| Next changeset 1:3aca88613abf (2017-06-28) |
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Commit message:
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added:
.shed.yml kaks_analysis.xml macros.xml plant_tribes_scaffolds.loc.sample test-data/output1.tabular test-data/output_blastn_results1.tabular test-data/output_paralogous_pairs.tabular test-data/species1_cds.fasta test-data/species1_pep.fasta tool_data_table_conf.xml.sample |
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| diff -r 000000000000 -r 2f0b8e19286b .shed.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.shed.yml Thu Jun 08 12:53:38 2017 -0400 |
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| @@ -0,0 +1,14 @@ +name: plant_tribes_kaks_analysis +owner: greg +description: | + Contains a tool that performs orthologous or paralogous ks analyses of coding sequences and amino acid sequences. +homepage_url: https://github.com/dePamphilis/PlantTribes +long_description: | + Contains a tool that tool is one of the PlantTribes collection of automated modular analysis pipelines that + utilize objective classifications of complete protein sequences from sequenced plant genomes to perform + comparative evolutionary studies. This tool performs orthologous or paralogous ks analyses of coding sequences + and amino acid sequences. +remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/plant_tribes/kaks_analysis +type: unrestricted +categories: +- Phylogenetics |
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| diff -r 000000000000 -r 2f0b8e19286b kaks_analysis.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/kaks_analysis.xml Thu Jun 08 12:53:38 2017 -0400 |
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| b'@@ -0,0 +1,308 @@\n+<tool id="plant_tribes_kaks_analysis" name="KaKsAnalysis" version="@WRAPPER_VERSION@.0">\n+ <description>estimates paralogous and orthologous pairwise synonymous (Ks) and non-synonymous (Ka) substitution rates</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements_kaks_analysis" />\n+ <command detect_errors="exit_code"><![CDATA[\n+#set output_dir = \'kaksAnalysis_dir\'\n+#set comparison = $comparison_cond.comparison\n+#if str($options_type.options_type_selector) == \'advanced\':\n+ #set codeml_ctl_file_cond = $options_type.codeml_ctl_file_cond\n+ #set codeml_ctl_file_select = $codeml_ctl_file_cond.codeml_ctl_file_select\n+ #set fit_components_cond = $options_type.fit_components_cond\n+ #set fit_components = $fit_components_cond.fit_components\n+ #set recalibrate_cond = $options_type.recalibrate_cond\n+ #set recalibrate = $recalibrate_cond.recalibrate\n+ #set set_min_coverage_cond = $options_type.set_min_coverage_cond\n+ #set set_min_coverage = $set_min_coverage_cond.set_min_coverage\n+ #set set_lower_ks_limit_cond = $options_type.set_lower_ks_limit_cond\n+ #set set_lower_ks_limit = $set_lower_ks_limit_cond.set_lower_ks_limit\n+ #set set_upper_ks_limit_cond = $options_type.set_upper_ks_limit_cond\n+ #set set_upper_ks_limit = $set_upper_ks_limit_cond.set_upper_ks_limit\n+#else:\n+ #set codeml_ctl_file_select = \'no\'\n+ #set fit_components = \'no\'\n+ #set set_lower_ks_limit = \'no\'\n+ #set set_upper_ks_limit = \'no\'\n+#end if\n+KaKsAnalysis\n+--num_threads \\${GALAXY_SLOTS:-4}\n+--coding_sequences_species_1 \'$coding_sequences_species_1\'\n+--proteins_species_1 \'$proteins_species_1\'\n+--comparison $comparison\n+#if str($comparison) == \'orthologs\':\n+ --coding_sequences_species_2 \'$comparison_cond.coding_sequences_species_2\'\n+ --proteins_species_2 \'$comparison_cond.proteins_species_2\'\n+#end if\n+#if str($options_type.options_type_selector) == \'advanced\':\n+ #if str($set_min_coverage) == \'yes\':\n+ --min_coverage $set_min_coverage_cond.min_coverage\n+ #end if\n+ #if str($recalibrate) == \'yes\':\n+ --recalibration_rate $recalibrate_cond.recalibration_rate\n+ #end if\n+ #if str($codeml_ctl_file_select) == \'yes\':\n+ --codeml_ctl_file \'$codeml_ctl_file_cond.codeml_ctl_file\'\n+ # No else block needed here because the default codeml_ctl config\n+ # will be used if the --codeml_ctl_file flag is missing.\n+ #end if\n+ #if str($fit_components) == \'yes\':\n+ --fit_components\n+ --num_of_components $fit_components_cond.num_of_components\n+ #end if\n+ #if str($set_lower_ks_limit) == \'yes\':\n+ --min_ks $set_lower_ks_limit_cond.min_ks\n+ #end if\n+ #if str($set_upper_ks_limit) == \'yes\':\n+ --max_ks $set_upper_ks_limit_cond.max_ks\n+ #end if\n+#end if\n+>/dev/null\n+&& mv $output_dir/species1.fna \'$output_species1_fna\'\n+&& mv $output_dir/species1.faa \'$output_species1_faa\'\n+#if str($comparison) == \'paralogs\':\n+ && mv $output_dir/species1.fna.blastn.paralogs \'$output_species1_paralog\'\n+#else:\n+ && mv $output_dir/species2.faa \'$output_species2_faa\'\n+ && mv $output_dir/species2.fna \'$output_species2_fna\'\n+ && mv $output_dir/species1.fna.blastn.orthologs \'$output_species1_ortholog\'\n+ && mv $output_dir/species2.fna.blastn.orthologs \'$output_species2_ortholog\'\n+#end if\n+&& mv $output_dir/*.rbhb \'$output_rbhb\'\n+&& mv $output_dir/*.kaks \'$output_kaks\'\n+#if str($fit_components) == \'yes\':\n+ && mv $output_dir/*.components \'$output_components\'\n+#end if\n+ ]]></command>\n+ <inputs>\n+ <param name="coding_sequences_species_1" format="fasta" type="data" label="Coding sequences for the first species" />\n+ <param name="proteins_species_1" format="fasta" type="data" label="Protein sequences for the first species" />\n+ <conditional name="comparison_cond">\n+ <param name="comparison" type="select" label="Type of sequence comparison">\n+ '..b'eml.ctl.args" can be found in the scaffold data installed into Galaxy via the PlantTribes Scaffolds Download Data Manager tool, and are also available at the PlantTribes GitHub `repository`_. Default settings shown in the template are used if \'No\' is selected.\n+ - **Rates clustering configuration** - select \'Yes\' to estimate clusters of synonymous substitution rates using a mixture of multivariate normal distributions which represent putative duplication event(s).\n+\n+ - **Number of components** - number of components to include in the normal mixture model.\n+\n+ - **Lower limit synonymous substitution rates configuration** - select \'Yes\' to set the minimum allowable synonymous substitution rate to use in the normal mixtures cluster analysis to exclude young paralogs that arise from normal gene births and deaths in a genome.\n+\n+ - **Minimum rate** - minimum allowable synonymous substitution rate.\n+\n+ - **Upper limit synonymous substitution rates configuration** - select \'Yes\' to set the maximum allowable synonymous substitution rate to use in the normal mixtures cluster analysis to exclude likely ancient paralogs in a genome.\n+\n+ - **Maximum rate** - maximum allowable synonymous substitution rate.\n+\n+.. _repository: https://github.com/dePamphilis/PlantTribes/blob/master/config/codeml.ctl.args\n+\n+ </help>\n+ <citations>\n+ <expand macro="citation1" />\n+ <citation type="bibtex">\n+ @article{Wall2008,\n+ journal = {Nucleic Acids Research},\n+ author = {2. Wall PK, Leebens-Mack J, Muller KF, Field D, Altman NS},\n+ title = {PlantTribes: a gene and gene family resource for comparative genomics in plants},\n+ year = {2008},\n+ volume = {36},\n+ number = {suppl 1},\n+ pages = {D970-D976},}\n+ </citation>\n+ <citation type="bibtex">\n+ @article{Altschul1990,\n+ journal = {Journal of molecular biology}\n+ author = {3. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ},\n+ title = {Basic local alignment search tool},\n+ year = {1990},\n+ volume = {215},\n+ number = {3},\n+ pages = {403-410},}\n+ </citation>\n+ <citation type="bibtex">\n+ @article{Katoh2013,\n+ journal = {Molecular biology and evolution},\n+ author = {4. Katoh K, Standley DM},\n+ title = {MAFFT multiple sequence alignment software version 7: improvements in performance and usability},\n+ year = {2013},\n+ volume = {30},\n+ number = {4},\n+ pages = {772-780},}\n+ </citation>\n+ <citation type="bibtex">\n+ @article{Yang2007,\n+ journal = {Molecular biology and evolution},\n+ author = {5. Yang Z},\n+ title = {PAML 4: phylogenetic analysis by maximum likelihood},\n+ year = {2007},\n+ volume = {24},\n+ number = {8},\n+ pages = {1586-1591},}\n+ </citation>\n+ <citation type="bibtex">\n+ @article{McLachlan1999,\n+ journal = {Journal of Statistical Software},\n+ author = {6. McLachlan GJ, Peel D, Basford KE, Adams P},\n+ title = {The EMMIX software for the fitting of mixtures of normal and t-components},\n+ year = {1999},\n+ volume = {4},\n+ number = {2},\n+ pages = {1-14},}\n+ </citation>\n+ <citation type="bibtex">\n+ @article{Cui2006,\n+ journal = {Genome Research},\n+ author = {7. Cui L, Wall PK, Leebens-Mack JH, Lindsay BG, Soltis DE, Doyle JJ, Soltis PS, Carlson JE, Arumuganathan K, Barakat A, Albert VA},\n+ title = {Widespread genome duplications throughout the history of flowering plants},\n+ year = {2006},\n+ volume = {16},\n+ number = {6},\n+ pages = {738-749},}\n+ </citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r 2f0b8e19286b macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Jun 08 12:53:38 2017 -0400 |
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| @@ -0,0 +1,130 @@ +<?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="1.0.0">plant_tribes_assembly_post_processor</requirement> + </requirements> + </xml> + <xml name="requirements_gene_family_aligner"> + <requirements> + <requirement type="package" version="1.0.0">plant_tribes_gene_family_aligner</requirement> + </requirements> + </xml> + <xml name="requirements_gene_family_classifier"> + <requirements> + <requirement type="package" version="1.0.0">plant_tribes_gene_family_classifier</requirement> + </requirements> + </xml> + <xml name="requirements_gene_family_integrator"> + <requirements> + <requirement type="package" version="1.0.0">plant_tribes_gene_family_integrator</requirement> + </requirements> + </xml> + <xml name="requirements_kaks_analysis"> + <requirements> + <requirement type="package" version="1.0.0">plant_tribes_kaks_analysis</requirement> + </requirements> + </xml> + <xml name="requirements_ks_distribution"> + <requirements> + <requirement type="package" version="1.3.0">r-optparse</requirement> + </requirements> + </xml> + <xml name="requirements_gene_family_phylogeny_builder"> + <requirements> + <requirement type="package" version="1.0.0">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> + <option value="orthofinder">OrthoFinder</option> + <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, + journal = {None}, + author = {1. Wafula EK}, + title = {Manuscript in preparation}, + year = {None}, + url = {https://github.com/dePamphilis/PlantTribes},} + </citation> + </xml> +</macros> |
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| diff -r 000000000000 -r 2f0b8e19286b plant_tribes_scaffolds.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plant_tribes_scaffolds.loc.sample Thu Jun 08 12:53:38 2017 -0400 |
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| @@ -0,0 +1,4 @@ +## Plant Tribes scaffolds +#Value Name Path Description +#22Gv1.0 22Gv1.0 /plant_tribes/scaffolds/22Gv1.0 22 plant genomes (Angiosperms clusters, version 1.0; 22Gv1.0) +#22Gv1.1 22Gv1.1 /plant_tribes/scaffolds/22Gv1.1 22 plant genomes (Angiosperms clusters, version 1.1; 22Gv1.1) |
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| diff -r 000000000000 -r 2f0b8e19286b test-data/output1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output1.tabular Thu Jun 08 12:53:38 2017 -0400 |
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| @@ -0,0 +1,4 @@ +SEQ1 SEQ2 Ka Ks Ka\Ks +contig_241; contig_241 1.5312 7.1619 0.2138 +contig_300 contig_300; 0.8653 3.7872 0.2285 +contig_586 contig_586; 1.7791 1.1181 1.5912 |
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| diff -r 000000000000 -r 2f0b8e19286b test-data/output_blastn_results1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_blastn_results1.tabular Thu Jun 08 12:53:38 2017 -0400 |
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| @@ -0,0 +1,25 @@ +contig_1; contig_1; 100.00 346 0 0 1 346 1 346 0.0 640 +contig_2 contig_2 100.00 511 0 0 1 511 1 511 0.0 944 +contig_3; contig_3; 100.00 379 0 0 1 379 1 379 0.0 701 +contig_5; contig_5; 100.00 418 0 0 1 418 1 418 0.0 773 +contig_7 contig_7 100.00 296 0 0 1 296 1 296 7e-158 547 +contig_9 contig_9 100.00 396 0 0 1 396 1 396 0.0 732 +contig_10; contig_10; 100.00 257 0 0 1 257 1 257 3e-136 475 +contig_11; contig_11; 100.00 426 0 0 1 426 1 426 0.0 787 +contig_12; contig_12; 100.00 330 0 0 1 330 1 330 1e-176 610 +contig_13 contig_13 100.00 211 0 0 1 211 1 211 8e-111 390 +contig_14 contig_14 100.00 250 0 0 1 250 1 250 2e-132 462 +contig_15 contig_15 100.00 258 0 0 1 258 1 258 8e-137 477 +contig_16 contig_16 100.00 282 0 0 1 282 1 282 4e-150 521 +contig_18; contig_18; 100.00 428 0 0 1 428 1 428 0.0 791 +contig_19 contig_19 100.00 236 0 0 1 236 1 236 1e-124 436 +contig_20 contig_20 100.00 309 0 0 1 309 1 309 4e-165 571 +contig_21; contig_21; 100.00 520 0 0 1 520 1 520 0.0 961 +contig_22; contig_22; 100.00 229 0 0 1 229 1 229 9e-121 424 +contig_23; contig_23; 100.00 213 0 0 1 213 1 213 7e-112 394 +contig_24; contig_24; 100.00 332 0 0 1 332 1 332 7e-178 614 +contig_25; contig_25; 100.00 122 0 0 1 122 1 122 1e-61 226 +contig_27; contig_27; 100.00 261 0 0 1 261 1 261 2e-138 483 +contig_28; contig_28; 100.00 219 0 0 1 219 1 219 3e-115 405 +contig_29 contig_29 100.00 849 0 0 1 849 1 849 0.0 1568 +contig_30 contig_30 100.00 478 0 0 1 478 1 478 0.0 883 |
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| diff -r 000000000000 -r 2f0b8e19286b test-data/output_paralogous_pairs.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_paralogous_pairs.tabular Thu Jun 08 12:53:38 2017 -0400 |
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| @@ -0,0 +1,3 @@ +contig_241; contig_241 +contig_300 contig_300; +contig_586 contig_586; |
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| diff -r 000000000000 -r 2f0b8e19286b test-data/species1_cds.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/species1_cds.fasta Thu Jun 08 12:53:38 2017 -0400 |
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| b'@@ -0,0 +1,4219 @@\n+>contig_1; 91 1 346 minus strand\n+XTTAAAAAATTATATGGAGACAAGGAAGATATCCTTGTCCCAGATATTTTCTGGGATTAC\n+ACGAGTGGAAAGGTGCTAACAATGGAGTGGGTTGAAGGTGTTAAATTAAATGAGCAAGAT\n+GCCGTTGAGAGTCAAGGGCTCAGTGTTCTGGATCTGGTGAATACCGGCATACAGTGCAGT\n+CTTCGACAGCTGCTTGAGTACGGCTATTTTCATGCAGATCCTCACCCAGGGAATCTCTTA\n+GCTACACCTGACGGGAAGCTTGCTTTTCTTGATTTTGGAATGATGAGTGAGACTCCTGAA\n+CAAGCAAGATCGGCCATAATTGGTCATGTTGTACACATGGTTAATCGX\n+>contig_2 218 1 511 \n+XXCCTTTCCAAGGTACCCATCCCATCCAACAACATATATGCTATAAATGATAAGAAGTCC\n+CCGGAAGATGCAGCAGACGACTACGAAAACCGCCTCAAGGAACTCGTCTCCGAAAAAATC\n+ATACCCGTTTCAACCATTAGCGGGTTCCCGAAGTTCGACCTCATGTTGCTTGGAATGGGG\n+CCCGACGGCCATGTGGCCTCTCTTTTCCCTTCTCACATGCAACGCTATGAGAAGGAGAAA\n+TGGGTCACTTTCATAACTGACTCTCCCAAACCGCCTCCGTCGAGAATCACTTTTACGTTT\n+CCGATGATCAACTCGGCTTCGGAGATCGCTATGGTGGTTACCGGGGCTGATTTGGCTGGT\n+ACAACTAAGATAGCATTGGGTACTACGGGCAATGTTAAGCCGGGTGAGACTCCTTTGCCT\n+TGTACTGAAGTTTCGGCTGAGGGAGAGGTTACTTGGTTCTTGGACAAAGATGCTGCTTCA\n+CAACTGTTAAATTATGTGCGCTTTGATGATTAA\n+>contig_3; 134 1 379 minus strand\n+XXTGTGGATGAAGGAGTTGTTGTTGCTGGCTTGTCAGAGCAGGAGAAGGCATCTGTTTCT\n+GAAATTCTGACAACTGCTAGAGCTCATTCAGAAACAATTGAGAACCTTAAGAGAGATCAT\n+TCCCAGCAGGTATCCTGTATCGAACAGCACACGAATGATACTTTCAGGCAAAAATACATG\n+GATTACGAGCCTACAGGGTCCACGCCAGTTAGGAGCGAGCCGGATATTCCCAGCAAAGGC\n+ACAATAGAGTCACTTCGTGCCATGCCTATAGATGCACTTGAAGAAGAATTTCGAGAAAAC\n+CATTCATACGAATCTGCTGTTACAGGAAAGGAACTAATGCCGTCTGTTACGACTCGTGCA\n+CCATTTTCACAGATCAACTAG\n+>contig_5; -67 1 418 minus strand\n+XXCGGTGGTCCGCCACAAACACACGTCAAGCGGGATCCCGCATCCCGCGGGCTCTTCCAC\n+GCGGTCGTCCCGGCGCTCGGCCCTCTCCGTGACGCACGTCGAGAGGGACGATTTGGCCGA\n+TGCCGCGTGATGCCAGGCCCCGACATCATgCAAGGAGCACTCCGTTGTGCCGACCCTCGC\n+CTTCGATGACGTCCTCGGGCGTCTAGCGAAGTATCGAAGAAGGGCGAGCTAAGGAGCCAT\n+GAATCCTGGAGATGCGAGCCAGGTCACGAGAGGCGCGGCAGGCGAGTCTTTGCTCGCTCT\n+CGCACCGTCTGCTCTCGTGCTTGGAGAAGAAGGACCGACTGCTGACGTCGAACCGGATGA\n+TGGAAGGTTCGAACAAGTCAGATCTGGAAAGGGGTAGCATGGAAAAGGCGACACTCTCAC\n+X\n+>contig_7 103 1 296 \n+GAGAATGAGTGGTCTGGGGCTGAGTTTTTGAATGAAATGGCGGCAATGATGACTCAAAAT\n+AAATCCAATGAAAACGGAACCGGAACTTTTGAAGAACTGCAACAATTGTTCGATGAAATG\n+TTTCAGAGCGACATCGAGTCCTTCAATGGTTGTTCTTCATCATCCAATGAAACATGTAGC\n+AACTCGAACAAGAGGAATTCCATTGAGTCGAGCTCGGCTAATTTCAGACCCGAAAATGcG\n+AAACGAAAGCGGCGAGATTAGCGGGAAGAAGAATACTAGGAAAGGTAAAGGTGACGXX\n+>contig_9 34 1 396 \n+XXACTTCGGTTAAAGGCAGATGAGGAGGCACAATGTTTGAATCAGATGCAGCGTATCATT\n+TTTGATGAAATTATGGAGCATGTGGAGTTAGAAAAGGGGGGCTTCTATTTCGTATATCGC\n+CCTGGGGGCAACGGAAAGACCTTGTGGTTGGCTATTATCTCAAAACTGAGAAGCGAGGGT\n+AGAATAGTTCTCGCAGTGGCTTCATCAGGTATAGCATTGCTTTTGGTTGAGGGTGGTAGA\n+ACAGCCCATTCTCGATTTAAAATACCCATAGATGTCAATGAATATAACAATTGTGAAATT\n+AAACAGAACATCTACCTCGCTGAACTTATATGTCACACCAATTTGGTCATTTGGGATGAG\n+GCACCTATGACTCAATATTTTGTCTTTGAGGCGGTTGAX\n+>contig_10; 78 87 343 minus strand\n+ATGGCAGAAGAGAACACCACTACAATGAACCTCGATCTCAATTTGGGCCCCATCAATAAC\n+TCAAGCGACGATAGCGAACCTTCATCACGCCCTTATACTGATGTCGCAATGAACTTGGAA\n+GATTGGTTAGATAGTCCCGTCCGAGTTCGTGAAGTCGTCCGCCACAGAAATCATAGGTGG\n+CGCTCTTTGTGGCGCCAAATCCCAATTCCGCCTGATACGCGAAACCTCGCGCTCGAATTA\n+ATCGGCGGCAATGCCCCX\n+>contig_11; 195 1 426 minus strand\n+XXCGCTGCTAAAGTCACGGTTGCTCCCGGATCTCGCGTCGCTGCTGCTGGAAGCGGCGTT\n+GCCTCAGAATCTCCGGCGACTGCTGAAGCCGGCGTTGCCCCAGGATCTCCCGCGGTCGAC\n+TTCAATAGCCACAGCGGGAGTTTCTGGAGCAACACCGACTGCAGCAGCAACAACGGGAGA\n+TTCGGAGCAACTCCGACGGGATATCATGGAGCAACCCCGACTTCAACAGTGGCGACGGGA\n+GATTTTGGAACAACGCCGACTTCAGGAGCCGCGGTGGGAGAGCTTGGAGXTAAATCCGAC\n+TTAAGCAGCACTGCGGGAGATCCTAGAACAATGCCTCCGACGACGGGAGATTCTGGAGTA\n+ACACCGCCTCCAACAACAACGACGGGAGATTCGGGAGCAACGCCACCCCAGAGTGTTCTC\n+ATATTTTGA\n+>contig_12; 4 1 330 minus strand\n+XCATCCTCATCCAAACGTTCTCTATAGCGATCAAAATCGCGGGGGGAAGAGACCAAGAAG\n+AAAATTGCAATTGAAAAGGAACGTCAAGAGCGGCTGAAATCTTTGGAAGCACGGTTTTCT\n+ACCAAGTCCGTAATCATGAGATCTACAGTCAGTAATAGGAGCTCATTTGATGGCACTGGT\n+GTAGAATTGCTGGGCGATATTTCTGCAGGTTACATAATTAATGTGGTGAGAGAGGAAGGT\n+GAAGAGCCAGTAAGAATCCCTCCAAGCATCTGTATAAAATTAAAGCCCCATCAGATTCAA\n+GGCATCAGGTTTATGTGGGAAAATATTATTCXX\n+>contig_13 86 218 428 \n+ATGTCGTCTGGAAGGTACATGTCATACTCACCGTCTCCTTCCGCCCCTCACTCACCTCAC\n+ATTGGCATCGCCGGCAGCGGCGGGGGTATGCGTACTGCCGCCTCTGTGCTCATCGAGCAA\n+GAAAAATACCTCTCAGAGTTGCTGTCTGAACGCAACAAACTCAGTCCC'..b'ACAATTCTACGTATAGGAATGATACAGGCAAC\n+CAGGCTCTTGCCTTGACGCGTGTGCCTCGTTCAGTGAATTTGGCATCAAACGCCTATCTC\n+GAATTTCTGCTTGGACCAACTACAAAAATGCTTTTCGAATTTGTCAAAGAAATGCCAAAG\n+CCTGGAACAACACTCAGGCTGGATTTATCGTCTCTTCTTGGGCCACTCTTCTTTACGTGG\n+GTTATCGTACAGCTGTTCCCTGTCGTGCTAATATCTTTGGTTTACGAGAAACAGCACAGA\n+CTAAGAATTATGATGAAAATGCATGGGCTTGGCGATGGACCTTATTGGATGATATCTTAT\n+GCTTATTTTCTTGCAATATCCTCCATCTACATGTTCTGCTTTGTGATATTTGGCTCAGCC\n+ATAGGGTTAAACTTCTTCAAACTAAATGATTATAGCATCCAGTTTGTGTTTTAX\n+>contig_685 255 60 583 \n+ATGCAGGAGAACAAAGGGGAAACGGCTTCCAACAAAAACCCTAAAAAGGCCAATCTTTTG\n+GATCATCATTCAATCAAGCACATTCTCGATGAATCAGTCACTGAGATCGTTACTAGCAAA\n+GGATATCCGGAAGATGTGAGGATGAGTAACATCCGGTTGTTGCTTGGGGTGGTGATCATT\n+GTGATCGCAATTTTTGCGCAGTTCTACAATAAGAAGTTTCCGGAGAATCGGAATTTCCTC\n+ATTAGTTGCATTGCGTTGTATGTTGTATTCAATGGGTTATTACAACTGATTATATACCTG\n+AAGGAAAAGAATGCCATCATGTTCACCTATCCTCTACCAGGCTCTTTCAACTCTACTGGG\n+TTAGTTGTAACTTCTAAGCTGCGAAGGTTTTCAGATTTGTACACACTCATCATAGCAAGT\n+GCAGATCCCAAATCGGTATCGGCAAAACCACCGGTTGAATTCACCAAAAGCGTGACTCAG\n+TGGTTCACCAAGGATGGAGTTTTGGTGGAGGGCCTTTTCTGGAAX\n+>contig_686 166 28 417 \n+ATGGGGAGCCTACTGAAGCTGGCCAACAGTGTCTTTCGTGGGCAAACACCGAGGATGGTT\n+CATGCGGTCCGCTTCGCTAGTGCCCAGTCTGGAAAGACTCTATACGTTACTGGGCTGTCA\n+GATGAAACTGATGACAAATCTCTTAAGGATGCATTTTCTAAATTTGGTGCTGTTGATAAT\n+GCTAAAGTTATTATCGACGAAAGTACCGGAAGGTCAAAGGGTTACGGTTACGTGAGATTT\n+GAAGAGTACGACCGTGATAAGGTAGCAAAGCATTTAATGGATGGGAAGGAATTGAATGGC\n+AGTAAGATTCGAGTTGAACGTGCGAAGGGGCCAATATCGTGCCTTGGTGCACCTCGCAAG\n+GGCCCAAAGCTTGTATACCTGGGTTTTTGA\n+>contig_687; 138 1 360 minus strand\n+GTCGCCGCCTCAGGCAGTGCACCCGGCGGTCCTCCGCCTAGAAACAAACGTGTGAGGGAT\n+CTGGTGAAGGAAAATGCTGTCGTGATTTTTGCTAGAAACGGCTGCTGCATGTGTCACGTG\n+GTGAAGCATTTGCTGCAAGGCCATGGCGTAAACCCCACAATCTTCGACGTCGACGAGCAA\n+AATGAAGCTGACGTGGTCAAAGATTTGCTCGGGTTTCCCGCGGCAGTAGGCGCCGGCGGC\n+GGAAGACCGGCGCTTCAGTTGCCGGCGGTGTTTGTTGGTGGGGAACTGTTTGGCGGGCTA\n+GATGAAATCATGCGTTCTCATATTTCCGGTGGATTGCTGCCGAAGTTAAGAGCAGCTGGG\n+>contig_688; 98 1 393 minus strand\n+GATAATATTTCCATATTCCAGAACGTAATGCGTGAAGATCCACAAAACGATTACGGGTTG\n+GGGAAAATGAGGGAGGGGCAAAATAGTCTTTTTCAGGATGAGAACCCGAATTGCGGCAGT\n+GAGAGATTCATATCAGCTGCATATCACATTTCAGAGCTGGATAGGTTTGGACATGTTAAT\n+CCGGTAACACTTACGCTTGGATTACAGCAGTGTGAGGGTGATAGCTTATCCATGCATGAT\n+AGCCATAATCATGGTTTTAATCCCCTGAGAGACGGTGTAGTTTATAACGATGCAGCTTCG\n+GCTATGGCCAATGATACAGCGGAATATGATTGCATGGATTCAGGAAATCGACAACATCAA\n+TTCGTCTCCTCACTCCTTCCATCCTTTTCATGA\n+>contig_689 126 1 240 \n+XGTACTAGGGTTGTATTTGATGATGAAGGCAACACCTTACCACCTCTTGCAAAGCTAGCT\n+GGCACCTTGACTGAGTCTGACTCTGTTATGCTGGACAAGGACAAAGTAAGCCAAAGATAC\n+GCCTTGTTGAGAGAAGAAATGAAAGTGGTGGACAAGGAAGATAAAGCATTAGAGCACCAA\n+CGTAGGAAAGAAAAACGCATCAAACAAAAGATGAAGTTGAAAAGAGGTAGAGACGATGAT\n+GXX\n+>contig_690; 82 1 226 minus strand\n+XGCTTGACAGAGGTTCGTGAGGTATTGAGCTCCGATCCAGGGTTTCAGATATCGGATTGT\n+GGGCTTGGCTTGTTCTACCTCGATCGGAAACCAGATTCTGGGATTTTGTCCTTCGTGGAT\n+CCGGAAAGCTCGGGCCGTGGGACAGCCTTTCACGCGATTTCTGGATGTGATTTCCGGCGG\n+CTCAGCCGTGGGACATCCTCTCACGCGATTTCTGGATGTGATTTCCGX\n+>contig_691; 13 1 366 minus strand\n+XCTGGAACACTCACGCAGCCTCTCTATGGGGCTTTTCCGGCTCTCTTAAGGAAGTACATT\n+AAGGTTGCACTTCATTTCTGGGGTACAGGTAACACCGCACTGTCAGTTGTTTCCTTTATA\n+TTCTTAAGAGACTGCTGCATAAGACTCGGTTCCGACTGCCTAGATGATTGCATCAGGGGA\n+ATGTATAAAGCTTATGTCTTGAATTGCCACTTTATTAATTCCACAAAATTGCAGCATATC\n+CAGTTTCTTGGTAATTGCCTTACCGAACTTCTCGGGGTGGACATTCCATCCTCATATCAA\n+CATGCCTTTGTTTACATCCGTCAGTTAGCAATGATATTGAAGGAGACACTTTCGTGTTCC\n+ACGAAAAXX\n+>contig_692; 55 1 217 minus strand\n+CCGAATCCTATTATTCCCATCTCTATCTCCTTGGAAGAGCGCCTTACTCAGTTTGCGACT\n+GAGGCCGAGGCAGACGAAGAGTGCAAGAAGCTCGGTGTCCAGTCGGCACTGCCCAAGGCT\n+ATTGTCACCATGCGCAAGGCTCTCCACCTTGCCTCGTTCTTCACCACCGGCGCAGATGAG\n+GTCAGGCAGTGGACCATCCGCGAGGACACCAAGGCACXX\n+>contig_693 4 1 417 \n+CTCCGCACCACTGGAGCGTGTACCTGGTCTTCCCAACACCTCCTTGCGCATGTCAATGCT\n+CTGCCAATGGAATCATTACTGAAAAAACTGCACATGACGAATGCCCATCCAAACCGGCCC\n+GCCGACACTCTTCACTGTGTTGAGCCGCCGCCTCAACGCCACTCGTAAAACAGAAGAACA\n+CTGCGGGCCTTCCGCCACACACAGCCGCCGCTAGCGTCTCGACCTCCGCTTCCTTTCGTG\n+CGACATTACCCTATCCGTCACGTCGTCAAGTGGGGAATCGTTCATTTCTTCTTGCTCTGG\n+TGCACCGTGTCGATGATCTTGTCAACCACCGAAGGGTCGGACAGCGTTGAGGTGTCGCCC\n+AGTTGGTCCTCCTCGCCAGCCAAGATCTTCCGCAAGATACGGCGCATGATCTTGCCG\n' |
| b |
| diff -r 000000000000 -r 2f0b8e19286b test-data/species1_pep.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/species1_pep.fasta Thu Jun 08 12:53:38 2017 -0400 |
| b |
| b'@@ -0,0 +1,2048 @@\n+>contig_1; 91 1 346 minus strand; translated\n+XKKLYGDKEDILVPDIFWDYTSGKVLTMEWVEGVKLNEQDAVESQGLSVLDLVNTGIQCS\n+LRQLLEYGYFHADPHPGNLLATPDGKLAFLDFGMMSETPEQARSAIIGHVVHMVNR\n+>contig_2 218 1 511 ; translated\n+XLSKVPIPSNNIYAINDKKSPEDAADDYENRLKELVSEKIIPVSTISGFPKFDLMLLGMG\n+PDGHVASLFPSHMQRYEKEKWVTFITDSPKPPPSRITFTFPMINSASEIAMVVTGADLAG\n+TTKIALGTTGNVKPGETPLPCTEVSAEGEVTWFLDKDAASQLLNYVRFDD\n+>contig_3; 134 1 379 minus strand; translated\n+XVDEGVVVAGLSEQEKASVSEILTTARAHSETIENLKRDHSQQVSCIEQHTNDTFRQKYM\n+DYEPTGSTPVRSEPDIPSKGTIESLRAMPIDALEEEFRENHSYESAVTGKELMPSVTTRA\n+PFSQIN\n+>contig_5; -67 1 418 minus strand; translated\n+XGGPPQTHVKRDPASRGLFHAVVPALGPLRDARREGRFGRCRVMPGPDIIKEHSVVPTLA\n+FDDVLGRLAKYRRRASXGAMNPGDASQVTRGAAGESLLALAPSALVLGEEGPTADVEPDD\n+GRFEQVRSGKGXHGKGDTLT\n+>contig_7 103 1 296 ; translated\n+ENEWSGAEFLNEMAAMMTQNKSNENGTGTFEELQQLFDEMFQSDIESFNGCSSSSNETCS\n+NSNKRNSIESSSANFRPENGNESGEISGKKNTRKGKGDX\n+>contig_9 34 1 396 ; translated\n+XLRLKADEEAQCLNQMQRIIFDEIMEHVELEKGGFYFVYRPGGNGKTLWLAIISKLRSEG\n+RIVLAVASSGIALLLVEGGRTAHSRFKIPIDVNEYNNCEIKQNIYLAELICHTNLVIWDE\n+APMTQYFVFEAVX\n+>contig_10; 78 87 343 minus strand; translated\n+MAEENTTTMNLDLNLGPINNSSDDSEPSSRPYTDVAMNLEDWLDSPVRVREVVRHRNHRW\n+RSLWRQIPIPPDTRNLALELIGGNAP\n+>contig_11; 195 1 426 minus strand; translated\n+XAAKVTVAPGSRVAAAGSGVASESPATAEAGVAPGSPAVDFNSHSGSFWSNTDCSSNNGR\n+FGATPTGYHGATPTSTVATGDFGTTPTSGAAVGELGXKSDLSSTAGDPRTMPPTTGDSGV\n+TPPPTTTTGDSGATPPQSVLIF\n+>contig_12; 4 1 330 minus strand; translated\n+XSSSKRSLXRSKSRGEETKKKIAIEKERQERLKSLEARFSTKSVIMRSTVSNRSSFDGTG\n+VELLGDISAGYIINVVREEGEEPVRIPPSICIKLKPHQIQGIRFMWENIIX\n+>contig_13 86 218 428 ; translated\n+MSSGRYMSYSPSPSAPHSPHIGIAGSGGGMRTAASVLIEQEKYLSELLSERNKLSPFVAV\n+LPNSYRLLNQX\n+>contig_14 88 1 250 ; translated\n+XLAATINKYQEEKIQRMKKLKVLVTTMLELWTFLDTHSEEQQSFEHVKCYVAAAAVDEHA\n+QKAYELPGILSLDCLNNVETEVSR\n+>contig_15 133 105 362 ; translated\n+MEEKLVFMWGYLPGALPQRMPILSPMVVRLPHGGGSWKDVCGGGCGFAMAISDSGKLITW\n+GSTDDLGQSYVTSGKHGEMPEPFPLP\n+>contig_16 58 1 282 ; translated\n+GVFPRRPRWVEADGVEDSGVGSIEADSSAMGXPGEIELVLKAVVTAAAGVEEGRERLVAR\n+VVGPGEADEVDASVRLRHRVSIQPTKSEIDVAD\n+>contig_18; 189 1 428 minus strand; translated\n+XTEVRRWNKQEDWGRKTWKEAKESTLPKIVGEGIYGVGPILAALSSGRRELYALYVQEGL\n+DLSSNSKKKDKKRFERVLKMVEKIGLSKKEVSKHDLNMVVDNRPHQGLLLDASALEMVSI\n+KELDPVSIDGEKCPLWLALDEVT\n+>contig_19 51 1 238 ; translated\n+XYKKRYPVVPTLLTRILWWRICLDEAQMVEGNAAAATELAVRLHAKHRWCITGTPIQRKL\n+DDLYGLLRFLQSSPFNVLRX\n+>contig_20 16 1 309 ; translated\n+XAYASMLTDMPYKIGNAICFNLILYFMTNLRREPGAFFFFLLISFTLTLVMSMLFRTIGS\n+VSRTLSQAMAPAAILILALVIYTGFVIPTRYMLGWSRWINYLDX\n+>contig_21; 181 1 520 minus strand; translated\n+XVSIVNQEPVLFSVSIGENIAYGLPDDYVSKVDVIKAAKAANAHEFIIALPQGYDTLVGE\n+RGGLLSGGQRQRVAIARALLKNAPILILDEATSALDAVSERLVQDALNRLMKGRTTLVIA\n+HRLSTVQNADQIALCSDGKISELGTHSELLEQKGLYASLVGTQRLAFEXHINMA\n+>contig_22; 76 1 229 minus strand; translated\n+XLEHLADHHGLAALLMSVLKPGYHFDELLVLDVEGNNLVLSAKCSLVNSTQQLPVDISDI\n+HTHSVVHGYICNIIETG\n+>contig_23; 77 1 213 minus strand; translated\n+XLVSCKNCAVLKQKMSNNVEPVKPIVLDSESDPEENASFEDASSDSDPEPEPNQLTKKSP\n+ALPPATLKNHGX\n+>contig_24; 156 1 332 minus strand; translated\n+XKTRELEIEQILLKSKDLESELESKGSMFIKETEALVAENSKLSQELGAFKSELNDIQMK\n+LNVVSSEKDGTVEELTSARKEIEELTQKLASEGQKLQSQISSIMEENNLLNX\n+>contig_25; 65 1 122 minus strand; translated\n+XGNDYDRGKSSTKSKKGGVKKAIRYQLATIGGGMNWRGRN\n+>contig_27; 61 1 261 minus strand; translated\n+LYKLWKQRIEERRPFQYVVGCEHWRDLILSVEEGVLIPRPETEVILDLVEDAVKKNGELK\n+NGLWADLGTGSGALAIGIARVLGPGCG\n+>contig_28; 14 1 219 minus strand; translated\n+XQFSPNACIIKHREKLPDLESTQTMLLLEESVLNKEKRQGSSHLDSSSSSPTVLVTANNN\n+SARSQTTTPNQSQX\n+>contig_29 303 1 849 ; translated\n+CWXIASKVRSSDRNFRTMKKSKLLQNSKDLLSRSFNPAKCKTSLRLAGSRLKLLRNKKEV\n+QLKQMKREIAQLLESGQDQTARIRVEHLIREEKMMAAYDLLDIYCELVVARLPVIESQKN\n+CPIDLKEAIASLVFAAPRCGDVPEFLDARKQFSAKYGKDFTTAATELRPQCGVGRMLVEK\n+LSATAPDVQSKTKILNAIAEEHNVKWEPTSFGENDSAPLNDRLTGPSSFTKEREQYPEPP\n+HFEAVQVQAHPSNNTLHSSPSNSSQQDDRTSVFVETSTFKTPS\n+>contig_30 158 1 478 ; translated\n+KASGLFSSKDSVDSTDSHMENVCSDILSMSINKNQILENGHVHNNRGAAIFELSGAATNV\n+IEDVGLSDVQSDTRLGMASQVCQVDMHEPEGGLLSFKNQRFKDAE'..b'NANARAYGGLEAEDCQIRCPLSTEPGQVV\n+LPALTQYKNASGEWENTIECWQVDTVSTELPGIDNAFRLDWEGGFDAAYQYVFHGQSFMP\n+AHPAPEPSLIVMSSGIGDLRVPSGRCLRVGAGDIFFSVGTDGRQTAWWSEGTVVSDFYFK\n+GGKIPKHDVVPEAPAGEGAFVVQASDEELLSPAMAGIALGSAALTLLASFQQGSSYTEHN\n+RTGILHLLLEHSMLITRSKTPAISRNRAWAGH\n+>contig_665 86 1 280 ; translated\n+XARVLADDYLHKRSSNTIQNGDTNNRICNQPSRAILLVLQHLEKASLPLPSNGVTCGSWL\n+SNGNGDGADLRSQQKAKTQQWQLVTAFCQMHNIP\n+>contig_666; 70 1 207 minus strand; translated\n+XDDTTNLSQANVVDLECDLSHGKWIHDSTGPLYTNNSCPVITQMQNCQGNGRPDKDYENW\n+RWKPSQCDVX\n+>contig_667; 47 1 278 minus strand; translated\n+XVSLRGRSDLSLLFSYWLLDTQVVSTGAFILNTMPTNDSTTSEPFSSAIAEIRDMLLQLT\n+DDVQNTRRDIEIQRLRTDNVYDVINAGINPNPNX\n+>contig_669 39 1 302 ; translated\n+XDAVEHAIELAELIHEWGPGYHVNLIPFNPVEGSEYQRPYKKSVLAFSAVLESRKVTVSI\n+RQTRGLDANAACGQLRNEFQKIPLLAGTEVEHELEMAVASXX\n+>contig_670 195 156 427 ; translated\n+MSDAKPVETPVAEAIPAAAPASETPVVAEAAPAEEAKTDAPAADAPAADAAAPAATEETT\n+ALPKEEKTGEEEVKITAEPIYSGALGYKAPG\n+>contig_672; 235 1 458 minus strand; translated\n+GIMPTEDELLKFEPSKKEESTDVQWLSQLFGEKEKKKKEVGSVKDKGDGKSEGSSSAFVG\n+NNFEMHDLVFFGRKDFGVVIGSEKDDGVKVLKEGLEGPLVVTVKQTELRSAFFDKKLFFV\n+LDKHSNTLLVNDNVRVLEGPLKDRQGIVKKIYX\n+>contig_673; 52 1 245 minus strand; translated\n+XSGTKVNTTNRSPKSTEQSPNPLNKPQIQSPDXRSLESLRENGTVKAQVDSKQQARASQP\n+PKQLRAPGVVASVSGFFNIARAX\n+>contig_674; 78 1 148 minus strand; translated\n+XNSVISSSEELKSRAHTGEAANGASVAVRSNSYTISVCKTFGRFSLCAS\n+>contig_676; 156 1 453 minus strand; translated\n+LVLFSDGKTIGACLDRNGLRPARYWRTVDNVVYVASEVGVIPTDDSKVVMKGRLGPGMMI\n+TVDLHKGQVFENTEVKKRVALSNPYGKWVNENLRPLKAANFMSTTVMDNETILKRQQAYG\n+YSSEDVQMVVEAMASQAKEPTFCMGDDIPLA\n+>contig_677; 23 1 259 minus strand; translated\n+XELNLGELWRDDENNLLKGFQQCILLALTEELTWCLRSTGDRTAEATTFEAALLIIPRIP\n+IIFNRSEKKSSSRSEERFSRNAETDLV\n+>contig_678 88 1 359 ; translated\n+XVLSEFCGDSALDFDGFGDSFRRKKLTAHWRTFIQPIMWRCKWTELQIKKLQSLAQKYDR\n+ELEAHNKPKLIQVEDSTLIDGVKSLPFSRMNAVNDLVKRKRRRVTEATTDVAEYMSRHNL\n+X\n+>contig_679; 122 45 224 minus strand; translated\n+MERDISTDPIYTEAEVFCDLDTIPPVLKQITGCCSATSLVDNISTICNRCLKKEKEKPIE\n+>contig_682; -120 1 364 minus strand; translated\n+XLGRHHLGRHHRSPPPGILLLXHLGCPVADRDRAHEPERAPLIPAAPSSSSSSGTPHTAS\n+LLRQPASPSSSSQNPPPRISGDDHDYNVQYGDIQPVLQPHSPALLAEMEKVKSSRVAHYA\n+HK\n+>contig_683 123 130 332 ; translated\n+KTLETSIETTRRELENPTEVEIELKRRLHHLTDHLIQKQAQVETLSSEKAMLLLRIEAVL\n+RMLDEYKP\n+>contig_684; 108 1 532 minus strand; translated\n+XNSEKKINEIVAAYDFTNSNENLFNVSIWYNSTYRNDTGNQALALTRVPRSVNLASNAYL\n+EFLLGPTTKMLFEFVKEMPKPGTTLRLDLSSLLGPLFFTWVIVQLFPVVLISLVYEKQHR\n+LRIMMKMHGLGDGPYWMISYAYFLAISSIYMFCFVIFGSAIGLNFFKLNDYSIQFVFX\n+>contig_685 255 60 583 ; translated\n+MQENKGETASNKNPKKANLLDHHSIKHILDESVTEIVTSKGYPEDVRMSNIRLLLGVVII\n+VIAIFAQFYNKKFPENRNFLISCIALYVVFNGLLQLIIYLKEKNAIMFTYPLPGSFNSTG\n+LVVTSKLRRFSDLYTLIIASADPKSVSAKPPVEFTKSVTQWFTKDGVLVEGLFWX\n+>contig_686 166 28 417 ; translated\n+MGSLLKLANSVFRGQTPRMVHAVRFASAQSGKTLYVTGLSDETDDKSLKDAFSKFGAVDN\n+AKVIIDESTGRSKGYGYVRFEEYDRDKVAKHLMDGKELNGSKIRVERAKGPISCLGAPRK\n+GPKLVYLGF\n+>contig_687; 138 1 360 minus strand; translated\n+VAASGSAPGGPPPRNKRVRDLVKENAVVIFARNGCCMCHVVKHLLQGHGVNPTIFDVDEQ\n+NEADVVKDLLGFPAAVGAGGGRPALQLPAVFVGGELFGGLDEIMRSHISGGLLPKLRAAG\n+>contig_688; 98 1 393 minus strand; translated\n+DNISIFQNVMREDPQNDYGLGKMREGQNSLFQDENPNCGSERFISAAYHISELDRFGHVN\n+PVTLTLGLQQCEGDSLSMHDSHNHGFNPLRDGVVYNDAASAMANDTAEYDCMDSGNRQHQ\n+FVSSLLPSFS\n+>contig_689 126 1 240 ; translated\n+XTRVVFDDEGNTLPPLAKLAGTLTESDSVMLDKDKVSQRYALLREEMKVVDKEDKALEHQ\n+RRKEKRIKQKMKLKRGRDDDX\n+>contig_690; 82 1 226 minus strand; translated\n+XLTEVREVLSSDPGFQISDCGLGLFYLDRKPDSGILSFVDPESSGRGTAFHAISGCDFRR\n+LSRGTSSHAISGCDFR\n+>contig_691; 13 1 366 minus strand; translated\n+XGTLTQPLYGAFPALLRKYIKVALHFWGTGNTALSVVSFIFLRDCCIRLGSDCLDDCIRG\n+MYKAYVLNCHFINSTKLQHIQFLGNCLTELLGVDIPSSYQHAFVYIRQLAMILKETLSCS\n+TKX\n+>contig_692; 55 1 217 minus strand; translated\n+PNPIIPISISLEERLTQFATEAEADEECKKLGVQSALPKAIVTMRKALHLASFFTTGADE\n+VRQWTIREDTKAX\n+>contig_693 4 1 417 ; translated\n+LRTTGACTWSSQHLLAHVNALPMESLLKKLHMTNAHPNRPADTLHCVEPPPQRHSXNRRT\n+LRAFRHTQPPLASRPPLPFVRHYPIRHVVKWGIVHFFLLWCTVSMILSTTEGSDSVEVSP\n+SWSSSPAKIFRKIRRMILP\n' |
| b |
| diff -r 000000000000 -r 2f0b8e19286b tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Jun 08 12:53:38 2017 -0400 |
| b |
| @@ -0,0 +1,6 @@ +<tables> + <table name="plant_tribes_scaffolds" comment_char="#"> + <columns>value, name, path, description</columns> + <file path="tool-data/plant_tribes_scaffolds.loc" /> + </table> +</tables> |