Mercurial > repos > iuc > data_manager_ncbi_taxonomy_sqlite
changeset 0:7a76cd412252 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
| author | iuc |
|---|---|
| date | Tue, 21 Jul 2020 17:04:41 -0400 |
| parents | |
| children | 54a0869d0051 |
| files | data_manager/data_manager_ncbi_taxonomy_sqlite.py data_manager/data_manager_ncbi_taxonomy_sqlite.xml data_manager_conf.xml test-data/ncbi_taxonomy.loc test-data/ncbi_taxonomy_sqlite.loc test-data/ncbi_taxonomy_sqlite_data_manager.json test-data/taxdb/names.dmp test-data/taxdb/nodes.dmp tool-data/ncbi_taxonomy.loc.sample tool-data/ncbi_taxonomy_sqlite.loc tool-data/ncbi_taxonomy_sqlite.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
| diffstat | 13 files changed, 1423 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_ncbi_taxonomy_sqlite.py Tue Jul 21 17:04:41 2020 -0400 @@ -0,0 +1,79 @@ +from __future__ import division, print_function + +import argparse +import datetime +import json +import os +import os.path +import shlex +import subprocess + +DATA_TABLE_NAME = "ncbi_taxonomy_sqlite" + + +def build_sqlite(taxonomy_dir, output_directory, name=None, description=None): + if not os.path.exists(output_directory): + os.mkdir(output_directory) + output_filename = os.path.join(output_directory, "tax.ncbitaxonomy.sqlite") + cmd_str = "taxonomy_util -d {} to_sqlite {}".format(output_filename, taxonomy_dir) + cmd = shlex.split(cmd_str) + subprocess.check_call(cmd) + + today_str = datetime.date.today().strftime("%Y-%m-%d") + if name is None or name.strip() == "": + name = "ncbitaxonomy_build_" + today_str + + if description is None or description.strip() == "": + description = "NCBI Taxonomy database (built on {})".format(today_str) + + data = [dict(value=name, description=description, path=output_filename)] + return data + + +if __name__ == "__main__": + parser = argparse.ArgumentParser( + description="Build SQLite database from NCBI taxonomy" + ) + parser.add_argument( + "--output_directory", default="tmp", help="Directory to write output to" + ) + parser.add_argument( + "taxonomy_dir", + help="Path to directory containing NCBI Taxonomy nodes.dml and names.dmp file" + ) + parser.add_argument( + "name", + help="Name to use for the entry in the data table" + ) + parser.add_argument( + "description", + help="Description to use for the entry in the data table" + ) + parser.add_argument( + "galaxy_datamanager_filename", + help="Galaxy JSON format file describing data manager inputs", + ) + args = parser.parse_args() + + config = json.load(open(args.galaxy_datamanager_filename)) + output_directory = config.get("output_data", [{}])[0].get("extra_files_path", None) + if output_directory is None: + output_directory = args.output_directory + + if not os.path.isdir(output_directory): + os.makedirs(output_directory) + + data_manager_dict = {} + data_manager_dict["data_tables"] = json.load( + open(args.galaxy_datamanager_filename) + ).get("data_tables", {}) + data_manager_dict["data_tables"] = data_manager_dict.get("data_tables", {}) + data_manager_dict["data_tables"][DATA_TABLE_NAME] = data_manager_dict[ + "data_tables" + ].get(DATA_TABLE_NAME, []) + + data = build_sqlite(args.taxonomy_dir, args.output_directory, args.name, args.description) + + data_manager_dict["data_tables"][DATA_TABLE_NAME].extend(data) + print(json.dumps(data_manager_dict)) + json.dump(data_manager_dict, open(args.galaxy_datamanager_filename, "w"))
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_ncbi_taxonomy_sqlite.xml Tue Jul 21 17:04:41 2020 -0400 @@ -0,0 +1,98 @@ +<tool id="data_manager_ncbi_taxonomy_sqlite" name="NCBI Taxonomy SQLite builder" tool_type="manage_data" profile="18.09" version="@PACKAGE_VERSION@+galaxy1" python_template_version="3.5"> + <macros> + <token name="@PACKAGE_VERSION@">1.0.5</token> + </macros> + <requirements> + <requirement type="package" version="@PACKAGE_VERSION@">rust-ncbitaxonomy</requirement> + <requirement type="package" version="3.7">python</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + #if $taxonomy.taxonomy_source == 'cached': + #set $taxonomy_dir = $taxonomy.taxonomy_table.fields.path + #else + mkdir taxonomy && ln -s '$taxonomy.nodes' taxonomy/nodes.dmp && ln -s '$taxonomy.names' taxonomy/names.dmp && + #set $taxonomy_dir = 'taxonomy' + #end if + python '$__tool_directory__/data_manager_ncbi_taxonomy_sqlite.py' '$taxonomy_dir' '$name' '$description' '$output_file' + ]]></command> + <inputs> + <conditional name="taxonomy"> + <param name="taxonomy_source" type="select" label="Choose source of NCBI Taxonomy"> + <option value="cached" selected="true">Use built-in NCBI Taxonomy database</option> + <option value="history">Datasets from history</option> + </param> + <when value="cached"> + <param type="select" name="taxonomy_table" label="NCBI Taxonomy database"> + <options from_data_table="ncbi_taxonomy"> + <filter type="sort_by" column="1" /> + <validator type="no_options" message="No NCBI Taxonomy downloads are available" /> + </options> + <validator type="no_options" message="No NCBI Taxonomy database download is available" /> + </param> + </when> + <when value="history"> + <param name="nodes" type="data" format="txt" label="NCBI Taxonomy nodes.dmp file" /> + <param name="names" type="data" format="txt" label="NCBI Taxonomy names.dmp file" /> + </when> + </conditional> + <param name="name" type="text" label="Name of taxonomy database" help="(leave blank to use name based on today's date)" /> + <param name="description" type="text" label="Description of taxonomy database" help="(leave blank to use name based on today's date)" /> + </inputs> + <outputs> + <data name="output_file" format="data_manager_json"/> + </outputs> + <tests> + <test> + <conditional name="taxonomy"> + <param name="taxonomy_source" value="history" /> + <param name="nodes" ftype="txt" value="taxdb/nodes.dmp" /> + <param name="names" ftype="txt" value="taxdb/names.dmp" /> + </conditional> + <param name="name" value="test" /> + <param name="description" value="test database" /> + <output name="output_file"> + <assert_contents> + <has_text text="tax.ncbitaxonomy.sqlite" /> + <has_text text="test database" /> + </assert_contents> + </output> + </test> + <test> + <conditional name="taxonomy"> + <param name="taxonomy_source" value="cached" /> + <param name="taxonomy_table" value="sample" /> + </conditional> + <param name="name" value="test" /> + <param name="description" value="test database" /> + <output name="output_file"> + <assert_contents> + <has_text text="tax.ncbitaxonomy.sqlite" /> + <has_text text="test database" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + The data manager creates a SQLite version the NCBI Taxonomy database, using the plain text files of the + NCBI database as input. Storing the database as a SQLite database allows for faster querying. + + Input is either from the individual files (nodes.dmp and names.dmp) from the NCBI Taxonomy database or + from a previously downloaded code of the database stored as "reference data" in the Galaxy server. + + .. class: infomark + + *Notice:** If you leave name, or description blank, it will be generated automatically from the current date. + ]]></help> + <citations> + <citation type="bibtex">@misc{vanHeusen2020, + author = {van Heusden, P.}, + title = {a Rust crate for working with a local copy of the NCBI Taxonomy database }, + year = {2020}, + publisher = {GitHub}, + journal = {GitHub repository}, + howpublished = {\url{https://github.com/pvanheus/ncbitaxonomy}}, + commit = {84d79cdcf2adb262c61511f8c7b9eceb5299b87d} + } + </citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Tue Jul 21 17:04:41 2020 -0400 @@ -0,0 +1,18 @@ +<?xml version="1.0"?> +<data_managers> + <data_manager tool_file="data_manager/data_manager_ncbi_taxonomy_sqlite.xml" id="data_manager_ncbi_taxonomy_sqlite" version="0.0.1"> + <data_table name="ncbi_taxonomy_sqlite"> + <output> + <column name="value" /> + <column name="description" /> + <column name="path" output_ref="output_file"> + <move type="directory" relativize_symlinks="True"> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">ncbi_taxonomy_sqlite/${value}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/ncbi_taxonomy_sqlite/${value}</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + </data_manager> +</data_managers>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ncbi_taxonomy.loc Tue Jul 21 17:04:41 2020 -0400 @@ -0,0 +1,2 @@ +#value name path +sample sample database ${__HERE__}/taxdb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ncbi_taxonomy_sqlite.loc Tue Jul 21 17:04:41 2020 -0400 @@ -0,0 +1,2 @@ +#value description path +test test database /tmp/tmpVxsQba/tmpUjPjFN/tmpjKzenM/database/data_manager_tool-data9y_VHy/ncbi_taxonomy_sqlite/test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ncbi_taxonomy_sqlite_data_manager.json Tue Jul 21 17:04:41 2020 -0400 @@ -0,0 +1,1 @@ +{"data_tables": {"ncbi_taxonomy_sqlite": [{"value": "test", "path": "tmp/tax.ncbitaxonomy.sqlite", "description": "test database"}]} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/taxdb/names.dmp Tue Jul 21 17:04:41 2020 -0400 @@ -0,0 +1,687 @@ +1 | all | | synonym | +1 | root | | scientific name | +10239 | Vira | | synonym | +10239 | Viridae | | synonym | +10239 | Viruses | | scientific name | +10239 | viruses | viruses <blast10239> | blast name | +12333 | bacterial virus | bacterial virus <unclassified bacterial viruses> | in-part | +12333 | bacterial viruses | bacterial viruses <unclassified bacterial viruses> | in-part | +12333 | prokaryotic virus | prokaryotic virus <unclassified bacterial viruses> | in-part | +12333 | unclassified bacterial viruses | | scientific name | +12333 | unclassified bacteriophages | | synonym | +12333 | unclassified phage | | synonym | +12333 | unclassified phages | | synonym | +12340 | Bacteriophage 933J | | synonym | +12340 | Coliphage 933J | | synonym | +12340 | Enterobacteria phage 933J | | scientific name | +12340 | phage 933J | | synonym | +12347 | Actinophage JHJ-1 | | scientific name | +12347 | Bacteriophage JHJ-1 | | synonym | +12366 | Bacteriophage h4489a | | synonym | +12366 | Streptococcus pyogenes bacteriophage H4489A | | synonym | +12366 | Streptococcus pyogenes phage H4489A | | scientific name | +12371 | Bacteriophage h30 | | synonym | +12371 | Phage h30 | | scientific name | +12374 | Lactococcus bacteriophage | | synonym | +12374 | Lactococcus phage | | scientific name | +12375 | Lactococcus 1 bacteriophage | | synonym | +12375 | Lactococcus bacteriophage (ISOLATE 7-9) | | synonym | +12375 | Lactococcus phage (ISOLATE 7-9) | | scientific name | +12386 | Lactococcus phage mi7-9 | | scientific name | +12388 | Mycobacterium phage FRAT1 | | scientific name | +12388 | mycobacteriophage FRAT1 | | synonym | +12392 | Bacteriophage mv4 | | synonym | +12392 | Lactobacillus delbrueckii subsp. bulgaricus phage mv4 | | synonym | +12392 | Lactobacillus phage mv4 | | scientific name | +12392 | Lactococcus delbrueckii bacteriophage MV4 | | synonym | +12392 | phage mv4 | | synonym | +12403 | Bacteriophage P32 | | synonym | +12403 | Leuconostoc oenos phage P32 | | synonym | +12403 | Leuconostoc phage P32 | | scientific name | +12404 | Bacteriophage P37 | | synonym | +12404 | Leuconostoc oenos phage P37 | | synonym | +12404 | Leuconostoc phage P37 | | scientific name | +12405 | Bacteriophage P54 | | synonym | +12405 | Leuconostoc oenos phage P54 | | synonym | +12405 | Leuconostoc phage P54 | | scientific name | +12406 | Bacteriophage PAt5-12 | | synonym | +12406 | Leuconostoc oenos phage PAt5-12 | | synonym | +12406 | Leuconostocphage PAt5-12 | | scientific name | +12408 | Bacteriophage PZt11-15 | | synonym | +12408 | Leuconostoc oenos phage PZt11-15 | | synonym | +12408 | Leuconostoc phage PZt11-15 | | scientific name | +12409 | Bacteriophage d-16 phi | | synonym | +12409 | Clostridium phage d-16 phi | | scientific name | +12412 | Staphylococcus aureus bacteriophage phi-42 | | synonym | +12412 | Staphylococcus aureus phage phi-42 | | synonym | +12412 | Staphylococcus phage phi-42 | | scientific name | +12412 | bacteriophage phi 42 | | synonym | +12412 | bacteriophage phi-42 | | synonym | +12413 | Bacteriophage phi 7-9 | | synonym | +12413 | Lactococcusphage phi7-9 | | scientific name | +12420 | Filamentous bacteriophage | | synonym | +12420 | Filamentous phage | | scientific name | +12424 | Bacteriophage 13 | | synonym | +12424 | Phage 13 | | scientific name | +12425 | Bacteriophage 16 | | synonym | +12425 | Phage 16 | | scientific name | +12427 | Lactococcus lactis phage phi 197 | | scientific name | +12427 | phage phi 197 | | synonym | +12427 | phage phi-197 | | synonym | +12428 | Retronphage phi R73 | | scientific name | +28368 | Corynebacterium diphtheriae phage | | scientific name | +28368 | Corynebacterium diphtheriae virus | | synonym | +31760 | Colitis phage | | scientific name | +33768 | Bacteriophage L10 | | synonym | +33768 | Leuconostoc oenos bacteriophage L10 | | synonym | +33768 | Leuconostoc oenos phage L10 | | synonym | +33768 | Leuconostoc phage L10 | | scientific name | +33769 | Bacteriophage mv1 | | synonym | +33769 | Lactobacillus delbrueckii bacteriophage mv1 | | synonym | +33769 | Lactobacillus delbrueckii subsp. bulgaricus phage mv1 | | synonym | +33769 | Lactobacillus phage mv1 | | scientific name | +38018 | Bacteriophage sp. | | synonym | +38018 | bacteriophage | | synonym | +38018 | bacteriophages | | synonym | +38018 | unidentified bacteriophage | | synonym | +38018 | unidentified phage | | scientific name | +39425 | Bacteriophage T270 | | synonym | +39425 | Streptococcus phage T270 | | scientific name | +39943 | Actinophage JHJ-3 | | scientific name | +39943 | Bacteriophage JHJ-3 | | synonym | +41669 | Bacteriophage LM4 | | synonym | +41669 | Phage LM4 | | scientific name | +42171 | Bacteriophage N 209 | | synonym | +42171 | Phage N 209 | | scientific name | +42172 | Bacteriophage 3/14 | | synonym | +42172 | Phage 3/14 | | scientific name | +42173 | Bacteriophage Cz | | synonym | +42173 | Phage Cz | | scientific name | +45331 | Bacteriophage fuse 5 | | synonym | +45331 | Phage fuse 5 | | scientific name | +45332 | Bacteriophage phi AR29 | | synonym | +45332 | Prevotella phage phi AR29 | | scientific name | +45441 | Bacteriophage L | | synonym | +45441 | Enterobacteria phage L | | scientific name | +48224 | Bacteriophage E | | synonym | +48224 | Phage E | | scientific name | +53480 | Virus-like particle CAK1 | | scientific name | +54392 | Leuconostoc oenos bacteriophage 10MC | | synonym | +54392 | Leuconostoc phage 10MC | | scientific name | +54392 | Oenococcus oeni bacteriophage 10MC | | synonym | +57476 | Bacillus cereus bacteriophage 12826 | | synonym | +57476 | Bacillus phage 12826 | | scientific name | +57476 | Bacteriophage 12826 | | synonym | +60457 | Bartonella henselae phage 60457 | | scientific name | +63117 | Vibrio cholerae V86 phage | | scientific name | +65388 | Mycobacteriophage Ms6 | | synonym | +65388 | Mycobacterium phage Ms6 | | scientific name | +73492 | Streptococcus pyogenes phage | | scientific name | +76262 | Bacteriophage phiU | | synonym | +76262 | Rhizobium phage phiU | | scientific name | +77920 | Bacteriophage #D | | synonym | +77920 | Phage #D | | scientific name | +86065 | Streptococcus pyogenes bacteriophage H10403 | | synonym | +86065 | Streptococcus pyogenes phage H10403 | | scientific name | +89551 | Corynephage phi16 | | scientific name | +100637 | Lactococcus lactis bacteriophage Q42 | | synonym | +100637 | Lactococcus phage Q42 | | scientific name | +100638 | Lactococcus lactis bacteriophage Q44 | | synonym | +100638 | Lactococcus phage Q44 | | scientific name | +100639 | Lactococcus lactis bacteriophage Q7 | | synonym | +100639 | Lactococcus phage Q7 | | scientific name | +100640 | Lactococcus lactis bacteriophage eb1 | | synonym | +100640 | Lactococcus phage eb1 | | scientific name | +105686 | Lambdoid phage HB-4 | | scientific name | +108916 | Bacteriophage F3 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| scientific name | +148339 | Bacteriophage GMSE-1 | | synonym | +148339 | Phage GMSE-1 | | scientific name | +156614 | environmental samples | environmental samples <bacteriophages> | scientific name | +156615 | Cyanophage clone GS2601 | | scientific name | +156616 | Cyanophage clone GS2602 | | scientific name | +156617 | Cyanophage clone GS2603 | | scientific name | +156618 | Cyanophage clone GS2607 | | scientific name | +156619 | Cyanophage clone GS2608 | | scientific name | +156620 | Cyanophage clone GS2614 | | scientific name | +156621 | Cyanophage clone GS2620 | | scientific name | +156622 | Cyanophage clone GS2624 | | scientific name | +156623 | Cyanophage clone GS2626 | | scientific name | +156624 | Cyanophage clone GS2633 | | scientific name | +156625 | Cyanophage clone GS2649 | | scientific name | +156626 | Cyanophage clone GS2650 | | scientific name | +156627 | Cyanophage clone GS2651 | | scientific name | +156653 | Cyanophage clone SE1 | | scientific name | +156654 | 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name | +156743 | Synechococcus phage 44A | | scientific name | +156745 | Synechococcus phage P6 | | scientific name | +156746 | Synechococcus phage P12 | | scientific name | +156747 | Synechococcus phage P17 | | scientific name | +156748 | Synechococcus phage P77 | | scientific name | +156749 | Synechococcus phage P79 | | scientific name | +156750 | Synechococcus phage P81 | | scientific name | +156767 | Cyanophage clone SS4016 | | scientific name | +156768 | Cyanophage clone SS4017 | | scientific name | +156769 | Cyanophage clone SS4018 | | scientific name | +156770 | Cyanophage clone SS4019 | | scientific name | +156771 | Cyanophage clone SS4020 | | scientific name | +156772 | Cyanophage clone SS4021 | | scientific name | +156773 | Cyanophage clone SS4026 | | scientific name | +156774 | Cyanophage clone SS4027 | | scientific name | +156775 | Cyanophage clone SS4028 | | scientific name | +156776 | Cyanophage clone SS4029 | | scientific name | +156777 | Cyanophage clone SS4033 | | 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SS4729 | | scientific name | +156800 | Cyanophage clone SS4726 | | scientific name | +156801 | Cyanophage clone SS4725 | | scientific name | +156802 | Cyanophage clone SS4723 | | scientific name | +156803 | Cyanophage clone SS4720 | | scientific name | +156804 | Cyanophage clone SS4718 | | scientific name | +156805 | Cyanophage clone SS4717 | | scientific name | +156806 | Cyanophage clone SS4716 | | scientific name | +156807 | Cyanophage clone SS4715 | | scientific name | +156808 | Cyanophage clone SS4714 | | scientific name | +156809 | Cyanophage clone SS4713 | | scientific name | +156810 | Cyanophage clone SS4710 | | scientific name | +156811 | Cyanophage clone SS4707 | | scientific name | +156812 | Cyanophage clone SS4706 | | scientific name | +156813 | Cyanophage clone SS4705 | | scientific name | +156814 | Cyanophage clone SS4703 | | scientific name | +156815 | Cyanophage clone SS4702 | | scientific name | +156816 | Cyanophage clone SS4701 | | scientific name | +156817 | Cyanophage clone SS4734 | | scientific name | +156818 | Cyanophage clone SS4736 | | scientific name | +156819 | Cyanophage clone SS4737 | | scientific name | +156820 | Cyanophage clone SS4738 | | scientific name | +156821 | Cyanophage clone SS4803 | | scientific name | +156822 | Cyanophage clone SS4804 | | scientific name | +156823 | Cyanophage clone SS4805 | | scientific name | +156824 | Cyanophage clone SS4809 | | scientific name | +156825 | Cyanophage clone SS4810 | | scientific name | +156826 | Cyanophage clone SS4813 | | scientific name | +156827 | Cyanophage clone SS4814 | | scientific name | +156828 | Cyanophage clone SS4821 | | scientific name | +156829 | Cyanophage clone SS4824 | | scientific name | +156830 | Cyanophage clone SS4827 | | scientific name | +156831 | Cyanophage clone SS4829 | | scientific name | +156832 | Cyanophage clone SS4832 | | scientific name | +156833 | Cyanophage clone SS4838 | | scientific name | +156834 | Cyanophage clone SS4845 | | scientific name | +156835 | Cyanophage clone SS4850 | | scientific name | +215796 | uncultured cyanophage | | scientific name | +278008 | uncultured bacteriophage | | synonym | +278008 | uncultured phage | | scientific name | +306552 | uncultured aquatic bacteriophage | | synonym | +306552 | uncultured aquatic phage | | scientific name | +432371 | Halophage AAJ-2005 | | synonym | +432371 | environmental halophage 1 AAJ-2005 | | scientific name | +436674 | environmental halophage | | scientific name | +445563 | uncultured desert soil virus | | scientific name | +445564 | uncultured prairie soil virus | | scientific name | +445565 | uncultured rainforest soil virus | | scientific name | +707152 | uncultured marine phage | | scientific name | +1168811 | environmental Halophage eHP-1 | | scientific name | +1168812 | environmental Halophage eHP-10 | | scientific name | +1168813 | environmental Halophage eHP-11 | | scientific name | +1168814 | environmental Halophage eHP-12 | | scientific name | +1168815 | environmental Halophage eHP-13 | | scientific name | +1168816 | environmental Halophage eHP-14 | | scientific name | +1168817 | environmental Halophage eHP-15 | | scientific name | +1168818 | environmental Halophage eHP-16 | | scientific name | +1168819 | environmental Halophage eHP-17 | | scientific name | +1168820 | environmental Halophage eHP-18 | | scientific name | +1168821 | environmental Halophage eHP-19 | | scientific name | +1168822 | environmental Halophage eHP-2 | | scientific name | +1168823 | environmental Halophage eHP-20 | | scientific name | +1168824 | environmental Halophage eHP-22 | | scientific name | +1168825 | environmental Halophage eHP-23 | | scientific name | +1168826 | environmental Halophage eHP-24 | | scientific name | +1168827 | environmental Halophage eHP-25 | | scientific name | +1168828 | environmental Halophage eHP-27 | | scientific name | +1168829 | environmental Halophage eHP-28 | | scientific name | +1168830 | environmental Halophage eHP-29 | | scientific name | +1168831 | environmental Halophage eHP-3 | | scientific name | +1168832 | environmental Halophage eHP-30 | | scientific name | +1168833 | environmental Halophage eHP-31 | | scientific name | +1168834 | environmental Halophage eHP-32 | | scientific name | +1168835 | environmental Halophage eHP-33 | | scientific name | +1168836 | environmental Halophage eHP-34 | | scientific name | +1168837 | environmental Halophage eHP-35 | | scientific name | +1168838 | environmental Halophage eHP-36 | | scientific name | +1168839 | environmental Halophage eHP-37 | | scientific name | +1168840 | environmental Halophage eHP-38 | | scientific name | +1168841 | environmental Halophage eHP-39 | | scientific name | +1168842 | environmental Halophage eHP-4 | | scientific name | +1168843 | environmental Halophage eHP-40 | | scientific name | +1168844 | environmental Halophage eHP-41 | | scientific name | +1168845 | environmental Halophage eHP-42 | | scientific name | +1168846 | environmental Halophage eHP-5 | | scientific name | +1168847 | environmental Halophage eHP-6 | | scientific name | +1168848 | environmental Halophage eHP-7 | | scientific name | +1168849 | environmental Halophage eHP-8 | | scientific name | +1168850 | environmental Halophage eHP-9 | | scientific name | +1168851 | environmental Halophage eHP-D7 | | scientific name | +1168852 | environmental Halophage eHP-E5 | | scientific name | +164125 | Mycobacteriophage L1 | | synonym | +164125 | Mycobacterium phage L1 | | scientific name | +167320 | Actinophage Q5 | | scientific name | +167533 | Bartonella quintana phage | | scientific name | +172666 | Bacteriophage 6220 | | synonym | +172666 | Enterobacteria phage 6220 | | scientific name | +173830 | Bacteriophage Lahn1 | | synonym | +173830 | Enterobacteria phage Lahn1 | | scientific name | +173831 | Bacteriophage Lahn3 | | synonym | +173831 | Enterobacteria phage Lahn3 | | scientific name | +176100 | Bacteriophage U153 | | synonym | +176100 | Listeria phage U153 | | scientific name | +181120 | Bacteriophage C1 | | synonym | +181120 | C1 bacteriophage | | synonym | +181120 | Enterobacteria phage C-1 | | scientific name | +181485 | Bacteriophage fOg44 | | synonym | +181485 | Oenococcus oeni bacteriophage fOg44 | | synonym | +181485 | Oenococcus oeni temperate bacteriophage fOg44 | | synonym | +181485 | Oenococcus phage fOg44 | | scientific name | +185368 | Lactococcus phage 409 | | scientific name | +185369 | Lactococcus phage F7/2 | | scientific name | +187176 | Escherichia coli K12 phage EH297 | | synonym | +187176 | Escherichia coli phage EH297 | | scientific name | +196194 | Lactobacillus helveticus phage f-0303 | | synonym | +196194 | Lactobacillus phage f-0303 | | scientific name | +198932 | Streptococcus canis phage phisc1 | | synonym | +198932 | Streptococcus phage phisc1 | | scientific name | +210927 | Bacteriophage SC370 | | synonym | +210927 | Enterobacteria phage SC370 | | scientific name | +219292 | Bacteriophage pMLP1 | | synonym | +219292 | Micromonospora phage pMLP1 | | scientific name | +221993 | Bacteriophage f237 | | synonym | +221993 | Vibrio phage f237 | | scientific name | +229343 | Bacillus anthracis phage lambda Ba01 | | synonym | +229343 | Bacillus phage lambda Ba01 | | scientific name | +229344 | Bacillus anthracis phage lambda Ba02 | | synonym | +229344 | Bacillus phage lambda Ba02 | | scientific name | +229345 | Bacillus anthracis phage lambda Ba03 | | synonym | +229345 | Bacillus phage lambda Ba03 | | scientific name | +229346 | Bacillus anthracis phage lambda Ba04 | | synonym | +229346 | Bacillus phage lambda Ba04 | | scientific name | +239740 | Hybrid phage HybP-Knphi | | scientific name | +241652 | Bacteriophage FIZ15 | | synonym | +241652 | Enterobacteria phage FIZ15 | | scientific name | +242708 | Bacteriophage HybRS-Knphi | | synonym | +242708 | Vibrio phage HybRS-Knphi | | scientific name | +262790 | Bacteriophage WOcauB1 | | synonym | +262790 | Wolbachia phage WOcauB1 | | scientific name | +264484 | Bacteriophage KPP95 | | synonym | +264484 | Klebsiella phage KPP95 | | scientific name | +268585 | Bacteriophage V11 | | synonym | +268585 | Enterobacteria phage V11 | | scientific name | +268586 | Bacteriophage C14 | | synonym | +268586 | Enterobacteria phage C14 | | scientific name | +268587 | Bacteriophage C1.2 | | synonym | +268587 | Enterobacteria phage C1.2 | | scientific name | +268588 | Bacteriophage L1 | | synonym | +268588 | E. coli O157:H7-specific bacteriophage L1 | | synonym | +268588 | Enterobacteria phage L1 | | scientific name | +268590 | Bacteriophage Ly1 | | synonym | +268590 | Enterobacteria phage Ly1 | | scientific name | +272473 | Bacteriophage TS2126 | | synonym | +272473 | Phage TS2126 | | scientific name | +272757 | Lactobacillus gasseri bacteriophage phigaY | | synonym | +272757 | Lactobacillus phage phigaY | | scientific name | +279276 | Equine faecal bacteriophage | | synonym | +279276 | Equine faecal phage | | scientific name | +280702 | Bacteriophage phiMFV1 | | synonym | +280702 | Mycoplasma phage phiMFV1 | | scientific name | +282372 | Phage Gifsy-3 | | scientific name | +282372 | Prophage Gifsy-3 | | acronym | +282372 | Salmonella phage Gifsy-3 | | synonym | +282690 | Bacteriophage A75 | | synonym | +282690 | Enterobacteria phage A75 | | scientific name | +282691 | Bacteriophage A534 | | synonym | +282691 | Enterobacteria phage A534 | | scientific name | +282692 | Bacteriophage A557 | | synonym | +282692 | Enterobacteria phage A557 | | scientific name | +282693 | Bacteriophage O157-572 | | synonym | +282693 | Enterobacteria phage O157-572 | | scientific name | +282698 | Bacteriophage A312 | | synonym | +282698 | Enterobacteria phage A312 | | scientific name | +282699 | Bacteriophage A315 | | synonym | +282699 | Enterobacteria phage A315 | | scientific name | +282700 | Bacteriophage A549 | | synonym | +282700 | Enterobacteria phage A549 | | scientific name | +282701 | Bacteriophage A580 | | synonym | +282701 | Enterobacteria phage A580 | | scientific name | +282702 | Bacteriophage O157-292 | | synonym | +282702 | Enterobacteria phage O157-292 | | scientific name | +282703 | Bacteriophage O157-330 | | synonym | +282703 | Enterobacteria phage O157-330 | | scientific name | +282704 | Bacteriophage O157-310 | | synonym | +282704 | Enterobacteria phage O157-310 | | scientific name | +282705 | Bacteriophage O157-379 | | synonym | +282705 | Enterobacteria phage O157-379 | | scientific name | +282709 | Bacteriophage A397 | | synonym | +282709 | Enterobacteria phage A397 | | scientific name | +282710 | Bacteriophage O157-469 | | synonym | +282710 | Enterobacteria phage O157-469 | | scientific name | +284052 | Bacteriophage phi WMY | | synonym | +284052 | Staphylococcus phage phiWMY | | scientific name | +291401 | Bacteriophage CP-1639 | | synonym | +291401 | Enterobacteria phage CP-1639 | | scientific name | +291401 | Prophage CP-1639 | | synonym | +292511 | Lactobacillus delbrueckii phage MZ-2004 | | synonym | +292511 | Lactobacillus delbrueckii subsp. lactis phage AI15 | | synonym | +292511 | Lactobacillus phage AI15 | | scientific name | +293378 | Streptococcus pyogenes phage phiRamid | | scientific name | +293378 | prophage Phi M1T1.Z | | synonym | +293711 | Streptococcus pyogenes phage 5005.1 | | scientific name | +293712 | Streptococcus pyogenes phage 5005.2 | | scientific name | +293713 | Streptococcus pyogenes phage 5005.3 | | scientific name | +294363 | Bacteriophage 020324 | | synonym | +294363 | Enterobacteria phage 020324 | | scientific name | +311221 | Bacillus thuringiensis phage MZTP02 | | scientific name | +319711 | Streptococcus pyogenes phage 6180.2 | | scientific name | +319712 | Streptococcus pyogenes phage 6180.3 | | scientific name | +319713 | Streptococcus pyogenes phage 6180.4 | | scientific name | +334523 | Phage SK137 | | scientific name | +338345 | Bacteriophage Nil3 | | synonym | +338345 | Enterobacteria phage Nil3 | | scientific name | +347331 | Bacteriophage PA16 | | synonym | +347331 | Pseudomonas phage PA16 | | scientific name | +350104 | Bacteriophage 700P1 | | synonym | +350104 | Streptococcus phage 700P1 | | scientific name | +350104 | Streptococcus uberis bacteriophage 700P1 | | synonym | +356350 | Phage 258-320 | | scientific name | +357204 | Bacteriophage PPA5 | | synonym | +357204 | Pseudomonas phage PPA5 | | scientific name | +360048 | Burkholderia phage 644-2 | | scientific name | +360048 | Burkholderia pseudomallei phage 644-2 | | synonym | +360049 | Burkholderia phage E12-2 | | scientific name | +360049 | Burkholderia pseudomallei phage E12-2 | | synonym | +360050 | Burkholderia phage E202 | | scientific name | +360050 | Burkholderia thailandensis phage E202 | | synonym | +362866 | Cyanophage AN-15 | | scientific name | +362866 | Temperate cyanophage AN-15 | | synonym | +364251 | Bacteriophage Sal2 | | synonym | +364251 | Lactobacillus phage Sal2 | | scientific name | +364252 | Bacteriophage Sal1 | | synonym | +364252 | Lactobacillus phage Sal1 | | scientific name | +364253 | Bacteriophage Sal4 | | synonym | +364253 | Lactobacillus phage Sal4 | | scientific name | +364254 | Bacteriophage Sal3 | | synonym | +364254 | Lactobacillus phage Sal3 | | scientific name | +370564 | Bacteriophage 2096.1 | | synonym | +370564 | Streptococcus phage 2096.1 | | scientific name | +370565 | Bacteriophage 2096.2 | | synonym | +370565 | Streptococcus phage 2096.2 | | scientific name | +374421 | Bacteriophage phiK38-1 | | synonym | +374421 | Streptomyces phage phiK38-1 | | scientific name | +375032 | Synechococcus phage S | | scientific name | +375033 | Synechococcus phage S-IO9 | | scientific name | +375034 | Synechococcus phage S-IO10 | | scientific name | +375035 | Synechococcus phage S-IO15 | | scientific name | +375036 | Synechococcus phage S-IO16 | | scientific name | +375037 | Synechococcus phage S-IO20 | | scientific name | +375038 | Synechococcus phage S-IO23 | | scientific name | +375039 | Synechococcus phage S-IO36 | | scientific name | +375040 | Synechococcus phage S-IO37 | | scientific name | +375041 | Synechococcus phage S-IO40 | | scientific name | +375042 | Synechococcus phage S-IO41 | | scientific name | +375043 | Synechococcus phage S-IO42 | | scientific name | +375044 | Synechococcus phage S-IO43 | | scientific name | +375045 | Synechococcus phage S-IO46 | | scientific name | +375046 | Synechococcus phage S-IO11 | | scientific name | +375047 | Synechococcus phage S-IO12 | | scientific name | +375048 | Synechococcus phage S-IO13 | | scientific name | +375049 | Synechococcus phage S-IO14 | | scientific name | +375050 | Synechococcus phage S-IO17 | | scientific name | +375051 | Synechococcus phage S-IO18 | | scientific name | +375052 | Synechococcus phage S-IO21 | | scientific name | +375053 | Synechococcus phage S-IO22 | | scientific name | +375054 | Synechococcus phage S-IO25 | | scientific name | +375055 | Synechococcus phage S-IO26 | | scientific name | +375056 | Synechococcus phage S-IO27 | | scientific name | +375057 | Synechococcus phage S-IO47 | | scientific name | +375058 | Synechococcus phage S-IO7 | | scientific name | +375059 | Synechococcus phage S-IO8 | | scientific name | +382277 | Synechococcus cyanophage S-SM1 | | scientific name | +382278 | Synechococcus cyanophage S-SSM1 | | scientific name | +382279 | Synechococcus cyanophage S-SSM2 | | scientific name | +382280 | Synechococcus cyanophage S-SSM3 | | scientific name | +382281 | Synechococcus cyanophage S-SSM5 | | scientific name | +382282 | Synechococcus cyanophage S-ShM1 | | scientific name | +382283 | Synechococcus cyanophage S-ShM2 | | scientific name | +376611 | Lactobacillus casei phage Lca1 | | scientific name | +382263 | Prochlorococcus cyanophage P-RSM2 | | scientific name | +382264 | Prochlorococcus cyanophage P-RSM3 | | scientific name | +382265 | Prochlorococcus cyanophage P-RSM5 | | scientific name | +382266 | Prochlorococcus cyanophage P-SSM1 | | scientific name | +382267 | Prochlorococcus cyanophage P-SSM10 | | scientific name | +382268 | Prochlorococcus cyanophage P-SSM12 | | scientific name | +382269 | Prochlorococcus cyanophage P-SSM3 | | scientific name | +382271 | Prochlorococcus cyanophage P-SSM8 | | scientific name | +382272 | Prochlorococcus cyanophage P-SSM9 | | scientific name | +382274 | Prochlorococcus cyanophage P-SSP5 | | scientific name | +387086 | Bacteriophage 10750 | | synonym | +387086 | Streptococcus pyogenes MGAS10750 phage | | scientific name | +370566 | Bacteriophage 10750.1 | | synonym | +370566 | Streptococcus phage 10750.1 | | scientific name | +370567 | Bacteriophage 10750.2 | | synonym | +370567 | Streptococcus phage 10750.2 | | scientific name | +370568 | Bacteriophage 10750.3 | | synonym | +370568 | Streptococcus phage 10750.3 | | scientific name | +370569 | Bacteriophage 10750.4 | | synonym | +370569 | Streptococcus phage 10750.4 | | scientific name | +387087 | Streptococcus pyogenes MGAS10270 phage | | scientific name | +370559 | Bacteriophage 10270.1 | | synonym | +370559 | Streptococcus phage 10270.1 | | scientific name | +370560 | Bacteriophage 10270.2 | | synonym | +370560 | Streptococcus phage 10270.2 | | scientific name | +370561 | Bacteriophage 10270.3 | | synonym | +370561 | Streptococcus phage 10270.3 | | scientific name | +370562 | Bacteriophage 10270.4 | | synonym | +370562 | Streptococcus phage 10270.4 | | scientific name | +370563 | Bacteriophage 10270.5 | | synonym | +370563 | Streptococcus phage 10270.5 | | scientific name | +387088 | Streptococcus pyogenes MGAS9429 phage | | scientific name | +370556 | Bacteriophage 9429.1 | | synonym | +370556 | Streptococcus phage 9429.1 | | scientific name | +370557 | Bacteriophage 9429.2 | | synonym | +370557 | Streptococcus phage 9429.2 | | scientific name | +370558 | Bacteriophage 9428.3 | | synonym | +370558 | Streptococcus phage 9428.3 | | scientific name | +405001 | Burkholderia phage E255 | | scientific name | +405001 | Burkholderia pseudomallei phage E255 | | synonym | +405001 | Burkholderia thailandensis phage E255 | | synonym | +409026 | Bacteriophage Swp3 | | synonym | +409026 | Phage Swp3 | | scientific name | +417289 | Saccharopolyspora erythraea prophage pSE101 | | scientific name | +417290 | Saccharopolyspora erythraea prophage pSE211 | | scientific name | +430512 | Streptococcus phage 370.1 | | scientific name | +430513 | Streptococcus phage 370.3 | | scientific name | +430514 | Streptococcus phage 370.2 | | scientific name | +430515 | Streptococcus phage 370.4 | | scientific name | +432197 | Enterobacteria phage CL707 | | scientific name | +432199 | Enterobacteria phage HK244 | | scientific name | +432202 | Enterobacteria phage mEp234 | | scientific name | +432203 | Enterobacteria phage mEp332 | | scientific name | +435305 | Vibrio phage KA-2007 | | scientific name | +435637 | Coliphage K1A | | synonym | +435637 | Enterobacteria phage K1A | | scientific name | +440576 | Leuconostoc phage L5 | | scientific name | +445701 | Cyanophage M4-283 | | scientific name | +447796 | Enterobacteria bacteriophage T5-D1 | | synonym | +447796 | Enterobacteria phage T5-D1 | | scientific name | +447800 | Enterobacteria phage T5-A1 | | scientific name | +449399 | Klebsiella phage PhiKPN | | scientific name | +458420 | Novosphingobium phage N-AFCM0615-3 | | scientific name | +458421 | Novosphingobium phage N-AFCa0615-4 | | scientific name | +458422 | Novosphingobium phage N-AFCa0615-5 | | scientific name | +458423 | Novosphingobium phage N-AFCa0615-6 | | scientific name | +458424 | Novosphingobium phage N-AFNF0628-7 | | scientific name | +458425 | Novosphingobium phage N-AFCF0628-8 | | scientific name | +458426 | Novosphingobium phage N-AFCF0628-9 | | scientific name | +458427 | Novosphingobium phage N-AFCa0628-10 | | scientific name | +458428 | Novosphingobium phage N-AFCM0628-11 | | scientific name | +458429 | Novosphingobium phage N-AFCa0628-12 | | scientific name | +458430 | Novosphingobium phage N-AFNF0707-13 | | scientific name | +458431 | Novosphingobium phage N-AFCF0707-14 | | scientific name | +458432 | Novosphingobium phage N-AFCF0707-15 | | scientific name | +458433 | Novosphingobium phage N-AFCF0707-16 | | scientific name | +458434 | Novosphingobium phage N-AFCa0707-17 | | scientific name | +458435 | Novosphingobium phage N-AFCa0707-18 | | scientific name | +458436 | Novosphingobium phage N-AFNF0802-19 | | scientific name | +458437 | Novosphingobium phage N-AFNF0802-20 | | scientific name | +458438 | Novosphingobium phage N-AFCF0802-21 | | scientific name | +458439 | Novosphingobium phage N-AFCF0802-22 | | scientific name | +458440 | Novosphingobium phage N-AFCa0802-56 | | scientific name | +458441 | Novosphingobium phage N-AFCa0802-23 | | scientific name | +458442 | Novosphingobium phage N-AFCa0802-57 | | scientific name | +458443 | Novosphingobium phage N-AFCa0802-24 | | scientific name | +458444 | Novosphingobium phage N-AFNF0810-25 | | scientific name | +458445 | Novosphingobium phage N-AFCF0810-26 | | scientific name | +458446 | Novosphingobium phage N-AFCM0810-27 | | scientific name | +458447 | Novosphingobium phage N-AFCM0810-28 | | scientific name | +458448 | Novosphingobium phage N-AFCa0810-29 | | scientific name | +458449 | Novosphingobium phage N-AFCa0810-30 | | scientific name | +458450 | Novosphingobium phage N-AFNF0824-31 | | scientific name | +458451 | Novosphingobium phage N-AFCF0824-32 | | scientific name | +458452 | Novosphingobium phage N-AFCM0824-33 | | scientific name | +458453 | Novosphingobium phage N-AFCa0824-34 | | scientific name | +458454 | Novosphingobium phage N-AFCa0824-35 | | scientific name | +458455 | Novosphingobium phage N-AFCa0824-36 | | scientific name | +458456 | Novosphingobium phage N-AFCF0901-37 | | scientific name | +458457 | Novosphingobium phage N-AFCM0901-40 | | scientific name | +458458 | Novosphingobium phage N-AFCa0901-41 | | scientific name | +458459 | Novosphingobium phage N-AFCa0901-42 | | scientific name | +458460 | Novosphingobium phage N-AFNF0913-43 | | scientific name | +458461 | Novosphingobium phage N-AFCM0913-47 | | scientific name | +458462 | Novosphingobium phage N-AFCF0714-51 | | scientific name | +458463 | Novosphingobium phage N-AFCM0714-52 | | scientific name | +458464 | Novosphingobium phage N-AFNF0922-55 | | scientific name | +458465 | Sphingomonas phage S-AFNF0615-61 | | scientific name | +458466 | Sphingomonas phage S-AFCF0802-69 | | scientific name | +458467 | Sphingomonas phage S-AFNF0810-70 | | scientific name | +458468 | Sphingomonas phage S-AFCa0824-71 | | scientific name | +458469 | Sphingomonas phage S-AFCa0901-72 | | scientific name | +458470 | Novosphingobium phage N-AFCa0707-83 | | scientific name | +458471 | Novosphingobium phage N-AFCa0714-84 | | scientific name | +458472 | Novosphingobium phage N-AFCa0802-85 | | scientific name | +458473 | Novosphingobium phage N-AFCM0802-86 | | scientific name | +458474 | Novosphingobium phage N-AFCF0901-89 | | scientific name | +458475 | Novosphingobium phage N-AFCa0901-90 | | scientific name | +458476 | Novosphingobium phage N-AFCM0901-91 | | scientific name | +458477 | Novosphingobium phage N-An-FWCa0913-92 | | scientific name | +462299 | Enterobacteria phage VT1-Sakai | | scientific name | +464033 | Campylobacter phage CGC-2007 | | scientific name | +472964 | Streptococcus phage NZ131.1 | | scientific name | +472965 | Streptococcus phage NZ131.2 | | scientific name | +472966 | Streptococcus phage NZ131.3 | | scientific name | +483783 | Bacillus phage bg1 | | scientific name | +483784 | Bacillus phage bg2 | | scientific name | +483785 | Bacillus phage bg3 | | scientific name | +498338 | Synechococcus phage SPGM99-02 | | scientific name | +498339 | Synechococcus phage SPGM99-07 | | scientific name | +498340 | Synechococcus phage SPGM99-10 | | scientific name | +498341 | Synechococcus phage SPGM99-12 | | scientific name | +498342 | Synechococcus phage SPGM99-14 | | scientific name | +498343 | Synechococcus phage SPGM99-15 | | scientific name | +498344 | Synechococcus phage SPGM99-16 | | scientific name | +498345 | Synechococcus phage SPGM99-20 | | scientific name | +498346 | Synechococcus phage SPGM99-21 | | scientific name | +498347 | Synechococcus phage SPGM99-24 | | scientific name | +498348 | Synechococcus phage SPGM99-27 | | scientific name | +498349 | Synechococcus phage SPGM99-28 | | scientific name | +498350 | Synechococcus phage SPGM99-29 | | scientific name | +498351 | Synechococcus phage SPGM99-30 | | scientific name | +498352 | Synechococcus phage SPGM99-31 | | scientific name | +498353 | Synechococcus phage SPGM99-39 | | scientific name | +504556 | Propionibacterium phage PAS7 | | scientific name |
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| +498347 | 12333 | species | SP | 3 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | +498348 | 12333 | species | SP | 3 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | +498349 | 12333 | species | SP | 3 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | +498350 | 12333 | species | SP | 3 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | +498351 | 12333 | species | SP | 3 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | +498352 | 12333 | species | SP | 3 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | +498353 | 12333 | species | SP | 3 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | +504556 | 12333 | species | PP | 3 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | |
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/ncbi_taxonomy.loc.sample Tue Jul 21 17:04:41 2020 -0400 @@ -0,0 +1,5 @@ +# Tab separated fields where +# value is unique key +# name is descriptive name +# path is path to directory containing names.dmp and nodes.dmp files +#value name path
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/ncbi_taxonomy_sqlite.loc Tue Jul 21 17:04:41 2020 -0400 @@ -0,0 +1,1 @@ +test test database /tmp/tmpvD64FQ/tmpIn01Xk/tmpcfHY_f/database/data_manager_tool-dataP323iD/ncbi_taxonomy_sqlite/test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/ncbi_taxonomy_sqlite.loc.sample Tue Jul 21 17:04:41 2020 -0400 @@ -0,0 +1,2 @@ +#This file describes the storage location for the NCBI Taxonomy SQLite database file +#<unique_name> <description> <file_path> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Jul 21 17:04:41 2020 -0400 @@ -0,0 +1,13 @@ +<?xml version="1.0"?> +<tables> + <!-- Locations of taxonomy data downloaded from NCBI --> + <table name="ncbi_taxonomy" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/ncbi_taxonomy.loc" /> + </table> + <!-- Locations of SQLite format NCBI Taxonomy database --> + <table name="ncbi_taxonomy_sqlite" comment_char="#"> + <columns>value, description, path</columns> + <file path="tool-data/ncbi_taxonomy_sqlite.loc" /> + </table> +</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Tue Jul 21 17:04:41 2020 -0400 @@ -0,0 +1,13 @@ +<?xml version="1.0"?> +<tables> + <!-- Locations of taxonomy data downloaded from NCBI --> + <table name="ncbi_taxonomy" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/test-data/ncbi_taxonomy.loc" /> + </table> + <!-- Locations of SQLite format NCBI Taxonomy database --> + <table name="ncbi_taxonomy_sqlite" comment_char="#"> + <columns>value, description, path</columns> + <file path="${__HERE__}/test-data/ncbi_taxonomy_sqlite.loc" /> + </table> +</tables>