| Next changeset 1:f415e44e71de (2023-04-03) |
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Commit message:
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 12282c16658b37858f49944796fd95515ef0fc0b |
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added:
README.md find_free_port.sh genenotebook_build.xml kill_gnb.sh launch_gnb.sh macros.xml test-data/annot.gff test-data/eggnog.tsv test-data/genome.fa test-data/interproscan.tsv test-data/output/genome.tar.bz2 test-data/output/genome_annot.tar.bz2 test-data/output/genome_annot_ips.tar.bz2 test-data/output/genome_annot_ips_en.tar.bz2 test-data/output/genome_reload.tar.bz2 |
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| diff -r 000000000000 -r 22f22c3e81bf README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Wed Jan 11 11:49:13 2023 +0000 |
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| @@ -0,0 +1,7 @@ +# GeneNoteBook Galaxy tool + +This tool will generate a MongoDB database ready to be used by a GeneNoteBook server. + +To achieve this, this tools starts a local MongoDB server, listening only on a UNIX socket within the job directory. + +It also starts a GeneNoteBook server within the job evironment, using a port >7000, that is detected to be free at the time of running the job. |
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| diff -r 000000000000 -r 22f22c3e81bf find_free_port.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/find_free_port.sh Wed Jan 11 11:49:13 2023 +0000 |
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| @@ -0,0 +1,43 @@ +#!/bin/bash + +set -e + +# This script finds a free port on the local machine in the 7000-65000 interval +# Should work in biocontainers derived from conda +# Taken from https://unix.stackexchange.com/a/358101 + +if command -v ss &> /dev/null +then + ss -alnut | awk ' + $2 == "LISTEN" { + if ($5 ~ "[.:][0-9]+$") { + split($5, a, /[:.]/); + port = a[length(a)]; + p[port] = 1 + } + } + END { + for (i = 7000; i < 65000 && p[i]; i++){}; + if (i == 65000) {exit 1}; + print i + } + ' +elif command -v netstat &> /dev/null +then + netstat -aln | awk ' + $6 == "LISTEN" { + if ($4 ~ "[.:][0-9]+$") { + split($4, a, /[:.]/); + port = a[length(a)]; + p[port] = 1 + } + } + END { + for (i = 7000; i < 65000 && p[i]; i++){}; + if (i == 65000) {exit 1}; + print i + } + ' +else + echo "This tool requires one of 'netstat' of 'ss' commands." +fi |
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| diff -r 000000000000 -r 22f22c3e81bf genenotebook_build.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/genenotebook_build.xml Wed Jan 11 11:49:13 2023 +0000 |
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| @@ -0,0 +1,126 @@ +<?xml version="1.0"?> +<tool id="genenotebook_build" name="Build a GeneNoteBook" version="@WRAPPER_VERSION@" profile="21.05"> + <description></description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="aggressive"><![CDATA[ +@START_GNB@ + +#for genome in $genomes: + genenotebook add genome @CONNECT_INFO@ --name '${genome.name}' '${genome.genome}'; + + #for annot in $genome.annots: + genenotebook add annotation @CONNECT_INFO@ --genome-name '${genome.name}' '${annot.annotation}'; + #if $annot.interproscan: + genenotebook add interproscan @CONNECT_INFO@ --format + #if $annot.interproscan.is_of_type('gff3'): + gff3 + #else: + tsv + #end if + '${annot.interproscan}'; + #end if + + #if $annot.eggnog: + genenotebook add eggnog @CONNECT_INFO@ '${annot.eggnog}'; + #end if + #end for +#end for + +@ZIP_GNB@ + ]]></command> + <inputs> + <param name="existing" type="data" format="genenotebook" optional="true" label="Load data in an existing GeneNoteBook database" help="Leave empty to start a new database from scratch" /> + <repeat name="genomes" title="Genomes"> + <param argument="--name" label="Name" type="text" help="Reference genome name" /> + <param name="genome" label="Genome sequence" type="data" format="fasta" /> + <repeat name="annots" title="Annotations"> + <param name="annotation" label="Annotation" type="data" format="gff3" /> + <param name="interproscan" label="InterProScan results" optional="true" type="data" format="tsv,gff3" /> + <param name="eggnog" label="EggNOG-Mapper results" optional="true" type="data" format="tsv" /> + </repeat> + </repeat> + </inputs> + <outputs> + <data format="genenotebook" name="gnb_db" label="GeneNoteBook on ${on_string}"/> + </outputs> + <tests> + <test> + <repeat name="genomes"> + <param name="name" value="Test org" /> + <param name="genome" value="genome.fa" /> + </repeat> + <output name="gnb_db" file="output/genome.tar.bz2" compare="sim_size" /> + <assert_stdout> + <has_text text="addGenome succesfully inserted 1 elements" /> + </assert_stdout> + </test> + <test> + <repeat name="genomes"> + <param name="name" value="Test org 2" /> + <param name="genome" value="genome.fa" /> + <repeat name="annots"> + <param name="annotation" value="annot.gff" /> + </repeat> + </repeat> + <output name="gnb_db" file="output/genome_annot.tar.bz2" compare="sim_size" /> + <assert_stdout> + <has_text text="addGenome succesfully inserted 1 elements" /> + <has_text text="addAnnotationTrack succesfully inserted 5 elements" /> + </assert_stdout> + </test> + <test> + <repeat name="genomes"> + <param name="name" value="Test org 2" /> + <param name="genome" value="genome.fa" /> + <repeat name="annots"> + <param name="annotation" value="annot.gff" /> + <param name="interproscan" value="interproscan.tsv" ftype="tsv" /> + </repeat> + </repeat> + <output name="gnb_db" file="output/genome_annot_ips.tar.bz2" compare="sim_size" /> + <assert_stdout> + <has_text text="addGenome succesfully inserted 1 elements" /> + <has_text text="addAnnotationTrack succesfully inserted 5 elements" /> + <has_text text="addInterproscan succesfully inserted 5 elements" /> + </assert_stdout> + </test> + <test> + <param name="existing" value="output/genome.tar.bz2" /> + <repeat name="genomes"> + <param name="name" value="Test org 2" /> + <param name="genome" value="genome.fa" /> + </repeat> + <output name="gnb_db" file="output/genome_reload.tar.bz2" compare="sim_size" /> + <assert_stdout> + <has_text text="addGenome succesfully inserted 1 elements" /> + </assert_stdout> + </test> + <test> + <repeat name="genomes"> + <param name="name" value="Test org 2" /> + <param name="genome" value="genome.fa" /> + <repeat name="annots"> + <param name="annotation" value="annot.gff" /> + <param name="interproscan" value="interproscan.tsv" ftype="tsv" /> + <param name="eggnog" value="eggnog.tsv" ftype="tsv" /> + </repeat> + </repeat> + <output name="gnb_db" file="output/genome_annot_ips_en.tar.bz2" compare="sim_size" delta="15000" /> + <assert_stdout> + <has_text text="addGenome succesfully inserted 1 elements" /> + <has_text text="addAnnotationTrack succesfully inserted 5 elements" /> + <has_text text="addInterproscan succesfully inserted 5 elements" /> + <has_text text="addEggnog succesfully inserted undefined elements" /> + </assert_stdout> + </test> + </tests> + <help><![CDATA[ +Build a GeneNoteBook by loading data into a MongoDB database. The resulting dataset can then be displayed with the "View a GeneNoteBook" interactive tool (to be written). + +The resulting GeneNoteBook will contain the default user accounts created on the first launch. You are responsible to change them if you ever want to put your result online. + ]]></help> + <expand macro="citation" /> +</tool> |
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| diff -r 000000000000 -r 22f22c3e81bf kill_gnb.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/kill_gnb.sh Wed Jan 11 11:49:13 2023 +0000 |
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| @@ -0,0 +1,14 @@ +#!/bin/bash + +# Make sure everything is cleaned (including job queue) +sleep 5 + +# Kill GeneNoteBook +kill $GNB_PID + +sleep 5 + +# Kill MongoDB +kill $(<"./mongo.pid") + +sleep 5 |
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| diff -r 000000000000 -r 22f22c3e81bf launch_gnb.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/launch_gnb.sh Wed Jan 11 11:49:13 2023 +0000 |
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| @@ -0,0 +1,33 @@ +#!/bin/bash + +set -e + +mongod --dbpath ./mongo_db/ --unixSocketPrefix `pwd` --bind_ip fake_socket --logpath ./mongod.log --pidfilepath ./mongo.pid & + +sleep 5 + +# "waiting for connections on port" is for mongodb 4x +#if ! grep -q "waiting for connections on port" ./mongod.log; then +# "Listening on" is for mongodb 5x +if ! grep -q "Listening on" ./mongod.log; then + echo "Failed to launch MongoDB:" 1>&2; + cat ./mongod.log 1>&2; + kill $GNB_PID; + exit 1; +fi; + +TMP_STORAGE=$(pwd)/tmp_storage +mkdir "$TMP_STORAGE" + +genenotebook run --storage-path "$TMP_STORAGE" --port ${GNB_PORT} --mongo-url mongodb://$MONGO_URI%2Fmongodb-27017.sock/genenotebook > ./gnb.log 2>&1 & + +export GNB_PID=$! + +sleep 15 + +if ! grep -q "GeneNoteBook server started, serving" ./gnb.log; then + echo "Failed to launch GeneNoteBook:" 1>&2; + cat ./gnb.log 1>&2; + kill $GNB_PID $(<"./mongo.pid"); + exit 1; +fi; |
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| diff -r 000000000000 -r 22f22c3e81bf macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Jan 11 11:49:13 2023 +0000 |
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| @@ -0,0 +1,48 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">genenotebook</requirement> + <yield/> + </requirements> + </xml> + + <token name="@TOOL_VERSION@">0.3.2</token> + <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy0</token> + + <xml name="citation"> + <citations> + <citation type="doi">10.1093/bioinformatics/btz491</citation> + </citations> + </xml> + + <token name="@CONNECT_INFO@">-u admin -p admin --port \$GNB_PORT</token> + + <!-- + This runs GeneNoteBook, and a local mongodb server listening only on a unix socket, created in the work dir. + The bind_ip option is a trick to prevent mongod from opening a TCP socket. + For some unknwon reason, unixSocketPrefix needs an absolute path + --> + <token name="@START_GNB@"><![CDATA[ + export GNB_PORT=\$(bash '$__tool_directory__/find_free_port.sh'); + export MONGO_URI=\$(pwd | sed 's|/|%2F|g'); + #if $existing + tar -xf '${existing}' mongo_db; + #else + mkdir ./mongo_db/; + #end if + . '$__tool_directory__/launch_gnb.sh'; + ]]></token> + + <token name="@ZIP_GNB@"><![CDATA[ + . '$__tool_directory__/kill_gnb.sh'; + + ## Zip the mongodb data dir + tar -cvjf '${gnb_db}' mongo_db > /dev/null; + + ## Make sure mongodb and GNB are really really stopped even if anything failed before + ## We assume the DRM or container exit will kill any remaining process after that, but who knows. + kill \$GNB_PID &> /dev/null || true ; + kill \$(<"./mongo.pid") &> /dev/null || true ; + ]]></token> +</macros> |
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| diff -r 000000000000 -r 22f22c3e81bf test-data/annot.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annot.gff Wed Jan 11 11:49:13 2023 +0000 |
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| @@ -0,0 +1,45 @@ +##gff-version 3 +scaffold_1 funannotate gene 300 1158 . - . ID=MMUCEDO_000001; +scaffold_1 funannotate mRNA 300 1158 . - . ID=MMUCEDO_000001-T1;Parent=MMUCEDO_000001;product=hypothetical protein; +scaffold_1 funannotate exon 880 1158 . - . ID=MMUCEDO_000001-T1.exon1;Parent=MMUCEDO_000001-T1; +scaffold_1 funannotate exon 407 800 . - . ID=MMUCEDO_000001-T1.exon2;Parent=MMUCEDO_000001-T1; +scaffold_1 funannotate exon 300 309 . - . ID=MMUCEDO_000001-T1.exon3;Parent=MMUCEDO_000001-T1; +scaffold_1 funannotate CDS 880 1158 . - 0 ID=MMUCEDO_000001-T1.cds;Parent=MMUCEDO_000001-T1; +scaffold_1 funannotate CDS 407 800 . - 0 ID=MMUCEDO_000001-T1.cds;Parent=MMUCEDO_000001-T1; +scaffold_1 funannotate CDS 300 309 . - 2 ID=MMUCEDO_000001-T1.cds;Parent=MMUCEDO_000001-T1; +scaffold_1 funannotate gene 4621 5580 . + . ID=MMUCEDO_000002; +scaffold_1 funannotate mRNA 4621 5580 . + . ID=MMUCEDO_000002-T1;Parent=MMUCEDO_000002;product=hypothetical protein; +scaffold_1 funannotate exon 4621 4715 . + . ID=MMUCEDO_000002-T1.exon1;Parent=MMUCEDO_000002-T1; +scaffold_1 funannotate exon 4812 5100 . + . ID=MMUCEDO_000002-T1.exon2;Parent=MMUCEDO_000002-T1; +scaffold_1 funannotate exon 5185 5250 . + . ID=MMUCEDO_000002-T1.exon3;Parent=MMUCEDO_000002-T1; +scaffold_1 funannotate exon 5312 5375 . + . ID=MMUCEDO_000002-T1.exon4;Parent=MMUCEDO_000002-T1; +scaffold_1 funannotate exon 5457 5488 . + . ID=MMUCEDO_000002-T1.exon5;Parent=MMUCEDO_000002-T1; +scaffold_1 funannotate exon 5557 5580 . + . ID=MMUCEDO_000002-T1.exon6;Parent=MMUCEDO_000002-T1; +scaffold_1 funannotate CDS 4621 4715 . + 0 ID=MMUCEDO_000002-T1.cds;Parent=MMUCEDO_000002-T1; +scaffold_1 funannotate CDS 4812 5100 . + 1 ID=MMUCEDO_000002-T1.cds;Parent=MMUCEDO_000002-T1; +scaffold_1 funannotate CDS 5185 5250 . + 0 ID=MMUCEDO_000002-T1.cds;Parent=MMUCEDO_000002-T1; +scaffold_1 funannotate CDS 5312 5375 . + 0 ID=MMUCEDO_000002-T1.cds;Parent=MMUCEDO_000002-T1; +scaffold_1 funannotate CDS 5457 5488 . + 2 ID=MMUCEDO_000002-T1.cds;Parent=MMUCEDO_000002-T1; +scaffold_1 funannotate CDS 5557 5580 . + 0 ID=MMUCEDO_000002-T1.cds;Parent=MMUCEDO_000002-T1; +scaffold_1 funannotate gene 6121 6864 . + . ID=MMUCEDO_000003; +scaffold_1 funannotate mRNA 6121 6864 . + . ID=MMUCEDO_000003-T1;Parent=MMUCEDO_000003;product=hypothetical protein; +scaffold_1 funannotate exon 6121 6146 . + . ID=MMUCEDO_000003-T1.exon1;Parent=MMUCEDO_000003-T1; +scaffold_1 funannotate exon 6198 6219 . + . ID=MMUCEDO_000003-T1.exon2;Parent=MMUCEDO_000003-T1; +scaffold_1 funannotate exon 6348 6358 . + . ID=MMUCEDO_000003-T1.exon3;Parent=MMUCEDO_000003-T1; +scaffold_1 funannotate exon 6447 6864 . + . ID=MMUCEDO_000003-T1.exon4;Parent=MMUCEDO_000003-T1; +scaffold_1 funannotate CDS 6121 6146 . + 0 ID=MMUCEDO_000003-T1.cds;Parent=MMUCEDO_000003-T1; +scaffold_1 funannotate CDS 6198 6219 . + 1 ID=MMUCEDO_000003-T1.cds;Parent=MMUCEDO_000003-T1; +scaffold_1 funannotate CDS 6348 6358 . + 0 ID=MMUCEDO_000003-T1.cds;Parent=MMUCEDO_000003-T1; +scaffold_1 funannotate CDS 6447 6864 . + 1 ID=MMUCEDO_000003-T1.cds;Parent=MMUCEDO_000003-T1; +scaffold_1 funannotate gene 6889 7683 . + . ID=MMUCEDO_000004; +scaffold_1 funannotate mRNA 6889 7683 . + . ID=MMUCEDO_000004-T1;Parent=MMUCEDO_000004;product=hypothetical protein; +scaffold_1 funannotate exon 6889 7683 . + . ID=MMUCEDO_000004-T1.exon1;Parent=MMUCEDO_000004-T1; +scaffold_1 funannotate CDS 6889 7683 . + 0 ID=MMUCEDO_000004-T1.cds;Parent=MMUCEDO_000004-T1; +scaffold_1 funannotate gene 9569 10657 . + . ID=MMUCEDO_000005; +scaffold_1 funannotate mRNA 9569 10657 . + . ID=MMUCEDO_000005-T1;Parent=MMUCEDO_000005;product=hypothetical protein; +scaffold_1 funannotate exon 9569 9699 . + . ID=MMUCEDO_000005-T1.exon1;Parent=MMUCEDO_000005-T1; +scaffold_1 funannotate exon 9763 9850 . + . ID=MMUCEDO_000005-T1.exon2;Parent=MMUCEDO_000005-T1; +scaffold_1 funannotate exon 9908 10657 . + . ID=MMUCEDO_000005-T1.exon3;Parent=MMUCEDO_000005-T1; +scaffold_1 funannotate CDS 9569 9699 . + 0 ID=MMUCEDO_000005-T1.cds;Parent=MMUCEDO_000005-T1; +scaffold_1 funannotate CDS 9763 9850 . + 1 ID=MMUCEDO_000005-T1.cds;Parent=MMUCEDO_000005-T1; +scaffold_1 funannotate CDS 9908 10657 . + 0 ID=MMUCEDO_000005-T1.cds;Parent=MMUCEDO_000005-T1; |
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| diff -r 000000000000 -r 22f22c3e81bf test-data/eggnog.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/eggnog.tsv Wed Jan 11 11:49:13 2023 +0000 |
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| @@ -0,0 +1,8 @@ +# emapper version: emapper-2.0.1 emapper DB: 2.0 +# command: ./emapper.py --data_dir /shared/ifbstor1/galaxy/mutable-data/tool-data/eggnog_data/2.0 -m diamond --matrix BLOSUM62 --gapopen 11 --gapextend 1 --query-cover 0 --subject-cover 0 --target_orthologs=all --go_evidence=non-electronic --seed_ortholog_evalue=0.001 --seed_ortholog_score=60 --output=results -i /shared/ifbstor1/galaxy/datasets/002/201/dataset_2201165.dat --cpu 8 +# time: Tue Nov 23 17:29:53 2021 +#query_name seed_eggNOG_ortholog seed_ortholog_evalue seed_ortholog_score best_tax_level Preferred_name GOs EC KEGG_ko KEGG_Pathway KEGG_Module KEGG_Reaction KEGG_rclass BRITE KEGG_TC CAZy BiGG_Reaction taxonomic scope eggNOG OGs best eggNOG OG COG Functional cat. eggNOG free text desc. +MMUCEDO_000002-T1 36080.S2J5L3 1.23e-186 523.0 Fungi incertae sedis ABP140 GO:0001510,GO:0003674,GO:0003779,GO:0003824,GO:0005488,GO:0005515,GO:0005575,GO:0005622,GO:0005623,GO:0005737,GO:0005856,GO:0005884,GO:0005937,GO:0005938,GO:0006139,GO:0006396,GO:0006399,GO:0006400,GO:0006725,GO:0006807,GO:0006996,GO:0007010,GO:0007015,GO:0008033,GO:0008092,GO:0008150,GO:0008152,GO:0008168,GO:0008173,GO:0008175,GO:0008757,GO:0009451,GO:0009987,GO:0010467,GO:0015629,GO:0016043,GO:0016070,GO:0016427,GO:0016740,GO:0016741,GO:0022607,GO:0030029,GO:0030036,GO:0030427,GO:0030479,GO:0030488,GO:0030674,GO:0030863,GO:0030864,GO:0032259,GO:0032432,GO:0034470,GO:0034641,GO:0034660,GO:0042995,GO:0043170,GO:0043226,GO:0043228,GO:0043229,GO:0043232,GO:0043332,GO:0043412,GO:0043414,GO:0044085,GO:0044237,GO:0044238,GO:0044260,GO:0044422,GO:0044424,GO:0044430,GO:0044444,GO:0044446,GO:0044448,GO:0044463,GO:0044464,GO:0044877,GO:0046483,GO:0051015,GO:0051017,GO:0051286,GO:0052735,GO:0060090,GO:0061572,GO:0061645,GO:0071704,GO:0071840,GO:0071944,GO:0090304,GO:0097435,GO:0099080,GO:0099081,GO:0099512,GO:0099513,GO:0099568,GO:0120025,GO:0120038,GO:0140098,GO:0140101,GO:1901360 2.1.1.268 ko:K17053 ko00000,ko01000,ko03016 Fungi 1GSMQ@112252,38G2U@33154,3NUGD@4751,KOG2361@1,KOG2361@2759 NA|NA|NA S Methyltransferase domain +MMUCEDO_000003-T1 36080.S2J001 0.0 948.0 Fungi Fungi 39PS9@33154,3Q616@4751,KOG3577@1,KOG3577@2759 NA|NA|NA T 7 transmembrane receptor (Secretin family) +MMUCEDO_000004-T1 36080.S2J485 7.4e-114 328.0 Fungi incertae sedis RPS9B GO:0000462,GO:0002181,GO:0003674,GO:0003676,GO:0003723,GO:0003735,GO:0005198,GO:0005488,GO:0005575,GO:0005622,GO:0005623,GO:0005737,GO:0005829,GO:0005840,GO:0006139,GO:0006364,GO:0006396,GO:0006412,GO:0006417,GO:0006450,GO:0006518,GO:0006725,GO:0006807,GO:0008150,GO:0008152,GO:0009058,GO:0009059,GO:0009889,GO:0009891,GO:0009893,GO:0009987,GO:0010467,GO:0010468,GO:0010556,GO:0010557,GO:0010604,GO:0010608,GO:0010628,GO:0015935,GO:0016070,GO:0016072,GO:0019222,GO:0019538,GO:0019843,GO:0022613,GO:0022626,GO:0022627,GO:0030490,GO:0030684,GO:0030686,GO:0031323,GO:0031325,GO:0031326,GO:0031328,GO:0032040,GO:0032268,GO:0032270,GO:0032991,GO:0034248,GO:0034250,GO:0034470,GO:0034641,GO:0034645,GO:0034660,GO:0042254,GO:0042274,GO:0043043,GO:0043170,GO:0043226,GO:0043228,GO:0043229,GO:0043232,GO:0043603,GO:0043604,GO:0044085,GO:0044237,GO:0044238,GO:0044249,GO:0044260,GO:0044267,GO:0044271,GO:0044391,GO:0044422,GO:0044424,GO:0044444,GO:0044445,GO:0044446,GO:0044464,GO:0045727,GO:0045903,GO:0046483,GO:0048518,GO:0048522,GO:0050789,GO:0050794,GO:0051171,GO:0051173,GO:0051246,GO:0051247,GO:0060255,GO:0065007,GO:0065008,GO:0071704,GO:0071840,GO:0080090,GO:0090304,GO:0097159,GO:1901360,GO:1901363,GO:1901564,GO:1901566,GO:1901576,GO:1990904,GO:2000112 ko:K02997 ko03010,map03010 M00177 br01610,ko00000,ko00001,ko00002,ko03011 Fungi 1GT32@112252,38B77@33154,3NU1W@4751,COG0522@1,KOG3301@2759 NA|NA|NA J Ribosomal protein S4/S9 N-terminal domain +MMUCEDO_000005-T1 36080.S2JYJ1 6.56e-107 308.0 Fungi incertae sedis RPL21A GO:0002181,GO:0003674,GO:0003735,GO:0005198,GO:0005575,GO:0005622,GO:0005623,GO:0005737,GO:0005829,GO:0005840,GO:0006412,GO:0006518,GO:0006807,GO:0008150,GO:0008152,GO:0009058,GO:0009059,GO:0009987,GO:0010467,GO:0015934,GO:0019538,GO:0022625,GO:0022626,GO:0032991,GO:0034641,GO:0034645,GO:0043043,GO:0043170,GO:0043226,GO:0043228,GO:0043229,GO:0043232,GO:0043603,GO:0043604,GO:0044237,GO:0044238,GO:0044249,GO:0044260,GO:0044267,GO:0044271,GO:0044391,GO:0044422,GO:0044424,GO:0044444,GO:0044445,GO:0044446,GO:0044464,GO:0071704,GO:1901564,GO:1901566,GO:1901576,GO:1990904 ko:K02889 ko03010,map03010 M00177,M00179 br01610,ko00000,ko00001,ko00002,ko03011 Fungi 1GTD9@112252,39YIF@33154,3P285@4751,COG2139@1,KOG1732@2759 NA|NA|NA J Ribosomal protein L21e |
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| diff -r 000000000000 -r 22f22c3e81bf test-data/genome.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome.fa Wed Jan 11 11:49:13 2023 +0000 |
| b |
| b'@@ -0,0 +1,171 @@\n+>scaffold_1\n+TGATTCGAAGTATCTTACTGAGTCTATGGGGACCAACACCGTGTTGAAAAAGGGGTCGCATTGTATTGGATAGATCCTTG\n+GAAATTCCAGACTTGTGCAGGAAAAGCTCTTTGATGATAAGGATTTAGTTGCTTGGCAATATTCTGATCGTATCCACTGA\n+ATGTTTTTTTACAACTCTTTTGTGTACATCTATAGTTCATGCTCATCAAATAAAAGCAACTAATGATAGATATACaaaat\n+aaacattaaaatttaaaggttgcaattaagataaatttaGCTGTGACAAGACTACTTACTCAAACTGATCTATTATTCTC\n+CTGCTTTAGTATTCTTTACAAATTCTTTTCGTTCTAAGTTACCAGTTTTACAGTCAGGACATTTTAAATATTTTTTTTTT\n+CTAAACCGTTAGCCCCACCGCCATTCAAAATATCAGGGAGCCAAATGAAGACTCTCGGGCGATAAAATATGTCAGGGTTT\n+ACTCTAGTGTTGTAATCAAATCCTTCGTACTCGACATTTACCCAATATGTCTTTCTTTGATATTCAATTGGTTTAACCCC\n+TCCTTTGAGCCTGTTTTGAATTTCAGTAACATATTTTCCAACAAAACTATCTTCTGGCGTACTGTTCCCAACTTGTTCAT\n+CAATAATCTCAAATTCTTCTTCTGTGAGCTCCTGTTCGGCAGCAGTATTGGCATAGTCATCACTGATATTTGTTACATTA\n+CCGACCATTTCTTCTTCATCACTTTCAGTACCTTCAACAACATTTTGCTCACTTTCTACAACAATTGGATCAACATTATT\n+CTAAAAACATTATTAATTTTATACAAAATAAGTCTGTGAAGTTATTAAAGCAGTGCACTACCTATTCATCACAATTAACT\n+TCCATTTGTCTATTCCGGATGTCTTCAGCCACAGGACTATGCATGGTGCTACCAACATTACCGTAGGAAAATGTTGACAT\n+GGATTGATCTTGTTCTCTTCCTGATCCTGTTCGGAATAGTGACATTTGATCAAGCCTTTGTAAATTTAAATTGGGTTGAT\n+TCATCATACGCTTAGGTCCTGAACGTGCTGCATGAGGATCTCTCTTTGATCCCACTTTTGGGCCTGGTTTACTTTTAGGA\n+ACACCTTCATTTTTATTTGAGGAGCTACCACTGAACATATTTTGAATAAAAACTAAATAAAATTATCAAAAAGCAAATTG\n+TGTATCCAGGAATGTTATATATATATATGAATGAGTACTATTTGCTGTCGAAATATAAATGTATTTGTTTATTCTAATGT\n+GCAAAGTTTAATAAAAAATAAACATTGGTGACATTTATATGGCATCTTTGTTTGGATGCCGGCGTCTTTTTAATGATTCT\n+GGCATGTTTTTATTGATGCTAGCATGTTTTTATTGATGCTGGCATCTTTTTTTGGATGCCGGTTTTTATTAGGCATCTTT\n+TTATTGATACTGGTGTTTTTTTAATGATGCTGGCGTCTTAGACGTTTGTTGATCCATAAGAGTTGACGGGAGCTTACCGT\n+AATTATTTGATCTAAAATAAGTACTTGTGATAATTCAACTGATATTGTGTTGGAAACGCTTGCAGATTATCCGGGTAAAT\n+CGTCCTGATTAACTGGAAGGTGGAAAAGTGAGTGGAGAGTTTGACCGTTTATATTAAATGCAGCTTTTCCTGTGAATGTA\n+CACTGCTTTTTCCTTAAACTGGTCTTCACAATCAATCTCATCCAAATCACGTTTTTGATCAGACCATGGGTAATACAGCA\n+TCATCATATGATAAAAATAGTCCTTTGGGTTCTTGTCACTGCGTGTTCTGTGATACTTTAAATAGTAAAGAATTTACACA\n+AGGCGGGGGTAGGAAAGAATACCGTCCATATACTGATGGAGATTGTGTTGCTGGTGTTGGACGTACAACTCCTATAAAGC\n+TACACGTATGTATATAATTTGATGTATTTAATTAAGTCAACCAAAATAGAATTCATTTATCCAGTCTAACTTATAGTACC\n+ACCAAATTTTTATAGCACTCTCGACAGAAATAATACCCTATTCCATATACAAGAAACTCTGAACATGCTTGCTAGAAACA\n+TGACCCAGTCTTCTTCCCTCCTCATTTGGATTTTAATGGTTTGAGTACTGAAGTAATCTACTCTCTTTATGTTTTTGTAT\n+AGATTCATAAACTCTGTCAGGTTATTCTAGTTTTTTTTTGCCTAGTTGAAACCAGAGGTTTTATTGTCTCTTGGTGTATT\n+GGGGAAGCTGCGGTGATGTAGTGCTAATTCGTTATTTTACACATTTATTAATGAGAAAACATGCTGGAGTGCGTTCTACT\n+ATAATTGAAAGTATTGTAAAAAGTATACCACTTAATTTTAAGCTAATTGGTAATCCATCATGAATTCAAAGTTTTTCTAC\n+ATGTAGCAAACCCGAGAAAAACAAGAAAAAAAGTGTTAAAATTTATATAAATTTTAAAACTGACGTCATGAGGCACATTT\n+CTCGACCAATGGAATTGGCCCAAAAATGAAACTACTCATGCAGCAGCTGCGGATTGTTGTGATGGGTTTAGCTGCACCTA\n+AATTGAGTAAAGCAGTAGTAATACATCATTGTTTATTGACCATTCAAACCCTTCTTCCCAAAACCAATCAATATTTAAAG\n+AAAAATCAGTTTATAGAACAGTTCCGTATTCTTAAAAGTTATGCTGACTTGACCAATTTGGATGCAGCCGTAAGTGAAAT\n+AGCTTTATCTTTGGGAAAAGATAAGAAACATGATGGAACATTAGACAGACAGACACAATGGGTACACCAAAAATAACGGG\n+CGCCATACTTCTTTATTAAATCTGACGTTATTTGTTCATCATACACATCCATCCTTCTGTGATAAGCCAGGTTTTCTGAA\n+ACAACCTTCTCGCTTACGTGCTGTCCGATCGATCAACCATTTTTCATAGCAAAAAGCTTCATGATGATCAGTTTATTTTT\n+CCTTTAGCGCTTCAGCATTGTTGGGGCTGTCGCTACAGACCTTCTTTGCACCGAACTAAGTAACTCTGAGCTACATTCAC\n+AGCAAAAAAGCACTTTTATGAAATACTTACAGACATCTGTAATTTCAGTTGTTTGTTTTGCGTACAAAATAATTTGACCA\n+AATATTAAAACGATTACAAATGTTCCTTATTCAAGCACTTAGGGGAATACATCGATTGAGTGCTGGGTGGAATTTTGTAT\n+GTGTCCAATATGAATATCCTTGCTGCCTTCAATTACTCTTGAAATAACTGTTTCCACATCTGTCAATTTACCTCTTCTGA\n+CTTGGTCCTTCATCACTTTCCAAAACATTTAAATAGGATTTAATTCAGGCGAGTAAGGAGAAAGGTATACTGGTATAAAA\n+CCATTCTCTAAAATGATAGGGATATTATCCATTGGCATAGCTTTCTCCCGTCAATGTTCTCTCAAGGAACAAAAGATCCG\n+AGTCTATTCATGGTTCTGAGAGCATTTTGTAAATTACCTGTACTTTAAGACACACAAAGCAGATATTACTAAAACACTAC\n+TTCTAAGAACGAGAAATAACAGGATAAAACAATAGAAGAGATAAAGAACTAATTTTTATTAAAAGAGTAACATTACCGGG\n+TATTTATATTCAGATGTATAAATGGTTTGTTTTGTATGATTTATGTAAGTTTTGACCTTATCCGTGGAAACAGCCAATCT\n+GCAAGGAAAGTTTGTCAGACTTCAGGCTCTCTACAAAACATTGTAAAAAATACAGGATCAATACGATCATAACCACCATT\n+CCTCTGTCTAATTAAGCAAACGTTGAGGATTTGATTGAGGCTGAATTCGTATCAGGAAGAACCAAATCAAAAAGGGAAAT\n+GTCTAGAACTCCGTATTTTTTAGAATCACGT'..b'TGTAAGTCAAGAAATTTTCTCTTTTCAAGAAGTCAAAAAGAAACTCATTATTTTTATATAAC\n+AGCTGGATCGGATGGAGAGAACAAATTCCTTTCCTTGTACAACTTGGTTACCGTGTTATTGTGCCTTCTCTTCGCGGTTT\n+TGGTGAAACAGTAGGTCAAAGATATATGCATGAAATTAATCGATACTAATATGTATAAAAATAAAAGGTATCACCAGCTG\n+ATCCTGCCGAATACGGTTATGGCACTGTCTCCAACGATTTAGCCGGTCTTTTAGACCACCTTCAAATTCCTACTGTCACT\n+GTCATTGGTCACGATTGGGGAGGAGCTGTGACTTGGCGATTCGGCCAATTCTATCCAGATCGAGTCAAGGCGCTTGCCAG\n+TTTTTGTACACCCTATCTTCCTGTGGCCCAAGAAGAAGTGACTTTGGAGCAAATTGTAAAAATTTTGCCCAACTTTAAAT\n+ACCAACTTTACTTGGCAGGACCTGATGCTGAAAAAGATATGAATGACAATTTCCCCAAATTCTTCAACCGTATTTTCCGT\n+CCTATTGCCGATATGGAACCCTTGATTGACCCTGAGCTTGGTACTTTGGCAGAAGGTCGTTCCGACCGACCTCGTAGTGA\n+TAAGATCCCTCAAAAAGTAATGGATTATTATGTAGAGGCTTATACAAAGCAAGGTGCTCGTGGTGGTTTAAATTGGTACC\n+GTCAAACACATAACAACTTTGTGCAATGCAAGAATTTAGATCCCATTATCAAGAAGCCTTCTATGTTGGTGCTTGCAGAA\n+GGTGATAGAGCGTTGCCTCCTTCCATGGCTAAAACCACACCTCAGTTTATCCCCGGTGTGGAGGTTCATCTTGTTGAAGA\n+CTCTGGACATTGGATTCTTTGGGAACAACCTGAAAAATGTAATGCCTATTTGAAGGATTTCCTCGCTCGTGTGGACCCTA\n+TCAATCACAAATTATAATTGTAAATAAACTTTTTTTTTTTATTCTTTGAATATACATGCATGGCTTTAAAAAAAAAAAGA\n+TGAAGAGGTATTATTAATCGAGTGAAGGTGGACACGAAGCACCTGCAGCAAGACATAAGTTACGTTGAGTAAATTGTACA\n+GTGTAAATGGGAGTATTTTTTGTAGGAAAAACAGATAAATGATCGTTGCTATGAAAGATTAATTTAGAAATATGTACACT\n+TTCTCTGGTAATGCATTTTGTTTACCTTTCCAATGTACCCTTTTTTCGCTTGTAATCCATGCTTGGCTTCATCTTTTCGT\n+TGTCTTTTTTATCCTTTTGTTTACCGTGCTGTTTAGACCGTTTCGAGTCTAATGTTTCTTGTACATCCAGCGGTGTATCT\n+TTAATCACGTCCCATACACGCACAGTTCCATCCGCACTTCCAGATACCAGGACGGTACTTTCTAAGTTAAAACTAACCGA\n+GTAAATGAAGCCTGTATGACCCGTCATGGTCTTTAATCTTTTTCCTGTGCCTAGATCCCACACAATGATTGTTTTATCCT\n+CTCCTGCTGACGCCATCAGTCGGCCATTCGGTGAGACGGCGACAGTATGTACCGACCCTGTATGACCTGTAAACACTCTA\n+ACGCAAGTACCTCGTTGCACGTCCCATAATCTAGCAGTGCGATCACTGGATGCCGTCACCACATATTTTGAATTGGGATG\n+AAATCTAACAGCCTAAGCAAAAAATAAAATAAAAAACGTTGGATCGTTTAGCAAAAAAATAAATCAGGATTATTTCTTTT\n+TTTTGCAATTGTACTTACGTTAACATCGGAAAGATGACCTGCAAAGATGCGTAATGGATTTACGTGATCGCAACTCCATA\n+ATCTAGCGGTTTTATCGTGCGATGCAGTAGCAAAATAAAATCCATAGGGTCCGAAATCCACATCCCAAATTGGATAATTA\n+TGACTCTTATAACAAACTAAATTTGTAAATGTATCTAGACTCCATAACCGAACTGTTTGCTTGCATGAGATTCTCTTATT\n+TAAAGTCTACTTATTTTTTTGCTTGTACCTGTTTGATCTTCAGAGCATGATATCAAGTATTGATTATCATGACTAAAGCT\n+CACTCCGTATACAGGCCCAGCATGGCCAATCATTTTTTTATACTGTGTGCCTGGAAGACCTAGAATATATGTGGTAAATT\n+TAAGAAAATGCACTTTTTTCTTTTTAAATGAATTTGTCATACCTTGGGCTTTTTCTGCTGCAGATGTTAATTTATTTCCT\n+TTTAAACTCCATACTTTAATATACGATTCGGAAAAACCGCCGGCTACCAGTGTCGTGTCTTGAGAAATGGTCAAACAATT\n+TAGCCTAAGATCATATGCGTGTGTTACTTATGGTATTGCATAAATTGGAAAATTATAATCTTATTACTACTACTTACAAA\n+TCATGCGTGTTGTGAAAAGTGTAAATGCAGACACTGGGTAATGCAGCACTGCCTAATGAGACGCGCTTTCTTAAGTCACT\n+GAGTGACTCTAATTCCGCTTGGATATCTGTGCCACGACTAGAATATAAAACTTAAGTTACAACATAAACGTGATTGTGGA\n+TATTCTTGATTTTTTTTTTACTAGGAAATGGCGGCAATTTCTTCCATATTCATCGTATCGACCAAAACCTCTTGTTTTAC\n+TTTATTCGTATCGGCCTATATATATGTATATCCAAATGTCAAAACTGAATACATGCATATATAAAAAAAAAAGTTGTGTA\n+TGTGTACGTTACATTATTGTTGACATGATTGATTTCGTGAAACTCTTCGATTTGATCATTGATATGACCGGCAATACCTT\n+CGTTTTCCGAAGTGACAGGCGATAATTTTCCAGTGACGAGATGAATGTTCAGATGCTGATTGACAATGCGTATCAAATTC\n+AAGAATTTCTTGTCCTGCAAGTACGAGATAAACAGTTCGAATGGGATGGAAGACATGCGAATATTGTATTTGTTGTTAAG\n+ATAAAGCGTGGCGATGGCATTTTCTTTCATGTCGTCTGTGCATTGGATTTGAGCGAGGGATTCGATATCGGTGGTATGGT\n+GTTGAATATGATCGTGCTTGTATTTATCGAACAGGTCCAAACCTATATTCATACTTTTTAAAGTTTATGTTTGACATTAT\n+GCATACAATTATTTTTTCTTACCTTGATCTACAAGCCCTTTGGACATGAGGTCGAGAAAGACGTGAACAAACATGGGGTA\n+TAGAACTGATTGTAGCTCGTGCTATAGAAAGATGCTTTAACATTGTGCTGTAGAGTGATAAAGTCAAAATATGGGGGTTA\n+CTTTGTATAAATCCAGGGCATTGAATATCCACTCTCTCAGACTTTGATAACTGTGCATGGTCGCATCCAGATCGCCACCT\n+CCTTGTTCAGCCTCTCGCTTAATAAACTGTACATGGTTAGGTAAAGTTGGTGAAGTGGTGAATTTCTTGGTCAATTGTTC\n+TAGCGAGACAATGTTGTGGTCTGCTGATTCTTGGATATACGCGAGTTCAGATTGACTGTATCCCTTTTTTAAAAAATAGG\n+TTTCAAGGATCTTGTTTACATCGTGATGAGAAGGCATGGGTTGCATGTCCTGCTTGTCCATGTCTCGATTCATATTGGTG\n+AATGAGTAGAAGAAAGGAAAACGGAGCGTCAAAAAAAAAATTAAAGAACGAGTCGACGTCATTCTTTTATTATTATTATT\n+GGAGAAAAAAATCtttttttttttttatttttctttgttCGTTGACAAAATGGAAAGCGCAATACTTGAAGAGGACTTAA\n+AGATCTTGGGATCCGATTCTATCAGGGAATCATGCAGTCGTTTCATGTTAGACATGGAAAGATTGGGTGATAAAAACGAG\n+GAACAGGAAGAGGAATACACGGAACCTGCCATTGAATTGGATCGTGTCTACAACGACATGCGAGAGATTCGTTCAGCAGC\n' |
| b |
| diff -r 000000000000 -r 22f22c3e81bf test-data/interproscan.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/interproscan.tsv Wed Jan 11 11:49:13 2023 +0000 |
| b |
| b'@@ -0,0 +1,5 @@\n+MMUCEDO_000001-T1\t1f9cb956ae0dcbdbd1b334d9b10ec0e9\t227\tMobiDBLite\tmobidb-lite\tconsensus disorder prediction\t1\t49\t-\tT\t27-01-2022\t-\t-\n+MMUCEDO_000002-T1\t2d68be6c38afea689ce7d6783b888576\t189\tCoils\tCoil\tCoil\t117\t137\t-\tT\t27-01-2022\t-\t-\n+MMUCEDO_000005-T1\t47cc622a1d31a46d5070a14eab3796f0\t322\tGene3D\tG3DSA:3.40.50.1820\talpha/beta hydrolase\t4\t316\t4.4E-84\tT\t27-01-2022\tIPR029058\tAlpha/Beta hydrolase fold\t-\tMetaCyc: PWY-1061|MetaCyc: PWY-1121|MetaCyc: PWY-1186|MetaCyc: PWY-1801|MetaCyc: PWY-181|MetaCyc: PWY-1822|MetaCyc: PWY-1901|MetaCyc: PWY-1921|MetaCyc: PWY-1961|MetaCyc: PWY-1981|MetaCyc: PWY-2002|MetaCyc: PWY-2021|MetaCyc: PWY-2055|MetaCyc: PWY-2083|MetaCyc: PWY-2321|MetaCyc: PWY-2343|MetaCyc: PWY-2541|MetaCyc: PWY-2601|MetaCyc: PWY-2881|MetaCyc: PWY-2901|MetaCyc: PWY-2902|MetaCyc: PWY-3162|MetaCyc: PWY-321|MetaCyc: PWY-3261|MetaCyc: PWY-3301|MetaCyc: PWY-3542|MetaCyc: PWY-361|MetaCyc: PWY-3722|MetaCyc: PWY-3841|MetaCyc: PWY-4021|MetaCyc: PWY-4161|MetaCyc: PWY-4202|MetaCyc: PWY-4381|MetaCyc: PWY-4421|MetaCyc: PWY-4801|MetaCyc: PWY-4922|MetaCyc: PWY-5048|MetaCyc: PWY-5059|MetaCyc: PWY-5094|MetaCyc: PWY-5098|MetaCyc: PWY-5101|MetaCyc: PWY-5105|MetaCyc: PWY-5109|MetaCyc: PWY-5129|MetaCyc: PWY-5139|MetaCyc: PWY-5142|MetaCyc: PWY-5147|MetaCyc: PWY-5160|MetaCyc: PWY-5161|MetaCyc: PWY-5163|MetaCyc: PWY-5209|MetaCyc: PWY-5268|MetaCyc: PWY-5271|MetaCyc: PWY-5283|MetaCyc: PWY-5284|MetaCyc: PWY-5286|MetaCyc: PWY-5287|MetaCyc: PWY-5292|MetaCyc: PWY-5301|MetaCyc: PWY-5305|MetaCyc: PWY-5307|MetaCyc: PWY-5310|MetaCyc: PWY-5312|MetaCyc: PWY-5313|MetaCyc: PWY-5316|MetaCyc: PWY-5319|MetaCyc: PWY-5320|MetaCyc: PWY-5321|MetaCyc: PWY-5338|MetaCyc: PWY-5339|MetaCyc: PWY-5342|MetaCyc: PWY-5343|MetaCyc: PWY-5344|MetaCyc: PWY-5353|MetaCyc: PWY-5366|MetaCyc: PWY-5367|MetaCyc: PWY-5379|MetaCyc: PWY-5380|MetaCyc: PWY-5392|MetaCyc: PWY-5397|MetaCyc: PWY-5399|MetaCyc: PWY-5400|MetaCyc: PWY-5407|MetaCyc: PWY-5437|MetaCyc: PWY-5473|MetaCyc: PWY-5475|MetaCyc: PWY-5477|MetaCyc: PWY-5479|MetaCyc: PWY-5489|MetaCyc: PWY-5490|MetaCyc: PWY-5497|MetaCyc: PWY-5499|MetaCyc: PWY-5519|MetaCyc: PWY-5531|MetaCyc: PWY-5629|MetaCyc: PWY-5632|MetaCyc: PWY-5641|MetaCyc: PWY-5642|MetaCyc: PWY-5651|MetaCyc: PWY-5652|MetaCyc: PWY-5660|MetaCyc: PWY-5665|MetaCyc: PWY-5666|MetaCyc: PWY-5667|MetaCyc: PWY-5672|MetaCyc: PWY-5679|MetaCyc: PWY-5706|MetaCyc: PWY-5707|MetaCyc: PWY-5710|MetaCyc: PWY-5729|MetaCyc: PWY-5748|MetaCyc: PWY-5751|MetaCyc: PWY-5754|MetaCyc: PWY-5756|MetaCyc: PWY-5759|MetaCyc: PWY-5765|MetaCyc: PWY-5773|MetaCyc: PWY-5774|MetaCyc: PWY-5782|MetaCyc: PWY-5784|MetaCyc: PWY-5793|MetaCyc: PWY-5794|MetaCyc: PWY-5797|MetaCyc: PWY-5800|MetaCyc: PWY-5818|MetaCyc: PWY-5821|MetaCyc: PWY-5822|MetaCyc: PWY-5830|MetaCyc: PWY-5835|MetaCyc: PWY-5837|MetaCyc: PWY-5846|MetaCyc: PWY-5848|MetaCyc: PWY-5867|MetaCyc: PWY-5875|MetaCyc: PWY-5882|MetaCyc: PWY-5883|MetaCyc: PWY-5903|MetaCyc: PWY-5922|MetaCyc: PWY-5926|MetaCyc: PWY-5927|MetaCyc: PWY-5936|MetaCyc: PWY-5954|MetaCyc: PWY-5955|MetaCyc: PWY-5966|MetaCyc: PWY-5971|MetaCyc: PWY-5972|MetaCyc: PWY-5973|MetaCyc: PWY-5975|MetaCyc: PWY-5976|MetaCyc: PWY-5978|MetaCyc: PWY-5981|MetaCyc: PWY-5984|MetaCyc: PWY-5987|MetaCyc: PWY-5989|MetaCyc: PWY-5994|MetaCyc: PWY-5996|MetaCyc: PWY-601|MetaCyc: PWY-6010|MetaCyc: PWY-6011|MetaCyc: PWY-6015|MetaCyc: PWY-6024|MetaCyc: PWY-6027|MetaCyc: PWY-6032|MetaCyc: PWY-6036|MetaCyc: PWY-6039|MetaCyc: PWY-6045|MetaCyc: PWY-6051|MetaCyc: PWY-6053|MetaCyc: PWY-6056|MetaCyc: PWY-6061|MetaCyc: PWY-6068|MetaCyc: PWY-6069|MetaCyc: PWY-6080|MetaCyc: PWY-6084|MetaCyc: PWY-6087|MetaCyc: PWY-6089|MetaCyc: PWY-6093|MetaCyc: PWY-6094|MetaCyc: PWY-6102|MetaCyc: PWY-6107|MetaCyc: PWY-6148|MetaCyc: PWY-6153|MetaCyc: PWY-6154|MetaCyc: PWY-6178|MetaCyc: PWY-6185|MetaCyc: PWY-6190|MetaCyc: PWY-6193|MetaCyc: PWY-6239|MetaCyc: PWY-6279|MetaCyc: PWY-6282|MetaCyc: PWY-6286|MetaCyc: PWY-6289|MetaCyc: PWY-6297|MetaCyc: PWY-6303|MetaCyc: PWY-6309|MetaCyc: PWY-6310|MetaCyc: PWY-6312|MetaCyc: PWY-6314|MetaCyc: PWY-6316|MetaC'..b'3560|Reactome: R-HSA-163765|Reactome: R-HSA-1660662|Reactome: R-HSA-192456|Reactome: R-HSA-193368|Reactome: R-HSA-199220|Reactome: R-HSA-2022377|Reactome: R-HSA-203615|Reactome: R-HSA-211945|Reactome: R-HSA-2132295|Reactome: R-HSA-2142670|Reactome: R-HSA-2426168|Reactome: R-HSA-3214847|Reactome: R-HSA-373760|Reactome: R-HSA-381340|Reactome: R-HSA-381771|Reactome: R-HSA-390247|Reactome: R-HSA-400511|Reactome: R-HSA-4085001|Reactome: R-HSA-418346|Reactome: R-HSA-422085|Reactome: R-HSA-426048|Reactome: R-HSA-4341670|Reactome: R-HSA-6794361|Reactome: R-HSA-6798695|Reactome: R-HSA-6803205|Reactome: R-HSA-6809371|Reactome: R-HSA-69273|Reactome: R-HSA-71240|Reactome: R-HSA-72764|Reactome: R-HSA-75105|Reactome: R-HSA-77289|Reactome: R-HSA-8963889|Reactome: R-HSA-8963901|Reactome: R-HSA-8964026|Reactome: R-HSA-8964038|Reactome: R-HSA-8964058|Reactome: R-HSA-9018682|Reactome: R-HSA-9029558|Reactome: R-HSA-9033241|Reactome: R-HSA-9648002|Reactome: R-HSA-9696273|Reactome: R-HSA-975634|Reactome: R-MMU-140837|Reactome: R-MMU-1482801|Reactome: R-MMU-1482839|Reactome: R-MMU-1482883|Reactome: R-MMU-1483115|Reactome: R-MMU-1483166|Reactome: R-MMU-1483191|Reactome: R-MMU-156584|Reactome: R-MMU-156588|Reactome: R-MMU-156590|Reactome: R-MMU-159418|Reactome: R-MMU-162791|Reactome: R-MMU-163765|Reactome: R-MMU-1660662|Reactome: R-MMU-192456|Reactome: R-MMU-193368|Reactome: R-MMU-199220|Reactome: R-MMU-2022377|Reactome: R-MMU-203615|Reactome: R-MMU-211945|Reactome: R-MMU-2132295|Reactome: R-MMU-2142670|Reactome: R-MMU-3214847|Reactome: R-MMU-373760|Reactome: R-MMU-381771|Reactome: R-MMU-390247|Reactome: R-MMU-400511|Reactome: R-MMU-4085001|Reactome: R-MMU-418346|Reactome: R-MMU-422085|Reactome: R-MMU-426048|Reactome: R-MMU-6794361|Reactome: R-MMU-6798695|Reactome: R-MMU-6809371|Reactome: R-MMU-69273|Reactome: R-MMU-72764|Reactome: R-MMU-75105|Reactome: R-MMU-77289|Reactome: R-MMU-8963889|Reactome: R-MMU-8963901|Reactome: R-MMU-8964026|Reactome: R-MMU-8964038|Reactome: R-MMU-8964058|Reactome: R-MMU-9018682|Reactome: R-MMU-9033241|Reactome: R-MMU-9648002|Reactome: R-MMU-9696273|Reactome: R-MMU-975634|Reactome: R-RNO-1482801|Reactome: R-RNO-1482883|Reactome: R-RNO-1483115|Reactome: R-RNO-156584|Reactome: R-RNO-156588|Reactome: R-RNO-156590|Reactome: R-RNO-159418|Reactome: R-RNO-162791|Reactome: R-RNO-163765|Reactome: R-RNO-192456|Reactome: R-RNO-193368|Reactome: R-RNO-199220|Reactome: R-RNO-2022377|Reactome: R-RNO-203615|Reactome: R-RNO-211945|Reactome: R-RNO-2142670|Reactome: R-RNO-3214847|Reactome: R-RNO-373760|Reactome: R-RNO-381771|Reactome: R-RNO-400511|Reactome: R-RNO-418346|Reactome: R-RNO-426048|Reactome: R-RNO-6794361|Reactome: R-RNO-6798695|Reactome: R-RNO-69273|Reactome: R-RNO-72764|Reactome: R-RNO-75105|Reactome: R-RNO-77289|Reactome: R-RNO-8963889|Reactome: R-RNO-8963901|Reactome: R-RNO-8964026|Reactome: R-RNO-8964038|Reactome: 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