Mercurial > repos > jjohnson > eggnog_mapper
changeset 2:a74d61dbd155 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_eggnog.py Mon Nov 04 16:38:44 2019 -0500 @@ -0,0 +1,57 @@ +#!/usr/bin/env python + +from __future__ import print_function + +import argparse +import json +import os.path +import sqlite3 +from sqlite3 import OperationalError +import sys + +def _get_db_version(sqlitedb_path): + version = '4.5' + try: + query = 'select version from version' + conn = sqlite3.connect(sqlitedb_path) + cur = conn.cursor() + cur.execute(query) + version = cur.fetchone()[0] + except OperationalError as e: + print('Assuming eggnog version %s because %s %s' % (version, sqlitedb_path, e), file=sys.stderr) + return version + +def main(): + parser = argparse.ArgumentParser() + parser.add_argument( '--config_file' ) + parser.add_argument( '--install_path' ) + parser.add_argument( '--dbs', default='') + args = parser.parse_args() + + eggnog_db_path = os.path.join(args.install_path,'eggnog.db') + if not os.path.exists(eggnog_db_path): + print('Can not open: %s' % eggnog_db_path, file=sys.stderr) + exit(1) + db_version = _get_db_version(eggnog_db_path) + + params = json.loads( open( args.config_file ).read() ) + data_manager_dict = {} + data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) + data_table = 'eggnog_mapper_db' + data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get( data_table, [] ) + data_table_entry = dict(value=db_version, name=db_version, path=eggnog_db_path) + data_manager_dict['data_tables'][data_table].append( data_table_entry ) + data_table = 'eggnog_mapper_hmm_dbs' + data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get( data_table, [] ) + if args.dbs: + dbs = [x.strip() for x in args.dbs.split(',')] + for db in dbs: + key = '%s_%s' % (db_version, db) + data_table_entry = dict(key=key, db_version=db_version, value=db, name=db, path=db) + data_manager_dict['data_tables'][data_table].append( data_table_entry ) + + # save info to json file + open( args.config_file, 'wb' ).write( json.dumps( data_manager_dict ) ) + +if __name__ == "__main__": + main()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_eggnog.xml Mon Nov 04 16:38:44 2019 -0500 @@ -0,0 +1,165 @@ +<tool id="data_manager_eggnog" name="EggNOG DB Download" version="@VERSION@" tool_type="manage_data"> + <description>Download a new database</description> + <macros> + <token name="@VERSION@">4.5.1</token> + </macros> + <requirements> + <requirement type="package" version="@VERSION@">eggnog-mapper</requirement> + </requirements> + <version_command>emapper.py --version</version_command> + <command detect_errors="exit_code"><![CDATA[ +#import json, os +#set params = json.loads(open(str($out_file)).read()) +#set install_path = $params['output_data'][0]['extra_files_path'].encode('ascii', 'replace') +#if $dbs: +#set $eggnogdbs = ' '.join($dbs.split(',')) +#else +#set $eggnogdbs = 'none' +#endif +#if $test == 'false' +mkdir -p '${target_directory}' && +download_eggnog_data.py + $diamond_database -y -q --data_dir $install_path $eggnogdbs +' '.join(dbs.split(',')) && +#end if +python '${__tool_directory__}/data_manager_eggnog.py --config_file $out_file --install_path $target_directory --dbs '$dbs' + ]]></command> + <inputs> + <param name="test" type="hidden" value="false" /> + <param name="target_path" type="text" label="Download Destination (full path)" /> + <param name="diamond_database" type="boolean" truevalue="" falsevalue="-D" checked="true" label="Install the diamond database"/> + <param argument="dbs" type="select" multiple="true" label="eggNOG HMM databases to download. If none are selected only diamond can be used'"> + <option value="arch" selected="true">eggnog_4.5.1 arch</option> + <option value="bact" selected="true">eggnog_4.5.1 bact</option> + <option value="euk" selected="true">eggnog_4.5.1 euk</option> + <option value="NOG" selected="true">All organisms (NOG)</option> + <option value="aciNOG">Acidobacteria (aciNOG)</option> + <option value="acidNOG">Acidobacteriia (acidNOG)</option> + <option value="acoNOG">Aconoidasida (acoNOG)</option> + <option value="actNOG">Actinobacteria (actNOG)</option> + <option value="agaNOG">Agaricales (agaNOG)</option> + <option value="agarNOG">Agaricomycetes (agarNOG)</option> + <option value="apiNOG">Apicomplexa (apiNOG)</option> + <option value="aproNOG">Proteobacteria_alpha (aproNOG)</option> + <option value="aquNOG">Aquificae (aquNOG)</option> + <option value="arNOG">Archaea (arNOG)</option> + <option value="arcNOG">Archaeoglobi (arcNOG)</option> + <option value="artNOG">Arthropoda (artNOG)</option> + <option value="arthNOG">Arthrodermataceae (arthNOG)</option> + <option value="ascNOG">Ascomycota (ascNOG)</option> + <option value="aveNOG">Aves (aveNOG)</option> + <option value="bacNOG">Bacilli (bacNOG)</option> + <option value="bactNOG">Bacteria (bactNOG)</option> + <option value="bacteNOG">Bacteroidia (bacteNOG)</option> + <option value="basNOG">Basidiomycota (basNOG)</option> + <option value="bctoNOG">Bacteroidetes (bctoNOG)</option> + <option value="biNOG">Bilateria (biNOG)</option> + <option value="bproNOG">Proteobacteria_beta (bproNOG)</option> + <option value="braNOG">Brassicales (braNOG)</option> + <option value="carNOG">Carnivora (carNOG)</option> + <option value="chaNOG">Chaetomiaceae (chaNOG)</option> + <option value="chlNOG">Chlorobi (chlNOG)</option> + <option value="chlaNOG">Chlamydiae (chlaNOG)</option> + <option value="chloNOG">Chloroflexi (chloNOG)</option> + <option value="chlorNOG">Chloroflexi (chlorNOG)</option> + <option value="chloroNOG">Chlorophyta (chloroNOG)</option> + <option value="chorNOG">Chordata (chorNOG)</option> + <option value="chrNOG">Chromadorea (chrNOG)</option> + <option value="cloNOG">Clostridia (cloNOG)</option> + <option value="cocNOG">Coccidia (cocNOG)</option> + <option value="creNOG">Crenarchaeota (creNOG)</option> + <option value="cryNOG">Cryptosporidiidae (cryNOG)</option> + <option value="cyaNOG">Cyanobacteria (cyaNOG)</option> + <option value="cytNOG">Cytophagia (cytNOG)</option> + <option value="debNOG">Debaryomycetaceae (debNOG)</option> + <option value="defNOG">Deferribacteres (defNOG)</option> + <option value="dehNOG">Dehalococcoidetes (dehNOG)</option> + <option value="deiNOG">Deinococcusthermus (deiNOG)</option> + <option value="delNOG">delta/epsilon (delNOG)</option> + <option value="dipNOG">Diptera (dipNOG)</option> + <option value="dotNOG">Dothideomycetes (dotNOG)</option> + <option value="dproNOG">Proteobacteria_delta (dproNOG)</option> + <option value="droNOG">Drosophilidae (droNOG)</option> + <option value="eproNOG">Proteobacteria_epsilon (eproNOG)</option> + <option value="eryNOG">Erysipelotrichi (eryNOG)</option> + <option value="euNOG">Eukaryotes (euNOG)</option> + <option value="eurNOG">Euryarchaeota (eurNOG)</option> + <option value="euroNOG">Eurotiomycetes (euroNOG)</option> + <option value="eurotNOG">Eurotiales (eurotNOG)</option> + <option value="fiNOG">Fishes (fiNOG)</option> + <option value="firmNOG">Firmicutes (firmNOG)</option> + <option value="flaNOG">Flavobacteriia (flaNOG)</option> + <option value="fuNOG">Fungi (fuNOG)</option> + <option value="fusoNOG">Fusobacteria (fusoNOG)</option> + <option value="gproNOG">Proteobacteria_gamma (gproNOG)</option> + <option value="haeNOG">Haemosporida (haeNOG)</option> + <option value="halNOG">Halobacteria (halNOG)</option> + <option value="homNOG">Hominidae (homNOG)</option> + <option value="hymNOG">Hymenoptera (hymNOG)</option> + <option value="hypNOG">Hypocreales (hypNOG)</option> + <option value="inNOG">Insects (inNOG)</option> + <option value="kinNOG">Kinetoplastida (kinNOG)</option> + <option value="lepNOG">Lepidoptera (lepNOG)</option> + <option value="lilNOG">Liliopsida (lilNOG)</option> + <option value="maNOG">Mammals (maNOG)</option> + <option value="magNOG">Magnaporthales (magNOG)</option> + <option value="meNOG">Animals (meNOG)</option> + <option value="metNOG">Methanobacteria (metNOG)</option> + <option value="methNOG">Methanococci (methNOG)</option> + <option value="methaNOG">Methanomicrobia (methaNOG)</option> + <option value="necNOG">Nectriaceae (necNOG)</option> + <option value="negNOG">Negativicutes (negNOG)</option> + <option value="nemNOG">Nematodes (nemNOG)</option> + <option value="onyNOG">Onygenales (onyNOG)</option> + <option value="opiNOG">Opisthokonts (opiNOG)</option> + <option value="perNOG">Peronosporales (perNOG)</option> + <option value="plaNOG">Planctomycetes (plaNOG)</option> + <option value="pleNOG">Pleosporales (pleNOG)</option> + <option value="poaNOG">Poales (poaNOG)</option> + <option value="prNOG">Primates (prNOG)</option> + <option value="proNOG">Proteobacteria (proNOG)</option> + <option value="rhaNOG">Rhabditida (rhaNOG)</option> + <option value="roNOG">Rodents (roNOG)</option> + <option value="sacNOG">Saccharomycetaceae (sacNOG)</option> + <option value="saccNOG">Saccharomycetes (saccNOG)</option> + <option value="sorNOG">Sordariales (sorNOG)</option> + <option value="sordNOG">Sordariomycetes (sordNOG)</option> + <option value="sphNOG">Sphingobacteriia (sphNOG)</option> + <option value="spiNOG">Spirochaetes (spiNOG)</option> + <option value="spriNOG">Supraprimates (spriNOG)</option> + <option value="strNOG">Streptophyta (strNOG)</option> + <option value="synNOG">Synergistetes (synNOG)</option> + <option value="tenNOG">Tenericutes (tenNOG)</option> + <option value="thaNOG">Thaumarchaeota (thaNOG)</option> + <option value="theNOG">Thermoplasmata (theNOG)</option> + <option value="therNOG">Thermotogae (therNOG)</option> + <option value="thermNOG">Thermococci (thermNOG)</option> + <option value="treNOG">Tremellales (treNOG)</option> + <option value="veNOG">Vertebrates (veNOG)</option> + <option value="verNOG">Verrucomicrobia (verNOG)</option> + <option value="verrNOG">Verrucomicrobiae (verrNOG)</option> + <option value="virNOG">Viridiplantae (virNOG)</option> + </param> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json" label="${tool.name}"/> + </outputs> + <tests> + <test> + <param name="test" value="true"/> + <param name="diamond_database" value="false"/> + <output name="out_file"> + <assert_contents> + <has_text text="eggnog_mapper_db" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +This tool downloads eggnog data using download_eggnog_data.py +and populates the data tables: eggnog_mapper_db and eggnog_mapper_hmm_dbs. + ]]></help> + <citations> + <citation type="doi">10.1093/nar/gkv1248</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Mon Nov 04 16:38:44 2019 -0500 @@ -0,0 +1,27 @@ +<?xml version="1.0"?> +<data_managers> + <data_manager tool_file="data_manager/data_manager_eggnog.xml" id="data_manager_eggnog" > + <data_table name="eggnog_mapper_db"> <!-- Defines a Data Table to be modified. --> + <output> <!-- Handle the output of the Data Manager Tool --> + <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool --> + <column name="name" /> <!-- columns that are going to be specified by the Data Manager Tool --> + <column name="path" output_ref="out_file" > + <move type="directory" relativize_symlinks="True"> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${value}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${value}</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + <data_table name="eggnog_mapper_hmm_dbs"> <!-- Defines a Data Table to be modified. --> + <output> <!-- Handle the output of the Data Manager Tool --> + <column name="key" /> <!-- columns that are going to be specified by the Data Manager Tool --> + <column name="db_version" /> <!-- columns that are going to be specified by the Data Manager Tool --> + <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool --> + <column name="name" /> <!-- columns that are going to be specified by the Data Manager Tool --> + <column name="path" /> <!-- columns that are going to be specified by the Data Manager Tool --> + </output> + </data_table> + </data_manager> +</data_managers>
--- a/eggnog_mapper.xml Tue Aug 08 12:40:56 2017 -0400 +++ b/eggnog_mapper.xml Mon Nov 04 16:38:44 2019 -0500 @@ -1,24 +1,23 @@ -<tool id="eggnog_mapper" name="eggNOG Mapper" version="0.1.0"> +<tool id="eggnog_mapper" name="eggNOG Mapper" version="@VERSION@.1"> <description>functional sequence annotation by orthology</description> + <macros> + <token name="@VERSION@">1.0.3</token> + </macros> <requirements> - <requirement type="package" version="0.99.2">eggnog-mapper</requirement> + <requirement type="package" version="@VERSION@">eggnog-mapper</requirement> </requirements> - <stdio> - <exit_code range="1:" /> - </stdio> - <version_command>python emapper.py --version</version_command> - <command><![CDATA[ - ### Load on demand - with changes to download_eggnog_data.py - ## #if $db.mode == 'hmmer': - ## download_eggnog_data.py -y -q --data_dir ~/src/eggnog-mapper/data $db.database && - ## #else - ## download_eggnog_data.py -y -q --data_dir ~/src/eggnog-mapper/data $db.database && - ## #end if - emapper.py - --data_dir '$eggnog_data.fields.data_dir' - -m $db.mode $translate - #if $db.mode == 'hmmer': - --database=$db.database + <version_command>emapper.py --version</version_command> + <command detect_errors="aggressive"><![CDATA[ + emapper.py + --data_dir '$eggnog_data.fields.path' + -m $db.mode + $translate + #if ($db.mode == 'hmmer'): + #if $db.database.fields.path: + --database=$db.database.fields.path + #else + --database=$db.database + #end if #if $db.hmm_options.hmm_settings == 'specified': --hmm_maxhits=$db.hmm_options.hmm_maxhits --hmm_evalue=$db.hmm_options.hmm_evalue @@ -29,13 +28,9 @@ #end if --Z=$db.hmm_options.Z #end if - #elif $db.mode == 'diamond': - ## $db.sensitive - ## $db.more_sensitive - --matrix '$db.matrix' - --gapopen '$db.gapopen' - --gapextend '$db.gapextend' - ## --seg '$db.seg' + #elif ($db.mode == 'diamond'): + --matrix '$db.matrix_gapcosts.matrix' + $db.matrix_gapcosts.gap_costs #end if #if $annotation_options.tax_scope: --tax_scope=$annotation_options.tax_scope @@ -49,75 +44,186 @@ #if $seed_ortholog_options.seed_ortholog_evalue: --seed_ortholog_evalue=$seed_ortholog_options.seed_ortholog_evalue #end if - #if $seed_ortholog_options.seed_ortholog_score: + #if str($seed_ortholog_options.seed_ortholog_score): --seed_ortholog_score=$seed_ortholog_options.seed_ortholog_score #end if - $output_options.file_comments + $output_options.no_file_comments $output_options.no_annot $output_options.report_orthologs --output='results' -i '${input}' + --cpu "\${GALAXY_SLOTS:-4}" ]]></command> - <inputs> - <param name="input" type="data" format="fasta" label="Fasta sequences to annotate"/> - <param name="translate" type="boolean" truevalue="--translate" falsevalue="" checked="false" - label="Are these CDS sequences that need to be translated"/> - <param name="eggnog_data" type="select" label="Eggnog Data"> - <options from_data_table="eggnog_mapper" > - <filter type="static_value" name="type" value="data" column="2"/> - <validator type="no_options" message="No cached eggnog data is available" /> - </options> - </param> - <conditional name="db"> - <param name="mode" type="select" label="Annotation Type"> - <option value="hmmer">HMM</option> - <option value="diamond">DIAMOND</option> + <inputs> + <param name="input" type="data" format="fasta" label="Fasta sequences to annotate"/> + <param name="eggnog_data" type="select" label="Version of eggNOG Database"> + <options from_data_table="eggnog_mapper_db"/> </param> - <when value="hmmer"> - <param name="database" type="select" multiple="true" min="1" label="HMM target database"> - <options from_data_table="eggnog_mapper" > - <!-- - --> - <filter type="param_value" ref="eggnog_data" column="3" /> - <filter type="static_value" name="type" value="hmmer" column="2"/> - <validator type="no_options" message="No HMM DBs are available, request from your galaxy admin" /> - </options> + <param name="translate" type="boolean" truevalue="--translate" falsevalue="" checked="false" + label="Are these coding DNA sequences that need to be translated?"/> + <conditional name="db"> + <param name="mode" type="select" label="Annotation Type"> + <option value="hmmer">HMM</option> + <option value="diamond">DIAMOND</option> </param> - <conditional name="hmm_options"> - <param name="hmm_settings" type="select" label="HMM Search Options"> - <option value="default">Use defaults</option> - <option value="specified">Set HMM Search Options</option> + <when value="hmmer"> + <param name="database" type="select" label="HMM target database" help="Choose either the full eggNOG database or a subset of it. Contact your Galaxy admin to have additional HMM databases installed."> + <options from_data_table="eggnog_mapper_hmm_dbs"> + <!-- + <filter type="param_value" ref="eggnog_data" column="1" /> + <filter type="unique_value" column="3" /> + <validator type="no_options" message="No HMM databases are available; request installation from your Galaxy admin." /> + --> + </options> </param> - <when value="default"/> - <when value="specified"> - <param name="hmm_maxhits" type="integer" value="1" label="Max number of hits to report. Default=1" /> - <param name="hmm_evalue" type="float" value="0.001" label="E-value threshold. Default=0.001" /> - <param name="hmm_score" type="integer" value="20" label="Bit score threshold. Default=20" /> - <param name="hmm_maxseqlen" type="integer" value="5000" label="Ignore query sequences larger than `maxseqlen`. Default=5000" /> - <param name="hmm_qcov" type="float" value="" min="0." max="1." optional="true" label="min query coverage (from 0 to 1). Default=(disabled)" /> - <param name="Z" type="integer" value="" label="Fixed database size used in phmmer/hmmscan (allows comparing e-values among databases). Default=40,000,000" /> - </when> - </conditional> - </when> - <when value="diamond"> - <param name="database" type="hidden" value="diamond"/> - <param argument="--sensitive" type="boolean" truevalue="--sensitive" falsevalue="" checked="false" label="Trigger the sensitive alignment mode with a 16x9 seed shape configuration?" help=""/> - <param name="more_sensitive" argument="--more-sensitive" type="boolean" truevalue="--more-sensitive" falsevalue="" checked="false" label="Trigger the more sensitive mode?" help="This mode provides some additional sensitivity compared to the sensitive mode."/> - <param argument="--seg" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Enable SEG masking of low complexity segments in the query?" help=""/> - <param argument="--matrix" type="select" label="Scoring matrix" help="In brackets are the supported values for (gap open)/(gap extend)"> - <option value="BLOSUM45">BLOSUM45 ((10-13)/3; (12-16)/2; (16-19)/1)</option> - <option value="BLOSUM50">BLOSUM50 ((9-13)/3; (12-16)/2; (15-19)/1)</option> - <option value="BLOSUM62" selected="True">BLOSUM62 ((6-11)/2; (9-13)/1)</option> - <option value="BLOSUM80">BLOSUM80 ((6-9)/2; 13/2; 25/2; (9-11)/1)</option> - <option value="BLOSUM90">BLOSUM90 ((6-9)/2; (9-11)/1)</option> - <option value="PAM250">PAM250 ((11-15)/3; (13-17)/2; (17-21)/1)</option> - <option value="PAM70">PAM70 ((6-8)/2; (9-11)/1)</option> - <option value="PAM30">PAM30 ((5-7)/2; (8-10)/1)</option> - </param> - <param argument="--gapopen" type="integer" value="11" label="Gap open penalty" help="" /> - <param argument="--gapextend" type="integer" value="1" label="Gap extension penalty" help="" /> - </when> - </conditional> + <conditional name="hmm_options"> + <param name="hmm_settings" type="select" label="HMM Search Options"> + <option value="default">Use defaults</option> + <option value="specified">Set HMM Search Options</option> + </param> + <when value="default"/> + <when value="specified"> + <param name="hmm_maxhits" type="integer" value="1" label="Max number of hits to report per query sequence"/> + <param name="hmm_evalue" type="float" min="0" value="0.001" label="E-value threshold" /> + <param name="hmm_score" type="integer" min="0" value="20" label="Bit score threshold" /> + <param name="hmm_maxseqlen" type="integer" value="5000" label="Ignore query sequences larger than `maxseqlen`. Default=5000" /> + <param name="hmm_qcov" type="float" value="" min="0." max="1." optional="true" label="min query coverage (from 0 to 1). Default=(disabled)" /> + <param name="Z" type="integer" value="40000000" min="0" label="Fixed database size used in phmmer/hmmscan (allows comparing e-values among databases). Default=40,000,000" /> + </when> + </conditional> + </when> + <when value="diamond"> + <!-- db.database is used in diamond mode only to name outputs --> + <param name="database" type="hidden" value="diamond"/> + <conditional name="matrix_gapcosts"> + <param argument="--matrix" type="select" label="Scoring matrix and gap costs"> + <option value="BLOSUM90">BLOSUM90</option> + <option value="BLOSUM80">BLOSUM80</option> + <option value="BLOSUM62" selected="true">BLOSUM62</option> + <option value="BLOSUM50">BLOSUM50</option> + <option value="BLOSUM45">BLOSUM45</option> + <option value="PAM250">PAM250</option> + <option value="PAM70">PAM70</option> + <option value="PAM30">PAM30</option> + </param> + <when value="BLOSUM90"> + <param name="gap_costs" type="select" label="Gap Costs"> + <option value="--gapopen 9 --gapextend 2">Existence: 9 Extension: 2</option> + <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option> + <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option> + <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option> + <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option> + <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option> + <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option> + </param> + </when> + <when value="BLOSUM80"> + <param name="gap_costs" type="select" label="Gap Costs"> + <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option> + <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option> + <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option> + <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option> + <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option> + <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option> + </param> + </when> + <when value="BLOSUM62"> + <param name="gap_costs" type="select" label="Gap Costs"> + <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option> + <option value="--gapopen 10 --gapextend 2">Existence: 10 Extension: 2</option> + <option value="--gapopen 9 --gapextend 2">Existence: 9 Extension: 2</option> + <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option> + <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option> + <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option> + <option value="--gapopen 13 --gapextend 1">Existence: 13 Extension: 1</option> + <option value="--gapopen 12 --gapextend 1">Existence: 12 Extension: 1</option> + <option value="--gapopen 11 --gapextend 1" selected="true">Existence: 11 Extension: 1</option> + <option value="--gapopen 10 --gapextend 1">Existence: 10 Extension: 1</option> + <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option> + </param> + </when> + <when value="BLOSUM50"> + <param name="gap_costs" type="select" label="Gap Costs"> + <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option> + <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option> + <option value="--gapopen 11 --gapextend 3">Existence: 11 Extension: 3</option> + <option value="--gapopen 10 --gapextend 3">Existence: 10 Extension: 3</option> + <option value="--gapopen 9 --gapextend 3">Existence: 9 Extension: 3</option> + <option value="--gapopen 16 --gapextend 2">Existence: 16 Extension: 2</option> + <option value="--gapopen 15 --gapextend 2">Existence: 15 Extension: 2</option> + <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option> + <option value="--gapopen 13 --gapextend 2" selected="true">Existence: 13 Extension: 2</option> + <option value="--gapopen 12 --gapextend 2">Existence: 12 Extension: 2</option> + <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option> + <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option> + <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option> + <option value="--gapopen 16 --gapextend 1">Existence: 16 Extension: 1</option> + <option value="--gapopen 15 --gapextend 1">Existence: 15 Extension: 1</option> + </param> + </when> + <when value="BLOSUM45"> + <param name="gap_costs" type="select" label="Gap Costs"> + <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option> + <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option> + <option value="--gapopen 11 --gapextend 3">Existence: 11 Extension: 3</option> + <option value="--gapopen 10 --gapextend 3">Existence: 10 Extension: 3</option> + <option value="--gapopen 15 --gapextend 2" selected="true">Existence: 15 Extension: 2</option> + <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option> + <option value="--gapopen 13 --gapextend 2">Existence: 13 Extension: 2</option> + <option value="--gapopen 12 --gapextend 2">Existence: 12 Extension: 2</option> + <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option> + <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option> + <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option> + <option value="--gapopen 16 --gapextend 1">Existence: 16 Extension: 1</option> + </param> + </when> + <when value="PAM250"> + <param name="gap_costs" type="select" label="Gap Costs"> + <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option> + <option value="--gapopen 14 --gapextend 3">Existence: 14 Extension: 3</option> + <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option> + <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option> + <option value="--gapopen 17 --gapextend 2">Existence: 17 Extension: 2</option> + <option value="--gapopen 16 --gapextend 2">Existence: 16 Extension: 2</option> + <option value="--gapopen 15 --gapextend 2">Existence: 15 Extension: 2</option> + <option value="--gapopen 14 --gapextend 2" selected="true">Existence: 14 Extension: 2</option> + <option value="--gapopen 13 --gapextend 2">Existence: 13 Extension: 2</option> + <option value="--gapopen 21 --gapextend 1">Existence: 21 Extension: 1</option> + <option value="--gapopen 20 --gapextend 1">Existence: 20 Extension: 1</option> + <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option> + <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option> + <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option> + </param> + </when> + <when value="PAM70"> + <param name="gap_costs" type="select" label="Gap Costs"> + <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option> + <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option> + <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option> + <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option> + <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option> + <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option> + <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option> + <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option> + </param> + </when> + <when value="PAM30"> + <param name="gap_costs" type="select" label="Gap Costs"> + <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option> + <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option> + <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option> + <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option> + <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option> + <option value="--gapopen 5 --gapextend 2">Existence: 5 Extension: 2</option> + <option value="--gapopen 14 --gapextend 1">Existence: 14 Extension: 1</option> + <option value="--gapopen 10 --gapextend 1">Existence: 10 Extension: 1</option> + <option value="--gapopen 9 --gapextend 1" selected="true">Existence: 9 Extension: 1</option> + <option value="--gapopen 8 --gapextend 1">Existence: 8 Extension: 1</option> + </param> + </when> + </conditional> + </when> + </conditional> <section name="annotation_options" expanded="false" title="Annotation Options"> <param name="tax_scope" type="select" optional="true" label="Set taxonomic scope"> <option value="NOG">All organisms (NOG)</option> @@ -228,38 +334,39 @@ <option value="verrNOG">Verrucomicrobiae (verrNOG)</option> <option value="virNOG">Viridiplantae (virNOG)</option> </param> - <param name="target_orthologs" type="select" optional="true" label="target orthologs for functional transfer"> + <param name="target_orthologs" type="select" label="target orthologs for functional transfer"> <option value="one2one">one2one</option> <option value="many2one">many2one</option> <option value="one2many">one2many</option> <option value="many2many">many2many</option> - <option value="all">all</option> + <option value="all" selected="true">all</option> </param> - <param name="go_evidence" type="select" optional="true" label="Type of GO terms should be used for annotation"> + <param name="go_evidence" type="select" + label="Select the set of GO terms that should be used for annotation"> <option value="experimental">experimental = Use only terms inferred from experimental evidence</option> - <option value="non-electronic">non-electronic = Use only non-electronically curated terms</option> + <option value="non-electronic" selected="true">non-electronic = Use only non-electronically curated terms</option> </param> </section> <section name="seed_ortholog_options" expanded="false" title="Seed Ortholog Search Options"> - <param name="seed_ortholog_evalue" type="float" value="0.001" optional="true" label="Min E-value threshold. Default=0.001"> + <param name="seed_ortholog_evalue" type="float" value="0.001" min="0" label="Min E-value threshold"> <help> Min E-value expected when searching for seed eggNOG ortholog. Applies to phmmer/diamond searches. - Queries not having a significant seed orthologs will not be annotated. + Queries not having a significant seed orthologs (E-value less than threshold) will not be annotated. </help> </param> - <param name="seed_ortholog_score" type="integer" value="60" optional="true" label="Bit score threshold. Default=60"> + <param name="seed_ortholog_score" type="integer" value="60" min="0" label="Minimum bit score threshold"> <help> - Min bit score expected when searching for seed eggNOG ortholog. Applies to phmmer/diamond searches. - Queries not having a significant seed orthologs will not be annotated. Default=60 + Min bit score expected when searching for seed eggNOG ortholog. + Queries not having a significant seed orthologs will not be annotated. </help> </param> </section> <section name="output_options" expanded="false" title="Output Options"> - <param name="file_comments" type="boolean" truevalue="--no_file_comments" falsevalue="" checked="false" + <param name="no_file_comments" type="boolean" truevalue="--no_file_comments" falsevalue="" checked="true" label="Exclude header lines and stats from output files"/> - <param name="no_annot" type="boolean" truevalue="--no_annot" falsevalue="" checked="false" + <param name="no_annot" type="boolean" truevalue="--no_annot" falsevalue="" checked="false" label="Skip functional annotation, reporting only hits"/> - <param name="report_orthologs" type="boolean" truevalue="--report_orthologs" falsevalue="" checked="false" + <param name="report_orthologs" type="boolean" truevalue="--report_orthologs" falsevalue="" checked="false" label="Output a file with the list of orthologs for each hits"/> </section> </inputs> @@ -272,7 +379,7 @@ <data name="annotations" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.annotations" from_work_dir="results.emapper.annotations"> <filter>not output_options['no_annot']</filter> <actions> - <action name="column_names" type="metadata" default="query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score,predicted_gene_name,GO_terms,KEGG_pathways,Annotation_tax_scope,Matching_OGs,best_OG|evalue|score,COG,functional,categories,eggNOG_HMM_model_annotation"/> + <action name="column_names" type="metadata" default="query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score,predicted_gene_name,GO_terms,KEGG_KO,BiGG_Reactions,Annotation_tax_scope,Matching_OGs,best_OG|evalue|score,COG_functional_categories,eggNOG_HMM_model_annotation"/> </actions> </data> <data name="hmm_hits" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.hmm_hits" from_work_dir="results.emapper.hmm_hits"> @@ -288,98 +395,84 @@ </actions> </data> </outputs> + <tests> + <test> + <param name="input" value="nlim_fragment.fasta" ftype="fasta"/> + <param name="database" value="ENOG411CB2I"/> + <param name="mode" value="hmmer"/> + <!-- + <param name="test" value="true"/> + --> + <param name="eggnog_data" value="4.5"/> + <param name="no_annot" value="true"/> + <param name="no_file_comments" value="true"/> + <output name="hmm_hits" file="HMM_nlim.emapper.hmm_hits" ftype="tabular"/> + </test> + <test> + <param name="input" value="nlim_fragment.fasta" ftype="fasta"/> + <param name="eggnog_data" value="4.5"/> <!-- not passed in test, but required for test to work --> + <param name="no_annot" value="true"/> + <param name="mode" value="diamond"/> + <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular"/> + </test> + </tests> <help><![CDATA[ eggnog-mapper - -optional arguments: - -h, --help show this help message and exit - --version +============= +Overview +-------- -Target HMM Database Options: - --guessdb guess eggnog db based on the provided taxid - --database , -d specify the target database for sequence searches. - Choose among: euk,bact,arch, host:port, or a local - hmmpressed database - --dbtype {hmmdb,seqdb} - --qtype {hmm,seq} +``eggnog-mapper`` is a tool for fast functional annotation of novel sequences (genes or proteins) using precomputed eggNOG-based orthology assignments. +Obvious examples include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs. +The use of orthology predictions for functional annotation is considered more precise than traditional homology searches, +as it avoids transferring annotations from paralogs (duplicate genes with a higher chance of being involved in functional divergence). + +EggNOG-mapper is also available as a public online resource: `<http://beta-eggnogdb.embl.de/#/app/emapper>`_. -Annotation Options: - --tax_scope Fix the taxonomic scope used for annotation, so only - orthologs from a particular clade are used for - functional transfer. By default, this is automatically - adjusted for every query sequence. - --target_orthologs {one2one,many2one,one2many,many2many,all} - defines what type of orthologs should be used for - functional transfer - --excluded_taxa (for debugging and benchmark purposes) - --go_evidence {experimental,non-electronic} - Defines what type of GO terms should be used for - annotation:experimental = Use only terms inferred from - experimental evidencenon-electronic = Use only non- - electronically curated terms +Options +------- + +``eggnog-mapper`` can use two search algorithms: `HMMER <http://hmmer.org/>`_ and `DIAMOND <https://github.com/bbuchfink/diamond>`_. +HMMER is more sensitive, while DIAMOND is faster and useful for larger sets of query sequences. -HMM search_options: - --hmm_maxhits Max number of hits to report. Default=1 - --hmm_evalue E-value threshold. Default=0.001 - --hmm_score Bit score threshold. Default=20 - --hmm_maxseqlen Ignore query sequences larger than `maxseqlen`. - Default=5000 - --hmm_qcov min query coverage (from 0 to 1). Default=(disabled) - --Z Fixed database size used in phmmer/hmmscan (allows - comparing e-values among databases). - Default=40,000,000 + +Outputs +------- + +**hmm_hits** -Seed ortholog search option: - --seed_ortholog_evalue - Min E-value expected when searching for seed eggNOG - ortholog. Applies to phmmer/diamond searches. Queries - not having a significant seed orthologs will not be - annotated. Default=0.001 - --seed_ortholog_score - Min bit score expected when searching for seed eggNOG - ortholog. Applies to phmmer/diamond searches. Queries - not having a significant seed orthologs will not be - annotated. Default=60 +For each query sequence, a list of significant +hits to eggNOG Orthologous Groups (OGs) is reported. +Each line in the file represents a hit, where evalue, bit-score, +query-coverage and the sequence coordinates of the match are reported. +If multiple hits exist for a given query, results are sorted by e-value. +Only returned when using HMMER mode. + +**seed_orthologs** + +each line in the file provides the best match of each query within the best Orthologous Group (OG) +reported in the [project].hmm_hits file, obtained running PHMMER against all sequences within the best OG. +The seed ortholog is used to fetch fine-grained orthology relationships from eggNOG. +If using the diamond search mode, seed orthologs are directly +obtained from the best matching sequences by running DIAMOND against the whole eggNOG protein space. -Output options: - --output , -o base name for output files - --resume Resumes a previous execution skipping reported hits in - the output file. - --override Overwrites output files if they exist. - --no_refine Skip hit refinement, reporting only HMM hits. - --no_annot Skip functional annotation, reporting only hits - --no_search Skip HMM search mapping. Use existing hits file - --report_orthologs The list of orthologs used for functional transferred - are dumped into a separate file - --scratch_dir Write output files in a temporary scratch dir, move - them to final the final output dir when finished. - Speed up large computations using network file - systems. - --output_dir Where output files should be written - --temp_dir Where temporary files are created. Better if this is a - local disk. - --no_file_comments No header lines nor stats are included in the output - files - --keep_mapping_files Do not delete temporary mapping files used for - annotation (i.e. HMMER and DIAMOND search outputs) +**annotations** + +This file provides final annotations of each query. Tab-delimited columns in the file are: -Execution options: - -m {hmmer,diamond} Default:hmmer - -i Computes annotations for the provided FASTA file - --translate Assume sequences are genes instead of proteins - --servermode Loads target database in memory and keeps running in - server mode, so another instance of eggnog-mapper can - connect to this sever. Auto turns on the --usemem flag - --usemem If a local hmmpressed database is provided as target - using --db, this flag will allocate the whole database - in memory using hmmpgmd. Database will be unloaded - after execution. - --cpu - --annotate_hits_table - Annotatate TSV formatted table of query->hits. 4 - fields required: query, hit, evalue, score. Implies - --no_search and --no_refine. +- ``query_name``: query sequence name +- ``seed_eggNOG_ortholog``: best protein match in eggNOG +- ``seed_ortholog_evalue``: best protein match (e-value) +- ``seed_ortholog_score``: best protein match (bit-score) +- ``predicted_gene_name``: Predicted gene name for query sequences +- ``GO_terms``: Comma delimited list of predicted Gene Ontology terms +- ``KEGG_pathways``: Comma delimited list of predicted KEGG pathways +- ``Annotation_tax_scope``: The taxonomic scope used to annotate this query sequence +- ``Matching_OGs``: Comma delimited list of matching eggNOG Orthologous Groups +- ``best_OG|evalue|score``: Best matching Orthologous Groups (only in HMM mode) +- ``COG functional categories``: COG functional category inferred from best matching OG +- ``eggNOG_HMM_model_annotation``: eggNOG functional description inferred from best matching OG ]]></help> <citations>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/DIA_nlim.emapper.seed_orthologs Mon Nov 04 16:38:44 2019 -0500 @@ -0,0 +1,1 @@ +Nlim_1033886738.Nlim_1033Cytidyltransferase-like 886738.Nlim_1033 5.4e-20 78.6
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/HMM_nlim.emapper.hmm_hits Mon Nov 04 16:38:44 2019 -0500 @@ -0,0 +1,1 @@ +Nlim_1033886738.Nlim_1033Cytidyltransferase-like ENOG411CB2I 2.3e-16 46.1 39 1 39 1 38 0.948717948718
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2A.fa Mon Nov 04 16:38:44 2019 -0500 @@ -0,0 +1,6 @@ +>1001994.MY1_1439 +MKIQIYILIGVVVLTLISVGIMTNQDQNTHENKIRVAYFPNISHAIPIVGIEKGFFSNHIGSDIDIQPILFDSGPQVIESIFAGSVDIAYVGPGPAINAFLKSEQHDVKILSGAASGGVSFIVHPKSEIKSVADFAGKRIAAPQIGNTQDISLRTYLSDNGLKPAEKGGSVIILNTGNSDIYILFAKGDIDGAWVPEPTATILVQQLGGTRLFNENELWPENKFATVVLIAKEEYVNSHPEIIQKWLEAHQQTADWINSNKEETKTIFFDFMKNEMGKSLPVELIDESLSNLEITSDPIVSSIDTIAKRADSLGYLGRHGYNLDGLFFDKNSNSQSQEVLVNNDQT +>436308.Nmar_1285 +MKIRSVIAAGIGAIIVFSALGIALSSSDTTYENKIRIAYFPNIGHAIPIVGMEKGFFAEHLGDDVKIETKVFDSGPQAIESLFANSIDIAYVGPGPAINGFLNSNNQNVKILAGAASGGASFIVHPDSEINTADDFAGKKIAAPQIGNTQDVSLRHFLAENQLKPAEKGGNVVVYNIPNPDIYTLFVKGDIDGAWVAEPWATILETELDGKRLFHEEELWPDKEFASVLLIGNVDYIDKNSVVWADYIRAHHETQIWIESNPIETRNVFNDFLDSYLGQSLSDDVVDVALSNIMITADPKPNSVVSFAEKADTLGYLGRNGYDLSGIFYSFDTNSLEEAST +>886738.Nlim_1020 +MKMRSIILAGIASIILILSVGIIVNTDGSTRENKIRVAYFPNITHVVPIIGLERGTFANEIGNTITIQPILFDSGPQVIESIFAGSVNIAYVGPGPAINGFLKSEHHNVKILSGAASGGVSFIVHPDSKINSAEDFIGKRIAAPQIGNSQDISLRTYLSANGLKPAEKGGSVIVLNVPNSDIYTLFAKGDIDAAWVAEPTATLLVQKLNGTRLFDEIDMWPDQKFASVLLIANEDYVNQHPEVIRKWLEAHQQTIDWINSNPEETRIIFNQFLKRELGKSLPDNLIDESLSKLQITSDPIVSSIETFAKRADSLGYLGRHGYSLDGIFFDINSNSQLQEVLIP
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2B.fa Mon Nov 04 16:38:44 2019 -0500 @@ -0,0 +1,6 @@ +>1001994.MY1_0167 +MSYDGAIEALSTDALKFVKDDFVIGLGSGRAATAFVKSLSSFIKIKNYNIRGVPTSLQIKLIAEKGGIPLVEAEQVDHIDIVFDGADQIDSQKFVIKGGGGALLRENILFNLAKKVVVMADKSKFVKNFTRSVPVEVHPQARNLVTYEIKKLGGKAELRLIDRGYPFFTENGNIILDCDFGVIKNPKILSQKIKQVAGVIESGIFIRKPDVIYRAKTGGKFDII +>436308.Nmar_0218 +MSYDGAITALSNNALKFVKDDYVVGLGSGRAATVLVKSLGKLIKLKNYNIKGVPTSLQIKLIAEKVGIPLIEADQVEHIDVVFDGADQIDSQKFVIKGGGGALLRENILFSLAKKVVVMADKTKFVKNFTRTVPVEVHPLARNSVSKSMKKLGGKAELRSLDRGYPFFTENGNIILDCDFGTIKNPKALTQKIKATTGVLESGIFLRKPDVIYRAKTGEKFDIL +>886738.Nlim_1248 +MSYDDAIEALSTDALKFVKDGFVIGLGSGRAATSFVKSLSSFIKIKNYSIKAVPTSLQIKLIAEKGGIPLVEADHVEYIDVVFDGADQIDSQKFVIKGGGGALLRENILFNLSKKVVVMADKSKFVKNFTREVPVEVHPLARNSVIDAIRKLGGNAQLRSLDRGYPFFTENGNIILDCNFGTIKNPKSLTQKIKQITGVMESGIFLRKPDVIYKAKTGGKFEII
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2C.fa Mon Nov 04 16:38:44 2019 -0500 @@ -0,0 +1,4 @@ +>1001994.MY1_1435 +MVQKEPFLTALQNRILLFDGAMGTEIQKYNPKPEDFPNNQDGFNDGLVITHPDWIKKIHKNYLDAGSDCIETNSFGSNKIKLDEYGFGDQTIEFNKKIAQLAVEVCSEYTDKPRYVIGSMGPSGYLPSSNDPDLGQKPLGEIRNAFELQAEGLILGGVDALLIETSQDILEVKLVIEACHNAMKKTGKKVPIIANTTLDQYGKMLLGTNIQAAYTTVSDMGIDVFGLNCSTGPAEMTPSVRWLDEQNEHNLLVVPNAGMPENQGGQAVYKMTPQKMGELLGDFLKQYKKVRIIGGCCGTNPEHIAVLRKVIDEKAYSVKG +>436308.Nmar_1268 +MTEKEPFLDALQNRVLLFDGAMGTEIQKFNPKPEDFPNNQDGFNDGLVVTRPDWIKQIHRHYLDAGADCIETNSFGSNKIKLDEYGFGDQTIEFNKKIAQLASEVCQEYSDRPRYVIGSMGPSGFLPSSNDPDLGQKPLDEIKEAFELQAEGLILGGVDALLIETSQDILEVKLVIEACHQAMEKTGKKIPIIANTTLDQYGKMLLGTNIQAAYTTVSDMGIDVFGMNCSTGPIEMTPSVRWLDEQNEHNILVVPNAGMPENEGGQAVYKMTPEKMGDALGDFLNQYKKVRIIGGCCGTNPEHIKVLRKVIDEKANSVEG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2D.fa Mon Nov 04 16:38:44 2019 -0500 @@ -0,0 +1,6 @@ +>1001994.MY1_0571 +MDKSGVIVGAISGAAIVAIIFAVILAVPPTAVKADVISDNKSIPSATGAILTDYSKKLSLIEIFEKSEPGVVRINVQRAEQSNGTSGVGSGFVFDKQGHIITNAHVVKNVKKVVVTFLDGRSYNAEIVGSDQYTDIGVIKVNADLSLLQPLPLGDSANLKVGEPIAAIGNPFGLSGSMTSGIISQLGRLLPSGAGYSIPDVIQTDAAINPGNSGGPLLNMRGEIVGINTAIQSTTGEFTGVGFAVPSQTLAKIVPKIIVDGKYIHPWIGIAGRDIDPDLAKVLNLNDAVGFLVITVVDDSPAAKAGIHGSNETVEVDGIKYLIGGDIILSVDGNQVRKIDDILIHLQRAKSVGDEMVLEVLRDGRTTNIIITLDERPNGN +>436308.Nmar_0594 +MDKSGVFVGGAIGAVIVVAIFAVLFVSPPESVKPDIVVSNGHGPSTVGEVTPVYSKDLSLIEIFEKSEPGVVRVNVQREEVSDVGGVGSGFVFDKQGHIITNEHVIDDAKKIIITFLDGRSYNAEIIGTDEFTDLAVVKVNADLALLHPLSIGDSSNLKVGEPIAAIGNPFGLSGSMTSGIVSQLGRLLPSGSGYSIPDVIQTDAAINPGNSGGPLLNMRGEIVGINTAIQSATGEFTGVGFAIPSQTVAKIVPTLIEDGDYKHPWIGISGRDIDPDLAKVLELPDAVGFLVVTVIEDSPASKAGLIGSEKTIDVDGVNYPMGGDIILAVDGIEVRKIDDILIHLQRAKSVGDEMVLEVLRDGRTTDISIILQERPNGN +>886738.Nlim_0162 +MSKSEMLVGAAIGASVVAVIFAIILISPAAITKSEINTSDKSIPSVTQTAPAYSTNLSLIDIFEKSEPGVVRVNVQRTDQSNGTSGLGSGFVFDKKGDIITNAHVVKNAKNIVVTFLDGRSYNADLIGSDEFTDIAVIKVNADLTRLHPLSLGDSSSLKVGESIAAIGNPFGLSGSMTSGIVSQLGRLLPSGSGYSIPDVIQTDAAINPGNSGGPLLNMRGEIVGINTAIQSTTGEFTGVGFAVPSQTIVKIVPSLIQDGTYHHPWIGITGRDIEPDLAKVLKLNDAVGFLIVSVIDDSPAAKAGLHGSNETVQVDGLNYQIGGDIILSVDGKQVRKIDDILVHLQRAKSVGDEMVLEILRDGRTTNITINLEERPNGN
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2E.fa Mon Nov 04 16:38:44 2019 -0500 @@ -0,0 +1,6 @@ +>1001994.MY1_1525 +MEPSLVTSIGKIQLERPVMLASGILGISLDVFNRLYRSGAGAVVSKSLSTEPWDGYPNPTIFGINGGGWINAVGLSNPGAPNFAKMIEPNKDVPIIISLVGSIPEDFSTMVEQFKNSKVIAYELNLSCPHVAKVGLEVGDDPELVKKIVSTVKNSTNVPVIAKVGLGTTHYLNTVSAAIDSGIDAITAINTIRAIAIDVETQRPILSNKFGGLSGTPIKPIALRCVYEISSKYDIPIIGCGGISTWEDALEFILAGASAIQIGSAIGDNWIHVFNDINKGILQYMKRKGYSKIDEMIGLAKKS +>436308.Nmar_1390 +MEPNLATSIGPIQLDRPVMLASGILGISLDVFSRLYRSGAGAVVTKSLSTEPWEGYPNPTIFSVKGGGWINAVGLSNPGAENFAKMIEPNQDVPIIVSLVGSIPEDFEKMIKQFENCKVTAYELNLSCPHVAKVGLEVGDDPELVKKIVTTVKNSTNVPVIAKVGLGTTHYLNTVGTAIESGIDAITAINTVRSMAIDVETQRPILSNKFGGLSGTPIKPIALRCVYEISSKYDIPIIGCGGISTWEDAVEFFLAGASSVQLGSAIGDNWIDVFNEINTGILQYMEKKNYSKIEEMIGLAKKS +>886738.Nlim_1764 +MEPSLVTSIGKIQLERPVMLASGILGISLDVFNRLYRSGAGAVVTKSLSTEPWDGYPNPTIFSVNGGGWINAVGLSNPGAPNFAKMIESNTTVPIIVSLVGSIAEDFEMMVSQFKNCKVTAYELNLSCPHVAKVGLEVGDDPELVKKIVSTVKNSTAVPVIAKVGLGTTHYLNTVKTAIDSGIDAITAINTVRAMAIDVETQRPILSNKFGGLSGTPIKPIALRCVYEISSKYDIPIIGCGGISTWEDAIEFILGGASAIQLGSAIGDRWLNVFNDINDGIIRYMKRKGYSKLDEMVGLAKKS
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2F.fa Mon Nov 04 16:38:44 2019 -0500 @@ -0,0 +1,6 @@ +>1001994.MY1_0238 +MLEISSTPLVIIAILGTVGILLPIISIARKEKGSNSFYAVIAFAALIVSIGYVAYQFVNGNILPSALFSEDVLVDDAFGGFFAIAMLIVAIFTTVGSFNYMRKKNYPAVYYSLILLSTIGMVLVAYSTDLVMLFVAWELMSIPTYVLAGFMKKNPSSNEAALKYFLFGALSSAIIVYGISLSYGLTGSTNIGEVIQGYATLDPSLLPLALLSVGMFIAGFGFKMGLVPFHQWLPDTYEGAPPTITTLLAAGTKKAGFAATIRIVVLGMVVLNLDWTLALGVIAVMTMTIGNIAAIMQKNLARMLAYSSIAHAGYILIGLAVSPYSSLGLQGSLYHILNHAVMKGMAFIAVTGIITTLAVTHIDKLKGLGRRMPITALGLIISLFALAGVPPLAGFWSKLVLFGGALDAGTSIWWAPWLAIAGVLNSALSLAYYGWITRKMYFEGENEKRVSEPKSIIAIMIFSIVFLVGFGIYPDPIIKFVEFAAPTFSLGVMP +>436308.Nmar_0286 +MLEITSTPLILIAILGTVGVILPIISIARKEKGSNSFYAVIAFAALIVSMAYVGYEFINENVAASALFSDDVIVDDAFGGFFAIAMLIVALFTTVGSFNYMRKHNSPAVYYSLILLATIGMILVAYSTDLVMLFVAWELMSIPTYILVGYMKKNPSSNEAALKYFLFGALSSAIIVYGIAISYGLTGSTNIGEVIEGYSTLDPSLLPLALLSVGMFIAGFGFKMGLVPFHQWLPDTYEGAPSPVTALLAAATKKAGFAAAIRIIVLGMMALNLDWTLALGIIAVMTMTIGNVAAIMQKNLSRMLAYSSIAHAGYILIGLAVAPYSSLGLQGSLYQIFNHAVMKGAAFIAIAGIVTTLAVTHIDKLKGLGRRMPITALGMVISLFALAGVPPLSGFWSKLMLFGSALDASTALWWAPWLAIAGVLNSALSLAYYGWITRKMYFEGETEKRVSEPKSIVAVMIFSIIFLVGFGVYPEPLLKFVEFATPVVSLGLMP +>886738.Nlim_1181 +MLEITSTPLVIIAILGTVGVLLPIISIARKEKGSNSFYAIIAFAALIVSIGYVAYQFINDNVLPSALFSEDVLVDDAFGGFFAIAMLIVAIFTTIGSFNYMRKKNYPAVYYSLILLSTIGMVLVAYSTDLVMLFVAWELMSIPTYVLVGFMKKNPSSNEAALKYFLFGALSSAIIVYGISLSYGLTGSTNIGEVIQGYATLDASLLPLALLSVGMFIAGFGFKMGLVPFHQWLPDTYEGAPPTITTLLAAGTKKAGFAATIRIVVLGMVVLNLDWTLALGVIAVMTMTIGNIAAIMQKNLARMLAYSSIAHAGYILIGLAVSPYSSLGLQGSLYQILNHAVMKGMAFIAVTGIVTTLAVTHIDKLKGLGRRMPITAFGLVISLFALAGVPPLAGFWSKLMLFGGALDAGSTIWWAPWLAIAGVLNSALSLAYYGWITRKMYFEGETEKRVREPKSIIAIMVFSIIFLVGFGVYPDPIIKFVEFAAPTFSLGIMP
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2G.fa Mon Nov 04 16:38:44 2019 -0500 @@ -0,0 +1,6 @@ +>1001994.MY1_1852 +MISLNRFVIILIVGIFVSGILTISFISNSYVDANSTKKINFTKTIISSQDPGQGHENHQLSLILSPNEGTLYDGSMTFTSNEPVDVVVLHEITGNDVKGQPTWTIDGKTIYAMSLIDLKSKSDSFEFTGAALALHSSNSKEFTATVSVDGWIRGQPTEVIMQKIQVEKDPSLMLSRANVEATMPMHEGLYKGNSIFYIITDTSREEYSKKITEKQDWKVQTSTLIEKMPEEILQKIFIFNNGVRGQGIYGHQKEIFSSTPVQESKYSALNSVIEVSWKKGQNAKVLESFEDVIDAEKNGRIEFTKTGVVINSPQIIWPNGQMLVRNDTKITDDLTFSGGQITKINKDEMTVTFVAHRMWGPDGKTIYAIVTDATPSNPSEIMGIPFSPVYDNLITNSSAADLFQFQNGIKGSGSLGYQPGITSVNSDQENYSPIWRIYNVEWHNPKDAKILQTMSDIDSFKAKDLISVSLARPMNSHHIINGPLIDPFQ +>436308.Nmar_1753 +MLRKLIAILIIGIFATSIITASSLSDQFADAGSRKKIHFTQTFTSSQDPGQGHENHQLSLILSPNQGTIYDGSMTFTSSEPVQIVVLHEINSDDAKGQPTWSIDGNTVYGLSLIDLQEKSGSFEFTGAALGLHSPNSKQFTSTVSVDGWIRGQPTEVIMQKIELEKEEPMSLLSRANVPATIPIHEGIYGGEKVLYIITDGSDEEYARELSEKQEWNVELAPVLADVPEDALQKIFVFKNGVKGEGLYGFQNEIFSSTPQQESEYSALSSVIEVTWKTGQKEIVFESANDVIAAEENGRIEFDETGVVLNTPHIVWPGGQMQVRADQEIADDMPYGGGQITEINEEEMTVTFVAHRGWGPDGRTIYYIVTDATPFGPAEMMGVTSSPTSANLIAHSGAVDLFQFKNGIKGTGPLGFQAGIAAASLGDENYSPMWRIYLIEWNDSENAKILETKSDIDSFRADDLITVSITRPTNSDHIVNCPFIDPFQ +>886738.Nlim_1479 +MNRFTIILIVGIFIIGALTVSFVSDNYVNANSTKKINFTKTITSSQDPGQGHENHQLALILSPNQGTLYVGSMTFTSSEPVEIVVLHEINNDDVKGQSTWTIDGKTVYAISLIELKAKSGSLEFTGAALALHSTNSKEFTATVSIDGWIRGQPTEVTMQKIQVQQNPPLELSRANIAASIPMHEGFYDGKSVFYIITDSSQKEYAEMITKKQNWKVEVAPEIKKISENTLQTIFIFKNGVNGDGIYGRQKEVFSSTPSQVQKYSALNSVIEVTWKKGQNASTLESYEDIINAEKNGRIEFSKTGIVINTPQIIWPDGQMLVRNNKEITNNLKFDGGQITEINKDEMTVTFVAHRGWGPDGKTIYYIITDTTPSGPAKIMGIPFSPVSEHLITNSSKSDLYQFKNGIKSSGSLGYQAEIISVMPGDDSYSPIWRVYNIEWNNPENASILETISDITSSKIKDLILVSLARSMNNQYVINGPIIDPFQ
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2H.fa Mon Nov 04 16:38:44 2019 -0500 @@ -0,0 +1,4 @@ +>436308.Nmar_0483 +MTALATKSENIEKQIISDPSDTIDSEKYKMIAENVTISYDGIQAVKNITMKFKEKSVTALIGPSGCGKTTFLRCLNRMHDMTKNAKVDGKVMIDNIDLYDQSIDPIYHRRKVGMVFQKPNPFPTMSIYDNVTAGLKLNGVKDKRILDEIVEDSLKMAYLWDEVKGDLKKSAIELSGGQQQRLCIARALAIQPEVLLMDEPASALDPIATQKIEETITELKKEYTIIIVTHNMQQAVRVSDYTGFMYLGDLVEFRETKKLFTDPKNELTAKYVQGQFG +>886738.Nlim_0922 +MTAMTTKPTHAETSFTSKSQPTLDSDKYKMIAENITVSYGGVDAVKNVTMKFKEKSVTALIGPSGCGKTTFLRCLNRMHDMTKNAKVTGKVMIDNIDLYAKDIDPIYHRRKVGMVFQKPNPFPTMSVYDNVTAGLRLNGVRDKRILDEIVEDSLKMAYLWDEVKNDLKKSAIELSGGQQQRLCIARALAIQPEVLLMDEPASALDPIATQKIEETIIELKKDYTIIIVTHNMQQAIRVSDYTGFMYLGDLIEFRETKKLFTDPKDDLTAKYVQGHFG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2I.fa Mon Nov 04 16:38:44 2019 -0500 @@ -0,0 +1,6 @@ +>1001994.MY1_1452 +MELIEKIILTQIYLSGITGKSYKDNLKTKKGFTENIINSKIDELVKNKLITEDKSALTELGRSSLRVVLAGGVFDIIHPGHIHTLNAAKILGDVLVVVVATDNTAIKMKKRQPLHSKEQRQELVNSLSMVDLCLIGQEDDIFKTVNLVKPQIIALGYDQVHQEKFIIEGCKKINLDAKVARLQSPIPESSSSKIQKEYGESIHGI +>436308.Nmar_1298 +MLEQSQRTILSTIYVCQIEGTNPIEKIKRKTAFSDDQINSKIEELIKKQLVNEDKKTLTESGRDSLKVVLAGGVFDIIHPGHIHTLNAAKELGDALVVVVATDNTAVKMKKRRPLHSQEQRQELVNSLSMVDLCLIGQEDDIFKTVNNVRPQIIALGYDQAHQEKFITEGCKKINLDAKVARLQSPIPDSSSSKIEKEYGESIHGI +>886738.Nlim_1033 +MELIKKSILTELYLSGITGKSHIDNLTKKGFTQKLIDLEIDELIKNKLVKEDRAILTELGRSSLRVVLAGGVFDIIHPGHIYTLNAAKSLGDVLIVVVATDNTALKMKKRQPLHSKEQRQELVNSLIMVDLCLIGQEDDIFKTVNLVKPQIIALGYDQVHQEKFIIDGCKKIQLDAKVARLQSPIPESSSSKIQKEYGESIHGI
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2J.fa Mon Nov 04 16:38:44 2019 -0500 @@ -0,0 +1,6 @@ +>1001994.MY1_1646 +MSCSGEIVDEEKLIQIKPGILQQLKKAKYGVADHSTVELCHWTKKSFKHEGSCYKHKFYGISTHRCMEFSPAGMHCENRCVYCWRPMEFYDSLKMEPEKVSEPKEILTKLMEERKKLIMGYYGDSRNDKQRLDESLLPSHYAISLSGEPTMYPKLPELIKYLKSLEATKSIFLVTNGQEPDMIQRLQDKDALPTQLYLSTNAADYDSFLKINRPKYDDSWQRWNRTLEMLKHLDTRTVLRITLIRNYNDQKEMIPAFAAMLKQASPHFIEIKSYMHIGRSTNRLEHSNMLEMEEVRRFSEEVAKHSEIFSIMDESLVSRIVILQNNQRSINRWISAYSNTN +>436308.Nmar_1529 +MSCSGEVVEEEQLIQIKPAISEQLKKAKYGVSDHSTVELCHWTKKSFKHEGSCYKHKFYGISTHRCMEFSPAGMHCENRCVYCWRPMEFYDSLEMKPEQVAEPEEILTKLMAERKKLINGYYGDSRNDKQRLDESLLPSHYAISLSGEPTMYPKLPELIKYLNSLEATKSIFLVTNGQEPDMIQKLQDEDALPTQLYLSTNAADYESFLKINKPKYDDSWERWNRTLGMLKHLNTRTVLRITLIRNYNDQKSMIPAFAKMFKEASPHFIEIKSYMHIGRSTNRLEHSNMLEMEEVKRFSEQIAKQSQIFSVMDESFVSRISILQNNERFIDRWIPAYVNTN +>886738.Nlim_1932 +MSCSGEIVDEERLIQIKPGISQQLKKAKYGVADHSTVELCHWTKKSFKHEGSCYKHKFYGISTHRCMEFSPAGMHCENRCVYCWRPMEFYDSLKMDPEKVAEPKEILTKLMAERKKLINGYYGDSRNDKQRLDESLLPSHYAISLSGEPTMYPKLPELIKYLKSLEETKSIFLVTNGQEPDMIQRLQDEDALPTQLYLSTNAADYESFLKINKPKYDDSWQRWNRTLEMLKKLDTRTVLRITLIRNYNDQEEMIPAFAAMLKQASPHFIEIKSYMHIGRSTNRLEHSNMLEMEEVRKFSESVAEHSQIFSVMDESLVSRIVILQNNQRTIDRWIPAYANTN
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2K.fa Mon Nov 04 16:38:44 2019 -0500 @@ -0,0 +1,4 @@ +>436308.Nmar_0061 +MPNFDKTWARQETQSVTGKLREAVKPQGALKPRIQTAVNKLQVQISKMDSMLGKLHERDAQLFQRVVTAMQQHDTSTSRVLSNELAEIRKVTKMLGNARMSLEQVQLRLTTIHDLGDAMVAIGPAMSTMKGLKSSLGRFMPEADSELNTMTQTLNGLMMDSLAGDSFNMESDVSSEETEKILQEASAVAEQQIGDKFPSVPSSTGLSSGTSTSTFE +>886738.Nlim_1611 +MPNFDKTWARQETPGVTEKLRETIKPQGALKPRIQTAVNKLQVQISKMDSMLGKLHERDAQLFQRVVTAMQQHDTSTSRVLSNELAEIRKVTKMLGNARMSLEQVQLRLTTIHDLGDAMVAIGPAMSTMKGLKSSLGRFMPEADSELNSMTQTLNGLMMDSLAGDSFSMETGASSEETERILQEASAVAEQQIGDKFPSVPTSTGLSQSSQSTY
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2M.fa Mon Nov 04 16:38:44 2019 -0500 @@ -0,0 +1,6 @@ +>1001994.MY1_0188 +MLSTGMWVEKYRPSKLSEIVNQKEIIGSLEALIKDPTDMPHLMFSGSAGVGKTTTALCISRQILGEYAKDYTLELNASDERGIGMVREKVKKFSRFAGMVDVPFKIIILDEADEMTSDAQTALRRIIEDTAKYCRFILIANNISKIIDPIQSRCATFKFTSIPEEDVINHLENIAKKEKVKSDKKGLKAIYDYSEGDLRHAINLMQATASIGEISEENVKSSAGLTKTSDVDIVLKMALSGKIVDAREKMIELTKVYGMSESDFLKYLNSAVFKIKHDNISDILEVIAKYDYRILVGANPEIQLTAMLAELGKLEK +>436308.Nmar_0240 +MAATGMWVEKYRPMKLSEVVNQTEIIGSLEALIKDPTDMPHLLFSGSAGVGKTTTALCISRQILGDYAKDYTLELNASDERGIGMVREKVKKFSRYAGMADVPFKIIILDEADEMTSDAQTALRRIIEDTAKICRFILIANNISKIIDPIQSRCATFKFTAVPEEDVIKRLEEIAKKEKVKADKKGLKAIYDYSEGDLRHAINLMQATASLGSISEDNVKASAGLTKTTDVDEVLKIALSGKVPEAREKMIELIKVYGMSESDFLKYLNSAVFKSKHDKLSDILEIIAKYDYRILVGSNSEIQLSAMLAELAKVEN +>886738.Nlim_1226 +MLSTGMWVEKYRPTKLSEIVNQTEIIGSLEALIKDPTDMPHLMFSGSAGVGKTTTALCIARQILGEYAKDYTLELNASDERGIGMVREKVKKFSRFAGMAEVPFKIIILDEADEMTADAQTALRRIIEDTAKYCRFILIANNISKIIDPIQSRCATFKFTSIPQEDVINHLESISKKEKIKSDKKGLKAIYDYSEGDLRHAINLLQATASLGEVTEENVKASAGLTKTSDVDEVLKMALAGKVLEAREKMIELIKVYGMSESDFLKYINSAVFKTKHEKLSDILQVIAKYDFRILSGANSEIQLSALLAELSTLK
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2N.fa Mon Nov 04 16:38:44 2019 -0500 @@ -0,0 +1,6 @@ +>1001994.MY1_0435 +MNKVNLNIKQRKIISDKIFKIGVTTAGAYVLIVVVLIAFQLVSESYPVWEEEGLSFITKTDWNAVEGRESFGALPYILGTLTTSAIAMMIGVPLSIGIAMFISDAPPKIGAPLGFLVELLAAVPSVIYGLWGLYVFRIYFRDWFETPLHDAFGDNIWLFSGNPYGLDILTASVILAIMIIPTVSAVSREIMKAVPQQQKEAAYMLGATKWEMFKLAIFPYSKTGLIGASILGLGRAVGETMAVTMLIGNATGLGAIPSSLFGPSQTMSSIIANEFVEASPASIHMPALIGIGLILLLIAIVINVVAHLLVTRMLKIKEGAINN +>436308.Nmar_0481 +MGRPKLNPPKVGRRPISDKIFKVGATVAGVYVLVVIVLLAFQLISESAPIWDEYGLSFIVKSEWNAIDDRQDFGVLPYIFGTLVTSALAMVIGVPLSIGIAMFISDAPSKIGGPLGFLVELLAAVPSVIYGLWGLFVFRVYFVDWVEKPLHNTFGDSIWLFSGTPFGLDILTASVILAIMIIPTVSAVSREVMKAVPQQQKEAAYMLGATKWEMFKLAVFPYSKTGLIGASILGLGRAVGETMAVTMLIGNATGPNAFADSLFDPSQTMSSIIANEFNEASLGTLHLPALIGVAVVLLLIAIAINVVAHILVTRMLKVKEGAINN +>886738.Nlim_0924 +MISDKVFKIGATVAGTYVLVVVVLIAFQLISESYPIWEKEGLSFITSTDWNAVEGRESFGALPYIIGTLTTSAIAMAIGVPLSIGIAMFISDAPAKIGGPLGFLVELLAAVPSVIYGLWGLFVFRIYFRDWIETPLHNAFGDNIWLFSGNPYGLDIITASVILAIMIIPTVSAVSREIMKAVPQQQKEAAYMLGATKWEMFKLAVFPYSKTGLIGASILGLGRAVGETMAVTMLIGNATGIGAIPSSLFGPSQTMSSIIANEFVEASPASVHMPALIGIGLILLLIAIVINVIAHLLVTKMLKIKEGAINN
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2P.fa Mon Nov 04 16:38:44 2019 -0500 @@ -0,0 +1,4 @@ +>1001994.MY1_1290 +MTPSELNEEKLVEIPAEHTFSELYDDVKYDPDIRPGRELQERDSLHEVLLKRRLRQKLVELNPGNPDIVYDIAVQKIELISEPTLIETNRAFHQMLLSGIKVAYQEDNQTKYSVMKLIDFDNPEKNDFIAVRQFLLVQHEERRLDHVIFVNGIPLIILEYKSMADKNATIVDAFHQLGKTKYQRDIPIIFRYNAFLVISDRLNAKYGTINAPFERFSDWNDLTQPDKKVANRLEILQKLLLNKTTILDVIKNFIEYESDGKNLIKKICQQHQYHAVNTIVKKTSDVYSQQGENRIGVVWHTTGSGKSLTMIYYVNSLSQIEKFENPTFIIITDRRDLDEQLNHFFRIAGFPYPKPETAILEADSILDLREKLQVPSGKIIFTTIQKFQTTEEEREGKVKYPKISDRRNIIIIADEAHRSQYKKMAQNLQTALPNALRIGFTGTPIELEDRSTTQVFGDIISSYKIPEAVRDGATVQISCETHPVTLLLLNKFIGKDFEEITQGLDEENVTTLARRGAEFTKLVEDPDRIKTIANDIVSHFNKKQKIFKGKAMIATSTKLAAARFADYISSLKVAPECTCIVSGATSQKPESTPEKRTREAIIQKHYKDKLTIENILTRFKDENDPLSLLIVCDMYLTGFDAPLIHTMYIDKPLRDHNLIQAISRVNRVWKNKPGGAIIDYIGIADDLDRAFSAYAQDDVKGAMIPTAEIIEIMKKKHSDLINFFDPKISNRQGLDESQELQLIYDAIDEIVYDDIVKREFIKIVTELTKAYAVCTPHPSCLDVEDDLRFFQKLRKILLKATSNVPVDLTEMESAISDLVEQGIGADQVVKGFKISFDPKKQDISKEYLNDIKKLKQKNLKAELAYKLLDDAIQAKFKRNLVKRKSFQDRIEEALSKYHARFWDNDDTIQKLEEVGKEITNESSREQELGLNDEEIAFYDVVSLGKDYVKSDAVIKQISLDLTKYLKGNIRIDWINQENIKAEIRMGVRKILLRADFPTDKIEEIVPKIMDQAETNYG +>436308.Nmar_0608 +MNFRIEDNEEGRQVELPALELITALGYTYIPNYELNIPKERPDHRQVLLYPRLRAAIKRLNDFDDDGIEQAIAQIHEDNFPIGMPMIDANEKIRIKLTGRAGENAIAQPITIKQYGKKGIEYPTVKFFDFDPKKIGTKEDKNEYLVTNQFKHLGNRTEIECDIVIFVNGIPLVLIECKKPTTIDLMKTVWKENLEKYQRDGSHSLGHEKLFFFNHVIMATSAIQARYGTLKALPNKYAKWTSLTNITTKELEKLVGRKPTPQDIMLAGMIKKETLLDMLKNFVLYEIEEHKKIKKVAKHQQYRVVTKSVDRISHHKKVEDKGGVIWHTQGSGKSLSMVWFATQLYYKFSRPTIMVITDRRQLNKQIFDTFRNCGFPEPEKPRNRSQLAKTLQYSKGKTIMVNLQKFDKPEKFVETKEKIYVLVDEAHRSQYKWTAGYMRKAMPNAVFFAFTGTPLDRENKNTYRRFGPLIDKYSFTESKEDGATVKVEHMGLLPEIEIEGGNSLNNIFDNLFGHLPKAQQAEIRRKYATKKKIASSPARIRKICEKIVDHYTKKILPNGYKAMIVAPTRAAAVTYKRELEDLTKLPARIIMDSKKDEVGPDEFSWADYYLPQNEALKKAEEFTNPDDPTKFLIVVDMLLVGYDAPIVQVMYLDRPLREHALLQAIARVNRIYDEHKDRGFIIDFWGVTRDLQNALKMFEEQDVQGALDNVDDDLLELDVRHKDFMEKIQGIDSKDHNEIAKRFEDEDEQEEFEYAFKRFAKALEAVLPDKEAVPYEKDLKKGYEIRGKIRAWFYGDRADLSEYGKKVQKIIDKHIRAIGISEISGSKEITYDNFLGFIAKFKGDNRAKAALIKKRATLVIREMSPDNPAFYQKLKERLEKLIQDEKERRVDDAQYFEGIRDIFEEALSGPEKLQKQTGIKDRFQLAIYMLLEEKHSDLKQNKKYSEEIFKKVKKAASVKDWRDKEPQENEIELAVIDTLDKKIFDEKTRDKLASEVYKMAVNNNEW
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2Q.fa Mon Nov 04 16:38:44 2019 -0500 @@ -0,0 +1,6 @@ +>1001994.MY1_1750 +MDRKILGISGGIAVIIAIVAVMLLTPNLESTPIQKHNEKIGLVINAPHSAISLQDLNQIYAEASSTGIGRSNVYMFWNIVEPVRGEYDWKQSDVLMSFNKNNNLKVTLFFSVINGETLGPFPNWIGKPSLNAIGEDRLVNVLDAILSRYDIIDTVVIAGETESQFRYHEQNIPVYKELFNGVYAKLKEKHPDVQIGNGFALHNVLNKNLEHIVSDLAIGDFVAFSYFPVDTLNDIVKTPEEAKADLQKTFEIIPDKKIGLFEVSWSTSDFVGGNETSQQIFLEKSFEFYTENESKIEFFTWYRQYDRPDGTCVIDKPEIANQTLTVGGGSGLGSSEYIMERLSHYICNSGLLDVDGTPKSSWNEFKNQIELIN +>436308.Nmar_1626 +MDKKILGVGIGVAVVIAIIAGVLSIPSDSNPEVTPVKTNEKIGLVINSPNQSVTLQELDEIYSTASESGIGRSNVYLFWNLIEPEHREYNWQYSDALMSFNQKNDLKVTLYFSIINGETLGPFPDWIGKPPIQSLNEDRVVSVLDAILSRYHIVDTVILAGETESQFRYYEQNIPPYKELFVGVYDKIKEKHPDVKIGNAFALHQVLNKDLQNIVTDLDVGDFVAFSYSPVDTVGDMVKTPQQAKEDLEQIIDLAGDRNAAIFEISWSTSDFVGGSEESQTEFLEKSFEFYAENESELEFFTWYRQNDKPEGTCAFEVQEVGEDKLTVGGSGFGSSEHVIERLDHYVCNAGLFDENGNPKSGWNEFKNQIQMLN +>886738.Nlim_1388 +MDKKILSIGIGIAIVIALVLVVIGFQSAEIITNQKQDEKIGLVINTPNPSISLKELHKIYADASSTGIGRSNVYIFWNVVEPVKGEFDWTQSDVLMSYNKNNDLKVTLYFSVINGETLGPFPNWIGKPSLNAIGEDRVVSVLDAILSRYDIIDTVVIAGETESQFRYYEQNIPVYKELFTGVYDKIKEKHPTVKIGNAFALHNVLNKNLEYIVTDLSLGDFVAFSYSPVDTLNEIVKTPQEAKEDLQKIFEIVPDKKIGLFEISWSTSDFVGGNSTSQQEFLEKSFEFYKENKSKIEFFTWYRQYDKPDGTCVIEKPEIGNKTLSVGGGSGLGSSEYVIERLSHYVCSVGLLDADGTPKPSWNEFKNQIELINQ
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2R.fa Mon Nov 04 16:38:44 2019 -0500 @@ -0,0 +1,4 @@ +>1001994.MY1_0222 +MWSEKYRPQNISDMIGNEESRSSIIEWFTKWKKGTKPLLLVGPPGIGKTTIAYLTAKQFQYDMVGLNASDVRSKSRINEILSPVLGNVSILGLPMIFIDEVDGIHGRGDYGGAEALIEILKEPTIPIILAANSDTSDKMKSIKKVVKTISFKPIPPRLLKIYLENILKKENVTLSPGSIIKVIDRSRGDVRSMINLTQSLVTGFNPQTEKSFESINVEDGINAFFKANSFDEARGVLYSMQIDPRLKIDAFYSSIVTSNLDNQTLAKLLEIISEADILYGKIMKTQNWRLLRYLNEILIRLYLNDERIRYSQYNLSWPLLNRIRWDGKKIKSLSSVMAKTLHLSSSAFVTICLPYILFCIKNKKLSLDLEETFGDVIEKEIELIK +>436308.Nmar_0270 +MWSEKYRPQIISDMVGNEESRAAIMEWFAKWKKGTKPLLLAGPPGIGKTTMAFLVAKQFGYDMIGLNASDVRSKSRINEILTPVLGNVSVLGTPMIFVDEVDGIHGRGDYGGVAALVDILKEPTVPIILAANDDTSDKMKNIKKVVKTISFKKIPPRLLRVYLENILKKESAKLSPGSLIKVIDKSRGDIRSMINLTQSMVTGFNPQTETTFENIDVEDGVNAFFKSKSVDEARGVLYSMQIDPREKINAFYSSIVMSSLDPETLAKYLEIISEADMLYGKIVRTQNWRLLRYLNDILIKLYHDDDRVRYAQYNLSWPLLNRIRWDGSKIKSLSSVMAKKLHLSSSAFVTFGLPFVLFCIKNNALELELEETFGDIIEKEIELIQ
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2S.fa Mon Nov 04 16:38:44 2019 -0500 @@ -0,0 +1,4 @@ +>1001994.MY1_0691 +MSFKSLIDEIENNLHKILEDMSIYDISFTVEPAKPGFGDASSNISFLLAKSLKKSPKEIANLMSEKYRQSQNILVLKVEPHQTGYLNFFADWEKLNQLILSESNLNEFGFIDLGHNSEIVVEHTSVNPNKALHIGHIRNIVLGDTVARILKKSNYKVNVLNYVDDSGLQVADIIVGFKHLGFAQQSPTGKKFDHYCGDDVYVKTTEKYEQDPNFEEIRKNTLKELEDGASETAKFADTITRRVLENQLETCWNLGVYYDCLNFESQIIRSGLWSKIFEKLKEMNLVEFENDGKNAGCWIIRGENNEEDKVIVRSNGTATYIAKDIPYAAWKLGLIEDPFSYKKYEKTQPGNKILWQTTLTATNEPKQNFTGNKVITVIDSRQARLQKIITGLMSKFKSTNDAYVHLGYESVTLSSDTAQTLGLDTDGKQAQMSGRKGLYVDADSVYDLLKNKTIEETKKRHPEMSDSEIEQIAHYVSVGTLRYEMIKQDLDKMITFDLTKSLSLEGDTAPYIQYTHARASRIIEKSARNPSIDVDFSLLNDASELSLIKIIGLFEIYVLDAAKNLSPKVIARYCHNLAVAFNSFYEHVKVLELGDEKLENSRLCLVNSFKITLEKALELLGITAPEKM +>436308.Nmar_0686 +MTFKSILDEIENNLNKILDDLSISDVKFSVEPAKPGFGDVSSNVSFLLAKQLKKSPKEISEMLSEKYSQCVSTLVSKSESHPSGYLNFYADWPKLNQLILSESNLPEFGDVDIGKNSTIVVEHTSVNPNKALHIGHIRNIIIGDTISRILQKANYKVNVLNYVDDSGLQVADIIVGFKHFGYPIEPPQGKKFDHYCGDDVYVKTTEKYEQDSSLEEIRKNVLKELEDGTSETAQFADKITRRVLSNQLETCWNLAVSYDCLNFESQIIRSGLWDGIFEKLKEMNLVEFENDGKNAGCWVIRGEGKEEDKVIVRSNGTATYIAKDIPYAAWKLGLLDDPFHYEKYEKEQPNSRVLWQTILNDGASESQNFSGDKVITVIDSRQARLQKIITSLMGKFKSIPDAYVHLGYESVTLSSDTAKILGLETDGKQAQMSGRKGLYVNADSVYDLLKEKTTEETKKRHPEMDDSEIEKISHSVSVATLRYEMIKQDLDKIIAFDLTKSLSLEGDTAPYIQYTHARASRILEKSGRTPSIDVDFSLLKEQSEIDLVKMIGLFNLQVRDAANNLSPKVISRYCHDLAVTFNSFYEKSKVLDLGDEKLENSRLCLVNSFKITIEKALNLLGISAPDKM
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2T.fa Mon Nov 04 16:38:44 2019 -0500 @@ -0,0 +1,6 @@ +>1001994.MY1_0879 +MSTEQIEKFQEVVDIPAGVKVTLKKNMMHFEGPLGKTHKNFRNIPVNIEIKEGKVILKSQGYRKRDYSILHTARSVIRNLCEGLVVGYTIKMKIAFAHFPITVKVQDRTVLIENFQGERSSRITKIIGNTKVVPKGEDVILTGEVWNHITQTAANIELRSKVKDKDHRVFLDGVYVYEKKKGIEK +>436308.Nmar_0794 +MSTSQLEKMQDQVEIPEGVTVTQNKNMLLFEGPLGKTHKNFRNIPVKIEIADGKVNLKTIGERKRDYAILHTARSIIRNICEGLVEGYTIKMKVVFAHFPITVKVEGKKILIENFQGERAPRSTHIMGNTKVIPKGEDVLLTGEVWTDITQTAANIELTTKVKNKDHRVFLDGIYVYEKKKGIEK +>886738.Nlim_0395 +MSTEQIEKFQEVVEIPKGVTVTLKKHMLHFQGPLGKTHKNFRNIPVNIEVKDGKVILKSQGYRKRDYSILHTARSIIRNICEGLITGYTIKMKIVFAHFPITVKVQDKTVLIENFQGERSARVTRIIGNTKVVPKGEDVILTGEVWNDITQTAANIELRSKVKDKDHRVFLDGVYSYEKKKGIDK
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2U.fa Mon Nov 04 16:38:44 2019 -0500 @@ -0,0 +1,6 @@ +>1001994.MY1_1727 +MVIEVVRIGQRLVRDDRVTTHVALVARAFGCSKIFMTEVNPEIKDTLEKINNTWGGDFVVEFIDNWKSIVKMKKKDSKIVHLTMYGESINEVDMQLRKEENLLIVVGAEKVPREIYELADYNVGIGNQPHSEISALAIILDRIQKGEQFKNSFPGAKRKIIPTRNGKNVLVRGTRD +>436308.Nmar_1606 +MVIEVVRIGQRLVRDDRVTTHVALVSRAFGAERIFMTEINPEIKDTLGKINDTWGGNFEIEFIDSWKPIVKKKKEEGFKIVHLSMYGEKINDAQEEIRKEENLLIVVGAEKVPREIYELADFNVGVGSQPHSEISALAILLDRIQGGQQFEKEFPNAKRKIIPTKTGKNVQVKETRD +>886738.Nlim_1365 +MVLEVVRIGQRLVRDDRVTTHVALVARAFGCTKIFMTEVNPEIKDTVEKINKTWGGDFVVEFIDNWKSIVKKKKEEYKIVHLTMYGESIDDVDEQLRKEKNLLIVVGAEKVPREIYELADYNISIGNQPHSEISALAITLDRIQKGKQFKNSFSGAKRKIIPTKKGKNVFVSGTRD
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2V.fa Mon Nov 04 16:38:44 2019 -0500 @@ -0,0 +1,6 @@ +>1001994.MY1_1241 +MKIRIFDTTLRDGEQTIGVSLSPDQKLAIAKKLDELGVDAIEAGFPVISAGEFKAVKMIAAAGLSCEIAGLTRTIKNDIDAAVDAGLNYIHTFIATSDIHLQYKLKMTREQALEKAIEAVEYGKSRGLQVEFSAEDATRTDREFLKKVFGDVAKAGADRVNIPDTVGYSTPEYMAVLTKDTVEVTKLPVSVHCHNDFGLAVANSLAGIHAGASCAHVTINGIGERAGNASLEEFSMALKCLPFEKKYETNIKSELIYDTSRFISKTVGIIVQPNKAIVGTNAFGHESGIHTHGVLSNPLTYEPISPELVGRKRWLQVGKHAGIHGMNAMLAEYGVKPTEEQSKQILDKVKTLGDAGKQITDVELLSIASDVLGEKELKRIVQLTGFSVSTGIGTMPYAFVKLNIDGQDHIGTDYGVGPVDAALNAIQKITGKISEIRIKDYGLASISGGSSALCEVTVKVEDAFGNKVSAKSVGEDIVTTSVKAVIDAINRIMLKKMLQEKQVR +>436308.Nmar_1070 +MTNVRIFDTTLRDGEQTLGVSLSPDQKLAIAKKLDELGVDAIEAGFPVISEGELQAVKMITAAGLSSEICGLTRTIKKDIDAAIDAGLNYVHTFIATSDIHLEHKLQMTREQALEKAIEAVEYGKSHGLQVEFSAEDASRTDREFLKKVFSEVAKAGADRVNIPDTVGYSTPEYMAQITKDTIEATNLPVSVHCHNDFGLAVANALAGIHVGAACAHVTINGIGERAGNASLEELSMALKCLPYEQKYETNIKSELIYDVSRFISKTVGIIVQPNKAIVGANAFGHESGIHTHGVLNNPLTYEPISPELVGRKRWLKVGKHAGVHGMNAMLEEYGVKPTEDQAKQILEKVKVLGDQGKQITDVELLSMASEVLGKKDLKRIVQLTGFSVSTGIGTMPYAFVKLNVDGQDHIGTDYGVGPVDAALNAIQKITGKISEIRIKDYGLASISGGSGALCEVTVKVEDPLGNKVSAKSVGEDIVTTSVKAVIDAINRIMLKKMLQEKQVS +>886738.Nlim_0759 +MKVRIFDTTLRDGEQTIGVSLSPDQKLAIAKKLDELGVDAIEAGFPVISSGEFKAVKMIASEGLSCEIAGLTRTIKNDVDAAVNAGLNYIHTFIATSDIHLQYKLKMTREQALEKAIEAVEYGKSRGLQVEFSAEDATRTDREFLKKVFGDVAKAGADRVNIPDTVGYSTPEYMAELTRDTVEATHLPVSVHCHNDFGLAVANSLAGIHAGASCAHVTINGIGERAGNASLEEFSMALKCLPFEQKYETNIKSELIYETSRFISKTVGIIVQPNKAIVGTNAFGHESGIHTHGVLSNPLTYEPISPELVGRKRWLQVGKHAGIHGMNAMLAEYGVKPTEEQSKQILDKVKTLGDAGKQITDVELLSIASDVLGEKELKRIVQLTGFSVSTGIGTMPYAFVKLNIDGQDHIGTDYGVGPVDAALNAIQKITGKISEIRIKDYGLASISGGSSALCEVTVKVEDALGNKVSAKSVGEDIVTTSVKAVIDAINRIMLKKMLQEKQVR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2W.fa Mon Nov 04 16:38:44 2019 -0500 @@ -0,0 +1,6 @@ +>1001994.MY1_1343 +MQNQKSEWATNESPRIMSYTLANFRQLPQIQKLGEEKQFEMEVVGNVLPFKTNNYVVEQLIDWNNIPDDPMFVLTFPQRGMLIPEHYAKMEAALKKGDKKEIQNTANEIRLQLNPHPAGQMELNVPTLKDGTKLYGMQHKYKETCLFFPSQSQTCHAYCSFCFRWPQFVGMDELKFAMKEGEQLVQYLQEHPEISDVLFTGGDPMIMKARIFSTYINPLLEANLPNLRTIRIGTKALSYWPYKFLTDDDAEEMLDIFKRVVDKGIHLALMGHFNHTVELKTDAVKEAIKKVRATGAQIRTQSPILRHINDDSEMWAEMWKTQVQLGCIPYYMFVVRDTGAQHYFGIPLIEAQRIFRDAYKKVTGLARTVRGPSMSATPGKVQILGIAEYGGEKLMVLRFLQGRNPDWVQIPFLAKYDEKAIWLDDLKPATGDKFFFEDELNEKMKVIKNQDYPES +>436308.Nmar_1772 +MTYQESVWDDSPSLKSYTLSNFRDLPQIQNISEEKQFEMEVVGNVLPFKANNYVVEQLINWNDIPNDPMYVLTFPQRGMLKPEHYAKMENTLKNTSDKKEIANVANEIRLQLNPHPAGQMELNVPTLKDGTKLYGMQHKYKETCLFFPSQSQTCHAYCSFCFRWPQFVGMDEMKFAMQEGEQLVQYVSEHPEISDVLFTGGDPMIMKAKMFSKYVDALIEAKLPNLKTIRIGTKALSYWPYKFLTDSDSQEMLQVFQKITDSGLHLAFMAHFNHLNELSTNAVKSAIKEVRKTGAQIRTQSPLLAHINDDAEMWANMWTKQVQLGCIPYYMFVVRDTGAQHYFGVPLVKAYEIFSQAYSTVSGLGRTVRGPSMSATPGKVQVVGTTQINGEKLLILRFLQGRNPNWIKEPFFAKYDENAIWLDDLKPAFGDKFFFEDELDAIKASKTS +>886738.Nlim_0892 +MQRQDSAWGVKESPRLKSYTLANFRELPQIQKMGAKKQFEMEVVGNVLPFKTNNYVIEQLIDWNNIPNDPMFVLTFPQRGMLIPEHYSKMESALKKGDKKEIQNTANEIRLQLNPHPAGQMELNVPTLKDGTKLYGMQHKYKETCLFFPSQSQTCHAYCSFCFRWPQFVGMDELKFAMREGEQLVQYLREHPEISDVLFTGGDPMIMKAKIFSTYINPLLEANLPNLRTIRIGTKALSYWPYKFLTEDDAEEMLDIFKRVVDKGIHLAVMGHFNHLVELKTDAVKEAIKKIRATGAQIRTQSPLLRHINDDADMWAEMWKVQVQLGCIPYYMFVVRDTGAQHYFGISLIDAQRIFRDAYKKVTGLARTVRGPSMSATPGKVQILGITEVNDEKFMVLRFLQGRNPDWVQIPFLAKYDEKAIWLDDLKPATGDKFFFENELKEMMMTIKNEDYPES
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2X.fa Mon Nov 04 16:38:44 2019 -0500 @@ -0,0 +1,6 @@ +>1001994.MY1_1050 +MKFLIIDNYDSFVYNIAQYLGELGVDCDVIRNDKITLEKIKQNNYDAVIISPGPGTPTDRKYFGICSDVIKDMGSTTPILGVCLGHQGIIHAFGGKVTNAGCVRHGKTSPVDHTNSDLFKDVKNPFRATRYHSLVGDKTIIPDVLEVTAVAADDGEVMAVRHKEYLIEGVQFHPESIMTEDGKKILANFIKQVKDRK +>436308.Nmar_0912 +MKFLIIDNYDSFVYNIAQYLGELGVDCDVIRNDKITLNEIQEKKYDAIIISPGPGTPEDKKYFGVCSEVIKDMGSSTPILGVCLGHQGIIDAFGGKVTNAGCVRHGKTSPVNHEDSKLFKDVKNPFRATRYHSLVGDKTIIPEVLKVTATASDDGEVMAIEHKDYLIQGVQFHPESIMTEDGKKILSNFIQQVKEKQK +>886738.Nlim_0576 +MKFLIIDNYDSFVYNIAQYLGELGVDSDVIRNDKITVEQIKQNKYDAIIISPGPGTPSDRKYFGVCGDVIKDIGPITPILGVCLGHQGIIEAFGGKVTNARCVRHGKTSPVDHTNSELFKDVKNPFRATRYHSLVGDKTIIPDALEITAIAADDGEVMAVRHKKYLIEGVQFHPESIMTEDGKKILANFIKQVKSKK
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2Y.fa Mon Nov 04 16:38:44 2019 -0500 @@ -0,0 +1,6 @@ +>1001994.MY1_1793 +MMGDRDYRSIIKNAVDSIGRELEIEIDAKDIKTIHLKEVVQCLRRSYYDRIEPKEVERRGFNDLLSGLLRKLQYGSDPKEFSIEDIKLRGHADMIADNSIILFRPTNASLESPLANDLLYLNACMWIYDKTDGVIIYITGDREEIMFSLTRDKKMFEEIIRRVRVLNDLLKEQKTPILEPSSDCMECQYYQRCFITKKNTKQVSLAEMLGLGKD +>436308.Nmar_1701 +MMGDRDFRTTIQNAIKSIGNELEIDIDSKDFETIHLQEVVRCMRRSYYDRVEPLEIERRGFNELLSGLLRKLEYGSNPKDFDINEIKLRGQADMMVDDAILLFRSATEELENPHASDVLYLNACMWIYDKEDGMIVYITGDRKESTFSLTRNKKMFEDTIRRVRVLNNLLKEQKTPILEPSAECTECQYYERCFTKRKNTKQTSLAEMLGLGKQD +>886738.Nlim_1425 +MMGDRDFRSIVKNAVDTIGRELEIQIDAKNIKTIHLKEVVQCLRRSYYDRIDPKEVERRGFNDLLSGLLRKLHYGSDPKEFSIDEIKLRGQADMIADDSIVLFRPSKTVIEAPVANDLLYLNACMWIYDKTDGIIVYITGDREEIMFSLTRDKKMFEEIIRRVRVLNDLLKEQKTPILEPSNDCAECQYYQRCFTTKKNTKQVSLAEMIGLGKD
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/OG_fasta/thaNOG/1CB2Z.fa Mon Nov 04 16:38:44 2019 -0500 @@ -0,0 +1,6 @@ +>1001994.MY1_1440 +MAEKGILAFSGGLDTSVVIKYLQEEYNMDVITVTVDVGQGDDQKKIEAKAKKLGVIKHYNIDARKEFVENFIFPSIKANALYQKKYCLATALARPLIAEKVLEIAKKEKVTSLAHGCSGKGNDQVRFDITLRSGSDLPIIAPIRDKNLDRVTELEFAKKHGIEIDSVAKRFSIDQNLWGRAIEGGVLEDPYNEPPEDAFIWVKTKNLPDKPTYLEIKFEKGIPVSVDGKILEPIKLIEYVNKKAGDAGVGIVDHIEDRVVGIKSREVYETPGALCLIEAHSDLEKMVHTKHENKFKSIIDDEWAYLAYSGLWQDPLKQDLDAFIQASQKPVSGTVKLKLFKGSIRVVGRKSDYSLYNHKIATYGTESTFDQRLAKGFVELWGIQSTEANKLQKKRSTKT +>436308.Nmar_1286 +MTQKGILAFSGGLDTSVVVKYLQDEHDMDVITVTVDVGQGDDNKKIAAKAKKLGVKKHYNIDARKEFVKDYIFPSIKANALYQKKYCLATALARPLIAEKVLEIAKKEKVTSLAHGCSGKGNDQVRFDITLRSGSNLPIIAPIRDKNLDRVTELKFAKKHGIEIDTVAKKFSIDQNLWGRAIEGGVLEDPYNEPPDDAFIWVKTKNLPDKPTYLEIKFEKGIPVGVDGKTMDGQKLIEYINKKAGDAGVGIVDHIEDRVVGIKSREVYETPAATCLIEAHSDLEKMVHTKHENKFKSIIDDEWAYLAYSGLWQDPLKSDLDGFIEASQKPVTGTVKLKLYKGSLRVVGRKSKNSLYSHEIATYGTESTFDQRLAKGFVELWGMQSTEANKLQKKRSTKI +>886738.Nlim_1021 +MTEKGILAFSGGLDTSVVVKYLQEEYDMDVITVTVDVGQGDDQRKIEAKAKKLGVKKHYNIDARKEFVEKFIFPSIKANALYQKKYCLATALARPLIAEKVLEIAKKEKVTSLAHGCSGKGNDQVRFDITLRSGSDLPIIAPIRDKNLDRVTELAFAKKHGIEIDSVAKRFSIDQNLWGRAIEGGVLEDPYSEPPDDAFIWVKTKNLPDKPTYIEIKFEKGIPVAVDGKILEPIKLIEYVNKKAGDAGVGIVDHIEDRVVGIKSREVYETPGALCLIEAHSDLEKMVHTKHENKFKSIIDDEWAYLAYSGLWQDPLKQDLDSFIETSQKPVTGTVKIKLFKGSMRVVGRKSDYSLYSHKIATYGSESTFDQKMAKGFVELWGIQSTEANKLQKKRSTKI
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/eggnog_mapper_db.loc Mon Nov 04 16:38:44 2019 -0500 @@ -0,0 +1,2 @@ +#value name path +4.5 eggNOG_4.5 ${__HERE__}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/eggnog_mapper_hmm_dbs.loc Mon Nov 04 16:38:44 2019 -0500 @@ -0,0 +1,2 @@ +#key db_version value name path +4.5_ENOG411CB2I 4.5 ENOG411CB2I ENOG411CB2I ${__HERE__}/hmmdb_levels/ENOG411CB2I/ENOG411CB2I
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/hmmdb_levels/ENOG411CB2I/ENOG411CB2I Mon Nov 04 16:38:44 2019 -0500 @@ -0,0 +1,637 @@ +HMMER3/f [3.1b1 | May 2013] +NAME ENOG411CB2I +LENG 205 +ALPH amino +RF no +MM no +CONS yes +CS no +MAP yes +DATE Thu Apr 16 06:29:18 2015 +NSEQ 3 +EFFN 0.454102 +CKSUM 2514733105 +STATS LOCAL MSV -10.6020 0.70508 +STATS LOCAL VITERBI -11.4006 0.70508 +STATS LOCAL FORWARD -4.9608 0.70508 +HMM A C D E F G H I K L M N P Q R S T V W Y + m->m m->i m->d i->m i->i d->m d->d + COMPO 2.60488 4.26537 2.86806 2.68812 3.48541 2.84597 3.68190 2.58658 2.57105 2.36046 3.71753 3.12796 3.51194 3.07828 3.00549 2.67857 2.91482 2.52396 5.16454 3.68907 + 2.68619 4.42226 2.77521 2.73125 3.46355 2.40514 3.72496 3.29355 2.67742 2.69356 4.24578 2.90348 2.73741 3.18148 2.89802 2.37888 2.77521 2.98520 4.58478 3.61505 + 0.17176 1.91497 4.55917 0.35031 1.21898 0.00000 * + 1 3.06761 4.52439 4.31327 3.78099 3.05250 4.16350 4.46561 2.17607 3.57234 1.30879 1.91901 4.09154 4.45690 3.86045 3.77957 3.51234 3.30962 2.23580 5.01687 3.83610 2 l - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510 + 2 2.92273 5.02492 2.47434 1.07719 4.36685 3.25185 3.83632 3.81369 2.71243 3.43683 4.41304 2.91439 3.85493 3.05312 3.11711 2.90913 3.22689 3.50145 5.54519 4.26810 3 e - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510 + 3 2.78351 4.58087 3.32911 2.88754 3.40933 3.59103 3.84122 2.81006 2.61259 1.66760 3.45029 3.30455 4.01739 2.39416 2.89621 2.95209 3.03282 2.70991 4.99124 3.67436 4 l - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510 + 4 2.53418 4.23705 3.59368 3.16853 3.49025 3.42404 4.06074 1.74993 3.06664 2.43412 3.49971 3.45907 3.96332 3.42386 3.35145 2.21772 2.86823 2.25074 5.06222 3.78462 5 i - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510 + 5 2.78589 5.09914 2.65704 2.00312 4.42838 3.36184 3.58271 3.84850 1.89046 3.35615 4.18804 2.85104 3.82604 2.22691 2.52714 2.75121 3.01078 3.49213 5.49453 4.17260 6 k - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510 + 6 2.93327 5.02405 3.29627 2.69847 4.43219 3.55593 3.56756 3.79912 1.41937 3.28272 4.16078 3.11215 3.94769 2.71245 1.76026 2.94298 3.11879 3.48852 5.35872 4.16856 7 k - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510 + 7 2.42315 4.21787 3.44026 2.97006 3.62502 3.28653 3.93296 2.25259 2.89478 2.62127 3.57447 3.29089 3.83488 3.23909 3.22031 2.19519 2.23227 2.47087 5.09408 3.85175 8 s - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510 + 8 3.00341 4.43279 4.28393 3.89883 3.35077 4.02713 4.63395 1.12320 3.72623 1.94475 3.29234 4.14920 4.46227 4.07854 3.92692 3.51945 3.30343 1.84653 5.23382 3.96866 9 i - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510 + 9 3.11581 4.58898 4.13200 3.77226 3.12310 3.93638 4.43920 2.32589 3.54034 0.92039 3.15824 4.05113 4.37826 3.91722 3.72201 3.50392 3.41191 2.35386 4.98887 3.70377 10 l - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510 + 10 2.21970 4.14708 3.27216 2.97236 4.05658 2.94753 4.04583 3.36566 2.97325 3.13664 4.01775 3.19548 3.65760 3.31810 3.28297 1.86435 1.69294 2.93575 5.43271 4.18954 11 t - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510 + 11 2.67125 4.89170 2.63995 2.01286 4.19991 3.30620 3.62584 3.60098 2.37369 3.19109 4.03621 2.84971 3.79086 2.33541 2.77812 2.67728 2.37271 3.26758 5.41474 4.07676 12 e - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510 + 12 3.08388 4.45892 4.50779 3.99931 3.20318 4.29602 4.67441 1.39467 3.81924 1.46323 3.07061 4.27722 4.58606 4.09884 4.01845 3.66823 3.33503 1.84767 5.18001 3.96570 13 i - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510 + 13 3.19664 4.70006 3.78606 3.50925 2.29569 3.78896 3.60349 3.21093 3.36780 2.67393 3.88982 3.68029 4.26389 3.68239 3.55861 3.33670 3.48329 3.07987 3.93791 1.02720 14 y - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510 + 14 2.98251 4.43779 4.31388 3.82115 3.20877 4.08952 4.54007 2.00695 3.64555 1.30599 3.09552 4.09798 4.45211 3.94746 3.86362 3.46665 3.25564 1.64211 5.13725 3.91385 15 l - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510 + 15 2.15254 2.45969 3.69479 3.31339 3.86059 2.92557 4.16344 3.17236 3.21287 2.97886 3.87676 3.36254 3.65358 3.52003 3.46091 1.53946 2.62341 2.77195 5.29578 4.07476 16 s - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510 + 16 2.59251 4.66552 2.70968 2.48311 4.18488 1.89749 3.77255 3.67484 2.56229 3.27203 4.14808 2.94825 3.77150 2.19715 2.92693 2.65455 2.93244 3.29447 5.43421 4.12493 17 g - 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- - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.02203 3.82629 * 0.61958 0.77255 0.00000 * +//
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/hmmdb_levels/thaNOG/thaNOG Mon Nov 04 16:38:44 2019 -0500 @@ -0,0 +1,637 @@ +HMMER3/f [3.1b1 | May 2013] +NAME thaNOG +LENG 205 +ALPH amino +RF no +MM no +CONS yes +CS no +MAP yes +DATE Thu Apr 16 06:29:18 2015 +NSEQ 3 +EFFN 0.454102 +CKSUM 2514733105 +STATS LOCAL MSV -10.6020 0.70508 +STATS LOCAL VITERBI -11.4006 0.70508 +STATS LOCAL FORWARD -4.9608 0.70508 +HMM A C D E F G H I K L M N P Q R S T V W Y + m->m m->i m->d i->m i->i d->m d->d + COMPO 2.60488 4.26537 2.86806 2.68812 3.48541 2.84597 3.68190 2.58658 2.57105 2.36046 3.71753 3.12796 3.51194 3.07828 3.00549 2.67857 2.91482 2.52396 5.16454 3.68907 + 2.68619 4.42226 2.77521 2.73125 3.46355 2.40514 3.72496 3.29355 2.67742 2.69356 4.24578 2.90348 2.73741 3.18148 2.89802 2.37888 2.77521 2.98520 4.58478 3.61505 + 0.17176 1.91497 4.55917 0.35031 1.21898 0.00000 * + 1 3.06761 4.52439 4.31327 3.78099 3.05250 4.16350 4.46561 2.17607 3.57234 1.30879 1.91901 4.09154 4.45690 3.86045 3.77957 3.51234 3.30962 2.23580 5.01687 3.83610 2 l - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510 + 2 2.92273 5.02492 2.47434 1.07719 4.36685 3.25185 3.83632 3.81369 2.71243 3.43683 4.41304 2.91439 3.85493 3.05312 3.11711 2.90913 3.22689 3.50145 5.54519 4.26810 3 e - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510 + 3 2.78351 4.58087 3.32911 2.88754 3.40933 3.59103 3.84122 2.81006 2.61259 1.66760 3.45029 3.30455 4.01739 2.39416 2.89621 2.95209 3.03282 2.70991 4.99124 3.67436 4 l - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510 + 4 2.53418 4.23705 3.59368 3.16853 3.49025 3.42404 4.06074 1.74993 3.06664 2.43412 3.49971 3.45907 3.96332 3.42386 3.35145 2.21772 2.86823 2.25074 5.06222 3.78462 5 i - 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- - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510 + 191 2.29842 4.21804 3.17637 2.99106 4.04109 2.94862 4.10162 3.55914 3.06240 3.28234 4.21181 3.22118 3.68461 3.41464 3.34915 1.14610 2.77598 3.10206 5.41656 4.12456 192 s - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510 + 192 2.29842 4.21804 3.17637 2.99106 4.04109 2.94862 4.10162 3.55914 3.06240 3.28234 4.21181 3.22118 3.68461 3.41464 3.34915 1.14610 2.77598 3.10206 5.41656 4.12456 193 s - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510 + 193 2.94036 4.90159 3.11392 2.74278 4.27986 3.43307 3.74090 3.70703 1.08817 3.28019 4.24408 3.16863 3.93637 2.93480 2.42690 2.98500 3.19656 3.41702 5.34960 4.15744 194 k - 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- - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510 + 197 2.92273 5.02492 2.47434 1.07719 4.36685 3.25185 3.83632 3.81369 2.71243 3.43683 4.41304 2.91439 3.85493 3.05312 3.11711 2.90913 3.22689 3.50145 5.54519 4.26810 198 e - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510 + 198 3.19664 4.70006 3.78606 3.50925 2.29569 3.78896 3.60349 3.21093 3.36780 2.67393 3.88982 3.68029 4.26389 3.68239 3.55861 3.33670 3.48329 3.07987 3.93791 1.02720 199 y - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510 + 199 2.62209 4.40041 3.28850 3.18371 4.32546 0.78630 4.30564 3.91689 3.36007 3.57539 4.55128 3.45295 3.79040 3.68714 3.59951 2.79308 3.10058 3.45214 5.42949 4.42634 200 g - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510 + 200 2.92273 5.02492 2.47434 1.07719 4.36685 3.25185 3.83632 3.81369 2.71243 3.43683 4.41304 2.91439 3.85493 3.05312 3.11711 2.90913 3.22689 3.50145 5.54519 4.26810 201 e - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510 + 201 2.29842 4.21804 3.17637 2.99106 4.04109 2.94862 4.10162 3.55914 3.06240 3.28234 4.21181 3.22118 3.68461 3.41464 3.34915 1.14610 2.77598 3.10206 5.41656 4.12456 202 s - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510 + 202 3.00341 4.43279 4.28393 3.89883 3.35077 4.02713 4.63395 1.12320 3.72623 1.94475 3.29234 4.14920 4.46227 4.07854 3.92692 3.51945 3.30343 1.84653 5.23382 3.96866 203 i - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510 + 203 2.95756 4.78041 3.09252 2.84941 3.26099 3.41845 1.21998 3.65490 2.69349 3.15313 4.19373 3.25996 3.96930 3.21533 2.96107 3.02872 3.25993 3.39076 4.72643 3.21297 204 h - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510 + 204 2.62209 4.40041 3.28850 3.18371 4.32546 0.78630 4.30564 3.91689 3.36007 3.57539 4.55128 3.45295 3.79040 3.68714 3.59951 2.79308 3.10058 3.45214 5.42949 4.42634 205 g - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.03256 3.83682 4.55917 0.61958 0.77255 0.48576 0.95510 + 205 3.00341 4.43279 4.28393 3.89883 3.35077 4.02713 4.63395 1.12320 3.72623 1.94475 3.29234 4.14920 4.46227 4.07854 3.92692 3.51945 3.30343 1.84653 5.23382 3.96866 206 i - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.02203 3.82629 * 0.61958 0.77255 0.00000 * +//
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/make_comp_file.sh Mon Nov 04 16:38:44 2019 -0500 @@ -0,0 +1,24 @@ +#!/bin/bash + +base_path=$1 + +emapper.py \ + -i $base_path/test-data/nlim_fragment.fasta \ + --output HMM_nlim \ + --output_dir $base_path/test-data \ + --override \ + --database $base_path/test-data/cached_locally/hmmdb_levels/ENOG411CB2I/ENOG411CB2I \ + --data_dir $base_path/test-data/cached_locally \ + --no_refine\ + --no_annot \ + --no_file_comments + +emapper.py \ + -i $base_path/test-data/nlim_fragment.fasta \ + --output DIA_nlim \ + --output_dir $base_path/test-data \ + --override \ + -m diamond \ + --data_dir $base_path/test-data/cached_locally \ + --no_file_comments \ + --no_annot
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/nlim_1033.fasta Mon Nov 04 16:38:44 2019 -0500 @@ -0,0 +1,7 @@ +>Nlim_1033886738.Nlim_1033Cytidyltransferase-like protein +MELIKKSILTELYLSGITGKSHIDNLTKKGFTQKLIDLE +IDELIKNKLVKEDRAILTELGRSSLRVVLAGGVFDIIHP +GHIYTLNAAKSLGDVLIVVVATDNTALKMKKRQPLHSKE +QRQELVNSLIMVDLCLIGQEDDIFKTVNLVKPQIIALGY +DQVHQEKFIIDGCKKIQLDAKVARLQSPIPESSSSKIQK +EYGESIHGI
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/nlim_fragment.fasta Mon Nov 04 16:38:44 2019 -0500 @@ -0,0 +1,2 @@ +>Nlim_1033886738.Nlim_1033Cytidyltransferase-like protein +MELIKKSILTELYLSGITGKSHIDNLTKKGFTQKLIDLE
--- a/tool-data/eggnog_mapper.loc.sample Tue Aug 08 12:40:56 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +0,0 @@ -#This is a sample file distributed with Galaxy that enables tools -#to use a directory of eggnog_mapper data files. -# -# eggnog-mapper requires the following files to be installed in the data directory: -# https://github.com/jhcepas/eggnog-mapper/blob/master/data/og2level.tsv.gz -# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/eggnog.db.gz -# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/OG_fasta.tar.gz -# In addition individual HMM DBs can be installed from: -# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/hmmdb_levels/ -# A complete diamond database is available from: -# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/eggnog_proteins.dmnd.gz -# -# -#name value type data_dir -#eggnog_4.5 eggnog_4.5 data /depot/data2/galaxy/eggnog/eggnog_4.5/data -#eggnog_4.5arcNOG arcNOG hmmer eggnog_4.5 -#eggnog_4.5euk euk hmmer eggnog_4.5 -#eggnog_4.5dmnd eggnog_proteins.dmnd diamond eggnog_4.5
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/eggnog_mapper_db.loc.sample Mon Nov 04 16:38:44 2019 -0500 @@ -0,0 +1,25 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of eggnog_mapper data files. +# +# eggnog-mapper requires the following files to be installed in the data directory: +# https://github.com/jhcepas/eggnog-mapper/blob/master/data/og2level.tsv.gz +# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/eggnog.db.gz +# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/OG_fasta.tar.gz +# In addition individual HMM DBs can be installed from: +# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/hmmdb_levels/ +# A complete diamond database is available from: +# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/eggnog_proteins.dmnd.gz +# +# The python script download_eggnog_data.py, +# included with eggnog_mapper, can be used to download the files to the correct directory +# +# The near-equivalence of columns "value" and "db" is needed for the tests to work, +# and for the setting of --data_dir to the parent directory of eggnog.db +# The complicated eggNOG database structure makes passing custom HMM databases somewhat tricky. +# See test-data/cached_locally/eggnog_mapper.loc for how this was done with the included test databases +# In all other cases, when the appropriate HMM database (for example, "thaNOG") was downloaded from eggnogdb.embl.de, +# value and db should be the same (in the example, both should be "thaNOG") +# +# +#db_version name path +#4.5.1 eggnog_4.5.1 /path/to/directory/that/contains/eggnog.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/eggnog_mapper_hmm_dbs.loc.sample Mon Nov 04 16:38:44 2019 -0500 @@ -0,0 +1,28 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of eggnog_mapper data files. +# +# eggnog-mapper requires the following files to be installed in the data directory: +# https://github.com/jhcepas/eggnog-mapper/blob/master/data/og2level.tsv.gz +# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/eggnog.db.gz +# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/OG_fasta.tar.gz +# In addition individual HMM DBs can be installed from: +# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/hmmdb_levels/ +# A complete diamond database is available from: +# http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/eggnog_proteins.dmnd.gz +# +# The python script download_eggnog_data.py, +# included with eggnog_mapper, can be used to download the files to the correct directory +# +# The near-equivalence of columns "value" and "db" is needed for the tests to work, +# and for the setting of --data_dir to the parent directory of eggnog.db +# The complicated eggNOG database structure makes passing custom HMM databases somewhat tricky. +# See test-data/cached_locally/eggnog_mapper.loc for how this was done with the included test databases +# In all other cases, when the appropriate HMM database (for example, "thaNOG") was downloaded from eggnogdb.embl.de, +# value and db should be the same (in the example, both should be "thaNOG") +# +# +#key db_version value name path +#4.5.1_NOG 4.5.1 NOG Full eggNOG database (NOG) +#4.5.1_euk 4.5.1 euk Eukaryotes (euk) +#4.5.1_aproNOG 4.5.1 aproNOG Proteobacteria_alpha (aproNOG) +#4.5.1_aproNOG 4.5.1 ENOG411CB2I ENOG411CB2I (custom) /path/to/custom/hmmdb/ENOG411CB2I
--- a/tool_data_table_conf.xml.sample Tue Aug 08 12:40:56 2017 -0400 +++ b/tool_data_table_conf.xml.sample Mon Nov 04 16:38:44 2019 -0500 @@ -1,7 +1,11 @@ <tables> <!-- Locations of all eggnog_mapper data --> - <table name="eggnog_mapper" comment_char="#"> - <columns>name,value,type,data_dir</columns> - <file path="tool-data/eggnog_mapper.loc" /> + <table name="eggnog_mapper_db" comment_char="#"> + <columns>value,name,path</columns> + <file path="tool-data/eggnog_mapper_db.loc" /> + </table> + <table name="eggnog_mapper_hmm_dbs" comment_char="#"> + <columns>key,db_version,value,name,path</columns> + <file path="tool-data/eggnog_mapper_hmm_dbs.loc" /> </table> </tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Mon Nov 04 16:38:44 2019 -0500 @@ -0,0 +1,11 @@ +<tables> + <!-- Locations of all eggnog_mapper data --> + <table name="eggnog_mapper_db" comment_char="#"> + <columns>value,name,path</columns> + <file path="${__HERE__}/test-data/cached_locally/eggnog_mapper_db.loc" /> + </table> + <table name="eggnog_mapper_hmm_dbs" comment_char="#"> + <columns>key,db_version,value,name,path</columns> + <file path="${__HERE__}/test-data/cached_locally/eggnog_mapper_hmm_dbs.loc" /> + </table> +</tables>