| Next changeset 1:c6c77d840993 (2020-01-08) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a" |
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added:
cat_contigs.xml macros.xml tabpad.py test-data/cached_locally/CAT_prepare_test/CAT_database/test.nr.dmnd test-data/cached_locally/CAT_prepare_test/CAT_database/test.nr.fastaid2LCAtaxid test-data/cached_locally/CAT_prepare_test/CAT_database/test.nr.gz test-data/cached_locally/CAT_prepare_test/CAT_database/test.nr.taxids_with_multiple_offspring test-data/cached_locally/CAT_prepare_test/taxonomy/names.dmp test-data/cached_locally/CAT_prepare_test/taxonomy/nodes.dmp test-data/cached_locally/CAT_prepare_test/taxonomy/test.prot.accession2taxid.gz test-data/cached_locally/cat_database.loc test-data/contigs.fasta test-data/genome2.fna test-data/genome3.fna test-data/test_contig.contig2classification.names.txt test-data/test_contig.contig2classification.txt tool-data/cat_database.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r 11a61934bfb3 cat_contigs.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cat_contigs.xml Tue Dec 10 16:05:34 2019 -0500 |
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| @@ -0,0 +1,92 @@ +<tool id="cat_contigs" name="CAT contigs" version="@VERSION@.0"> + <description>annotate with taxonomic classification</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="version_command" /> + <command detect_errors="exit_code"><![CDATA[ + CAT contigs + -c '$contigs_fasta' + @CAT_DB@ + @USE_INTERMEDIATES@ + @CUSTOM_SETTINGS@ + @DIAMOND_OPTIONS@ + && @TXT2TSV@ *.ORF2LCA.txt *.contig2classification.txt + @ADD_NAMES@ + @SUMMARISE@ + ]]></command> + <inputs> + <param name="contigs_fasta" type="data" format="fasta" label="Contigs fasta"/> + <expand macro="cat_db" /> + <expand macro="use_intermediates" /> + <expand macro="custom_settings" /> + <expand macro="diamond_options" /> + <expand macro="add_names" /> + <expand macro="summarise" /> + <expand macro="select_cat_outputs" /> + </inputs> + <outputs> + <expand macro="outputs" /> + </outputs> + <tests> + <test> + <param name="contigs_fasta" ftype="fasta" value="contigs.fasta"/> + <expand macro="test_catdb"/> + <param name="select_outputs" value="contig2classification"/> + <output name="contig2classification"> + <assert_contents> + <has_text text="contig_38063" /> + </assert_contents> + </output> + </test> + <test> + <param name="contigs_fasta" ftype="fasta" value="contigs.fasta"/> + <expand macro="test_catdb"/> + <param name="select_outputs" value="predicted_proteins_faa"/> + <conditional name="names"> + <param name="add_names" value="both"/> + </conditional> + <param name="summarise" value="classification"/> + <output name="predicted_proteins_faa"> + <assert_contents> + <has_text text=">contig_9952" /> + </assert_contents> + </output> + <output name="orf2lca_names"> + <assert_contents> + <has_text text="Listeria" /> + </assert_contents> + </output> + <output name="classification_summary"> + <assert_contents> + <has_text text="Listeria" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +**CAT contigs** + +Classifiy metagenomics contigs. + +@COMMON_HELP@ + +@OUTPUTS_HELP@ + + +**CAT contigs** + +Run Contig Annotation Tool (CAT). + +Required arguments: + -c, --contigs_fasta Path to contigs fasta file. + -d, --database_folder Path to folder that contains database files. + -t, --taxonomy_folder Path to folder that contains taxonomy files. + + +@OPTIONS_HELP@ + + ]]></help> + <expand macro="citations" /> +</tool> |
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| diff -r 000000000000 -r 11a61934bfb3 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Dec 10 16:05:34 2019 -0500 |
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| b'@@ -0,0 +1,389 @@\n+<macros>\n+ <token name="@VERSION@">5.0.3</token>\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="@VERSION@">cat</requirement>\n+ <yield/>\n+ </requirements>\n+ </xml>\n+ <xml name="version_command">\n+ <version_command><![CDATA[CAT --version]]></version_command>\n+ </xml>\n+ <token name="@DATABASE_FOLDER@">CAT_database</token>\n+ <token name="@TAXONOMY_FOLDER@">taxonomy</token>\n+ <xml name="cat_db">\n+ <conditional name="db">\n+ <param name="db_src" type="select" label="CAT database (--database_folder,--taxonomy_folder) from">\n+ <option value="cached">local cached database</option>\n+ <option value="history">history</option>\n+ </param>\n+ <when value="cached">\n+ <param name="cat_builtin" type="select" label="Use a built-in CAT database" help="If the CAT database of interest is not listed, contact your Galaxy administrator">\n+ <options from_data_table="cat_database">\n+ <filter type="sort_by" column="2" />\n+ <validator type="no_options" message="No CAT database is available." />\n+ </options>\n+ </param>\n+ </when>\n+ <when value="history">\n+ <param name="cat_db" type="data" format="txt" label="A history dataset from CAT prepare tool"/>\n+ </when>\n+ </conditional>\n+ </xml>\n+ <token name="@CAT_DB@"><![CDATA[\n+ #if $db.db_src == \'cached\':\n+ --database_folder \'$db.cat_builtin.fields.database_folder\'\n+ --taxonomy_folder \'$db.cat_builtin.fields.taxonomy_folder\'\n+ #else\n+ #import os.path\n+ #set $catdb = $db.cat_db.extra_files_path\n+ --database_folder \'$os.path.join($catdb,"@DATABASE_FOLDER@")\'\n+ --taxonomy_folder \'$os.path.join($catdb,"@TAXONOMY_FOLDER@")\'\n+ #end if\n+]]></token>\n+ <token name="@CAT_TAXONOMY@"><![CDATA[\n+ #if $db.db_src == \'cached\':\n+ --taxonomy_folder \'$db.cat_builtin.fields.taxonomy_folder\'\n+ #else\n+ #import os.path\n+ #set $catdb = $db.cat_db.extra_files_path\n+ --taxonomy_folder \'$os.path.join($catdb,"@TAXONOMY_FOLDER@")\'\n+ #end if\n+]]></token>\n+ <xml name="test_catdb">\n+ <conditional name="db">\n+ <param name="db_src" value="cached"/>\n+ <param name="cat_builtin" value="CAT_prepare_test"/>\n+ </conditional>\n+ </xml>\n+ <xml name="use_intermediates">\n+ <conditional name="previous">\n+ <param name="use_previous" type="select" label="Use previous prodigal gene prediction and diamond alignment">\n+ <help>predicted_proteins.faa and alignment.diamond from previous CAT run.</help> \n+ <option value="yes">Yes</option>\n+ <option value="no" selected="true">No</option>\n+ </param>\n+ <when value="yes">\n+ <param argument="--proteins_fasta" type="data" format="fasta" label="prodigal predicted proteins fasta"/>\n+ <param argument="--diamond_alignment" type="data" format="tabular" label="alignment.diamond file"/>\n+ </when>\n+ <when value="no"/>\n+ </conditional>\n+ </xml>\n+ <token name="@USE_INTERMEDIATES@"><![CDATA[\n+ #if $previous.use_previous == \'yes\'\n+ --proteins_fasta \'$previous.proteins_fasta\'\n+ --diamond_alignment \'$previous.diamond_alignment\'\n+ #end if\n+ --out_prefix \'cat_output\'\n+]]></token>\n+ <xml name="custom_settings">\n+ <param argument="--range" type="integer" value="10" min="0" max="49" label="range"/>\n+ <param argument="--fraction" type="float" value="0.5" min="0" max="0.99" label="fraction"/>\n+ </xml>\n+ <token name="@CUSTOM_SETTINGS@"><![CDATA[\n+ --range \'$range\'\n+ --fraction \'$fraction\'\n+]]></token>\n+ <xml name="diamon'..b'tputs with taxonomic names. \n+ - CAT summerise - reports number of assignments to each taxonomic name.\n+\n+A CAT database can either be installed by data_manager_cat or in the local history by CAT prepare tool.\n+\n+.. _Prodigal: https://github.com/hyattpd/Prodigal\n+.. _Diamond: https://github.com/bbuchfink/diamond\n+\n+]]></token>\n+ <token name="@OUTPUTS_HELP@"><![CDATA[\n+\n+**OUTPUTS**\n+\n+Any of the files produced by the CAT workflow are available as outputs\n+ - Prodigal\n+\n+ - predicted_proteins.faa\n+ - predicted_proteins.gff\n+\n+ - Diamond\n+\n+ - alignment.diamond\n+\n+ - CAT contigs/bins\n+\n+ - contigs/bin2classification.txt\n+ - ORF2LCA.txt\n+\n+ - CAT add_names (optional)\n+\n+ - contigs/bin2classification.names.txt\n+ - ORF2LCA.names.txt\n+\n+ - CAT summarise (optional)\n+\n+ - contigs/bin2classification.summary.txt\n+\n+\n+]]></token>\n+ \n+ <token name="@OPTIONS_HELP@"><![CDATA[\n+\n+Optional arguments:\n+ -r, --range cut-off range after alignment [0-49] (default: 10).\n+ -f, --fraction fraction of bit-score support for each classification\n+ [0-0.99] (default: 0.5).\n+ -p, --proteins_fasta\n+ Path to predicted proteins fasta file. If supplied,\n+ CAT will skip the protein prediction step.\n+ -a, --diamond_alignment\n+ Path to DIAMOND alignment table. If supplied, CAT will\n+ skip the DIAMOND alignment step and directly classify\n+ the sequences. A predicted proteins fasta file should\n+ also be supplied with argument [-p / --proteins].\n+\n+\n+DIAMOND specific optional arguments:\n+ --sensitive Run DIAMOND in sensitive mode (default: not enabled).\n+\n+ --block_size DIAMOND block-size parameter (default: 2.0). Lower\n+ numbers will decrease memory and temporary disk space\n+ usage.\n+\n+ --index_chunks\n+ DIAMOND index-chunks parameter (default: 4). Set to 1\n+ on high memory machines. The parameter has no effect\n+ on temporary disk space usage.\n+\n+ --top\n+ DIAMOND top parameter [0-50] (default: 50). Governs\n+ hits within range of best hit that are written to the\n+ alignment file. This is not the [-r / --range]\n+ parameter!\n+\n+\n+Setting the DIAMOND --top parameter\n+\n+You can speed up DIAMOND considerably, and at the same time greatly reduce disk usage, by setting the DIAMOND --top parameter to lower values. This will govern hits within range of the best hit that are written to the alignment file.\n+\n+You have to be very carefull to 1) not confuse this parameter with the r / --range parameter, which does a similar cut-off but after alignment and 2) be aware that if you want to run CAT or BAT again afterwards with different values of the -r / --range parameter, your options will be limited to the range you have chosen with --top earlier, because all hits that fall outside this range will not be included in the alignment file. Importantly, CAT and BAT currently do not warn you if you choose -r / --range in a second run higher than --top in a previous one, so it\'s up to you to remember this!\n+\n+If you have understood all this, or you do not plan to tune -r / --range at all afterwards, you can enjoy a huge speedup with much smaller alignment files! For CAT you can for example set --top 11 and for BAT --top 6.\n+\n+]]></token>\n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">https://doi.org/10.1101/072868</citation>\n+ <citation type="doi">https://doi.org/10.1186/s13059-019-1817-x</citation>\n+ <citation type="doi">https://doi.org/10.1038/nmeth.3176</citation>\n+ <citation type="doi">https://doi.org/10.1186/1471-2105-11-119</citation>\n+ <yield />\n+ </citations>\n+ </xml>\n+</macros>\n' |
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| diff -r 000000000000 -r 11a61934bfb3 tabpad.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tabpad.py Tue Dec 10 16:05:34 2019 -0500 |
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| @@ -0,0 +1,67 @@ +#!/usr/bin/env python + +import argparse +import re + + +def padfile(infile, outfile, fieldcnt=None): + with open(infile, 'r') as fh: + out = open(outfile, 'w') + commentlines = [] + tabs = '\t' * fieldcnt if fieldcnt is not None else None + + def pad_line(txtline, tabs=None): + line = txtline.rstrip('\r\n') + fields = line.split('\t') + if not tabs: + tabs = '\t' * len(fields) + out.write('%s%s\n' % (line, tabs[len(fields):])) + + for i, txtline in enumerate(fh): + if txtline.lstrip().startswith('#'): + commentlines.append(txtline) + else: + if commentlines: + for i in range(len(commentlines) - 1): + out.write(commentlines[i]) + pad_line(commentlines[-1], tabs=tabs) + commentlines = [] + pad_line(txtline, tabs=tabs) + out.close() + + +def fieldcount(infile): + fieldcnt = 0 + with open(infile, 'r') as fh: + for i, line in enumerate(fh): + fieldcnt = max(fieldcnt, len(line.rstrip('\r\n').split('\t'))) + return fieldcnt + + +def tsvname(infile): + return re.sub('.txt$', '', infile) + '.tsv' + + +def __main__(): + parser = argparse.ArgumentParser( + description='Pad a file with TABS for equal field size across lines') + parser.add_argument( + '-i', '--input', help='input file') + parser.add_argument( + '-o', '--output', help='output file') + parser.add_argument( + 'files', nargs='*', help='.txt files') + args = parser.parse_args() + + if args.input: + outfile = args.output if args.output else tsvname(args.input) + fieldcnt = fieldcount(args.input) + padfile(args.input, outfile, fieldcnt=fieldcnt) + for infile in args.files: + outfile = tsvname(infile) + fieldcnt = fieldcount(infile) + padfile(infile, outfile, fieldcnt=fieldcnt) + + +if __name__ == "__main__": + __main__() |
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| diff -r 000000000000 -r 11a61934bfb3 test-data/cached_locally/CAT_prepare_test/CAT_database/test.nr.dmnd |
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| diff -r 000000000000 -r 11a61934bfb3 test-data/cached_locally/CAT_prepare_test/CAT_database/test.nr.fastaid2LCAtaxid --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/CAT_prepare_test/CAT_database/test.nr.fastaid2LCAtaxid Tue Dec 10 16:05:34 2019 -0500 |
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| @@ -0,0 +1,10 @@ +WP_000159554.1 2 +WP_000214552.1 91061 +WP_000346214.1 91061 +WP_000568619.1 666 +WP_000958804.1 1301 +WP_000991933.1 666 +WP_000996146.1 666 +WP_003722398.1 1639 +WP_005378126.1 662 +XP_961517.1 5141 |
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| diff -r 000000000000 -r 11a61934bfb3 test-data/cached_locally/CAT_prepare_test/CAT_database/test.nr.gz |
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| diff -r 000000000000 -r 11a61934bfb3 test-data/cached_locally/CAT_prepare_test/CAT_database/test.nr.taxids_with_multiple_offspring --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/CAT_prepare_test/CAT_database/test.nr.taxids_with_multiple_offspring Tue Dec 10 16:05:34 2019 -0500 |
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| @@ -0,0 +1,17 @@ +91061 +1 +641 +1224 +1236 +131567 +1637 +1639 +1783272 +2 +662 +13562 +13562 +641 +662 +666 +91061 |
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| diff -r 000000000000 -r 11a61934bfb3 test-data/cached_locally/CAT_prepare_test/taxonomy/names.dmp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/CAT_prepare_test/taxonomy/names.dmp Tue Dec 10 16:05:34 2019 -0500 |
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| b'@@ -0,0 +1,252 @@\n+1\t|\tall\t|\t\t|\tsynonym\t|\n+1\t|\troot\t|\t\t|\tscientific name\t|\n+2\t|\tBacteria\t|\tBacteria <prokaryotes>\t|\tscientific name\t|\n+2\t|\tMonera\t|\tMonera <Bacteria>\t|\tin-part\t|\n+2\t|\tProcaryotae\t|\tProcaryotae <Bacteria>\t|\tin-part\t|\n+2\t|\tProkaryota\t|\tProkaryota <Bacteria>\t|\tin-part\t|\n+2\t|\tProkaryotae\t|\tProkaryotae <Bacteria>\t|\tin-part\t|\n+2\t|\tbacteria\t|\tbacteria <blast2>\t|\tblast name\t|\n+2\t|\teubacteria\t|\t\t|\tgenbank common name\t|\n+2\t|\tprokaryote\t|\tprokaryote <Bacteria>\t|\tin-part\t|\n+2\t|\tprokaryotes\t|\tprokaryotes <Bacteria>\t|\tin-part\t|\n+641\t|\tVibrionaceae\t|\t\t|\tscientific name\t|\n+641\t|\tVibrionaceae Veron 1965\t|\t\t|\tauthority\t|\n+641\t|\tgamma-3 proteobacteria\t|\tgamma-3 proteobacteria <#3>\t|\tin-part\t|\n+662\t|\t"Microspira" Schroeter 1886\t|\t\t|\tauthority\t|\n+662\t|\t"Pacinia" Trevisan 1885\t|\t\t|\tauthority\t|\n+662\t|\tBeneckea\t|\t\t|\tsynonym\t|\n+662\t|\tBeneckea Campbell 1957\t|\t\t|\tauthority\t|\n+662\t|\tListonella\t|\t\t|\tsynonym\t|\n+662\t|\tListonella MacDonell and Colwell 1986\t|\t\t|\tauthority\t|\n+662\t|\tMicrospira\t|\t\t|\tsynonym\t|\n+662\t|\tPacinia\t|\t\t|\tsynonym\t|\n+662\t|\tVibrio\t|\t\t|\tscientific name\t|\n+662\t|\tVibrio Pacini 1854\t|\t\t|\tauthority\t|\n+666\t|\t"Bacillo virgola del Koch" Trevisan 1884\t|\t\t|\tauthority\t|\n+666\t|\t"Bacillus cholerae" (Pacini 1854) Trevisan 1884\t|\t\t|\tauthority\t|\n+666\t|\t"Bacillus cholerae-asiaticae" Trevisan 1884\t|\t\t|\tauthority\t|\n+666\t|\t"Kommabacillus" Koch 1884\t|\t\t|\tauthority\t|\n+666\t|\t"Liquidivibrio cholerae" (Pacini 1854) Orla-Jensen 1909\t|\t\t|\tauthority\t|\n+666\t|\t"Microspira comma" Schroeter 1886\t|\t\t|\tauthority\t|\n+666\t|\t"Pacinia cholerae-asiaticae" (Trevisan 1884) Trevisan 1885\t|\t\t|\tauthority\t|\n+666\t|\t"Spirillum cholerae" (Pacini 1854) Mac1889\t|\t\t|\tauthority\t|\n+666\t|\t"Spirillum cholerae-asiaticae" (Trevisan 1884) Zopf 1885\t|\t\t|\tauthority\t|\n+666\t|\t"Vibrio cholera" (sic) Pacini 1854\t|\t\t|\tauthority\t|\n+666\t|\t"Vibrio cholerae-asiaticae" (Trevisan 1884) Pfeiffer 1896\t|\t\t|\tauthority\t|\n+666\t|\t"Vibrio comma" (Schroeter 1886) Blanchard 1906\t|\t\t|\tauthority\t|\n+666\t|\tATCC 14035\t|\tATCC 14035 <type strain>\t|\ttype material\t|\n+666\t|\tATCC 14547 [[Vibrio albensis]]\t|\tATCC 14547 [[Vibrio albensis]] <type strain>\t|\ttype material\t|\n+666\t|\tBacillo virgola del Koch\t|\t\t|\tsynonym\t|\n+666\t|\tBacillus cholerae\t|\t\t|\tsynonym\t|\n+666\t|\tBacillus cholerae-asiaticae\t|\t\t|\tsynonym\t|\n+666\t|\tCCUG 48664 [[Vibrio albensis]]\t|\tCCUG 48664 [[Vibrio albensis]] <type strain>\t|\ttype material\t|\n+666\t|\tCCUG 9118 A\t|\tCCUG 9118 A <type strain>\t|\ttype material\t|\n+666\t|\tCECT 514\t|\tCECT 514 <type strain>\t|\ttype material\t|\n+666\t|\tCIP 62.13\t|\tCIP 62.13 <type strain>\t|\ttype material\t|\n+666\t|\tKommabacillus\t|\t\t|\tsynonym\t|\n+666\t|\tLMG 4406 [[Vibrio albensis]]\t|\tLMG 4406 [[Vibrio albensis]] <type strain>\t|\ttype material\t|\n+666\t|\tLMG:4406 [[Vibrio albensis]]\t|\tLMG:4406 [[Vibrio albensis]] <type strain>\t|\ttype material\t|\n+666\t|\tLiquidivibrio cholerae\t|\t\t|\tsynonym\t|\n+666\t|\tMicrospira comma\t|\t\t|\tsynonym\t|\n+666\t|\tNCIMB 41 [[Vibrio albensis]]\t|\tNCIMB 41 [[Vibrio albensis]] <type strain>\t|\ttype material\t|\n+666\t|\tNCTC 8021\t|\tNCTC 8021 <type strain>\t|\ttype material\t|\n+666\t|\tPacinia cholerae-asiaticae\t|\t\t|\tsynonym\t|\n+666\t|\tSpirillum cholerae\t|\t\t|\tsynonym\t|\n+666\t|\tSpirillum cholerae-asiaticae\t|\t\t|\tsynonym\t|\n+666\t|\tVibrio albensis\t|\t\t|\tsynonym\t|\n+666\t|\tVibrio albensis Lehmann and Neumann 1896\t|\t\t|\tauthority\t|\n+666\t|\tVibrio cholera\t|\t\t|\tsynonym\t|\n+666\t|\tVibrio cholerae\t|\t\t|\tscientific name\t|\n+666\t|\tVibrio cholerae Pacini 1854\t|\t\t|\tauthority\t|\n+666\t|\tVibrio cholerae biovar albensis\t|\t\t|\tsynonym\t|\n+666\t|\tVibrio cholerae bv. albensis\t|\t\t|\tsynonym\t|\n+666\t|\tVibrio cholerae-asiaticae\t|\t\t|\tsynonym\t|\n+666\t|\tVibrio comma\t|\t\t|\tsynonym\t|\n+1224\t|\tAlphaproteobacteraeota\t|\t\t|\tsynonym\t|\n+1224\t|\tAlphaproteobacteraeota Oren et al. 2015\t|\t\t|\tauthority\t|\n+1224\t|\tAlphaproteobacteriota\t|\t\t|\tsynonym\t|\n+1224\t|\tProteobacteria\t|\t\t|\tscientific name\t|\n+1224\t|\tProteobacteria Garrity et al. 2005\t|\t\t|\tauthority\t|\n+1224\t|\tProteobacteria [class] Stackebrandt et al. 1988\t|\t\t|\tauthority\t|\n+1224\t|\tproteobacteria\t|\tproteobacteria <blast1224>\t|\tblast name\t|\n+1224\t|\tpu'..b'teria sp. FDA00013574\t|\t\t|\tincludes\t|\n+1639\t|\tListeria sp. FDA00013575\t|\t\t|\tincludes\t|\n+1639\t|\tListeria sp. FDA00013576\t|\t\t|\tincludes\t|\n+1639\t|\tListeria sp. FDA00013577\t|\t\t|\tincludes\t|\n+1639\t|\tListeria sp. FDA00013578\t|\t\t|\tincludes\t|\n+1639\t|\tListeria sp. FDA00013579\t|\t\t|\tincludes\t|\n+1639\t|\tListeria sp. FDA00013607\t|\t\t|\tincludes\t|\n+1639\t|\tNCTC 10357\t|\tNCTC 10357 <type strain>\t|\ttype material\t|\n+1639\t|\tSLCC 53\t|\tSLCC 53 <type strain>\t|\ttype material\t|\n+2157\t|\t"Archaea" Woese et al. 1990\t|\t\t|\tauthority\t|\n+2157\t|\t"Archaebacteria" (sic) Woese and Fox 1977\t|\t\t|\tauthority\t|\n+2157\t|\tArchaea\t|\t\t|\tscientific name\t|\n+2157\t|\tArchaebacteria\t|\t\t|\tsynonym\t|\n+2157\t|\tMendosicutes\t|\t\t|\tsynonym\t|\n+2157\t|\tMetabacteria\t|\t\t|\tsynonym\t|\n+2157\t|\tMonera\t|\tMonera <Archaea>\t|\tin-part\t|\n+2157\t|\tProcaryotae\t|\tProcaryotae <Archaea>\t|\tin-part\t|\n+2157\t|\tProkaryota\t|\tProkaryota <Archaea>\t|\tin-part\t|\n+2157\t|\tProkaryotae\t|\tProkaryotae <Archaea>\t|\tin-part\t|\n+2157\t|\tarchaea\t|\tarchaea <blast2157>\t|\tblast name\t|\n+2157\t|\tprokaryote\t|\tprokaryote <Archaea>\t|\tin-part\t|\n+2157\t|\tprokaryotes\t|\tprokaryotes <Archaea>\t|\tin-part\t|\n+2158\t|\tMethanobacteriales\t|\t\t|\tscientific name\t|\n+2158\t|\tMethanobacteriales Balch and Wolfe 1981\t|\t\t|\tauthority\t|\n+2159\t|\tMethanobacteriaceae\t|\t\t|\tscientific name\t|\n+2159\t|\tMethanobacteriaceae Barker 1956\t|\t\t|\tauthority\t|\n+2172\t|\tMethanobrevibacter\t|\t\t|\tscientific name\t|\n+2172\t|\tMethanobrevibacter Balch and Wolfe 1981\t|\t\t|\tauthority\t|\n+28890\t|\t"Euryarchaeota" Woese et al. 1990\t|\t\t|\tauthority\t|\n+28890\t|\tEuryarchaeota\t|\t\t|\tscientific name\t|\n+28890\t|\tEuryarchaeota Garrity and Holt 2002\t|\t\t|\tauthority\t|\n+28890\t|\tMethanobacteraeota\t|\t\t|\tsynonym\t|\n+28890\t|\tMethanobacteraeota Oren et al. 2015\t|\t\t|\tauthority\t|\n+28890\t|\tMethanobacteriota\t|\t\t|\tsynonym\t|\n+28890\t|\teuryarchaeotes\t|\teuryarchaeotes <blast28890>\t|\tblast name\t|\n+83816\t|\tATCC 35063\t|\tATCC 35063 <type strain>\t|\ttype material\t|\n+83816\t|\tDSM 1093\t|\tDSM 1093 <type strain>\t|\ttype material\t|\n+83816\t|\tJCM 13430\t|\tJCM 13430 <type strain>\t|\ttype material\t|\n+83816\t|\tMethanobacterium ruminantium\t|\t\t|\tsynonym\t|\n+83816\t|\tMethanobacterium ruminantium Smith and Hungate 1958 (Approved Lists 1980)\t|\t\t|\tauthority\t|\n+83816\t|\tMethanobrevibacter ruminantium\t|\t\t|\tscientific name\t|\n+83816\t|\tMethanobrevibacter ruminantium (Smith and Hungate 1958) Balch and Wolfe 1981\t|\t\t|\tauthority\t|\n+83816\t|\tOCM 146\t|\tOCM 146 <type strain>\t|\ttype material\t|\n+83816\t|\tstrain M1\t|\tstrain M1 <type strain> <taxid 83816>\t|\ttype material\t|\n+91061\t|\tBacilli\t|\t\t|\tscientific name\t|\n+91061\t|\tBacilli Ludwig et al. 2010\t|\t\t|\tauthority\t|\n+91061\t|\tBacillus/Lactobacillus/Streptococcus group\t|\t\t|\tsynonym\t|\n+91061\t|\tFirmibacteria\t|\t\t|\tsynonym\t|\n+91061\t|\tFirmibacteria Murray 1988\t|\t\t|\tauthority\t|\n+131567\t|\tbiota\t|\t\t|\tsynonym\t|\n+131567\t|\tcellular organisms\t|\t\t|\tscientific name\t|\n+135623\t|\t\'Vibrionales\'\t|\t\t|\tsynonym\t|\n+135623\t|\tVibrionaceae group\t|\t\t|\tsynonym\t|\n+135623\t|\tVibrionales\t|\t\t|\tscientific name\t|\n+183925\t|\tArchaeobacteria\t|\t\t|\tsynonym\t|\n+183925\t|\tArchaeobacteria Murray 1988\t|\t\t|\tauthority\t|\n+183925\t|\tMethanobacteria\t|\t\t|\tscientific name\t|\n+183925\t|\tMethanobacteria Boone 2002\t|\t\t|\tauthority\t|\n+183967\t|\tThermoplasmata\t|\t\t|\tscientific name\t|\n+183967\t|\tThermoplasmata Reysenbach 2002\t|\t\t|\tauthority\t|\n+186820\t|\tListeriaceae\t|\t\t|\tscientific name\t|\n+186820\t|\tListeriaceae Ludwig et al. 2010\t|\t\t|\tauthority\t|\n+1235850\t|\t"Methanoplasmatales" Paul et al. 2012\t|\t\t|\tauthority\t|\n+1235850\t|\tMethanomassiliicoccales\t|\t\t|\tscientific name\t|\n+1235850\t|\tMethanomassiliicoccales Iino et al. 2013\t|\t\t|\tauthority\t|\n+1235850\t|\tMethanoplasmatales\t|\t\t|\tsynonym\t|\n+1783272\t|\tTerrabacteria group\t|\t\t|\tscientific name\t|\n+2283794\t|\t"Methanomada" Petitjean et al. 2015\t|\t\t|\tauthority\t|\n+2283794\t|\tMethanogen Class I\t|\t\t|\tsynonym\t|\n+2283794\t|\tMethanomada\t|\t\t|\tequivalent name\t|\n+2283794\t|\tMethanomada group\t|\t\t|\tscientific name\t|\n+2283796\t|\tDiaforarchaea\t|\t\t|\tequivalent name\t|\n+2283796\t|\tDiaforarchaea Petijean et al. 2015\t|\t\t|\tauthority\t|\n+2283796\t|\tDiaforarchaea group\t|\t\t|\tscientific name\t|\n' |
| b |
| diff -r 000000000000 -r 11a61934bfb3 test-data/cached_locally/CAT_prepare_test/taxonomy/nodes.dmp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/CAT_prepare_test/taxonomy/nodes.dmp Tue Dec 10 16:05:34 2019 -0500 |
| b |
| @@ -0,0 +1,27 @@ +1 | 1 | no rank | | 8 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | | +2 | 131567 | superkingdom | | 0 | 0 | 11 | 0 | 0 | 0 | 0 | 0 | | +641 | 135623 | family | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +662 | 641 | genus | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +666 | 662 | species | VC | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | +1224 | 2 | phylum | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +1236 | 1224 | class | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +1239 | 1783272 | phylum | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +1385 | 91061 | order | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +1637 | 186820 | genus | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +1639 | 1637 | species | LM | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | +2157 | 131567 | superkingdom | | 0 | 0 | 11 | 0 | 0 | 0 | 0 | 0 | | +2158 | 183925 | order | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +2159 | 2158 | family | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +2172 | 2159 | genus | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +28890 | 2157 | phylum | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +83816 | 2172 | species | MR | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | +91061 | 1239 | class | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +131567 | 1 | no rank | | 8 | 1 | 1 | 1 | 0 | 1 | 1 | 0 | | +135623 | 1236 | order | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +183925 | 2283794 | class | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +183967 | 2283796 | class | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +186820 | 1385 | family | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +1235850 | 183967 | order | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +1783272 | 2 | no rank | | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | +2283794 | 28890 | no rank | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +2283796 | 28890 | no rank | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | |
| b |
| diff -r 000000000000 -r 11a61934bfb3 test-data/cached_locally/CAT_prepare_test/taxonomy/test.prot.accession2taxid.gz |
| b |
| Binary file test-data/cached_locally/CAT_prepare_test/taxonomy/test.prot.accession2taxid.gz has changed |
| b |
| diff -r 000000000000 -r 11a61934bfb3 test-data/cached_locally/cat_database.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/cat_database.loc Tue Dec 10 16:05:34 2019 -0500 |
| b |
| @@ -0,0 +1,8 @@ +## A typical download from https://tbb.bio.uu.nl/bastiaan/CAT_prepare/CAT_prepare_20190719.tar.gz +# ls CAT_prepare_20190719/ +# 2019-07-19.CAT_prepare.fresh.log +# 2019-07-19_CAT_database +# 2019-07-19_taxonomy +#value name database_folder taxonomy_folder +#2019-07-19_CAT_database 2019-07-19_CAT_database /opt/galaxy/tool-data/cat_database/CAT_prepare_20190719/2019-07-19_CAT_database /opt/galaxy/tool-data/cat_database/CAT_prepare_20190719/2019-07-19_taxonomy +CAT_prepare_test CAT_prepare_test ${__HERE__}/CAT_prepare_test/CAT_database ${__HERE__}/CAT_prepare_test/taxonomy |
| b |
| diff -r 000000000000 -r 11a61934bfb3 test-data/contigs.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/contigs.fasta Tue Dec 10 16:05:34 2019 -0500 |
| b |
| b'@@ -0,0 +1,93 @@\n+>contig_9952\n+TGGTTATGTACGCAGACAGCTTACTCCTCCTCGGAGACCACTCGCGGTACTCTATTCCCTCCACGGTTGCGAGGCGCTCGCCGTAGATCCGCTTCCCGGG\n+ACAGGCAGACAGGGTGTATAGCCTCCCCCTCTCGGAAAAAACCCCGGGCACGCGGTCCAAAGACTCCATGCCCGTAACAACGCCGTGGTTTTAGAAATAA\n+TCTGTGCCGTCGGTTGCAAACCCTAAATACAGGGGGATATCAATGCGGTTGCATGGATATCCACATCCTTCGTGAGATCGCCGACGCAGTTCAGGCGGCG\n+GTATCTCTCATACCCGACCCCTGCAGCAGGGGCAACGAGATATGCATGGGCAACGACGGCACACCCACATCCGAGATAGACAAAGTGGCTGAGAACGCGG\n+TGCTCGGGTACATAGAGTCCAACCGCCTGGCTCTGAACGTGCTCAGCGAAGAGATAGGCTTCGTGGACAACGGCGCGTCGGAGGTTCTGGTCCTCGATCC\n+CATCGATGGGACAAGCAATTCAGTGGCCGAGATACCTTTCTATACGATATCCATGGCCGTCGGCAAGGATTCGCTCTGCGGCATGCACACGGCCTACATC\n+AGGAACCTGGCGACAGGGGACGAGTTCTGGGCGCACAAAGGGGATGGCGCTTATTACAACGGAAGGAGGATAAACGTCAGGAAGCCGGATTTCTCCAAAC\n+TGTTCGCCCTTATATACATGGGGAACGCCGCTGTCGATGAAGCGTTCGCCCTTGCAAAGAACGTCAAGACCTCCCGCTCCATGGGCTGCGCCTCCCTTGA\n+GATGACGCTCGTGGCACTAGGACACGCCGATATCTATTACATGAACACCTACCGTTACAACCGTGCCGTCAGGACTGTGGACATCGCCGCCAGCGCCCTG\n+ATACTCAGGGAGGCGGGCGGCGAGATATTCGATATCGGCGGCAACAAGCTGGATATGCCGCTGGACAACGCTTACCACGCAAGCTTCGTGGCGTGCTCCT\n+GCAAAGAGGTATTCGACCACATCATGAGGGCCCACATCGAGGAGCACGGCGCTACGCGTTACGGGATATACGCCAACGAGACCGTCCCCGGGGCGGCCGA\n+GTATGTGAGGAGGGCGTACGATGCTTTGAGGGGGGAGAAGGTAACCCTCGACACGGCGGCCGCCAGGCTGATCGGGGCGGAAGGCGTGCCTATTTCGGAG\n+ATCGAGGCGGACATCGTCGTGGTGATAGGAGGGGACGGCACGATACTCAGGGCGCTCAAGAAGACGGATGCCGCCGTGATAGGGATCAACGCCGGAGGCG\n+TGGGGTTCCTGGCCGAGGTCGAGCCGGACGAGATAGAGGAGAGCATATCCCGCATCAGGCGCGGAGAGTACTCGGTTGAGGAGAGGATCAAGCTCAGGAC\n+TTTTTACGAGGGGGAATATCTCTCGGAGGCCGTGAACGAGACAGTGATACACACTGATTCCGTGGCGAAGATCAGGCAGTTCAAGATATATGTCAACGAA\n+CACCTGGCAACGGAGGTCCGCGCGGACGGCATAATCATCTCGACGCCCACAGGCTCCACCTGCTACGCCATGAGCCTCGGCGCGCCCATAACCGACCCGG\n+GGGTCGGAGCTTTCCTGATAGTCCCCATGGCGGCGTTCAAGTTCGCTTCCCGTCCGTTCGTCGTTCCCTATACGGCGAAGATAACCGTCGAGGCGGTCAT\n+GGACAAGGGCTGCCTCATCGTGGTGGACGGCCAGCACGAGTACCCGATGAGGGGAGGGACGCGGGCGGAATTCTCGCTTTCCGACAACCTCGCCAAATTC\n+TCGGCCCCGGCGTTCCTGGCATCGACGGGCATCTCGAAGTAGATCTCGCCGCCCATCATGTTGATGTCGGCCTTAAAAGGTAAAGAAAGCCAGATGGCGT\n+TCGAGACATCGGAGTCGTCCAGCTCGGCGAAGTAATCGCCGCTCGTCGTGACAATCTTCATTCTGCTCAAAGCGCCACCCGGCCGTCGGTTCAGTTCTTT\n+TTCTTCTTTTCGAAGAGCTTCCTGATCTCCCTGCCCGTGACCTCGATCTGGAGGTCCTTCTCCTTCTCCTCCATTGCCTTCAGGCCCTTCAGGTCGTTGG\n+CCCATTCGGAGGTCCAGTCGGCTTTGAATTTTCCGGATTCGATGTCGTCCAGAATCTTCTTCATGCCCTTCTCGGACTCTTCGGTGATCACCAGGTCCCT\n+CCTGGTAAGGCCTCCGTACTCGGCAGTGTTGGAAACGACGTGCCACATCTTCTCGAAACCGCCCTCGTTTATGAGGTCGACGATGAGCTTCGCCTCATGG\n+CATACTTCGAAGTAGGCCATTTCGGGAGGGTATCCTCCCTCGACCAGGGTCTTGAATCCCGACTTTATGAGGCCGGTGGTCCCTCCGCACAGCACGGCCT\n+GCTCTCCGAACAGGTCTGTGAGCGTCTCGTTGTCGAAAGTGGTCTCGAAGACGCCGGCGCGGGTGGCTCCGAGCCCCTTTGCAAGTGCAAGGGCGATCTT\n+CTTGGCGTTGCCGGTATAGTCCTGGTGGACGCAAACGAGGGCCGGAACTCCGAATCCCTCGACGAACACATCCCTTTCTTTGTCCCCGGGGGCCTTGGGA\n+GCCATCATTATGACGTCGATGTTTTTCGGAGGAACGATGGTCTTGTAGGTCACAGCGAAACCGTGGGCGAACTCAAGTGCGCAGCCCTCCCTGATGTTGG\n+GCTCGACGAATTCTTTGTATACCTTTGGCTGGACCTCGTCGGGCAGAAGCATCATGATGACGTCCGCGGTCTTGGCGGCCTCGGCGAAATCTACGACCTT\n+GAAGCCGTCCTCTTTCGCTTTGTTCCATGATCTTCCGTCTTTCCTGAGCCCGATCACTACGTTGAGGCCGGAGTCCCTGAAGCACAGGGCCTGCGCTCTC\n+CCCTGGGATCCGTAGCCCATGACGGCGACCGTTTTTCCTTTAAGGACATCTATGTCCACATCTGCATCGTGGTAAATCTTCATTATATCCACCTGTTTAG\n+AGGTCCAACTGCTTTATAGACTAAAAGGTATCGTTCCCGCTCCGACATATAGGTCAGTTCAGTACTGGCAGCGTCCTTTGACCAGGGCCTGATTCGGATT\n+GGCAGGCAGCATGGGCAACACGTCCTCCTCGGGATCGATGTGGATGTCCAGCAGGCACGTCTCGCCGCTGTCTATTGCGGTCTTCAGGGCGTCGGCTATC\n+TCTCCCGGCTTCTCGACCAGCATTCCTCTGGCCCCGTAGGCCTCGGCTATCTTGGAGAAGTCCGGGTCGGCGCCAAGCTCGGTCTCGCTGTACCTCTTGT\n+TCCAGAACAGCTTCTGCCACTGTTTGACCATTCCCAGCCATCCGTTGTTCAGCAGGACTATGACGACCGGCAGGTCCTCGGCCACCGAGGTGGCCAGCTC\n+CTGTTGGACCATCTGGAATCCCCCGTCCCCTGTTATGGTCAGGACGGTGCTGTCGGGCTTGGCGGCCTTCGCCCCTATGGCGGAGGGGAGCCCGAAACCC\n+ATCGTGCCGAAGCTTCCCGAGGAGAGGAGCTGTCTGGGCCTGTGGACGTGCAGATGGTGCATGGCCCACATTTGGTTCTGTCCCACGTCGGTGGTGACTA\n+TCATGTCGTCGTCCTTGTCGATCAGCCTGTTGATCTCGTATATGACCTTCTGAGGGACGATCGGTGTAAGGTCTATGTCGATCTTGCACCTGCAACGCCT\n+CCTGTACTCCGCATAGGTGCTGTTCCAGTCGGCATGGGTATCCCTGTATCCGGAGAGCCCGTCGATGAGCGCCGCGGTACCCTTCTTAGCATCGCAGAGA\n+AGGTTGACGTCGTTGTTCTTGTGCTTGTCGAACTCCGTCGCGTCTATGTCTATCTGGACGACCCTGCATGCGCCGTCGAACCTGGTGTGGG'..b'CGGGGGCCATATGCCCACGCAGGTGTTTCATGGCTGTAATAAAGGTCGGTATCAACGGATTCGGAACCATAGGGAAA\n+AGGGTCGCCTCCGCAGTGAGCGCACAGGATGACATGGAAGTCGTAGGTGTGACGAAGACCCGCCCGTCCTTCGAGTCGGAGGTCGCAAGGTACAGGGGAT\n+TCGACCTGTACGCGCCTCAGAAAAGCGTCGAACTGTTCGACAAAGCGAACGTGCCGGTCGGGGGGACCGTCGAAGACCTCTGCGGCAAGGTAGACATCAT\n+GGTCGACTGCACGCCCGGAAACGTAGGGCAGGAATACAAGGCGATGTACGCCAAAGCAGGCATAAAGGCGATATTCCAGGGAGGGGAGGACCACAGCCTG\n+ACGGGGATATCCTTCAACTCCACCGCCAACTACAAGGAGTCCTGGGGCGCCCAGTTCTCCCGTGTCGTTTCTTGCAACACCACGGGGCTGCTGAGGACGC\n+TCTACCCCATAGACCGCGAGTTCGGTATCGAGAAGGCGTACGTAACGTTGGTCAGAAGGGCCGCGGACCCCGGTGACAGCAAGAACGGGCCGATCAACGG\n+GCTGGAGCCCACCGTCAAGCTGCCGACCCACCACGGGCCGGACGTCCAGAGCATCATGCCATGGGTCAACATCAACACCATGGCGATAAAGGCCTCCACT\n+ACGTTGATGCACATGCACACGGTCACGCTGGAGCTGAAGAACTCCGCTTCCACCGAGGCCGCGGTCGAAGCGATAAGGAACTCCTCGCGCGTCAGGATGG\n+TGGACGCGGCGTCCGGCATCAGGTCCACGGCGGAGGTCATGGAGCTGTCGAGGGACCTGGCCAGGGACAGGTCCGACATGTACGAGATCGTGGTATGGGA\n+\n+>contig_38063\n+CTATCTCCTCAGGAGGTCTGGGAATCTCTGATCGGGAAGAACAGTAACTACCGCATCATAGTCGTGGACCTCAATCTGACCCGTGTGCTGTTCGGCATGA\n+TAGTGGGCGCCGGCCTGGCGGTGGCCGGTGCGGTCATGCAGGCCCTGTTCAAGAACCCGATGGCCTCGCCTTATACTCTCGGGCTCTCGTCAGGCGCCGC\n+ATTGGGCGCCGCATTGGGGATTCTCTTCCCTCTTTCGTTCGTACCTGAGGTCGCATCGGTCCCAATCCTGGCTTTCGTTTTCTGTCTGGGGACCATGTTC\n+CTCGTGTACTCTATTGCCAGAGTGGGCAACCAGACGCACATGGAGACTCTTCTGCTGGCCGGAATAGCCGTAGCGGCATTGGCGCAGGCGGCGGTCTCCC\n+TGCTCACGTACATAGCGGGCGAGAGCATCACGGAGATAGTCTTCTGGGGAATGGGCAGCCTGACCGTCAGCCTCCCATGGGTCAAGATCCCGATAGTGCT\n+GGTCCTCAGCGCCGTGGGCATATTCGCAATGCTCTACTACGCCAAGGACCTGAACGCCATGATGCTGGGGGACGCCCACGCCATGGACCTTGGAATAGAC\n+GTAAAAAAGACAAGGCTGGCACTGTTGATCGCCTCGTCTCTCGTCACCGCGGCTGCGGTATGTTTCGTGGGGACCATCGGCTTCGTAGGCCTTGTGATCC\n+CGCACATACTCAGGATACTTCTTGGTCCGGACAACCGTCTGCTTCTGCCGATGTGCGTGCTGACCGGAGGGATATATCTTGTAGGATGCGACTATCTGGC\n+ACATCTCTTCGCCCAATCTCTGGGCGTCATGCCCATAGGCATAGTGACATCTCTGATAGGCGCCCCGTATTTCATCTATCTGCTCAGGAGAAGAAAAAAG\n+GAGGTGGGATGGGTATGAGCCTGGATATCCGTGACTTATTCTACAATTACGATGGGAAGCCTGTTCTCAAAGACGTTTCGTTCCTGGTCAAGGAAGGAGA\n+GGTCCTGGGGATACTGGGGCCCAACGGATGCGGAAAGACGACCCTGCTGGGCAATCTGAACAGGAATCTGAGCCCCAAAGGCGGATGCGTGCTTCTGGAC\n+GGGGAGGACCTTCACAATTACAAGAAAAAAGACATCGCGAAGGAGATAGCGGTGGTTCCGCAGGACAGTCGCGTAGGTTTCTCGTTCACCGTAAGAGAGA\n+TCGTCTCCATGGGCAGGATGCCATTCCAGGACGCCTTCCAGGGAGACTCCTCGGAAGACCTCAGGATAATCGAAGACGCGATGAGGAAGACCAACGTACT\n+GGATATGGCAGACCGTTACGTGAACACCATGAGCGGCGGGGAAAGGCAGAAGGTCATAATCGCCAGGGCCATGGCGCAGACGCCCAAGATACTGCTGATG\n+GACGAGCCC\n+\n+>contig_44250\n+GGTGATGTACTGGGGCTTGTAGGCTACTTTGACCTTTGCGTCTATCTTGCCGCCGTCTGGAGGGATCTCTCCGGCCAGCATCTTTACGAAAGTGGTCTTT\n+CCTGTGGCGTTGGGACCGACGACCCCGACGGATTCCCCCATCTTTATGGAACCGCCGACGACATCCAAAGTGAACTCTCCGAAGTCCTTGGACAGGCCCT\n+CGAAGGAAAGCAGGTCGGAAGTGACCCAGTCGCTCCTGGGAGGAGACGCGAAGAACTCTATCGGCCTATCCCTGAAACGGATATTCTCTTCGGGAAGGTA\n+ACCGTCCAGATATACGTTTATGGCGGTCCTGACCTGTCTTGCAAGAGTGAACACGCCGTACGCCCCCTCGGTACCGTATACAACGCTGACGATGTCGGCG\n+AGGAAATCGAGTATGGCAAGATCGTGTTCTATCACGACCACCTGCTTTTCTGCGCTGAGTTCTTTGATGATGCGTGCCATCCTGATCCTCTGGTAGATGT\n+CAAGGTACGAGGTGGGCTCGTCGAAGAAGTATACGTCCGCGTCCTTCATGACCGTGGCAGCCATGGCGACCCTCTGAAGCTCTCCTCCTGAAAGTTTCTT\n+TATATCCCTGTCCAGAAGCTCGGTCAGCTCGAACATGATGGCGGCCTCCTCGAGTGTCAGGCGGCCTTTTATGCCGGAAAGCAGGTCCTTCACGGGCCCC\n+GATGCGGCTTTGGGTATGAGGTCCACGTACTGTGGCTTTATGGCCGTCCTCACCTTGCCGGCGTAGACGTCCGTGAGATAGGATTTGACCTCGGTACCGT\n+CGTAGTGCTGCAGCACTTCCTCTTTGGATGGAGGTTTCTCATAGTTGCCCAGGTTGGGGACGAGTTCCCCGGAAAGTATCTTGATCGCCGTGGATTTTCC\n+GATCCCGTTCGGTCCAAGTATGCCCGTGACCATGCCTTTCTTCGGCACCGGGAGCCTATAGAGGCGGAAGGCGTTCTCGCCGTACTGGTGGACCATCTCC\n+GTCTTCAGCTCGTCGGCCAGGCCTATGATCTTTATGGCGTCGAACTGGCATTTGTTGACGCATATCCCGCATCCCTGGCACAGGGATTCGGATATGATGG\n+GCTTGCCCCTCTCGCCGAACACTATGCATTCCACGCCCGTTCTGACCAACGGGCAGAACTTATAGCATTCCTTGTTGCATTTTCTGTTCTGGCATCTGTC\n+CTGCAGGACGGCCGCAATACGCATGTCCCCGCTTAGACCGATTTAAGATATAACCTTTAAGGATGGTATCGCAGATAAGCTGATAAGGGAAGACGGAGAC\n+AGATGGGCATGGCCGAAGCGGATGGGACCACCGAGGACGTCAGGATACTTACGGGCGACTACAGGAGGGCGATAAGGCATCTCTCCATACCGATAGCCGT\n+GGCTCTTGCGATACAGCATATCAACATACTCGTAGACACGTTCTGGGTCGCGGGCCTGGGGGCGGACCCGATGGCTTCAATAAGCATAGTATACCCGGTT\n+TTCGCCACGGTCATGGGCATCGGAAGCGGGCTGGGGATCGGTGCTTCTTCCGCGATAGCCAGAAGCATCGGGCATAACAGGAGGAAGGAAGCCGGCACGA\n' |
| b |
| diff -r 000000000000 -r 11a61934bfb3 test-data/genome2.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome2.fna Tue Dec 10 16:05:34 2019 -0500 |
| b |
| @@ -0,0 +1,51 @@ +>contig_11394 +GCTTTTTACGCCCAACGGGCTTGTTCTTGCTCAGACAGTCCAAGGCTTTCCAGATATGATAATCGCTGAATTTCGGTATCGGGCCGCCTGCACCCCTGTG +CTGCTGATTGGACATATGGATGTATCATTCATCCATTAAATAAAGTAATTGATTGTCATGTCGCAAGATACGGTATTAACGCCGTCAATAGCTGTTAAGC +CAGTGCCCGCCGTCGCTTTCCATCCGTAATACTCGCGCGTTTTTTATATCGAAGGAACTCTTCACATCCATGGTTCAAAAGTCGGTGGACTTTGTTATTA +TTGAGAATGTTTCCAAGAGGTTCGGGAACAAGACGGTCCTTAATAATGTGAGCGCCACTATACAGACCGGTAAGATACTGGGCCTGATAGGCAAGAGCGC +CGCGGGCAAGAGCGTTTTGATAATGATGCTGAGGGGAAGCGAAGATTACGCACCCGACTCCGGAAGGGTGCTGTACAGGGTCAATAGGTGTTCCGGATGC +GGAAACCTCGACCTCCCCCATGAAGGAACGCCCTGCTCGAAATGCGGGTGTGAAACAGGAACGATCACCGTGGATTTCTGGTCTTTGAAAGATGACGACC +CTTTAAGACGCCAGCTCAAGAGCCGCATCGCCATAATGCTGCAGAGGACGTTCGCCCTTTTCGGGGATAAGACCGTGATCGAGAACATCTTCGAGGCCAT +AGGCGACCGTGCAGAGGGCAAGGCCAGGACGGACATGGCGCTCCAGCTGCTGGAATTCGTGGGGATGACTCACAGGACCACACACATAGCCAGGGACCTG +TCCGGAGGAGAGAAGCAGAGGATAGTCCTCGCAAGGCAGATAGCCAGGGATCCTCTCTTCTTCTTGGCGGACGAGCCGACGGGAACGCTTGACCCGTACA +CGGCGGAATTGATGCACGAGCGTCTTGTGGACTACGTCGGGAAGAGAGGGATCTCGATGGTCTTCGCGTCCCATTGGCCCGAGGCCGTGGATAAGATGGC +CGACGAGGCCATATGGCTGGATTCCGGCAACGTGCTGATGCAGGGCGACCCGAAGGAGATCGCCGATAAATTTATGGAAGGATACTCGTTCGAAAGGACA +AAGGCCGCCGACCTGGGAGAGCCGATAATATCGCTCAAGGATGCGGAGAAGCACTTTTTCTCTGTCGTCAGAGGAGTCGTCAAGGCAGTGGACGGTGTAA +CCTTCGATATAATGGAGCGCGAGGTGTTCGGCCTTGTGGGAAAGTCGGGCGCCGGCAAGACCACGACGTCAAGAATGGTCGCCGGCATGACGCCCGCCAC +CCGCGGGTCCGTGAAGATAAGGATCGGCGACGACTGGGTTGATATGTCAGAGATGGGGCCGAGCGGGAAAGGCCGCGCCACCCCCTATATCGGGTTCCTC +CATCAGGAATACACGCTCTATCCCTTCGACAACATACTCAGCAACCTTACGACCAGCATAGGCACCAGGATGCCAGCGGAACTTGCAAAGTTCAAGGCCA +TACAAGTGCTTCAGAGCGTAGGGTTCGACAAGAAGAACATGGAGAGTCTTCTCTACTCTTACCCCGACACACTGAGCGTCGGAGAGTGCCAGAGGATAGC +CTTCGCACAGGTCCTGATAAGGGAGCCCCGCATCATAGTGCTGGATGAGCCTACAGGGACAATGGACCCGATAACAAAGACCATCATAGCAAAATCCGTC +ATCCGGGCGAGGGAGACCCTGGGCGAGACCTTCGTCGTGGTGAGCCACGACATGGATTTTGTCGAGAACGTCTGCGACCGCGTAGCGTTCATAAGGAACG +GCGTCGTGGAAGACATGGGAACTCCCGAGTCGGTCATCCAGAGGTTCGGTCTGAAAGAGCTTCAGGATGACGACTCCGAGGGTGAATGAATGAAGCAGCA +GATCGGGCGCCACCTCAGCTTCGTTGAATGCAGAGAGGCCATGGGGCTCGGCGTGGGCGGTGCCCTGGCACAGAGGGCGACCATCTCTGACAGCGGAAGG +GACGTCGTTGCGGTGGCCATGGGCCCGGGCAAGAGGCACATAACCAAACCGGTATGCGAGATAACATATGCCCTCAGAGAAGAGGGCATAGATACCAGCG +TCGCCTGAGCGCCTGGCACTTATTGCGGAGTATGTCAAGGACATGATGACCGAACTCGAACCGGACAACGCGGCCGTCTTCGAAGCGGGATGCGCCAGCT +ACCGGGCCAAGGTAGATGTGCTGATAGGGCTTGAACAAGAATATCTGACAGGCAAGGCGACTACCGAGATCATCGTCTGGCACCCTTCCTGGGCGTATCT +TCTTCCGGATAATGTGACCGAGGCAGAGCTCATGGAAGCAGCCGAGGCGGCATCCACGCCCTCATCGATCGCGATGCTGCAGGGAGGGACGCCGGAAAAT +CCTATCAACGTGTTCCTTTCGGAACCCGAAGAGATCAACGGTCTTACCCAGCAGGGGCTTTGTGAAATGGGAATATATGTAAACATAATAGTGATTAACA +TACTCGCCGGGGACTGGGTCGAATATCTGGGCCAGGTCATCGAGATACTGGGAGATAATATTCCGGATGCGGGGACATGAATTGATGATACCAATAGAAA +TTAAGGACCTTACCGCTGGATATGACGGCCGAGCCGTTTTCAGCAACGTCGACCTGGAGCTCAGGGACAAAGACTTCCTGGCGGTCATAGGGCCCAACGG +CGGCGGGAAGACAACGCTCTTCAGGGCGATCCTGGGCCTAATAAAACCCATGGGGGGGACCGTAAAAGTGTTCGGCAAGGAGCCGGCAGGTTCGCCCCCG +GGCATAGGATACGTTCCGCAGAACGAGAATCTGGACTCAGAATATCCAATAAGTGCCAGGGAAGTCGTCCTTATGGGAATGAGGTGCAAGAAGGGCCTTA +GGCCGTTCTATTCCAGTGAGGAGAAGGAGTCCGCAGAGAGGGCCATGGAGTACGCCGAGGTCTCGGATTTCGCAGACAGCCGAATAAGCAACCTGTCGGG +AGGGCAGAGACAGAGAGTATACCTCGCAAGGGCTCTTGCCCCGGAACCGAAGATACTCATGCTGGACGAACCCACCGCGAGCCTGGACCCGTCGATGAAG +GACTGCACCTACGACATACTCAGGAAGCTGAACAGGGACGGGATAGCCATAATGGTGATAACTCACGATATGAGCAGCATCTCTCATGATGTCAAACGTG +TAGCATGCATGAACCGCAGGCTGATAGTCAACGATGCGCCCGAGATAACCCAGGAGATGATCGCATTGGGATTCCACTGCATCCCCGAGCTAGTGCACAT +AGGTCCCTGCGATTGCGGAGGTCACAACGATGGTTGATTGGGTCGCGGCATTCTCGATGCCTCTGATTCAGAACATGTTCATGGTCGCGGCCATAGCATG +CGTTCTTTGCGGAGTCGTGGGAACCCTGGTGGTCGTGAAACGGATGGTGTTCGTAACGGGTGGCATAGCACACACCACTTTCGGAGGTGTGGGTCTTGCA +TATTATGTTATGTCCGTCGTCGCAGTCTCATGGTTCACCCCCATGATCGGCGCCGCACTGTTCGCGGTCGTTTCGGCGGTCATAATGGCGCTTCCCGCGG + +>contig_159 +TATAGCTCAGCTCGTTGGCGGAGACGCTGCTTCCGTACATCTGGCCGCCGCCGTTGATGCCGCCGCCCCAGGCGGCCGTCCCGATCCCCACGGGAGAAAT +GTCCGTACCTCGGAACCTTATGTTTCTCACGGATTCCCGTATATGTTCCTGGATTATAACTGATACGCAATCCTGTTTCCGACGTCCGCCATGTTTAGAT +AAATTGACGGTATAGCCGAAGGCATGGATATGGCAATGGAGCTGAGGAACGTCTCCGTAGTGAGGGACGGGAAGCGGATACTGGATTCCGTCTGCCTCGA +TATCGGCGCCTCCGAGAACGTTGCCGTCATAGGGCCGAACGGTTCGGGGAAGACGACGCTCATCAAACTGCTGAGGGGCGATATTTATCCCTACTACGAC +GAGGACCGCCCCGCGGAGATGAGGATCTTCGGTGAGAAGATATGGTCCATCTACGACATACGGAGCCGCATGGGCGTGGTCTCCATGGACCTCCAGGGCA +TGTTCGGCGGCGAAACGCTGGTCGGAGACGTCATAATGTCGGGATACTTCAGCAGCCTGGACATTTTCCGCAACCATGAGGTCACCGACAACATGCGCTC +CGGGGCCTCGCGAGCGGCCGGGTACATGGGAGTGGAACATCTCGTCGGCAGAGATCTGTCCGGCCTTTCTCTGGGAGAGATGAGGCGGACGCTGATCGCC +CGGGCGCTGGTCACCGCCCCCGAGATGCTCGTCCTCGACGAACCGATGACGGGCCTCGATATTGTAATGAAATCCAAATTCAGGAAGATGTTCGACATCA +TGACGGAAACGGGAGTGAGCATCGTCATGATAACCCACGACCTCACCGACATCCCCGTTTCCTTGAACCGCATAATAATGATCAAGGATGGGAAAGTGTT +CGCGGACGGTCCTAAAAAAGACGTCCTGACGTCCGAGGTCGTCAGCGGGCTTTTCGATGAACCTATTAATGTACAATGCGTTAACGGGATATATTCAATG +AGGATGGATGAGTGACAAGGTATATCTGTTCCGAATGCGGGAACGAGATTCCGTACGTTTCGGATTTCTGCTACCAGTGCGGTAGCCTGAAGAGCAAGGC +GTTCAAGATAGACGAGGGCGGCGAGATGGAGGGCGGGGAGGTCCCGTGCCCCAACTGCGGAAAGCCCATAGAGGAGGACGCCCGGTACTGCAGGCACTGC |
| b |
| diff -r 000000000000 -r 11a61934bfb3 test-data/genome3.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome3.fna Tue Dec 10 16:05:34 2019 -0500 |
| b |
| @@ -0,0 +1,60 @@ +>contig_4003 +ATCAAAGAGGAACTGAAGGCGGCGATGCTGCTGACCGGTTCCTCTGACATAAGAGAGCTCTCTGATGCAGAGTATATCGTCATGGGAGAGACACGCAAAT +GGATGGAAGGCCTGAAATGACCGACGTCAAGAAGATATTGAAACAGATGTCCGACGAGCTGAGCAAGCCGATCGAATCATACATAGAAGACGAACTGCCC +GCCAATCTCATCGAAGCGGCAAGACAGTACCCCTATGCCGGCGGAAAGAGGATGAGACCGGCCATGGTCATCGCCGCGTGCAGGGCGGTGGGAGGGGATG +GCAGGAAGGCCGTTCCCCTTGCGGTTGCCATAGAGTACATACACAATTTCACGCTGATCCATGATGACCTCATGGACGGGGACGAGAAGNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTCATGGACGGGGACGAGAAGCGCC +GGGGCATGACCACATCCCATGTGAAGTACGGCATGCCCACAGCGGTGTTGGCGGGAGATGCCCTGTTCGCTAAGGCCTTCCAGATAATCGCCGACCTCGA +TGCGGACGGCGAAACGGTCAGAGATGTCCTTAGAGTGGTCTCCCAATCCGTCTGGGACCTGGCCAGAGGTCAGCAGATGGATATAAACAACGAGAACGGG +ACCGAGGTCACCATGGATGAGTACATCGAGACCATCAGACTGAAGACCAGCGTTCTGTTCGCCGCCGGTGCCGCCGGAGGCGCTATGATCGGAGGTGCGA +GCAAGGAGGTCGTGGACGCCGTCCACGGCTACGCCATGAACCTGGGCGTCGCCTTCCAGATGTATGACGATATACTTGGGATAGTCGGGGACCCGGCCGT +TACCGGTAAATCGTCCGGTAATGACATTCGCAAAGGGAAGAGCACCGTCATCGTGTGCCACGCCCTGAAGAACATAGCTGACAGGGCGGACCTGCTGGTC +TTCCGCGATATCCTCGGCAAGACAGACGCCACCGATGCGGAGATAGACGAGGTCAGGAGCATACTCCGAAGAGCCTGCAGCCTGGATTACGCCATAGAGA +CCGCAGAGGATTACATCAACAAAGCCGTCGACTGCCTGGATGCGCTGGAGCCCTCAAAGGACAAGGACTTCATGATAGCCCTGGCAGAATACACGATGAC +CAGGACCCTTTAGTCGGAGATCCCCTTCTCCGTTATGGAGTATGTGGCTTTCCGGCCTTCCGGTATGCTGCGGTGCTTGACCATGATCGCGGCCCTGCGG +CCGTTGCCTTTCTTCTCCAAGCGGATTATGGTCTTCGCGTTATGATGCATGGCGTGGCCTCCGAGGAACTCTATCGTACCGGCGCCTATGTTGGTGTATA + +>contig_4403 +CACCGGTCACCCGAAGGTCACGCGCGTATCGATGCGTGACATCGCAGACCTGGGAGAGAGGGGCCTGTACATCCTTCACGAGATCGGTACGGACCTCGTC +GGCAAGATGGAGGGCTGCACCGGGTGCAAGAAGTGCGAGCACGAATGCCCCGAGAACGCGTTGACCGTAAGCAAGGACAAGACGATCACCGTGAAGACCA +AGAACTGCCTCGGAACGGCATGCTACAGATGCCAGTACGTCTGTCCCGAGAAGGTCATGCAGTTCGACTCCCTAAGGCTGTCGTGATAAACGGTTTTGGG +CGGGGCCGGCCCCGCCCTTTTTTCATTTACCGCCGTTCAGGGCCTCGGCGTGCACGGCAGGCCTGACATTCTCGTCCTCCAGCTCCGTAAGTATCTGCTT +GCGCAGCCTGATGAACTCGGGCGAAGCGCGGTCCCTGGGCCGCGGAATGCCTATGTCCACGATGTCCTTGATGCTGGCAGGACGCTTGGTAAGGACGACT +ATCCTGTCTGAAAGATAAACGGCCTCGTCGACCGAGTGGGTCACGAACAGGATCGTAGTGTCCGTCTTCTCGACTATCCTCAGCAGCTCGCCCTGCATGA +TGTTGCGCGTCTGGGCGTCCAACGCGCCGAACGGCTCGTCCATGAGCAGCACGTCGGGCTTGGTAACAAGGGCCCTTGCGATGCCCACGCGCTGCTTCAT +ACCTCCGCTGAGCTCGTGGACACGATGGTCCTCGAAACCTTCGAGGCCGACCGCCCTGATGTAGCGTTCGGCGGTCTTCCTGCGCTGCTCCGCCGGGACG +CCGGCGATCTCCAGGCCGAACTCGACATTCTTCCTTACAGAACGCCAAGGGAACAGTGCGAACTCCTGGAACACCATGCCTCTGTCGGGGCCTGGCCCGG +TGCACTTCTTCCCGCCTATCGACACTTCTCCGGAGGACGGCTCCATGAGCCCTGCTATAAGCCTGAGCAGAGTCGTCTTTCCGCATCCCGAGGGACCGAC +TATGGATATAAGCTCGCCCTTCTGGATCTCCAGAGAGAAATCCTCCAGGGCCACGGTCTCCTGTTCATCGGTCTTGTAGACCTTCCTCAGATGATTGATA +ACGATCTTCTCGCTCATTCTATCCCCATCCTTCTTGTTATGACCTTGTGCAGATAGTCGGCGAGGCTGGTCGTCAGTATTCCGAGGATTGCGATTATGAC +TATGCCCGCGTAGACGTTGGGCCAGTACCCCATCTGCGCCTGTATGCTGATGAAGTATCCGACGCCTCCTCCGAACGATGCGTACAGCTCGGAGGCAACT +ATGCACATCCACCCGACCCCCATGCCTATGCGGAGGCCGTTCATTATGTATGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN + +>contig_14302 +GATGTGGAATGCGGCCAAATGCCGCCTCGGTTTCAGCGGGGCAAGGCGTTCCATGTCCACGACCGCTGGAATACTGGTGAACGTTTTCATTACTTCTCTG +GAGATAGCCGAACGTTCTCAGCCTGCGCTCGAAAGCAGGAACTACAACGGCAGTTTCCCCATTTATAGGATGCCCAACAAGATCGGTCTCTACTGGTTCG +CCATCACGGCCGCCGCGTGCGCCTCGCTATACATCATCGGATACTACATCTCGACCCCGAACATGGCGGCAATACTCCTGGGGGCGGTCTGACGGTCTGC +GACCTTCGTACGGATAAAGTGAGCTACAGGTACGGCAATTCGAATTACAATGCTATCGATTCTGTGGATTTCACAGCCTCCCATGGCAGAAGGACCGTCA +TCCTGGGAGAGAACGGGTGCGGCAAGTCGACGCTGATATATCAGCTCAACGGAGTATACAAGCCTGTTTCCGGTACTGTGTTCTATGGAGATATGCCCAT +ATCATACGACAAGGAGTTCCTTACGGAGCTGCGTTCCGACGTTTCCGTTGTTCTGCAGAATCCAGACGATCAGATTTTCTCTTCCACCGTCGAGGAGGAC +GTGGCATTTGGACCGTTAAACTTGGGCCTTTCCCGGGAAGAGGTTGGAGAAAGAATCGGCCGGTCTTTGGAATGCGTGGGGATGTCGGGATTTGCCGAAG +TGCCTGTTCAGCGCCTTTCATACGGTCAGAAAAAAAGAGTGTCACTCGCAGGCGCCCTAGCATCACATCCAAAGATACTGGTCCTGGACGAGCCTACCGC +AGGCCTGGACCCGCAGATGTCCAGAGAGGTGATGGAGATCGCAAATTCTCTCATCAGAGAAGGGATCTCCGTCGTAGTATCCACCCATGACGTGAATCTG +ATCTACAATTGGGTCGAGGACCTTTACGTGATGCGGAACGGACACATGGTCTTCTCCGGAGATGCGGACGAGTTCTTCTCCGACCGTCCGTCCGTTTATC +TTTCAGGTCTGGAACAGCCCTCGATATTCAGCATAAACCACAATATGGAGACGTTAAGAGGGACGATTCCCGCGTCATATCCCAAGACCATGAGCCAGAT +GGTCAGCAGATTATTCCCTTCAGGATCCTCGGCCGGAAGGATATTCATCTATCAGACTGAAGGCGAGCGCATCGACCAGGATGCGATCGAGGAGGCCGTG +GGAAAGAAAGGGATGCCCATTGCAGTATACGGCCCCTCCGCGCGCAGGTCGGTGACCCGATCGAAGCTCAGGGTTGATTTCTATTTTAACGGCATAGAGT +GTTGCATCAGGGAGGCCATGGTAAACCATGATTCCCTGATAATAGTCGACCGGGGCTTGAAGGGGATCGTCACGGAGGCGATTGAAGAGCTTAGGGCATA +CGGAACCCGGATCAGTATCAGGGAGTTGGTTTTTTGAGCGCTCCCCTTTTCCGCACCGAAGGTCTTTTCTTCAGATACGAAGGCGGCCGGGGGGACGCGT +TGGCAGACGTGAACATCACGATCAAAGAGGGTGCCAGAACTGTCATCATGGGAGCCAACGGAGCTGGAAAATCCACGTTCTTCTATCATCTTAACGGAGT +CTTGAGGCCGTCGAAGGGCTCGGTGTTTTTCCGGGGAGAAAAAATACCGCACAGGGGAAAAGCTCTCAGGAAGCTGCGCTCGGAGGTCGCGGTGATGCTC +CAAGACCCCAACGACCAGCTTTTTGCACCAAAAGTATCTGACGACATAGCATTCGGCCCGAAGAACCTGGGACTCGACGCTCAGACTGTAGGGGAGAGGG +TCAGGGACGCCCTCTACATCACAGGCATCGAATCTCTGGAGGGTCGCAGCGTGATGCAGCTGTCGTTCGGCCAGAAGAAGAGGGTGGTGCTGGCCGGTGC +CTTGGCGATGCATCCGAAGGTGCTTATAATGGACGAGCCCACCGCAGGTCTCGATCCCCAGATGTCCAAGGAGCTCATCGAGCTCGCGGACGAGCTGCAC +CATCTTGGAACGACCGTTATTTTTTCAACCCATGACGTGGACCTCTCATATTCTTGGGCGGACGAGGTCCATGTCCTAAGAGGGGGCCGTAATGTATATT +CGGGGAGCTCAGAAAGATTCTATGACGATACTTCGGAAGTTTATCTTTCGGGCCTTGTCGAACCGGCCATGTACGACATCAACGTCAGCATCTCCGAGCT +TGCCGGATGCCCCGTTGAACCGTTTCCCAAAACCCTGCCTCAGCTTGTGGCCAAGGCAGTGCCGTCAGAGGGGCCGGGCACGGTTCACATCCTTCCCGTG +GAAGGTCCGGTCGACCGGGAGCTGTTCTCCTCTCTGACGTCCGGGTCCGGGATGTCCGCAACAGGCGTCTACGGTACTAATGCAAGAAAATCTGCGGAGG +CTTCCAAATTGCCGATAGATTATTTCTTCGGGGCCGACGAGGGATGCATAATAGAGGCTTTGCACGGCAAAGACACGCTGATATGCTGCGACAGGTCCCT +TACAGATCTGCTGATATCGAAGATAGGCAGTATGTCCCGGTTCGGGACAGAGGTCCCTTATTCTCTGCACTGAACATTTCTTTTTTCCGGGGGTTCGAAC |
| b |
| diff -r 000000000000 -r 11a61934bfb3 test-data/test_contig.contig2classification.names.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_contig.contig2classification.names.txt Tue Dec 10 16:05:34 2019 -0500 |
| b |
| @@ -0,0 +1,4 @@ +# contig classification reason lineage lineage scores superkingdom phylum class order family genus species +contig_38063 classified based on 1/2 ORFs 1;131567;2;1783272;1239;91061;1385;186820;1637;1639 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00 Bacteria: 1.00 Firmicutes: 1.00 Bacilli: 1.00 Bacillales: 1.00 Listeriaceae: 1.00 Listeria: 1.00 Listeria monocytogenes: 1.00 +contig_44250 classified based on 1/2 ORFs 1;131567;2;1224;1236;135623;641;662;666 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00 Bacteria: 1.00 Proteobacteria: 1.00 Gammaproteobacteria: 1.00 Vibrionales: 1.00 Vibrionaceae: 1.00 Vibrio: 1.00 Vibrio cholerae: 1.00 +contig_9952 classified based on 1/5 ORFs 1;131567;2;1783272;1239;91061* 1.00;1.00;1.00;1.00;1.00;1.00 Bacteria: 1.00 Firmicutes: 1.00 Bacilli*: 1.00 not classified not classified not classified not classified |
| b |
| diff -r 000000000000 -r 11a61934bfb3 test-data/test_contig.contig2classification.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_contig.contig2classification.txt Tue Dec 10 16:05:34 2019 -0500 |
| b |
| @@ -0,0 +1,4 @@ +# contig classification reason lineage lineage scores +contig_38063 classified based on 1/2 ORFs 1;131567;2;1783272;1239;91061;1385;186820;1637;1639 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00 +contig_44250 classified based on 1/2 ORFs 1;131567;2;1224;1236;135623;641;662;666 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00 +contig_9952 classified based on 1/5 ORFs 1;131567;2;1783272;1239;91061* 1.00;1.00;1.00;1.00;1.00;1.00 |
| b |
| diff -r 000000000000 -r 11a61934bfb3 tool-data/cat_database.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/cat_database.loc.sample Tue Dec 10 16:05:34 2019 -0500 |
| b |
| @@ -0,0 +1,7 @@ +## A typical download from https://tbb.bio.uu.nl/bastiaan/CAT_prepare/CAT_prepare_20190719.tar.gz +# ls CAT_prepare_20190719/ +# 2019-07-19.CAT_prepare.fresh.log +# 2019-07-19_CAT_database +# 2019-07-19_taxonomy +#value name database_folder taxonomy_folder +#2019-07-19_CAT_database 2019-07-19_CAT_database /opt/galaxy/tool-data/cat_database/CAT_prepare_20190719/2019-07-19_CAT_database /opt/galaxy/tool-data/cat_database/CAT_prepare_20190719/2019-07-19_taxonomy |
| b |
| diff -r 000000000000 -r 11a61934bfb3 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Dec 10 16:05:34 2019 -0500 |
| b |
| @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of CAT databases --> + <table name="cat_database" comment_char="#" allow_duplicate_entries="False"> + <columns>value, name, database_folder, taxonomy_folder</columns> + <file path="tool-data/cat_database.loc" /> + </table> +</tables> |
| b |
| diff -r 000000000000 -r 11a61934bfb3 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Tue Dec 10 16:05:34 2019 -0500 |
| b |
| @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of CAT databases --> + <table name="cat_database" comment_char="#" allow_duplicate_entries="False"> + <columns>value, name, database_folder, taxonomy_folder</columns> + <file path="${__HERE__}/test-data/cached_locally/cat_database.loc" /> + </table> +</tables> |