAKKWHPDKCSSSSSVKHMEEAKEKFQEIQGAYSVL\n+SDANKRLLYDVGVYDDEDDEDSMQGMGDFIGEMAQMMSQVRPTRQESFEELQQLFVDMFQSDIDSGFCNGSAKDQVQGQA\n+KSRTCSTSPSSSPSPPPPPTIVKEAEVSSCNGFNKRGSSAMDSGKPPRPVEGGAGQAGFCFGVSDTKQTPKPRGPNTSRR\n+RNGRKQKLSSKHDVSSEDETAGS\n+>gnl_Thepa2.0_Tp3g12470\n+MASNNSEKGNDDLYGVLGLKKECTTTELRTAYKKLALRWHPDRCSSMGTPEFVDEAKKKFQAIQEAYSVLSDSNKRFLYD\n+VGAYNSDDEDQNGMGDFLNEMAAMMNQSKPSENNSGDSFEQLQDLFNEMFQGDAAAFSSSSSSSCSASTFTSSCSFVFDT\n+NSQRSPFETSSMGTNDLFGFDHSAHTFSLGVEHQQDFKKGKNSGGRRNRRKNNAQSAAHETASSNNYGVPTS\n+>gnl_Theca1.0_Tc06_g010450\n+MANGEEKNNDFYAVLGLNKECTPTELRTAYKKLALRWHPDRCSASGNSKFVEEAKKKFQAIQQAYSVLSDSNKRFLYDVG\n+AYDSDDDENGMGDFLNEMAGMMSQTKSNENGGESFEELQELFEEMFQADIDSFESTGQSTPSCSASSSFGSYGESSSSNK\n+RNSSEMSSVETRLESSSSFDAQFHSFCLGVEHRQDIKQHRGARGGMRGAAGGSRRRNGRKQKVSSGHDVTSNDCGISAS\n+>gnl_Vitvi12X_PACid_17827068\n+MAAGEEKSNDFYAVLGLKKECTASELRNAYKRLALMWHPDRCSSSGNSKFVEEAKKKFQAIQEAYSVLSDANKRFLYDVG\n+AYDSDDDENGMGDFLNEMAVMMSQTKSNENGKESFEELQELFEDMFQRDVDAFNSASHHPMNSFPSSTSTSSYCESSNAN\n+NKRNSAEMGSGRMMSAGESSAFDAHFQSFCFGTGGTPGRFQEGERSKRRNSRRSQR\n+>gnl_Selmo1.0_PACid_15401289\n+MEKRKEDPYTVLGVQKSSSSSEIRSAYRKLAMKWHPDKQHSLEDQAKAKFQGIQEAYSVLSDDKKRVLYDSGLYDEGDDE\n+VS\n+>gnl_Orysa6.0_PACid_16864430\n+MARGGGGGGGADADLYAVLGLSRECTDADLRLAYRKLAMIWHPDRCSVAGGSASAAGVDEAKERFQEIQGAYSVLSDSNK\n+RFLYDVGVYDGNDGDDDDDEADLSGMGDFLGEMAQMMSQATPAESFEELQQLFVDMFQDDIDAGLCQSTPPPPSWPSPPA\n+AANARSPAAAATSRKGVNKRCSPAAMDMDSGLSSLLGISGFCFEAPWTSQDASTAAGGGGGKRRKQRPPPASHNV\n+>gnl_Sorbi1.4_PACid_1982925\n+MAATSHCGNIQDQDEEASAPGAADLYAVLGLNRECTDAELRVAYRRLAMIWHPDRCSASGSSPARMEEAKERFQEIQGAY\n+SVLSDSNKRLLYDVGVYDSDDDEADLSGMGDFLGEMADMMSQATPTETFEELQQVFVDMFQDDLDDAGFFGGLPTTGRRA\n+QAPSTSLPPSVSSSPLRPTPAAGRSKGPQATPSSSFKGVERRGSTSTAKRPRPNGSAGLESDLGLSGFCFMVSKEMSKSK\n+ERQAVWASDDGDRSTDGKQRLSTSRDVSGGGMSRSLQGQSSKNLLQCMASKS\n+>gnl_Medtr3.5_Medtr8g022310.3\n+MANEGNKSNDFYAVLGLNKECSDSELRNAYKKLALKWHPDRCSASGNVKFVEEAKKKFQAIQEAYSVLSDSNKRLMYDVG\n+VYDSDDDENVRHLFHTIHELGTLFCVMFCFFISLRGEKRSNLNLTFSLSH\n+>gnl_Nelnu1.0_NNU_000115-RA\n+MEVDSHRSSPSYYTILGVDQNSSASEIRNAYRKLAMQWHPDKWTKTPSLLEKAKSKFQQIQEAYSGGLLVFMLSDQGKRT\n+LYDVGLYDPDDETNDEVGLRRFHAGDDISHERCEETGEEIQLGGTTGDVSGNVTRAGVEDGECWWCVVVRWSCSLKEELK\n+EGQMGIISESDDAGHDTPSLPHLHGSELELLGRTGCCN\n+>contig_7\n+ENEWSGAEFLNEMAAMMTQNKSNENGTGTFEELQQLFDEMFQSDIESFNGCSSSSNETCSNSNKRNSIESSSANFRPENG\n+NESGEISGKKNTRKGKGDX\n' |
| b |
| diff -r a322e5e668a3 -r 276f0f31ddb0 test-data/3722_integrated.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3722_integrated.fna Mon Oct 30 09:53:09 2017 -0400 |
| b |
| b'@@ -0,0 +1,378 @@\n+>gnl_Glyma1.01_PACid_16266208\n+ATGGCTAATGAAGGAAAGAAAAGCAATAACTTCTATTCGATCTTGGGCTTGAGCAAGGAGTGCACTGAATTGGAGCTAAA\n+GAATGCTTATAGGAAACTTGCAAAGAAATGGCACCCAGATCGTTGTTCAGCCACCGGGAATTTAGAGTTAGTGGAAGAAG\n+CTAAGAAAAAATTTCAGGAAATTCGGGAAGCCTATTCTGTTTTATCTGACGCCAACAAAAGGTTAATGTACGACGTGGGA\n+GTCTACGACAGTGATGACGACGAAAACGGCATGGGGGACTTCTTGGACGAAATGTTAACAATGATGAGTCATACCAAATC\n+AAATGAAAATGGAGAGGAGAGCTTTGAGGAGTTGCAACAGCTTTTTGAAGACATGTTTCAAGCGGATATTGGATTGGATG\n+GAGGCCCTTCTCTTGCTTCTTCTGATTCCTCAACTTCATCTGCTTACATGACTTACAGTGAAAGTTCTAGTTCAAATAAA\n+CGCAATTCCTCTGAGATGAATTTCGGGAAGGCAGAGAATTCTTCTGTCTTTGATGCCAGTTACCAGAATTTCTGTTTTGG\n+GGTGAACCAACTCCAAGATATAAAGAAGGGAAAGGGGGGAATTCTAGGAGGAGGAGGTAGAAGTAGACACAGAAGTGGCA\n+GAAAGCAAAAAATGTTCTATGGCCATGATGTT\n+>gnl_Glyma1.01_PACid_16266209\n+ATGGCTAATGAAGGAAAGAAAAGCAATAACTTCTATTCGATCTTGGGCTTGAGCAAGGAGTGCACTGAATTGGAGCTAAA\n+GAATGCTTATAGGAAACTTGCAAAGAAATGGCACCCAGATCGTTGTTCAGCCACCGGGAATTTAGAGTTAGTGGAAGAAG\n+CTAAGAAAAAATTTCAGGAAATTCGGGAAGCCTATTCTGTTTTATCTGACGCCAACAAAAGGTTAATGTACGACGTGGGA\n+GTCTACGACAGTGATGACGACGAAAACGGCATGGGGGACTTCTTGGACGAAATGTTAACAATGATGAGTCATACCAAATC\n+AAATGAAAATGGAGAGGAGAGCTTTGAGGAGTTGCAACAGCTTTTTGAAGACATGTTTCAAGCGGATATTGGATTGGATG\n+GAGGCCCTTCTCTTGCTTCTTCTGATTCCTCAACTTCATCTGCTTACATGACTTACAGTGAAAGTTCTAGTTCAAATAAA\n+CGCAATTCCTCTGAGATGAATTTCGGGAAGGCAGAGAATTCTTCTGTCTTTGATGCCAGTTACCAGAATTTCTGTTTTGG\n+GACAGGTGAACCAACTCCAAGATATAAAGAAGGGAAAGGGGGGAATTCTAGGAGGAGGAGG\n+>gnl_Glyma1.01_PACid_16266210\n+ATGGCTAATGAAGGAAAGAAAAGCAATAACTTCTATTCGATCTTGGGCTTGAGCAAGGAGTGCACTGAATTGGAGCTAAA\n+GAATGCTTATAGGAAACTTGCAAAGAAATGGCACCCAGATCGTTGTTCAGCCACCGGGAATTTAGAGTTAGTGGAAGAAG\n+CTAAGAAAAAATTTCAGGAAATTCGGGAAGCCTATTCTGTTTTATCTGACGCCAACAAAAGGTTAATGTACGACGTGGGA\n+GTCTACGACAGTGATGACGACGAAAACGGCATGGGGGACTTCTTGGACGAAATGTTAACAATGATGAGTCATACCAAATC\n+AAATGAAAATGGAGAGGAGAGCTTTGAGGAGTTGCAACAGCTTTTTGAAGACATGTTTCAAGCGGATATTGGATTGGATG\n+GAGGCCCTTCTCTTGCTTCTTCTGATTCCTCAACTTCATCTGCTTACATGACTTACAGTGAAAGTTCTAGTTCAAATAAA\n+CGCAATTCCTCTGAGATGAATTTCGGGAAGGCAGAGAATTCTTCTGTCTTTGATGCCAGTTACCAGAATTTCTGTTTTGG\n+GGTCGGTCATGTAAACTATCATTACCAA\n+>gnl_Glyma1.01_PACid_16301083\n+ATGGCCGATGAAGGAAACAAAAGCAATAACTTCTATTCGATCTTGGGGTTGAAGAAGGAGTGCACTGAATTGGAGCTAAA\n+GAATGCTTATAGGAAACTTGCAAAGAAATGGCACCCAGATCGTTGTTCAGCGACCGGGAATTCAGAGTTAGTGGAAGAAG\n+CTAAGAAAAAATTTCAGGAAATTCGGGAAGCCTATTCAGTTTTATCTGACGCCAACAAAAGGTTAATGTACGACGTGGGA\n+GTCTACGACAGTGATGACGACGAGAACGGCATGGGGGACTTCTTGGACGAAATGCTAACAATGATGAGTCAGACCAAATC\n+GAATGAAAACGGAGAGGAGAGCTTTGAGGAGTTGCAACAGTTGTTTGAAGACATGTTTGAAGCAGATATTGGATTGGACG\n+GAGGCCCTTCTCTTGCTTCTTCTGATTGCTCAACTTCATCTGCTTACATGACTTATAGTGAAAGTTCTAGTTCAAATAAA\n+CACAATTCCTCTGAGATGAATTTCGGGAAGGCAGAGAATTCTTCTGTCTTTGATGCTGGTTACCAGAATTTCTGTTTTGG\n+GGTGAACCAACTCCAAGATATAAAGAAGAAAAAGGGGGGAATTCTAGGAGGAGGTAGAAGTAGACACAGAAATGGCAGAA\n+AGCAAAATATGTCCTATGGCCATGATGTTTCATCGAATGACTACCCTGGAATTTCCACAAAG\n+>gnl_Glyma1.01_PACid_16301085\n+ATGGCCGATGAAGGAAACAAAAGCAATAACTTCTATTCGATCTTGGGGTTGAAGAAGGAGTGCACTGAATTGGAGCTAAA\n+GAATGCTTATAGGAAACTTGCAAAGAAATGGCACCCAGATCGTTGTTCAGCGACCGGGAATTCAGAGTTAGTGGAAGAAG\n+CTAAGAAAAAATTTCAGGAAATTCGGGAAGCCTATTCAGTTTTATCTGACGCCAACAAAAGGTTAATGTACGACGTGGGA\n+GTCTACGACAGTGATGACGACGAGAACGGCATGGGGGACTTCTTGGACGAAATGCTAACAATGATGAGTCAGACCAAATC\n+GAATGAAAACGGAGAGGAGAGCTTTGAGGAGTTGCAACAGTTGTTTGAAGACATGTTTGAAGCAGATATTGGATTGGACG\n+GAGGCCCTTCTCTTGCTTCTTCTGATTGCTCAACTTCATCTGCTTACATGACTTATAGTGAAAGTTCTAGTTCAAATAAA\n+CACAATTCCTCTGAGATGAATTTCGGGAAGGCAGAGAATTCTTCTGTCTTTGATGCTGGTTACCAGAATTTCTGTTTTGG\n+GGTAGGTCATGTAAACTATCATTACCAA\n+>gnl_Glyma1.01_PACid_16301084\n+ATGGCCGATGAAGGAAACAAAAGCAATAACTTCTATTCGATCTTGGGGTTGAAGAAGGAGTGCACTGAATTGGAGCTAAA\n+GAATGCTTATAGGAAACTTGCAAAGAAATGGCACCCAGATCGTTGTTCAGCGACCGGGAATTCAGAGTTAGTGGAAGAAG\n+CTAAGAAAAAATTTCAGGAAATTCGGGAAGCCTATTCAGTTTTATCTGACGCCAACAAAAGGTTAATGTACGACGTGGGA\n+GTCTACGACAGTGATGACGACGAGAACGGCATGGGGGACTTCTTGGACGAAATGCTAACAATGATGAGTCAGACCAAATC\n+GAATGAAAACGGAGAGGAGAGCTTTGAGGAGTTGCAACAGTTGTTTGAAGACATGTTTGAAGCAGATATTGGATTGGACG\n+GAGGCCCTTCTCTTGCTTCTTCTGATTGCTCAACTTCATCTGCTTACATGACTTATAGTGAAAGTTCTAGTTCAAATAAA\n+CACAATTCCTCTGAGATGAATTTCGGGAAGGCAGAGAATTCTTCTGT'..b'AGAAGAGCAATGATTTTTATGCCGTTCTAGGGTTGAAAAAGGAATGCACCGCCTCCGAGCTCAG\n+AAATGCGTACAAGAGACTTGCCCTGATGTGGCACCCAGATCGTTGCTCCTCGTCGGGAAACTCGAAATTCGTGGAAGAAG\n+CGAAGAAGAAATTTCAGGCCATACAAGAAGCCTATTCAGTTCTCTCTGATGCGAATAAAAGGTTTCTGTACGACGTTGGA\n+GCCTACGACAGCGATGATGACGAAAACGGAATGGGGGATTTTTTGAATGAGATGGCGGTTATGATGAGCCAAACCAAGTC\n+CAATGAAAATGGGAAGGAGAGCTTTGAGGAGTTGCAGGAGCTCTTTGAGGATATGTTCCAAAGGGATGTCGACGCATTCA\n+ACTCTGCCTCTCATCACCCCATGAACTCTTTCCCCAGTTCTACTTCCACTTCTTCCTACTGCGAAAGCTCCAATGCCAAC\n+AACAAGCGGAATTCGGCTGAAATGGGCTCTGGAAGGATGATGAGTGCAGGGGAGTCCTCTGCTTTTGATGCCCACTTTCA\n+GAGCTTCTGCTTTGGGACAGGCGGCACGCCAGGGAGATTTCAGGAGGGGGAAAGGAGCAAGAGGAGGAATTCCAGGAGGA\n+GCCAACGG\n+>gnl_Selmo1.0_PACid_15401289\n+ATGGAGAAGAGGAAAGAGGATCCCTACACTGTTCTTGGTGTCCAAAAGTCGAGTTCTAGCTCGGAAATTCGCTCCGCTTA\n+TCGGAAGCTCGCCATGAAATGGCATCCAGATAAGCAACACTCTTTAGAGGATCAAGCAAAAGCGAAGTTCCAGGGCATTC\n+AAGAAGCTTATTCAGTGCTATCCGACGACAAAAAAAGAGTTCTTTATGATTCGGGACTTTATGACGAGGGAGATGACGAG\n+GTGAGT\n+>gnl_Orysa6.0_PACid_16864430\n+ATGGCCCGCGGCGGCGGCGGCGGCGGCGGCGCGGACGCCGACCTGTACGCCGTCCTCGGCCTCAGCAGGGAGTGCACCGA\n+CGCCGACCTCAGGCTCGCCTACCGCAAGCTCGCCATGATATGGCATCCGGACAGGTGCTCGGTGGCCGGCGGCAGCGCGA\n+GCGCGGCGGGCGTCGACGAGGCCAAGGAGCGATTCCAGGAGATCCAGGGCGCCTACTCCGTGCTCTCCGACTCCAACAAG\n+CGCTTCCTCTACGACGTCGGCGTCTACGACGGCAACGACGGCGACGACGACGACGACGAAGCAGATCTGTCGGGGATGGG\n+CGATTTCCTCGGCGAGATGGCGCAGATGATGAGCCAGGCGACGCCTGCGGAGAGCTTCGAGGAGTTGCAGCAGCTGTTCG\n+TGGACATGTTCCAGGACGACATCGACGCCGGCCTCTGCCAGTCGACGCCGCCGCCGCCGTCATGGCCGTCGCCTCCGGCG\n+GCCGCCAATGCACGATCGCCGGCGGCGGCGGCGACTTCACGCAAGGGCGTGAACAAGCGGTGCTCACCGGCGGCGATGGA\n+CATGGACTCCGGTTTGAGCAGCCTGCTGGGCATTTCGGGCTTCTGTTTCGAGGCGCCATGGACGTCGCAGGACGCGAGCA\n+CTGCCGCCGGCGGTGGCGGCGGCAAGAGGAGAAAGCAGAGGCCGCCGCCGGCGAGCCACAACGTG\n+>gnl_Sorbi1.4_PACid_1982925\n+ATGGCTGCTACAAGTCACTGCGGCAACATCCAGGACCAGGACGAAGAAGCTTCGGCTCCTGGCGCCGCCGACCTCTACGC\n+CGTGCTCGGGCTCAACAGGGAGTGCACCGACGCCGAGCTCAGGGTCGCGTACCGGCGGCTCGCCATGATATGGCATCCGG\n+ACAGGTGCTCGGCGTCCGGCAGCTCGCCGGCGCGCATGGAGGAGGCCAAGGAGCGGTTCCAGGAGATCCAGGGCGCCTAC\n+TCCGTGCTCTCCGACTCCAACAAGCGGCTCCTCTACGACGTCGGCGTCTACGACAGCGACGACGACGAGGCTGACCTGTC\n+GGGGATGGGCGACTTCCTCGGAGAGATGGCCGACATGATGAGCCAGGCCACGCCAACGGAGACCTTCGAGGAGCTGCAGC\n+AGGTGTTCGTGGACATGTTCCAGGACGACCTGGACGACGCCGGCTTCTTCGGCGGGCTTCCGACGACGGGCCGCAGGGCC\n+CAGGCACCCAGCACCTCGCTGCCGCCGTCGGTGTCGTCGTCGCCGTTGCGGCCGACGCCTGCCGCTGGAAGAAGCAAGGG\n+TCCGCAAGCGACGCCGTCGTCGTCGTTTAAAGGCGTCGAGAGGCGGGGTTCGACGTCGACGGCGAAACGGCCGAGGCCCA\n+ACGGGTCGGCGGGCCTGGAATCGGACCTGGGCCTCTCCGGATTCTGCTTCATGGTGAGTAAGGAGATGAGCAAGTCGAAG\n+GAGAGGCAAGCGGTATGGGCCAGTGACGACGGTGACAGGAGCACCGATGGCAAGCAGAGGTTGTCGACGAGCCGCGATGT\n+CTCCGGTGGTGGGATGTCACGCTCACTGCAGGGCCAAAGCAGCAAAAACTTGTTGCAGTGTATGGCCTCTAAGTCT\n+>gnl_Medtr3.5_Medtr8g022310.3\n+ATGGCTAACGAAGGAAACAAAAGCAATGATTTCTATGCAGTTTTGGGATTGAATAAGGAATGCTCTGATTCAGAGCTAAG\n+GAATGCTTATAAGAAACTTGCACTGAAATGGCATCCAGATCGTTGTTCAGCTTCAGGGAATGTGAAGTTTGTGGAAGAAG\n+CTAAGAAGAAATTTCAGGCAATTCAAGAAGCCTATTCTGTTTTATCTGACTCGAACAAGAGATTAATGTACGACGTTGGA\n+GTTTACGACAGTGATGATGACGAAAATGTAAGGCACTTGTTTCACACCATTCATGAGTTGGGGACCCTCTTTTGCGTTAT\n+GTTTTGTTTCTTCATTTCCTTGAGGGGAGAGAAGAGAAGCAACCTTAATTTAACCTTTTCACTTTCACAT\n+>gnl_Nelnu1.0_NNU_000115-RA\n+ATGGAGGTGGACTCCCATCGATCATCTCCATCTTACTACACCATCCTTGGTGTAGATCAGAATTCCTCCGCTTCCGAGAT\n+ACGCAATGCTTACAGGAAGCTCGCGATGCAATGGCATCCAGACAAATGGACGAAAACTCCGTCGCTCTTAGAGAAAGCCA\n+AGAGTAAATTCCAGCAAATCCAGGAGGCTTATTCGGGTGGGTTACTCGTTTTCATGTTATCGGATCAGGGGAAGAGAACA\n+CTGTATGATGTCGGTCTGTATGACCCGGACGATGAAACGAATGACGAGGTGGGGCTTCGCAGATTTCATGCAGGAGATGA\n+TATCTCTCATGAACGATGTGAAGAAACAGGAGAAGAAATACAGCTTGGAGGAACTACAGGAGATGTTAGTGGAAATGTCA\n+CAAGGGCTGGAGTTGAAGATGGAGAGTGCTGGTGGTGTGTGGTTGTTAGATGGAGCTGCAGCCTCAAGGAGGAGCTCAAA\n+GAGGGCCAGATGGGAATCATCAGCGAGTCCGACGACGCTGGACACGACACACCTTCTCTCCCCCACTTGCACGGTTCAGA\n+GCTGGAATTGTTAGGAAGAACCGGCTGTTGCAAT\n+>contig_7\n+GAGAATGAGTGGTCTGGGGCTGAGTTTTTGAATGAAATGGCGGCAATGATGACTCAAAATAAATCCAATGAAAACGGAAC\n+CGGAACTTTTGAAGAACTGCAACAATTGTTCGATGAAATGTTTCAGAGCGACATCGAGTCCTTCAATGGTTGTTCTTCAT\n+CATCCAATGAAACATGTAGCAACTCGAACAAGAGGAATTCCATTGAGTCGAGCTCGGCTAATTTCAGACCCGAAAATGGA\n+AACGAAAGCGGCGAGATTAGCGGGAAGAAGAATACTAGGAAAGGTAAAGGTGACGNN\n' |
| b |
| diff -r a322e5e668a3 -r 276f0f31ddb0 test-data/38889.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/38889.faa Mon Oct 30 09:53:09 2017 -0400 |
| b |
| @@ -0,0 +1,4 @@ +>contig_2 +XLSKVPIPSNNIYAINDKKSPEDAADDYENRLKELVSEKIIPVSTISGFPKFDLMLLGMGPDGHVASLFPSHMQRYEKEK +WVTFITDSPKPPPSRITFTFPMINSASEIAMVVTGADLAGTTKIALGTTGNVKPGETPLPCTEVSAEGEVTWFLDKDAAS +QLLNYVRFDD |
| b |
| diff -r a322e5e668a3 -r 276f0f31ddb0 test-data/38889.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/38889.fna Mon Oct 30 09:53:09 2017 -0400 |
| b |
| @@ -0,0 +1,8 @@ +>contig_2 +NNCCTTTCCAAGGTACCCATCCCATCCAACAACATATATGCTATAAATGATAAGAAGTCCCCGGAAGATGCAGCAGACGA +CTACGAAAACCGCCTCAAGGAACTCGTCTCCGAAAAAATCATACCCGTTTCAACCATTAGCGGGTTCCCGAAGTTCGACC +TCATGTTGCTTGGAATGGGGCCCGACGGCCATGTGGCCTCTCTTTTCCCTTCTCACATGCAACGCTATGAGAAGGAGAAA +TGGGTCACTTTCATAACTGACTCTCCCAAACCGCCTCCGTCGAGAATCACTTTTACGTTTCCGATGATCAACTCGGCTTC +GGAGATCGCTATGGTGGTTACCGGGGCTGATTTGGCTGGTACAACTAAGATAGCATTGGGTACTACGGGCAATGTTAAGC +CGGGTGAGACTCCTTTGCCTTGTACTGAAGTTTCGGCTGAGGGAGAGGTTACTTGGTTCTTGGACAAAGATGCTGCTTCA +CAACTGTTAAATTATGTGCGCTTTGATGAT |
| b |
| diff -r a322e5e668a3 -r 276f0f31ddb0 test-data/38889_integrated.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/38889_integrated.faa Mon Oct 30 09:53:09 2017 -0400 |
| b |
| @@ -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 |
| b |
| diff -r a322e5e668a3 -r 276f0f31ddb0 test-data/38889_integrated.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/38889_integrated.fna Mon Oct 30 09:53:09 2017 -0400 |
| b |
| @@ -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 |
| b |
| diff -r a322e5e668a3 -r 276f0f31ddb0 test-data/39614.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/39614.faa Mon Oct 30 09:53:09 2017 -0400 |
| b |
| @@ -0,0 +1,3 @@ +>contig_3 +XVDEGVVVAGLSEQEKASVSEILTTARAHSETIENLKRDHSQQVSCIEQHTNDTFRQKYMDYEPTGSTPVRSEPDIPSKG +TIESLRAMPIDALEEEFRENHSYESAVTGKELMPSVTTRAPFSQIN |
| b |
| diff -r a322e5e668a3 -r 276f0f31ddb0 test-data/39614.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/39614.fna Mon Oct 30 09:53:09 2017 -0400 |
| b |
| @@ -0,0 +1,6 @@ +>contig_3 +NNTGTGGATGAAGGAGTTGTTGTTGCTGGCTTGTCAGAGCAGGAGAAGGCATCTGTTTCTGAAATTCTGACAACTGCTAG +AGCTCATTCAGAAACAATTGAGAACCTTAAGAGAGATCATTCCCAGCAGGTATCCTGTATCGAACAGCACACGAATGATA +CTTTCAGGCAAAAATACATGGATTACGAGCCTACAGGGTCCACGCCAGTTAGGAGCGAGCCGGATATTCCCAGCAAAGGC +ACAATAGAGTCACTTCGTGCCATGCCTATAGATGCACTTGAAGAAGAATTTCGAGAAAACCATTCATACGAATCTGCTGT +TACAGGAAAGGAACTAATGCCGTCTGTTACGACTCGTGCACCATTTTCACAGATCAAC |
| b |
| diff -r a322e5e668a3 -r 276f0f31ddb0 test-data/39614_integrated.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/39614_integrated.faa Mon Oct 30 09:53:09 2017 -0400 |
| b |
| @@ -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 |
| b |
| diff -r a322e5e668a3 -r 276f0f31ddb0 test-data/39614_integrated.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/39614_integrated.fna Mon Oct 30 09:53:09 2017 -0400 |
| b |
| @@ -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 |
| b |
| diff -r a322e5e668a3 -r 276f0f31ddb0 test-data/tool-data/plant_tribes/scaffolds/README.txt --- /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 |
| b |
| @@ -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. |
| b |
| diff -r a322e5e668a3 -r 276f0f31ddb0 utils.py --- 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') |