| Previous changeset 5:a73c2e65098e (2017-08-25) Next changeset 7:2ac7090847f9 (2017-12-21) |
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Commit message:
Uploaded |
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modified:
.shed.yml gene_family_aligner.xml macros.xml utils.py |
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added:
test-data/3722.faa test-data/3722.faa.aln test-data/3722.fna test-data/3722.fna.aln test-data/38889.faa test-data/38889.faa.aln test-data/38889.fna test-data/38889.fna.aln test-data/39614.faa test-data/39614.faa.aln test-data/39614.fna test-data/39614.fna.aln |
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removed:
gene_family_aligner.py |
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| diff -r a73c2e65098e -r 3384b6a842b0 .shed.yml --- a/.shed.yml Fri Aug 25 13:01:25 2017 -0400 +++ b/.shed.yml Mon Oct 30 09:52:00 2017 -0400 |
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| @@ -7,7 +7,7 @@ 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 aligns gene family sequences. -remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/plant_tribes/gene_family_aligner +remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/phylogenetics/plant_tribes/gene_family_aligner type: unrestricted categories: - Phylogenetics |
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| diff -r a73c2e65098e -r 3384b6a842b0 gene_family_aligner.py --- a/gene_family_aligner.py Fri Aug 25 13:01:25 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,58 +0,0 @@ -#!/usr/bin/env python -import argparse -import os - -import utils - -OUTPUT_DIR = 'geneFamilyAlignments_dir' - -parser = argparse.ArgumentParser() -parser.add_argument('--alignment_method', dest='alignment_method', help='Multiple sequence alignments method') -parser.add_argument('--automated_trimming', dest='automated_trimming', default=None, help='Trims alignments using trimAls ML heuristic trimming approach') -parser.add_argument('--codon_alignments', dest='codon_alignments', default=None, help='Flag for constructing orthogroup multiple codon alignments') -parser.add_argument('--gap_trimming', dest='gap_trimming', default=0, type=float, help='Remove sites in alignments with gaps of') -parser.add_argument('--iterative_realignment', dest='iterative_realignment', type=int, default=0, help='Maximum number of iterations') -parser.add_argument('--num_threads', dest='num_threads', type=int, help='Number of threads to use for execution') -parser.add_argument('--orthogroup_faa', dest='orthogroup_faa', help='Directory of input fasta datasets') -parser.add_argument('--output', dest='output', help='Output dataset') -parser.add_argument('--output_dir', dest='output_dir', help='Output dataset files_path directory') -parser.add_argument('--output_dataset_collection', dest='output_dataset_collection', default=None, help='Output additional dataset collection of files.') -parser.add_argument('--pasta_iter_limit', dest='pasta_iter_limit', type=int, default=None, help='Maximum number of iteration that the PASTA algorithm will execute') -parser.add_argument('--pasta_script_path', dest='pasta_script_path', default=None, help='Path to script for executing pasta') -parser.add_argument('--remove_sequences', dest='remove_sequences', default=0, type=float, help='Remove sequences with gaps of') - -args = parser.parse_args() - -# Build the command line. -cmd = 'GeneFamilyAligner' -cmd += ' --orthogroup_faa %s' % args.orthogroup_faa -cmd += ' --alignment_method %s' % args.alignment_method -if args.alignment_method == 'pasta': - if args.pasta_script_path is not None: - cmd += ' --pasta_script_path %s' % args.pasta_script_path - if args.pasta_iter_limit is not None: - cmd += ' --pasta_iter_limit %d' % args.pasta_iter_limit -cmd += ' --num_threads %d' % args.num_threads -if args.codon_alignments is not None: - cmd += ' --codon_alignments' -if args.automated_trimming is not None: - cmd += ' --automated_trimming' -if args.gap_trimming > 0: - cmd += ' --gap_trimming %4f' % args.gap_trimming -if args.remove_sequences > 0: - cmd += ' --remove_sequences %4f' % args.remove_sequences -if args.iterative_realignment > 0: - cmd += ' --iterative_realignment %d' % args.iterative_realignment - -# Run the command. -utils.run_command(cmd) - -# Handle outputs. -if args.codon_alignments is None: - src_output_dir = OUTPUT_DIR -else: - src_output_dir = os.path.join(OUTPUT_DIR, 'orthogroups_aln') -if args.output_dataset_collection is not None: - utils.move_directory_files(src_output_dir, args.output_dataset_collection, copy=True) -utils.move_directory_files(src_output_dir, args.output_dir) -utils.write_html_output(args.output, 'Aligned gene family sequences', args.output_dir) |
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| diff -r a73c2e65098e -r 3384b6a842b0 gene_family_aligner.xml --- a/gene_family_aligner.xml Fri Aug 25 13:01:25 2017 -0400 +++ b/gene_family_aligner.xml Mon Oct 30 09:52:00 2017 -0400 |
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| b'@@ -1,36 +1,30 @@\n-<tool id="plant_tribes_gene_family_aligner" name="GeneFamilyAligner" version="@WRAPPER_VERSION@.2">\n+<tool id="plant_tribes_gene_family_aligner" name="GeneFamilyAligner" version="@WRAPPER_VERSION@.3.0">\n <description>aligns integrated orthologous gene family clusters</description>\n <macros>\n <import>macros.xml</import>\n </macros>\n- <expand macro="requirements_gene_family_aligner" />\n+ <requirements>\n+ <requirement type="package" version="1.0.3">plant_tribes_gene_family_aligner</requirement>\n+ </requirements>\n <command detect_errors="exit_code"><![CDATA[\n-#set input_format = $input_format_cond.input_format\n-#set alignment_method_cond = $input_format_cond.alignment_method_cond\n #set alignment_method = $alignment_method_cond.alignment_method\n-#if str($input_format_cond.input_format) == \'ptortho\':\n- #set output_codon_alignments = False\n-#else if str($input_format_cond.input_format) == \'ptorthocs\' and str($input_format_cond.codon_alignments ) == \'no\':\n- #set output_codon_alignments = False\n-#else:\n- #set output_codon_alignments = True\n-#end if\n-\n-python \'$__tool_directory__/gene_family_aligner.py\'\n+#set input_dir = \'input_dir\'\n+mkdir $input_dir &&\n+#for $i in $input:\n+ #set filename = $i.file_name\n+ #set name = $i.name\n+ ln -s $filename $input_dir/$name &&\n+#end for\n+GeneFamilyAligner\n --alignment_method $alignment_method\n #if str($alignment_method) == \'pasta\':\n --pasta_script_path \'$__tool_directory__/run_pasta.py\'\n --pasta_iter_limit $alignment_method_cond.pasta_iter_limit\n #end if\n --num_threads \\${GALAXY_SLOTS:-4}\n-#if str($input_format) == \'ptortho\':\n- --orthogroup_faa \'$input_format_cond.input_ptortho.extra_files_path\'\n-#else:\n- ## str($input_format) == \'ptorthocs\'\n- --orthogroup_faa \'$input_format_cond.input_ptorthocs.extra_files_path\'\n- #if str($input_format_cond.codon_alignments) == \'yes\':\n- --codon_alignments true\n- #end if\n+--orthogroup_faa \'$input_dir\'\n+#if str($codon_alignments) == \'yes\':\n+ --codon_alignments\n #end if\n #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences\n #if str($remove_gappy_sequences) == \'yes\':\n@@ -40,7 +34,7 @@\n --gap_trimming $trim_type_cond.gap_trimming\n #else:\n ## str($trim_type) == \'automated_trimming\'\n- --automated_trimming true\n+ --automated_trimming\n #end if\n #set remove_sequences_with_gaps_cond = $remove_gappy_sequences_cond.remove_sequences_with_gaps_cond\n #set remove_sequences_with_gaps = $remove_sequences_with_gaps_cond.remove_sequences_with_gaps\n@@ -51,90 +45,116 @@\n #if str($remove_sequences_with_gaps_cond.iterative_realignment):\n --iterative_realignment $remove_sequences_with_gaps_cond.iterative_realignment\n #end if\n- #if $output_codon_alignments:\n- --output \'$output_aln_filtered_ca\'\n- --output_dir \'$output_aln_filtered_ca.files_path\'\n- #else:\n- --output \'$output_aln_filtered\'\n- --output_dir \'$output_aln_filtered.files_path\'\n- #end if\n- #else:\n- #if $output_codon_alignments:\n- --output \'$output_aln_trimmed_ca\'\n- --output_dir \'$output_aln_trimmed_ca.files_path\'\n- #else:\n- --output \'$output_aln_trimmed\'\n- --output_dir \'$output_aln_trimmed.files_path\'\n- #end if\n- #end if\n-#else:\n- #if $output_codon_alignments:\n- --output \'$output_aln_ca\'\n- --output_dir \'$output_aln_ca.files_path\'\n- #else:\n- --output \'$output_aln\'\n- --output_dir \'$output_aln.files_path\'\n #end if\n #end if\n-#if str($output_dataset_collection) == \'yes\':\n- --output_dataset_collection dataset_collection\n-#end if\n+&>proc.log\n ]]></command>\n <inputs>\n- <conditional name="input_format_cond">\n- <param name="input_format" type="select" label="Classified orthogroup fasta files">\n- <option value="ptortho">Prot'..b'y_sequences_cond[\'remove_sequences_with_gaps_cond\'][\'remove_sequences_with_gaps\'] == \'yes\'</filter>\n+ </collection>\n+\n </outputs>\n <tests>\n- <!-- Test framework does not currently support inputs whose associated extra_files_path contains files to be analyzed.\n <test>\n+ <param name="input">\n+ <collection type="list">\n+ <element name="3722.faa" value="3722.faa"/>\n+ <element name="3722.fna" value="3722.fna"/>\n+ <element name="38889.faa" value="38889.faa"/>\n+ <element name="38889.fna" value="38889.fna"/>\n+ <element name="39614.faa" value="39614.faa"/>\n+ <element name="39614.fna" value="39614.fna"/>\n+ </collection>\n+ </param>\n+ <param name="codon_alignments" value="yes"/>\n+ <output_collection name="primary_faa" type="list">\n+ <element name="3722.faa.aln" file="3722.faa.aln" ftype="fasta"/>\n+ <element name="38889.faa.aln" file="38889.faa.aln" ftype="fasta"/>\n+ <element name="39614.faa.aln" file="39614.faa.aln" ftype="fasta"/>\n+ </output_collection>\n+ <output_collection name="primary_fna" type="list">\n+ <element name="3722.fna.aln" file="3722.fna.aln" ftype="fasta"/>\n+ <element name="38889.fna.aln" file="38889.fna.aln" ftype="fasta"/>\n+ <element name="39614.fna.aln" file="39614.fna.aln" ftype="fasta"/>\n+ </output_collection>\n </test>\n- -->\n </tests>\n <help>\n This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary\n@@ -145,13 +165,13 @@\n \n **Required options**\n \n- * **Classified orthogroup fasta files** - orthogroup fasta files produced by the GeneFamilyClassifier tool selected from your history. Depending on how the GeneFamilyClassifier tool was executed, these could either be proteins or proteins and their corresponding coding sequences.\n+ * **Integrated orthogroup fasta files** - orthogroup fasta files produced by the GeneFamilyIntegrator tool selected from your history. Depending on how the GeneFamilyClassifier tool was executed, these could either be proteins or proteins and their corresponding coding sequences.\n \n * **Multiple sequence alignment method** - method for estimating orthogroup multiple sequence alignments. PlantTribes estimates alignments using either MAFFT\'s L-INS-i algorithm or the divide and conquer approach implemented in the PASTA pipeline for large alignments.\n \n - **PASTA iteration limit** - number of PASTA iterations. By default, PASTA performs 3 iterations.\n \n- * **Codon alignments** - select \'Yes\' to create codon multiple sequence alignments. This option requires protein and their corresponding coding sequences to be provided as input data.\n+ * **Codon alignments** - select \'Yes\' to create codon multiple sequence alignments. This option requires both protein and their corresponding coding sequence orthogroup fasta files to be present in the GeneFamilyAligner input data that was produced by the GeneFamilyIntegrator.\n \n **Other options**\n \n@@ -167,7 +187,7 @@\n \n - **Realignment iteration limit** - number of iterations to perform trimming, removal of sequences, and realignment of orthogroup sequences. Zero value has no effect.\n \n- * **Output additional dataset collection of files** - selecting \'Yes\' will produce an additional output dataset collection whose elements are copies of the directories of files (these elements can be viewed with visualization tools).\n+ * **Output primary and intermediate alignments** - selecting \'Yes\' will produce a dataset collection of primary and intermediate alignments, the elements of which can be viewed with viaula tools, in addition to the final trimmed and/or filtered alignments dataset collection.\n \n .. _trimAl: http://trimal.cgenomics.org\n \n' |
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| diff -r a73c2e65098e -r 3384b6a842b0 macros.xml --- a/macros.xml Fri Aug 25 13:01:25 2017 -0400 +++ b/macros.xml Mon Oct 30 09:52:00 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 a73c2e65098e -r 3384b6a842b0 test-data/3722.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3722.faa Mon Oct 30 09:52:00 2017 -0400 |
| b |
| 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 a73c2e65098e -r 3384b6a842b0 test-data/3722.faa.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3722.faa.aln Mon Oct 30 09:52:00 2017 -0400 |
| b |
| b'@@ -0,0 +1,312 @@\n+>gnl_Glyma1.01_PACid_16266208\n+---MANE-------------------------------------------------GKKS\n+NNFYSILGLSKECTELELKNAYRKLAKKWHPDRCSATG---NLELVEEAKKKFQEIREAY\n+S------VLSDANKRLMYDVGVYDS--------DDDENGMGDFLDEMLTMMSHTKSNENG\n+--EESFEELQ------QLFEDMFQADI--GL----------DGGPSL-------------\n+----ASSDSSTSSA------------------YMTYSESSS---------SNKRNSS-EM\n+NFGK---AENSSVFDASY------QNFCFG-VN--QLQDIKKGK---GGILGGGGRSRHR\n+SGRKQKMFY-GHDV--------------------------\n+>gnl_Glyma1.01_PACid_16266209\n+---MANE-------------------------------------------------GKKS\n+NNFYSILGLSKECTELELKNAYRKLAKKWHPDRCSATG---NLELVEEAKKKFQEIREAY\n+S------VLSDANKRLMYDVGVYDS--------DDDENGMGDFLDEMLTMMSHTKSNENG\n+--EESFEELQ------QLFEDMFQADI--GL----------DGGPSL-------------\n+----ASSDSSTSSA------------------YMTYSESSS---------SNKRNSS-EM\n+NFGK---AENSSVFDASY------QNFCFG-TG--EPTPRYKEG--------KGGNSRRR\n+R---------------------------------------\n+>gnl_Glyma1.01_PACid_16266210\n+---MANE-------------------------------------------------GKKS\n+NNFYSILGLSKECTELELKNAYRKLAKKWHPDRCSATG---NLELVEEAKKKFQEIREAY\n+S------VLSDANKRLMYDVGVYDS--------DDDENGMGDFLDEMLTMMSHTKSNENG\n+--EESFEELQ------QLFEDMFQADI--GL----------DGGPSL-------------\n+----ASSDSSTSSA------------------YMTYSESSS---------SNKRNSS-EM\n+NFGK---AENSSVFDASY------QNFCFG-VG--HVNYHYQ------------------\n+----------------------------------------\n+>gnl_Glyma1.01_PACid_16301083\n+---MADE-------------------------------------------------GNKS\n+NNFYSILGLKKECTELELKNAYRKLAKKWHPDRCSATG---NSELVEEAKKKFQEIREAY\n+S------VLSDANKRLMYDVGVYDS--------DDDENGMGDFLDEMLTMMSQTKSNENG\n+--EESFEELQ------QLFEDMFEADI--GL----------DGGPSL-------------\n+----ASSDCSTSSA------------------YMTYSESSS---------SNKHNSS-EM\n+NFGK---AENSSVFDAGY------QNFCFG-VN--QLQDIKKKK---GGIL-GGGRSRHR\n+NGRKQNMSY-GHDVSSNDYPGISTK---------------\n+>gnl_Glyma1.01_PACid_16301085\n+---MADE-------------------------------------------------GNKS\n+NNFYSILGLKKECTELELKNAYRKLAKKWHPDRCSATG---NSELVEEAKKKFQEIREAY\n+S------VLSDANKRLMYDVGVYDS--------DDDENGMGDFLDEMLTMMSQTKSNENG\n+--EESFEELQ------QLFEDMFEADI--GL----------DGGPSL-------------\n+----ASSDCSTSSA------------------YMTYSESSS---------SNKHNSS-EM\n+NFGK---AENSSVFDAGY------QNFCFG-VG--HVNYHYQ------------------\n+----------------------------------------\n+>gnl_Glyma1.01_PACid_16301084\n+---MADE-------------------------------------------------GNKS\n+NNFYSILGLKKECTELELKNAYRKLAKKWHPDRCSATG---NSELVEEAKKKFQEIREAY\n+S------VLSDANKRLMYDVGVYDS--------DDDENGMGDFLDEMLTMMSQTKSNENG\n+--EESFEELQ------QLFEDMFEADI--GL----------DGGPSL-------------\n+----ASSDCSTSSA------------------YMTYSESSS---------SNKHNSS-EM\n+NFGK---AENSSVFDAGY------QNFCFG-TG--EPTPRYKEE--------KGGNSRRR\n+----------------------------------------\n+>gnl_Medtr3.5_Medtr8g022310.1\n+---MANE-------------------------------------------------GNKS\n+NDFYAVLGLNKECSDSELRNAYKKLALKWHPDRCSASG---NVKFVEEAKKKFQAIQEAY\n+S------VLSDSNKRLMYDVGVYDS--------DDDENGMGDFLNEMVTMMSQTKSNENG\n+--EESFEELQ------QLFDDMFQADI--GL----------NGSTSL-------------\n+----NASGCSTSST------------------FMTFSESSN---------SNKRNST-QM\n+NFGK---AEDSSSFGANY------QNFCFG-MK--HLQEDVEKE--KGGILEGGGSKKQR\n+KGRKQKISC-GH-VSSNDHPGISAN---------------\n+>gnl_Medtr3.5_Medtr8g022310.2\n+---MANE-------------------------------------------------GNKS\n+NDFYAVLGLNKECSDSELRNAYKKLALKWHPDRCSASG---NVKFVEEAKKKFQAIQEAY\n+S------VLSDSNKRLMYDVGVYDS--------DDDENGMGDFLNEMVTMMSQTKSNENG\n+--EESFEELQ------QLFDDMFQADI--GL----------NGSTSL-------------\n+----NASGCSTSST------------------FMTFSESSN---------SNKRNST-QM\n+NFGK---AEDSSSFGANY------QNFCFG-VN--LVNYHYQ------------------\n+----------------------------------------\n+>gnl_Musac1.0_GSMUA_Achr6T31040_001\n+---MAAE-------------------------------------------------EDKS\n+GDFYAVLGLRKECSETELRNAYKKLAMRWHPDKCLASG---NAQIVGEAKEKFQEIQKAY\n+S------VLSDSNKRFLYDVGVYDND------DDNDENGMGDFIGEMLEMMSQTKPNENS\n+--QDSFQELQ------ELFVEMFQDDL--DAG---------FGGSIFH-DCPWAQP----\n+---TNGQDCWTSSG------------------LHFANGRSK--------CGNKRGNS-AV\n+NLGK----VNLEELEHGT------SDFYFG-LN--DAAQPSQGKGGS--------NNKRR\n+NGRKQKVSS-N'..b'HDVSSEDETAGS-----------------\n+>gnl_Thepa2.0_Tp3g12470\n+---MASNN-----------------------------------------------SEKGN\n+DDLYGVLGLKKECTTTELRTAYKKLALRWHPDRCSSMG---TPEFVDEAKKKFQAIQEAY\n+S------VLSDSNKRFLYDVGAYNS-------DDEDQNGMGDFLNEMAAMMNQSKPSENN\n+-SGDSFEQLQ------DLFNEMFQGDA--AA----------FSSSSS-------------\n+------SSCSASTF------------------TSSCSFVFD--------TNSQRSPF-ET\n+SSMG---TNDLFGFDHSA------HTFSLG-VE--HQQDFKKGKN----------SGGRR\n+NRRKNNAQSAAHETASSNNYGVPTS---------------\n+>gnl_Theca1.0_Tc06_g010450\n+---MANG-------------------------------------------------EEKN\n+NDFYAVLGLNKECTPTELRTAYKKLALRWHPDRCSASG---NSKFVEEAKKKFQAIQQAY\n+S------VLSDSNKRFLYDVGAYDS--------DDDENGMGDFLNEMAGMMSQTKSNENG\n+--GESFEELQ------ELFEEMFQADI--DS----------FESTGQ-------------\n+----STPSCSASSS------------------FGSYGESSS---------SNKRNSS-EM\n+SSVE-TRLESSSSFDAQF------HSFCLG-VE--HRQDIKQHRGARGGMRGAAGGSRRR\n+NGRKQKVSS-GHDVTSND-CGISAS---------------\n+>gnl_Vitvi12X_PACid_17827068\n+---MAAG-------------------------------------------------EEKS\n+NDFYAVLGLKKECTASELRNAYKRLALMWHPDRCSSSG---NSKFVEEAKKKFQAIQEAY\n+S------VLSDANKRFLYDVGAYDS--------DDDENGMGDFLNEMAVMMSQTKSNENG\n+--KESFEELQ------ELFEDMFQRDV--DA----------FNSASHH------------\n+----PMNSFPSSTS------------------TSSYCESSN--------ANNKRNSA-EM\n+GSGRMMSAGESSAFDAHF------QSFCFG-T-----------GGTPGRFQEGE-RSKRR\n+NSRRSQR---------------------------------\n+>gnl_Selmo1.0_PACid_15401289\n+---M----------------------------------------------------EKRK\n+EDPYTVLGVQKSSSSSEIRSAYRKLAMKWHPDK--------QHSLEDQAKAKFQGIQEAY\n+S------VLSDDKKRVLYDSGLYDEG------DDE-------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+-------------------------------VS---------------------------\n+----------------------------------------\n+>gnl_Orysa6.0_PACid_16864430\n+---MARGGG-----------------------------------G----------GGGAD\n+ADLYAVLGLSRECTDADLRLAYRKLAMIWHPDRCSVAGGSASAAGVDEAKERFQEIQGAY\n+S------VLSDSNKRFLYDVGVYDGNDGDDDDDEADLSGMGDFLGEMAQMMSQATP----\n+--AESFEELQ------QLFVDMFQDDI--DAG---------LCQSTP-------------\n+----PPPSWPSPPA-------------------AANARSPAAAAT-SRKGVNKRCSP-AA\n+MDMD-----SGLSSLLGI------SGFCFE-AP--WTSQDASTAAGGG-------GGKRR\n+KQRPPPA---SHNV--------------------------\n+>gnl_Sorbi1.4_PACid_1982925\n+---MAATSH-----------------------------------CGNIQDQDEEASAPGA\n+ADLYAVLGLNRECTDAELRVAYRRLAMIWHPDRCSASG--SSPARMEEAKERFQEIQGAY\n+S------VLSDSNKRLLYDVGVYDSDD-----DEADLSGMGDFLGEMADMMSQATP----\n+--TETFEELQ------QVFVDMFQDDLD-DAG---------FFGGLPT-TGRRAQA--PS\n+TSLPPSVSSSPLRP----------------TPAAGRSKGPQATPSSSFKGVERRGST-ST\n+AKRPRPNGSAGLESDLGL------SGFCFM-VS--KEMSKSKERQAV---WASD-DGDRS\n+TDGKQRLST-SRDVSGGG-MSRSLQGQSSKNLLQCMASKS\n+>gnl_Medtr3.5_Medtr8g022310.3\n+---MANE-------------------------------------------------GNKS\n+NDFYAVLGLNKECSDSELRNAYKKLALKWHPDRCSASG---NVKFVEEAKKKFQAIQEAY\n+S------VLSDSNKRLMYDVGVYDS--------DDDENVRHLF-----------------\n+---HTIHELG------TLFCVMFCFFISLR------------GE----------------\n+---------KRSNL------------------NLTFSLSH--------------------\n+------------------------------------------------------------\n+----------------------------------------\n+>gnl_Nelnu1.0_NNU_000115-RA\n+---MEVD------------------------------------------------SHRSS\n+PSYYTILGVDQNSSASEIRNAYRKLAMQWHPDKWTKTP-----SLLEKAKSKFQQIQEAY\n+SGGLLVFMLSDQGKRTLYDVGLYDPDD-----ETNDEVGLRRF--HAGDDISHERC----\n+--EETGEEIQLGGTTGDVSGNVTRAGV--EDGECWWCVVVRWSCSLKE------------\n+----------------------------------------------------------EL\n+KEGQ--------------------MGIISE-SD--DA-----------------------\n+----------GHDTPSLPHLHGSEL-----ELLGRTGCCN\n+>contig_7\n+------------------------------------------------------------\n+------------------------------------------------------------\n+----------------------------------ENEWSGAEFLNEMAAMMTQNKSNENG\n+--TGTFEELQ------QLFDEMFQSDI--ES----------FNGCSSS------------\n+----SNETCS---------------------------------------NSNKRNSI-ES\n+SSAN----------------FRPENGNESG-----------------------E-ISGKK\n+NTRKGKGDX-------------------------------\n' |
| b |
| diff -r a73c2e65098e -r 3384b6a842b0 test-data/3722.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3722.fna Mon Oct 30 09:52:00 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 a73c2e65098e -r 3384b6a842b0 test-data/3722.fna.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3722.fna.aln Mon Oct 30 09:52:00 2017 -0400 |
| b |
| b'@@ -0,0 +1,819 @@\n+>gnl_Glyma1.01_PACid_16266208\n+---------ATGGCTAATGAA---------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------GGAAAGAAAAGC\n+AATAACTTCTATTCGATCTTGGGCTTGAGCAAGGAGTGCACTGAATTGGAGCTAAAGAAT\n+GCTTATAGGAAACTTGCAAAGAAATGGCACCCAGATCGTTGTTCAGCCACCGGG------\n+---AATTTAGAGTTAGTGGAAGAAGCTAAGAAAAAATTTCAGGAAATTCGGGAAGCCTAT\n+TCT------------------GTTTTATCTGACGCCAACAAAAGGTTAATGTACGACGTG\n+GGAGTCTACGACAGT------------------------GATGACGACGAAAACGGCATG\n+GGGGACTTCTTGGACGAAATGTTAACAATGATGAGTCATACCAAATCAAATGAAAATGGA\n+------GAGGAGAGCTTTGAGGAGTTGCAA------------------CAGCTTTTTGAA\n+GACATGTTTCAAGCGGATATT------GGATTG---------------------------\n+---GATGGAGGCCCTTCTCTT---------------------------------------\n+------------GCTTCTTCTGATTCCTCAACTTCATCTGCT------------------\n+------------------------------------TACATGACTTACAGTGAAAGTTCT\n+AGT---------------------------TCAAATAAACGCAATTCCTCT---GAGATG\n+AATTTCGGGAAG---------GCAGAGAATTCTTCTGTCTTTGATGCCAGTTAC------\n+------------CAGAATTTCTGTTTTGGG---GTGAAC------CAACTCCAAGATATA\n+AAGAAGGGAAAG---------GGGGGAATTCTAGGAGGAGGAGGTAGAAGTAGACACAGA\n+AGTGGCAGAAAGCAAAAAATGTTCTAT---GGCCATGATGTT------------------\n+------------------------------------------------------------\n+>gnl_Glyma1.01_PACid_16266209\n+---------ATGGCTAATGAA---------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------GGAAAGAAAAGC\n+AATAACTTCTATTCGATCTTGGGCTTGAGCAAGGAGTGCACTGAATTGGAGCTAAAGAAT\n+GCTTATAGGAAACTTGCAAAGAAATGGCACCCAGATCGTTGTTCAGCCACCGGG------\n+---AATTTAGAGTTAGTGGAAGAAGCTAAGAAAAAATTTCAGGAAATTCGGGAAGCCTAT\n+TCT------------------GTTTTATCTGACGCCAACAAAAGGTTAATGTACGACGTG\n+GGAGTCTACGACAGT------------------------GATGACGACGAAAACGGCATG\n+GGGGACTTCTTGGACGAAATGTTAACAATGATGAGTCATACCAAATCAAATGAAAATGGA\n+------GAGGAGAGCTTTGAGGAGTTGCAA------------------CAGCTTTTTGAA\n+GACATGTTTCAAGCGGATATT------GGATTG---------------------------\n+---GATGGAGGCCCTTCTCTT---------------------------------------\n+------------GCTTCTTCTGATTCCTCAACTTCATCTGCT------------------\n+------------------------------------TACATGACTTACAGTGAAAGTTCT\n+AGT---------------------------TCAAATAAACGCAATTCCTCT---GAGATG\n+AATTTCGGGAAG---------GCAGAGAATTCTTCTGTCTTTGATGCCAGTTAC------\n+------------CAGAATTTCTGTTTTGGG---ACAGGT------GAACCAACTCCAAGA\n+TATAAAGAAGGG------------------------AAAGGGGGGAATTCTAGGAGGAGG\n+AGG---------------------------------------------------------\n+------------------------------------------------------------\n+>gnl_Glyma1.01_PACid_16266210\n+---------ATGGCTAATGAA---------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------GGAAAGAAAAGC\n+AATAACTTCTATTCGATCTTGGGCTTGAGCAAGGAGTGCACTGAATTGGAGCTAAAGAAT\n+GCTTATAGGAAACTTGCAAAGAAATGGCACCCAGATCGTTGTTCAGCCACCGGG------\n+---AATTTAGAGTTAGTGGAAGAAGCTAAGAAAAAATTTCAGGAAATTCGGGAAGCCTAT\n+TCT------------------GTTTTATCTGACGCCAACAAAAGGTTAATGTACGACGTG\n+GGAGTCTACGACAGT------------------------GATGACGACGAAAACGGCATG\n+GGGGACTTCTTGGACGAAATGTTAACAATGATGAGTCATACCAAATCAAATGAAAATGGA\n+------GAGGAGAGCTTTGAGGAGTTGCAA------------------CAGCTTTTTGAA\n+GACATGTTTCAAGCGGATATT------GGATTG---------------------------\n+---GATGGAGGCCCTTCTCTT---------------------------------------\n+------------GCTTCTTCTGATTCCTCAACTTCATCTGCT------------------\n+------------------------------------TACATGACTTACAGTGAAAGTTCT\n+AGT---------------------------TCAAATAAACGCAATTCCTCT---GAGATG\n+AATTTCGGGAAG---------GCAGAGAATTCTTCTGTCTTTGATGCCAGTTAC------\n+------------CAGAATTTCTGTTTTGGG---GTCGGT------CATGTAAACTATCAT\n+TACCAA------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+>gnl_Glyma1.01_PACid_16301083\n+---------ATGGCCGATGAA---------------------------------------\n+------------------------------------------------------------\n+------------'..b'------AAGGAGATGAGCAAG\n+TCGAAGGAGAGGCAAGCGGTA---------TGGGCCAGTGAC---GACGGTGACAGGAGC\n+ACCGATGGCAAGCAGAGGTTGTCGACG---AGCCGCGATGTCTCCGGTGGTGGG---ATG\n+TCACGCTCACTGCAGGGCCAAAGCAGCAAAAACTTGTTGCAGTGTATGGCCTCTAAGTCT\n+>gnl_Medtr3.5_Medtr8g022310.3\n+---------ATGGCTAACGAA---------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------GGAAACAAAAGC\n+AATGATTTCTATGCAGTTTTGGGATTGAATAAGGAATGCTCTGATTCAGAGCTAAGGAAT\n+GCTTATAAGAAACTTGCACTGAAATGGCATCCAGATCGTTGTTCAGCTTCAGGG------\n+---AATGTGAAGTTTGTGGAAGAAGCTAAGAAGAAATTTCAGGCAATTCAAGAAGCCTAT\n+TCT------------------GTTTTATCTGACTCGAACAAGAGATTAATGTACGACGTT\n+GGAGTTTACGACAGT------------------------GATGATGACGAAAATGTAAGG\n+CACTTGTTT---------------------------------------------------\n+---------CACACCATTCATGAGTTGGGG------------------ACCCTCTTTTGC\n+GTTATGTTTTGTTTCTTCATTTCCTTGAGG------------------------------\n+------GGAGAG------------------------------------------------\n+---------------------------AAGAGAAGCAACCTT------------------\n+------------------------------------AATTTAACCTTTTCACTTTCACAT\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+>gnl_Nelnu1.0_NNU_000115-RA\n+---------ATGGAGGTGGAC---------------------------------------\n+------------------------------------------------------------\n+---------------------------------------------TCCCATCGATCATCT\n+CCATCTTACTACACCATCCTTGGTGTAGATCAGAATTCCTCCGCTTCCGAGATACGCAAT\n+GCTTACAGGAAGCTCGCGATGCAATGGCATCCAGACAAATGGACGAAAACTCCG------\n+---------TCGCTCTTAGAGAAAGCCAAGAGTAAATTCCAGCAAATCCAGGAGGCTTAT\n+TCGGGTGGGTTACTCGTTTTCATGTTATCGGATCAGGGGAAGAGAACACTGTATGATGTC\n+GGTCTGTATGACCCGGACGAT---------------GAAACGAATGACGAGGTGGGGCTT\n+CGCAGATTT------CATGCAGGAGATGATATCTCTCATGAACGATGT------------\n+------GAAGAAACAGGAGAAGAAATACAGCTTGGAGGAACTACAGGAGATGTTAGTGGA\n+AATGTCACAAGGGCTGGAGTT------GAAGATGGAGAGTGCTGGTGGTGTGTGGTTGTT\n+AGATGGAGCTGCAGCCTCAAGGAG------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------GAGCTC\n+AAAGAGGGCCAG------------------------------------------------\n+------------ATGGGAATCATCAGCGAG---TCCGAC------GACGCT---------\n+------------------------------------------------------------\n+------------------------------GGACACGACACACCTTCTCTCCCCCACTTG\n+CACGGTTCAGAGCTG---------------GAATTGTTAGGAAGAACCGGCTGTTGCAAT\n+>contig_7\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------GAGAATGAGTGGTCTGGG\n+GCTGAGTTTTTGAATGAAATGGCGGCAATGATGACTCAAAATAAATCCAATGAAAACGGA\n+------ACCGGAACTTTTGAAGAACTGCAA------------------CAATTGTTCGAT\n+GAAATGTTTCAGAGCGACATC------GAGTCC---------------------------\n+---TTCAATGGTTGTTCTTCATCA------------------------------------\n+------------TCCAATGAAACATGTAGC------------------------------\n+------------------------------------------------------------\n+---------------------------AACTCGAACAAGAGGAATTCCATT---GAGTCG\n+AGCTCGGCTAAT------------------------------------------------\n+TTCAGACCCGAAAATGGAAACGAAAGCGGC------------------------------\n+---------------------------------------GAG---ATTAGCGGGAAGAAG\n+AATACTAGGAAAGGTAAAGGTGACGNN---------------------------------\n+------------------------------------------------------------\n' |
| b |
| diff -r a73c2e65098e -r 3384b6a842b0 test-data/38889.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/38889.faa Mon Oct 30 09:52:00 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 a73c2e65098e -r 3384b6a842b0 test-data/38889.faa.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/38889.faa.aln Mon Oct 30 09:52:00 2017 -0400 |
| b |
| @@ -0,0 +1,18 @@ +>gnl_Mimgu1.0_PACid_17675619 +MAETKTK--VLKFDAEEDVAVALAKYTAYLSEKYIKEKNSFSVVLSGGTLIDTLRKLVEF +PYKDSVDWSKWLIFWVDERVVPLDHEDSNYLLAYRGFLSKVPIPPSNIYAINDKKSPEGA +ADDYEERIKNLVEEKTLPISD-SGFPKFDLMLLGMGPDGHVASLFPSHNQRYEKKRWVTF +ITDSPKPPPPRITFTFPVINSASDIAMVVTGAELADTTKKALGNEKHTLP---PLPCTEV +SAERELTWFLDKDAASKL-------- +>gnl_Solly2.3_Solyc06g053200.2.1 +MATQKGKKTVLKFDSEEDVSKALAKYTAELSEKFIKQKGSFTVVLSGGSLIDTMRKLVEP +PYKDSIDWSKWWIFWVDERVVPLGHDDSNYKLASDGFLSKVPIPSSNIYAINDKESPEGA +AADYEARLKQLIESKVLPLSAITGFPKFDLMLLGMGPDGHVASLFPLHPHRHEKERLVTF +ITDSPKPPPPRITFTFPVINSASEIAMVVTGAELAHMVDVALGNAP--PPDGIPPPCTEV +SAEEELTWFLDKDAASEL----QTSR +>contig_2 +------------------------------------------------------------ +------------------------------------XLSKVPIPSNNIYAINDKKSPEDA +ADDYENRLKELVSEKIIPVSTISGFPKFDLMLLGMGPDGHVASLFPSHMQRYEKEKWVTF +ITDSPKPPPSRITFTFPMINSASEIAMVVTGADLAGTTKIALGTTGNVKPGETPLPCTEV +SAEGEVTWFLDKDAASQLLNYVRFDD |
| b |
| diff -r a73c2e65098e -r 3384b6a842b0 test-data/38889.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/38889.fna Mon Oct 30 09:52:00 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 a73c2e65098e -r 3384b6a842b0 test-data/38889.fna.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/38889.fna.aln Mon Oct 30 09:52:00 2017 -0400 |
| b |
| @@ -0,0 +1,45 @@ +>gnl_Mimgu1.0_PACid_17675619 +ATGGCCGAAACCAAAACAAAA------GTACTGAAATTCGACGCGGAGGAAGATGTGGCC +GTCGCTCTAGCAAAGTACACCGCCTATCTCTCCGAAAAGTACATCAAGGAAAAGAATTCT +TTCTCGGTGGTTCTCTCCGGCGGCACCCTAATAGATACACTCAGGAAACTAGTAGAGTTT +CCATACAAGGATTCTGTGGATTGGTCGAAATGGCTGATATTTTGGGTTGACGAGAGAGTG +GTTCCTCTTGATCATGAAGACAGCAACTACTTACTTGCATACCGTGGTTTTCTTTCAAAG +GTACCTATTCCTCCAAGCAACATTTACGCAATCAACGACAAGAAGTCTCCGGAAGGTGCA +GCCGATGATTACGAGGAGCGTATCAAGAATCTGGTCGAGGAAAAAACCCTACCTATTTCA +GAC---AGTGGCTTCCCTAAATTCGACCTTATGCTTCTCGGAATGGGGCCCGATGGCCAC +GTGGCGTCTCTTTTCCCCTCTCACAATCAACGGTACGAAAAGAAACGGTGGGTGACATTC +ATAACTGACTCTCCCAAACCGCCGCCACCTAGGATCACTTTCACATTCCCAGTCATCAAC +TCTGCTTCGGACATTGCAATGGTGGTCACTGGTGCTGAGCTGGCGGATACTACGAAGAAA +GCATTGGGAAACGAGAAGCATACTCTTCCT---------CCTCTTCCTTGTACTGAAGTT +TCGGCTGAGAGAGAGCTCACTTGGTTCTTGGACAAAGATGCTGCTTCTAAACTG------ +------------------ +>gnl_Solly2.3_Solyc06g053200.2.1 +ATGGCAACCCAGAAAGGGAAGAAGACGGTGCTAAAATTCGACTCCGAAGAAGATGTATCA +AAGGCACTTGCTAAATACACTGCTGAGCTATCGGAAAAATTCATCAAACAAAAAGGTTCT +TTCACTGTTGTGCTCTCTGGTGGTTCTCTTATCGATACCATGAGGAAATTGGTAGAGCCG +CCGTACAAAGACTCAATTGATTGGTCGAAATGGTGGATTTTTTGGGTAGACGAAAGAGTG +GTTCCTCTAGGTCACGATGATAGCAATTATAAACTTGCTTCGGATGGGTTTCTTTCTAAG +GTTCCGATCCCCTCTTCTAACATTTATGCGATTAATGACAAGGAGTCACCTGAGGGTGCA +GCTGCTGATTACGAAGCTCGTCTGAAACAATTGATTGAGAGCAAAGTTCTTCCGTTATCA +GCAATTACTGGATTCCCCAAATTTGATCTTATGCTATTAGGTATGGGGCCAGATGGACAT +GTAGCGTCTTTGTTTCCTTTGCATCCTCACCGCCACGAGAAGGAGCGGCTGGTCACCTTC +ATTACAGACTCACCAAAACCTCCTCCACCAAGGATTACTTTCACCTTTCCGGTAATTAAT +TCGGCTTCAGAGATAGCAATGGTGGTCACAGGAGCAGAGTTAGCTCATATGGTTGATGTC +GCTTTGGGTAATGCGCCT------CCTCCTGATGGAATTCCTCCCCCTTGTACTGAGGTT +TCAGCTGAAGAGGAACTGACCTGGTTTTTAGACAAGGATGCTGCATCAGAACTA------ +------CAGACCTCTAGA +>contig_2 +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------NNCCTTTCCAAG +GTACCCATCCCATCCAACAACATATATGCTATAAATGATAAGAAGTCCCCGGAAGATGCA +GCAGACGACTACGAAAACCGCCTCAAGGAACTCGTCTCCGAAAAAATCATACCCGTTTCA +ACCATTAGCGGGTTCCCGAAGTTCGACCTCATGTTGCTTGGAATGGGGCCCGACGGCCAT +GTGGCCTCTCTTTTCCCTTCTCACATGCAACGCTATGAGAAGGAGAAATGGGTCACTTTC +ATAACTGACTCTCCCAAACCGCCTCCGTCGAGAATCACTTTTACGTTTCCGATGATCAAC +TCGGCTTCGGAGATCGCTATGGTGGTTACCGGGGCTGATTTGGCTGGTACAACTAAGATA +GCATTGGGTACTACGGGCAATGTTAAGCCGGGTGAGACTCCTTTGCCTTGTACTGAAGTT +TCGGCTGAGGGAGAGGTTACTTGGTTCTTGGACAAAGATGCTGCTTCACAACTGTTAAAT +TATGTGCGCTTTGATGAT |
| b |
| diff -r a73c2e65098e -r 3384b6a842b0 test-data/39614.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/39614.faa Mon Oct 30 09:52:00 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 a73c2e65098e -r 3384b6a842b0 test-data/39614.faa.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/39614.faa.aln Mon Oct 30 09:52:00 2017 -0400 |
| b |
| @@ -0,0 +1,36 @@ +>gnl_Orysa6.0_PACid_16878968 +M----------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------------SHMEAFQNVVLLHKANSNS +TLEDISSLSAASCCSLDQLLACVEGEAQKIFGDIQNLLADHRSEVAHFTQELRESFRISL +DRTKDMSSFILGLFDKYVEETSKLQSHSNHTHEAQVKSLEDFQKAYEEQSKSEEQKLLAD +ITSLVSKHVTRQRELVGGRLNSLGDAARGNKAFLDEHTSAMEVVTKDAKRKWEMFAEQAE +NDCKVGSNFSAAKHCRMETILQECACTVDTAAQQWKASHATVNDLCRKQIAEVEALVRSA +IETNEQHEAEIASSRATAEEHASNSSKDLLQDVDNMLQEARNSSSRVVSTVEAHLGESQH +LQESHSSHTAGINTHADNAFQSSYKDYEPTGETPVRSEPEVPSKDAIESLRAMPMESLMD +EFRENHPYEPS---KDRRPSLIPRSPLATINN +>gnl_Phoda3.0_PDK_30s1023721g001 +VNQKMMKCTLIKDLYGEIERLKAEVYAAREKVGVYIPKERYHQEESERKAMAEQIEQMGV +LLENNQKQIEDLQERYNTQLQQSDDLSKKLDATEILCVSLSKKLDATEKSLEHTSKLLAA +AREDLKQAQYTLKEKDFVISEQRKAAREDKLNTANRSIVNNFRADLATRVGTLCNTVVAS +LDRQNEHLQSVEKLCQSSLDFHDKAVSELKRKVSASRALYTSHMEALQNVVRLHKASSNA +SLEEMSSMISANTCSLDQLLALGQSEADLIFSDLQSILSIHRGEIANFTRELREKFQVNL +DRTKEMSNFILELLEKIGKGTKEFQNDSTLVHEAQVKSIGDFQKAYE------------- +---------------VEVRLTGLGDAARDSKAIMDNHASSMDIVTTDAKRKWEEYSKQAE +QDSEDGSNFSAAKHCRMELMLQQCVNSVDATSQQWKKTHASVSEMSSKHVAEIEALVRSA +IESNDQHDAEVASARMAAEEDVAKNSKDVLQHFDTVIDHERNSAAGVMAAVEAHSATLHK +LQEEQSSQATEINSHAEDTFQNTYMDYEPTGETPTRSEPDIPSRGTIESLRAMPIEALLE +EFRENHPYES----KEPKPSLIPRSPLVQLN- +>contig_3 +X----------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------VD------------------------EGVV--- +--------------------------------VAGLSEQEKASVSEILTTARAHSETIEN +LKRDHSQQVSCIEQHTNDTFRQKYMDYEPTGSTPVRSEPDIPSKGTIESLRAMPIDALEE +EFRENHSYESAVTGKELMPSVTTRAPFSQIN- |
| b |
| diff -r a73c2e65098e -r 3384b6a842b0 test-data/39614.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/39614.fna Mon Oct 30 09:52:00 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 a73c2e65098e -r 3384b6a842b0 test-data/39614.fna.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/39614.fna.aln Mon Oct 30 09:52:00 2017 -0400 |
| b |
| @@ -0,0 +1,99 @@ +>gnl_Orysa6.0_PACid_16878968 +ATG--------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---TCACATATGGAAGCCTTCCAAAATGTTGTGCTCCTGCATAAAGCAAATTCAAATTCT +ACACTAGAGGATATATCATCCCTATCTGCTGCAAGCTGTTGCAGCCTTGATCAGCTTCTA +GCTTGTGTCGAGGGAGAGGCACAGAAGATATTTGGTGATATCCAGAATTTGCTAGCTGAT +CATCGAAGCGAAGTGGCACATTTCACTCAAGAGTTGCGGGAGAGTTTCCGCATTAGCTTG +GATAGGACGAAGGACATGTCTAGTTTCATCCTTGGGTTGTTCGATAAGTATGTGGAGGAA +ACTTCGAAGTTGCAGAGCCACTCCAATCACACACATGAAGCACAAGTCAAAAGCCTTGAA +GATTTCCAGAAGGCTTATGAGGAGCAATCAAAATCAGAAGAACAAAAGCTTCTGGCGGAC +ATCACCAGTTTGGTTTCTAAACACGTTACTCGACAACGAGAACTGGTGGGTGGTAGACTA +AACTCTCTTGGTGACGCCGCTCGTGGAAACAAAGCATTTTTGGATGAGCACACGTCCGCC +ATGGAGGTGGTCACGAAGGACGCCAAGAGAAAGTGGGAAATGTTTGCAGAGCAGGCAGAG +AATGACTGCAAAGTTGGGTCCAACTTCTCTGCAGCTAAGCATTGTCGCATGGAAACCATT +CTGCAGGAATGTGCATGCACCGTCGACACTGCTGCTCAACAATGGAAAGCATCACATGCA +ACTGTTAACGATCTATGCAGAAAACAAATAGCTGAAGTTGAAGCACTCGTCAGGAGTGCA +ATCGAAACCAACGAGCAGCACGAAGCAGAGATTGCATCTTCCCGTGCCACGGCCGAGGAG +CATGCGTCCAACAGCAGCAAGGACCTACTCCAAGATGTTGACAATATGCTGCAGGAGGCG +CGCAATTCGTCGTCGAGAGTGGTGTCGACGGTGGAAGCTCATTTGGGAGAGAGCCAGCAT +CTACAGGAGAGCCACTCCAGCCATACCGCCGGCATCAACACCCACGCCGACAACGCTTTC +CAGAGCAGCTACAAGGACTACGAGCCGACCGGCGAAACTCCGGTGAGGTCGGAGCCGGAG +GTGCCGAGCAAAGACGCGATCGAGTCGCTGCGAGCGATGCCGATGGAGTCCCTGATGGAC +GAGTTCCGCGAGAACCACCCCTACGAGCCGAGC---------AAGGACCGCAGGCCATCG +CTCATCCCTCGCTCGCCGCTCGCCACCATCAACAAC +>gnl_Phoda3.0_PDK_30s1023721g001 +GTAAACCAAAAAATGATGAAATGTACATTAATCAAAGATCTCTATGGAGAAATTGAGCGT +CTAAAAGCAGAGGTGTATGCTGCTCGTGAGAAAGTTGGAGTTTACATACCAAAAGAACGC +TACCATCAAGAAGAGAGCGAACGGAAGGCAATGGCAGAACAAATTGAACAAATGGGGGTC +TTGCTCGAAAACAATCAAAAGCAAATTGAGGATCTACAAGAAAGGTATAATACTCAACTT +CAACAGTCTGATGACCTGAGCAAAAAGCTTGATGCCACCGAGATTCTCTGTGTTTCTCTG +AGCAAAAAGCTTGATGCCACCGAGAAAAGTTTGGAGCACACTAGCAAGTTATTGGCTGCT +GCCAGAGAAGATCTGAAGCAAGCTCAGTATACTCTGAAGGAGAAAGATTTTGTTATATCA +GAGCAGAGGAAAGCAGCTAGAGAAGACAAACTGAATACTGCCAACAGATCTATTGTGAAC +AATTTTCGGGCTGATCTTGCAACAAGGGTTGGAACACTTTGTAATACTGTTGTTGCATCC +TTGGATCGGCAAAATGAACACCTTCAGTCTGTTGAGAAACTATGTCAATCTAGCCTTGAT +TTCCATGACAAGGCAGTATCAGAGCTGAAAAGGAAAGTGTCAGCTTCAAGAGCTTTGTAT +ACTTCCCATATGGAAGCACTACAAAATGTAGTGCGTTTGCATAAGGCAAGCAGCAATGCC +AGCTTAGAAGAGATGTCATCCATGATTTCTGCCAATACCTGCTCTCTTGATCAGTTACTT +GCCTTGGGGCAAAGCGAAGCAGATCTGATTTTTAGTGATCTGCAAAGCATATTGTCAATT +CACCGAGGAGAGATTGCAAATTTCACCCGTGAACTTCGTGAGAAATTTCAAGTTAATTTG +GATCGGACAAAGGAGATGTCCAATTTTATTCTTGAGCTGCTTGAAAAGATAGGGAAGGGA +ACAAAAGAATTTCAGAATGACTCAACTTTGGTACATGAGGCTCAGGTGAAGAGCATTGGT +GATTTCCAAAAGGCATATGAG--------------------------------------- +---------------------------------------------GTGGAAGTGAGGCTC +ACTGGACTGGGAGATGCTGCTCGAGATAGCAAAGCAATTATGGATAACCATGCATCATCA +ATGGACATCGTCACAACTGATGCTAAGAGGAAGTGGGAAGAATATTCCAAGCAGGCAGAG +CAAGATTCAGAGGACGGTTCTAACTTTTCAGCAGCAAAACATTGTCGCATGGAACTCATG +CTCCAACAGTGTGTAAACTCTGTTGATGCTACTTCTCAACAGTGGAAGAAGACACATGCA +TCTGTTAGTGAGATGAGCAGCAAACACGTTGCTGAAATTGAAGCACTTGTAAGGAGTGCC +ATTGAGAGCAATGATCAGCATGATGCTGAGGTTGCTTCAGCAAGAATGGCAGCAGAAGAG +GATGTAGCGAAAAATAGCAAAGATGTTCTTCAGCATTTTGATACTGTGATTGATCATGAG +CGCAACTCAGCCGCTGGAGTGATGGCAGCAGTCGAAGCTCACTCAGCAACCCTGCATAAA +CTGCAAGAGGAACAATCAAGCCAGGCAACAGAGATTAATAGCCATGCGGAGGACACATTC +CAAAACACCTACATGGACTATGAACCAACGGGAGAAACCCCAACAAGGTCGGAACCAGAT +ATACCAAGCAGGGGAACAATCGAATCTCTTCGAGCCATGCCGATAGAAGCCCTCCTTGAA +GAGTTCCGGGAGAACCATCCATACGAGTCC------------AAGGAGCCCAAACCGTCT +CTCATACCACGCTCTCCACTCGTCCAGCTCAAC--- +>contig_3 +NNT--------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------GTGGAT--------------------------------- +---------------------------------------GAAGGAGTTGTT--------- +------------------------------------------------------------ +------------------------------------GTTGCTGGCTTGTCAGAGCAGGAG +AAGGCATCTGTTTCTGAAATTCTGACAACTGCTAGAGCTCATTCAGAAACAATTGAGAAC +CTTAAGAGAGATCATTCCCAGCAGGTATCCTGTATCGAACAGCACACGAATGATACTTTC +AGGCAAAAATACATGGATTACGAGCCTACAGGGTCCACGCCAGTTAGGAGCGAGCCGGAT +ATTCCCAGCAAAGGCACAATAGAGTCACTTCGTGCCATGCCTATAGATGCACTTGAAGAA +GAATTTCGAGAAAACCATTCATACGAATCTGCTGTTACAGGAAAGGAACTAATGCCGTCT +GTTACGACTCGTGCACCATTTTCACAGATCAAC--- |
| b |
| diff -r a73c2e65098e -r 3384b6a842b0 utils.py --- a/utils.py Fri Aug 25 13:01:25 2017 -0400 +++ b/utils.py Mon Oct 30 09:52:00 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') |