| Next changeset 1:c409a495841f (2021-05-19) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b" |
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added:
customizemapping.py customizemetadata.py humann_genefamilies_genus_level humann_infer_taxonomy humann_regroup_table.xml macros.xml static/images/731303924-page_DENITRIFICATION-PWY.png test-data/barplot1.png test-data/barplot2.pdf test-data/barplot3.svg test-data/barplot4.png test-data/cpm_community_renormalized_pathway_abundance.tsv test-data/demo-taxonomic-profile.tabular test-data/demo.fasta.gz test-data/demo.fastq.gz test-data/demo.sam test-data/demo_genefamilies.tsv test-data/demo_joined_pathabundance_pathcoverage.tsv test-data/demo_pathabundance.tsv test-data/demo_pathcoverage.tsv test-data/genus-level-gene-families.tsv test-data/hmp_pathabund.txt test-data/humann_nucleotide_database.loc test-data/humann_protein_database.loc test-data/humann_utility_mapping.loc test-data/metaphlan_database.loc test-data/regrouped_gene_families_to_infogo1000.tsv test-data/relab_levelwise_renormalized_pathway_abundance.tsv test-data/rna_dna_norm-dna.txt test-data/rna_dna_norm-rna.txt test-data/strain_profiler-input.txt test-data/test-db/metaphlan-db/demo-db-v30.1.bt2 test-data/test-db/metaphlan-db/demo-db-v30.2.bt2 test-data/test-db/metaphlan-db/demo-db-v30.3.bt2 test-data/test-db/metaphlan-db/demo-db-v30.4.bt2 test-data/test-db/metaphlan-db/demo-db-v30.fasta test-data/test-db/metaphlan-db/demo-db-v30.json test-data/test-db/metaphlan-db/demo-db-v30.pkl test-data/test-db/metaphlan-db/demo-db-v30.rev.1.bt2 test-data/test-db/metaphlan-db/demo-db-v30.rev.2.bt2 test-data/test-db/metaphlan-db/humann_markers.tabular test-data/test-db/nucleotide-db/g__Bacteroides.s__Bacteroides_dorei.centroids.v296_201901b.ffn.gz test-data/test-db/nucleotide-db/g__Bacteroides.s__Bacteroides_vulgatus.centroids.v296_201901b.ffn.gz test-data/test-db/protein-db/uniref90_demo_prots_v201901b.dmnd test-data/test-db/protein-db/uniref90_demo_prots_v201901b.fasta test-data/test-db/utility_mapping/map_go_uniref90.txt test-data/test-db/utility_mapping/map_uniref90_name.txt tool-data/humann_nucleotide_database.loc.sample tool-data/humann_protein_database.loc.sample tool-data/humann_utility_mapping.loc.sample tool-data/metaphlan_database.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test transform_json_to_pkl.py |
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| diff -r 000000000000 -r 26ce946f4da9 customizemapping.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/customizemapping.py Wed May 12 08:59:30 2021 +0000 |
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| @@ -0,0 +1,47 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- + +import argparse +from pathlib import Path + + +if __name__ == '__main__': + # Read command line + parser = argparse.ArgumentParser(description='Customize HUMAnN utility mapping') + parser.add_argument('--in_mapping', help="Path to mapping file to reduce") + parser.add_argument('--features', help="Path to tabular file with features to keep in first column") + parser.add_argument('--elements', help="Path to tabular file with elements to keep in other columns") + parser.add_argument('--out_mapping', help="Path to reduced mapping file") + args = parser.parse_args() + + in_mapping_fp = Path(args.in_mapping) + feature_fp = Path(args.features) + element_fp = Path(args.elements) + out_mapping_fp = Path(args.out_mapping) + + # extract features to keep + features = set() + with open(feature_fp, 'r') as feature_f: + for line in feature_f.readlines(): + features.add(line.split("\t")[0]) + print(features) + + # extract elements to keep + elements = set() + with open(element_fp, 'r') as element_f: + for line in element_f.readlines(): + elements.add(line.split("\t")[0]) + print(elements) + + # write mapping for features to keep while keeping only elements + with open(in_mapping_fp, 'r') as in_mapping_f: + with open(out_mapping_fp, 'w') as out_mapping_f: + for line in in_mapping_f.readlines(): + l_split = line.split("\t") + feat = l_split[0] + if feat in features: + to_write = [feat] + for e in l_split[1:]: + if e in elements: + to_write.append(e) + out_mapping_f.write("%s\n" % '\t'.join(to_write)) |
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| diff -r 000000000000 -r 26ce946f4da9 customizemetadata.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/customizemetadata.py Wed May 12 08:59:30 2021 +0000 |
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| b"@@ -0,0 +1,480 @@\n+#!/usr/bin/env python\n+# -*- coding: utf-8 -*-\n+\n+import argparse\n+import bz2\n+import json\n+import pickle\n+import re\n+from pathlib import Path\n+\n+\n+def load_from_json(json_fp):\n+ '''\n+ Read JSON file with marker metadata\n+\n+ :param json_fp: Path to JSON file\n+ '''\n+ with open(json_fp, 'r') as json_f:\n+ data = json.load(json_f)\n+\n+ for m in data['markers']:\n+ data['markers'][m]['ext'] = set(data['markers'][m]['ext'])\n+\n+ for t in data['taxonomy']:\n+ if isinstance(data['taxonomy'][t], list):\n+ data['taxonomy'][t] = tuple(data['taxonomy'][t])\n+ return data\n+\n+\n+def dump_to_json(data, json_fp):\n+ '''\n+ Dump marker metadata to JSON file\n+\n+ :param json_fp: Path to JSON file\n+ '''\n+ for m in data['markers']:\n+ data['markers'][m]['ext'] = list(data['markers'][m]['ext'])\n+\n+ with open(json_fp, 'w') as json_f:\n+ json.dump(data, json_f)\n+\n+\n+def transform_pkl_to_json(pkl_fp, json_fp):\n+ '''\n+ Read Pickle file and drop it to a JSON file\n+\n+ :param pkl_fp: Path to input Pickle file\n+ :param json_fp: Path to output JSON file\n+ '''\n+ # load metadata from Pickle file\n+ with bz2.BZ2File(pkl_fp, 'r') as pkl_f:\n+ in_metadata = pickle.load(pkl_f)\n+\n+ out_metadata = {\n+ 'markers': in_metadata['markers'],\n+ 'taxonomy': in_metadata['taxonomy'],\n+ 'merged_taxon': {}\n+ }\n+ # transform merged_taxons tuple keys to string\n+ for k in in_metadata['merged_taxon']:\n+ n = ' , '.join(k)\n+ out_metadata[n] = in_metadata['merged_taxon'][k]\n+\n+ # dump metadata to JSON file\n+ dump_to_json(out_metadata, json_fp)\n+\n+\n+def transform_json_to_pkl(json_fp, pkl_fp):\n+ '''\n+ Read JSON file and drop it to a Pickle file\n+\n+ :param json_fp: Path to input JSON file\n+ :param pkl_fp: Path to output Pickle file\n+ '''\n+ # load metadata from JSON file\n+ in_metadata = load_from_json(json_fp)\n+\n+ out_metadata = {\n+ 'markers': in_metadata['markers'],\n+ 'taxonomy': in_metadata['taxonomy'],\n+ 'merged_taxon': {}\n+ }\n+ # transform merged_taxons keys to tuple\n+ for k in in_metadata['merged_taxon']:\n+ n = ' , '.split(k)\n+ out_metadata[n] = in_metadata['merged_taxon'][k]\n+\n+ # dump metadata to Pickle file\n+ with bz2.BZ2File(pkl_fp, 'w') as pkl_f:\n+ pickle.dump(out_metadata, pkl_f)\n+\n+\n+def add_marker(in_json_fp, out_json_fp, name, m_length, g_length, gca, k_name, k_id, p_name, p_id, c_name, c_id, o_name, o_id, f_name, f_id, g_name, g_id, s_name, s_id, t_name):\n+ '''\n+ Add marker to JSON file\n+\n+ :param in_json_fp: Path to input JSON file\n+ :param out_json_fp: Path to output JSON file\n+ :param name: Name of new marker\n+ :param m_length: Length of new marker\n+ :param g_length: List with lengths of genomes from which the new marker has been extracted\n+ :param gca: List with GCA of genomes from which the new marker has been extracted\n+ :param k_name: List with Name of Kingdom for genomes from which the new marker has been extracted\n+ :param k_id: List with NCBI id of Kingdom for genomes from which the new marker has been extracted\n+ :param p_name: List with Name of Phylum for genomes from which the new marker has been extracted\n+ :param p_id: List with NCBI id of Phylum for genomes from which the new marker has been extracted\n+ :param c_name: List with Name of Class for genomes from which the new marker has been extracted\n+ :param c_id: List with NCBI id of Class for genomes from which the new marker has been extracted\n+ :param o_name: List with Name of Order for genomes from which the new marker has been extracted\n+ :param o_id: List with NCBI id of Order for genomes from which the new marker has been extracted\n+ :param f_name: List with Name of Family for genomes from which the new marker has been extracted\n+ :param f_id: List with NCBI id of Family for genomes from which th"..b'for genome from which the new marker has been extracted", action="append")\n+ add_marker_parser.add_argument(\'--p_name\', help="Name of Phylum for genome from which the new marker has been extracted", action="append")\n+ add_marker_parser.add_argument(\'--p_id\', help="NCBI id of Phylum for genome from which the new marker has been extracted", action="append")\n+ add_marker_parser.add_argument(\'--c_name\', help="Name of Class for genome from which the new marker has been extracted", action="append")\n+ add_marker_parser.add_argument(\'--c_id\', help="NCBI id of Class for genome from which the new marker has been extracted", action="append")\n+ add_marker_parser.add_argument(\'--o_name\', help="Name of Order for genome from which the new marker has been extracted", action="append")\n+ add_marker_parser.add_argument(\'--o_id\', help="NCBI id of Order for genome from which the new marker has been extracted", action="append")\n+ add_marker_parser.add_argument(\'--f_name\', help="Name of Family for genome from which the new marker has been extracted", action="append")\n+ add_marker_parser.add_argument(\'--f_id\', help="NCBI id of Family for genome from which the new marker has been extracted", action="append")\n+ add_marker_parser.add_argument(\'--g_name\', help="Name of Genus for genome from which the new marker has been extracted", action="append")\n+ add_marker_parser.add_argument(\'--g_id\', help="NCBI id of Genus for genome from which the new marker has been extracted", action="append")\n+ add_marker_parser.add_argument(\'--s_name\', help="Name of Species for genome from which the new marker has been extracted", action="append")\n+ add_marker_parser.add_argument(\'--s_id\', help="NCBI id of Species for genome from which the new marker has been extracted", action="append")\n+ add_marker_parser.add_argument(\'--t_name\', help="Name of Strain for genome from which the new marker has been extracted", action="append")\n+ # remove_markers subcommand\n+ remove_markers_parser = subparsers.add_parser(\'remove_markers\', help=\'Remove markers from JSON file\')\n+ remove_markers_parser.add_argument(\'--in_json\', help="Path to input JSON file")\n+ remove_markers_parser.add_argument(\'--markers\', help="Path to file with markers to remove (1 per line)")\n+ remove_markers_parser.add_argument(\'--out_json\', help="Path to output JSON file")\n+ remove_markers_parser.add_argument(\'--kept_markers\', help="Path to file with kept markers")\n+ # keep_markers subcommand\n+ keep_markers_parser = subparsers.add_parser(\'keep_markers\', help=\'Keep markers from JSON file, others will be removed\')\n+ keep_markers_parser.add_argument(\'--in_json\', help="Path to input JSON file")\n+ keep_markers_parser.add_argument(\'--markers\', help="Path to file with markers to keep (1 per line)")\n+ keep_markers_parser.add_argument(\'--out_json\', help="Path to output JSON file")\n+\n+ args = parser.parse_args()\n+\n+ if args.function == \'transform_pkl_to_json\':\n+ transform_pkl_to_json(Path(args.pkl), Path(args.json))\n+ elif args.function == \'transform_json_to_pkl\':\n+ transform_json_to_pkl(Path(args.json), Path(args.pkl))\n+ elif args.function == \'add_marker\':\n+ add_marker(\n+ args.in_json,\n+ args.out_json,\n+ args.name,\n+ args.m_length,\n+ args.g_length,\n+ args.gca,\n+ args.k_name,\n+ args.k_id,\n+ args.p_name,\n+ args.p_id,\n+ args.c_name,\n+ args.c_id,\n+ args.o_name,\n+ args.o_id,\n+ args.f_name,\n+ args.f_id,\n+ args.g_name,\n+ args.g_id,\n+ args.s_name,\n+ args.s_id,\n+ args.t_name)\n+ elif args.function == \'remove_markers\':\n+ remove_markers(args.in_json, args.markers, args.out_json, args.kept_markers)\n+ elif args.function == \'keep_markers\':\n+ keep_markers(args.in_json, args.markers, args.out_json)\n' |
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| diff -r 000000000000 -r 26ce946f4da9 humann_genefamilies_genus_level --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/humann_genefamilies_genus_level Wed May 12 08:59:30 2021 +0000 |
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| @@ -0,0 +1,52 @@ +<!-- The tool is broken with current version of HUMAnN. Once it will be fixed (PR merged), we can update this wrapper and add the XML extension to enable it --> +<tool id="humann_genefamilies_genus_level" name="Create a genus level" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>gene families and pathways from HUMAnN species level gene families</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="edam_ontology"/> + <expand macro="requirements"/> + <expand macro="version"/> + <command detect_errors="exit_code"><![CDATA[ +humann_genefamilies_genus_level + --input '$input' + --output '$gene_families' +&& +humann + --input '$gene_families' + --output '$pathways' + ]]></command> + <inputs> + <param argument="--input" type="data" format="tsv,tabular" label="Species level gene families" help="Direct output from HUMAnN"/> + </inputs> + <outputs> + <data name="gene_families" format="tabular" label="${tool.name} on ${on_string}: Genus level gene families"/> + <data name="pathways" format="tabular" label="${tool.name} on ${on_string}: Genus level pathways"/> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="input" value="demo_genefamilies.tsv"/> + <output name="gene_families" ftype="tabular" value="genus-level-gene-families.tsv" compare="sim_size"> + <assert_contents> + <has_text text="humann_Abundance"/> + <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis|unclassified"/> + <has_n_columns n="2"/> + </assert_contents> + </output> + <output name="pathways" ftype="tabular" value="genus-level-pathways.tsv" compare="sim_size"> + <assert_contents> + <has_text text="humann_Abundance"/> + <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis|unclassified"/> + <has_n_columns n="2"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +@HELP_HEADER@ + +By default, the gene families and pathways output files from HUMAnN are species level. +This tool generates genus level gene families and pathways + ]]></help> + <expand macro="citations"/> +</tool> |
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| diff -r 000000000000 -r 26ce946f4da9 humann_infer_taxonomy --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/humann_infer_taxonomy Wed May 12 08:59:30 2021 +0000 |
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| @@ -0,0 +1,81 @@ +<!-- The tool is broken with current version of HUMAnN. Once it will be fixed, we can update this wrapper and add the XML extension to enable it --> +<tool id="humann_infer_taxonomy" name="Infex taxonomy" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>for "unclassified" taxonomy in HUMAnN generated gene families</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="edam_ontology"/> + <expand macro="requirements"/> + <expand macro="version"/> + <command detect_errors="exit_code"><![CDATA[ +humann_infer_taxonomy + --input '$input' + --output '$output' + --level '$level' + --database '$database.fields.path' + --mode '$mode' + --lca-choice '$lca_choice' + --threshold $threshold + ]]></command> + <inputs> + <param argument="--input" type="data" format="tsv,tabular" label="Gene family table"/> + <param argument="--level" type="select" label="Desired level for taxonomic estimation/summation"> + <option value="Kingdom">Kingdom</option> + <option value="Phylum">Phylum</option> + <option value="Class">Class</option> + <option value="Order">Order</option> + <option value="Family" selected="true">Family</option> + <option value="Genus">Genus</option> + </param> + <param argument="--database" type="select" label="UniRef-specific taxonomy database"> + <options from_data_table="humann_utility_mapping"> + <validator message="No utility mapping is available" type="no_options" /> + <filter type="regexp" column="2" value="tol-lca" /> + </options> + </param> + <param argument="--mode" type="select" label="Rows to include in the estimation/summation"> + <option value="c_tmode" selected="true">Totals</option> + <option value="c_umode">Unclassified</option> + <option value="c_smode">Stratified</option> + </param> + <param argument="--lca-choice" type="select" label="Per-gene taxonomic annotation to consider"> + <option value="source_tax">Source taxonomy</option> + <option value="uniref_lca">UniRef lowest common ancestor (LCA)</option> + <option value="humann_lca" selected="true">HUMAnN lowest common ancestor (LCA)</option> + </param> + <param argument="--threshold" type="float" value="1e-3" label="Minimum frequency for a new taxon to be included"/> + </inputs> + <outputs> + <data format="tabular" name="output"/> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="input" value=""/> + <param name="level" value="Kingdom"/> + <param name="database" value=""/> + <param name="mode" value="c_tmode"/> + <param name="lca_choice" value="source_tax"/> + <param name="threshold" value="1e-3"/> + <output name="output" ftype="tabular"> + <assert_contents> + <has_text text=""/> + <has_line line=""/> + <has_line_matching expression=""/> + <has_n_columns n=""/> + <has_size value="" delta=""/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +@HELP_HEADER@ + +Based on the lowest common ancestor (LCA) annotation +of each UniRef50/90 cluster, this tool infers approximate taxonomy +for unclassified features at a target level of resolution. + +It will modify features of known genus/species to match +target level. + ]]></help> + <expand macro="citations"/> +</tool> |
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| diff -r 000000000000 -r 26ce946f4da9 humann_regroup_table.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/humann_regroup_table.xml Wed May 12 08:59:30 2021 +0000 |
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| b'@@ -0,0 +1,182 @@\n+<tool id="humann_regroup_table" name="Regroup" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n+ <description>HUMAnN table features</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="edam_ontology"/>\n+ <expand macro="requirements"/>\n+ <expand macro="version"/>\n+ <command detect_errors="exit_code"><![CDATA[\n+humann_regroup_table\n+ --input \'$input\'\n+ --output \'$output\'\n+ --function \'$function\'\n+#if $grouping.type == "standard"\n+ --groups \'$grouping.groups\'\n+#else if $grouping.type == "large"\n+ --custom \'$grouping.grouping.fields.path\'\n+ $grouping.reversed\n+#else:\n+ --custom \'$grouping.custom\'\n+ $grouping.reversed\n+#end if\n+ --precision $precision\n+ --ungrouped \'$ungrouped\'\n+ --protected \'$protected\'\n+ ]]></command>\n+ <inputs>\n+ <param argument="--input" type="data" format="tsv,tabular" label="Gene families table"/>\n+ <param argument="--function" type="select" label="How to combine grouped features?">\n+ <option value="sum" selected="true">Sum</option>\n+ <option value="mean">Mean</option>\n+ </param>\n+ <conditional name="grouping">\n+ <param name="type" type="select" label="Grouping">\n+ <option value="standard">Basic grouping (to MetaCyc pathways)</option>\n+ <option value="large">Grouping with larger mapping</option>\n+ <option value="custom">Grouping with custom mapping</option>\n+ </param>\n+ <when value="standard">\n+ <param argument="--groups" type="select" label="Grouping">\n+ <option value="uniref90_rxn">UniRef90 to MetaCyc pathways</option>\n+ <option value="uniref50_rxn">UniRef50 to MetaCyc pathways</option>\n+ </param>\n+ </when>\n+ <when value="large">\n+ <param name="grouping" type="select" label="Mapping to use for the grouping">\n+ <options from_data_table="humann_utility_mapping">\n+ <validator message="No utility mapping is available" type="no_options" />\n+ <filter type="regexp" column="0" value=".*map.*(?!_name)" keep="true"/>\n+ </options>\n+ </param>\n+ <param argument="--reversed" type="boolean" checked="false" truevalue="--reversed" falsevalue="" label="Mapping from features to groups?"/>\n+ </when>\n+ <when value="custom">\n+ <param argument="--custom" type="data" format="tsv,txt,tabular" label="Custom mapping file for grouping" help="The format is explained in the help"/>\n+ <param argument="--reversed" type="boolean" checked="false" truevalue="--reversed" falsevalue="" label="Is the groups file reversed?" help="Mapping from features to groups"/>\n+ </when>\n+ </conditional>\n+ <param argument="--precision" type="integer" value="3" label="Decimal places to round to after applying function"/>\n+ <param argument="--ungrouped" type="boolean" checked="true" truevalue="Y" falsevalue="N" label="Include an \'UNGROUPED\' group to capture features that did not belong to other groups?"/>\n+ <param argument="--protected" type="boolean" checked="true" truevalue="Y" falsevalue="N" label="Carry through protected features, such as \'UNMAPPED\'?"/>\n+ </inputs>\n+ <outputs>\n+ <data name="output" format="tabular"/>\n+ </outputs>\n+ <tests>\n+ <test expect_num_outputs="1">\n+ <param name="input" value="demo_genefamilies.tsv"/>\n+ <param name="function" value="sum"/>\n+ <conditional name="grouping">\n+ <param name="type" value="standard"/>\n+ <param name="groups" value="uniref90_rxn"/>\n+ </conditional>\n+ <param name="precision" value="3"/>\n+ <param name="ungrouped" value="Y"/>\n+ '..b' <has_text text="GO:0003866|g__Bacteroides.s__Bacteroides_vulgatus" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test expect_num_outputs="1">\n+ <param name="input" value="demo_genefamilies.tsv"/>\n+ <param name="function" value="sum"/>\n+ <conditional name="grouping">\n+ <param name="type" value="custom"/>\n+ <!-- file generated using customizemapping file -->\n+ <param name="custom" value="test-db/utility_mapping/map_go_uniref90.txt"/>\n+ </conditional>\n+ <param name="precision" value="3"/>\n+ <param name="ungrouped" value="Y"/>\n+ <param name="protected" value="Y"/>\n+ <output name="output" ftype="tabular">\n+ <assert_contents>\n+ <has_text text="GO:0000049|g__Bacteroides.s__Bacteroides_vulgatus" />\n+ <has_text text="GO:0003866|g__Bacteroides.s__Bacteroides_vulgatus" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+@HELP_HEADER@\n+\n+This tool takes a table of feature values and a mapping of groups to component features to produce \n+a new table with group values in place of feature values.\n+\n+HUMAnN gene family output can contain a very large number of features depending on the complexity \n+of your underlying sample. One way to explore this information in a simplified manner is via HUMAnN\'s \n+own pathway coverage and abundance, which summarize the values of their member genes. However, this \n+approach does not apply to gene families that are not associated with metabolic pathways.\n+\n+To further simplify the exploration of gene family abundance data, users can regroup gene families \n+into other functional categories using the current tool. This tool takes as arguments a gene \n+family abundance table and a mapping (groups) file that indicates which gene families belong to which \n+groups.\n+\n+Out of the box, HUMAnN can regroup gene families to MetaCyc reactions (a step which is also \n+used internally as part of MetaCyc pathway quantification). Users can use additional mapping files \n+for both UniRef90 and UniRef50 gene families to the following systems:\n+\n+- MetaCyc Reactions\n+- KEGG Orthogroups (KOs)\n+- Pfam domains\n+- Level-4 enzyme commission (EC) categories\n+- EggNOG (including COGs)\n+- Gene Ontology (GO)\n+- Informative GO\n+\n+In most cases, mappings are directly inferred from the annotation of the corresponding UniRef centroid sequence in UniProt.\n+\n+One exception to this are the "informative GO" (infogo1000) maps: These are informative subsets of GO computed from UniProt\'s \n+annotations and the structure of the GO hierarchy specifically for HUMAnN (each informative GO term has >1,000 UniRef centroids \n+annotated to it, but none of its progeny terms have >1,000 centroids so annotated).\n+\n+If the "UNMAPPED" gene abundance feature is included in a user\'s input, it will automatically be carried forward to the final output. \n+In addition, genes that do not group with a non-trivial feature are combined as an "UNGROUPED" group. By default, UNGROUPED reflects \n+the total abundance of genes that did not belong to another group (similar in spirit to the "UNINTEGRATED" value reported in the pathway \n+abundance file).\n+\n+\n+Some groups are not associated by default with human-readable names. To attach names to a regrouped table, use the HUMAnN rename tool\n+(The "GO" name map can be used for both raw GO and informative GO.) \n+\n+Inputs\n+======\n+\n+Users are free to create and use additional mapping files and pass them to this tool. The format of a mapping file is:\n+\n+``\n+group1 uniref1 uniref2 uniref3 ...\n+``\n+\n+``\n+group2 uniref1 uniref5 ...\n+``\n+\n+Where spaces between items above denote TABS. By default, feature abundances (such as gene families) are summed to produce group abundances.\n+\n+\n+\n+]]></help>\n+ <expand macro="citations"/>\n+</tool>\n' |
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| @@ -0,0 +1,38 @@ +<?xml version="1.0"?> +<macros> + <token name="@TOOL_VERSION@">3.0.0</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">20.01</token> + <xml name="edam_ontology"> + <edam_topics> + <edam_topic>topic_3174</edam_topic> + <edam_topic>topic_0194</edam_topic> + </edam_topics> + <edam_operations> + <edam_operation>operation_2478</edam_operation> + <edam_operation>operation_0324</edam_operation> + </edam_operations> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">humann</requirement> + <yield/> + </requirements> + </xml> + <xml name="version"> + <version_command>humann --version</version_command> + </xml> + <token name="@HELP_HEADER@"> +What it does +============ + +HUMAnN is a pipeline for efficiently and accuretly profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data. + +Read more about the tool: http://huttenhower.sph.harvard.edu/humann + </token> + <xml name="citations"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1002358</citation> + </citations> + </xml> +</macros> |
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| diff -r 000000000000 -r 26ce946f4da9 test-data/cpm_community_renormalized_pathway_abundance.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cpm_community_renormalized_pathway_abundance.tsv Wed May 12 08:59:30 2021 +0000 |
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| @@ -0,0 +1,5 @@ +# Pathway humann_Abundance +PWY-5423: oleoresin monoterpene volatiles biosynthesis 578694 +PWY-5423: oleoresin monoterpene volatiles biosynthesis|unclassified 578694 +PWY-4203: volatile benzenoid biosynthesis I (ester formation) 421306 +PWY-4203: volatile benzenoid biosynthesis I (ester formation)|unclassified 421306 |
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| diff -r 000000000000 -r 26ce946f4da9 test-data/demo-taxonomic-profile.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demo-taxonomic-profile.tabular Wed May 12 08:59:30 2021 +0000 |
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| @@ -0,0 +1,12 @@ +#full-db +#metaphlan in --input_type fasta --read_min_len 70 --bt2_ps very-sensitive --min_mapq_val 5 --bowtie2db test-data/test-db/metaphlan-db --index demo-db-v30 -t rel_ab --tax_lev a --min_cu_len 2000 --add_viruses --stat_q 0.2 --perc_nonzero 0.33 --avoid_disqm --sample_id_key SampleID --sample_id Metaphlan_Analysis -o /tmp/tmp7hcectnz/files/000/dataset_2.dat --bowtie2out bowtie2out -s /tmp/tmp7hcectnz/files/000/dataset_4.dat --biom /tmp/tmp7hcectnz/files/000/dataset_5.dat --nproc 1 +#SampleID Metaphlan_Analysis +#clade_name NCBI_tax_id relative_abundance additional_species +k__Bacteria 2 100.0 +k__Bacteria|p__Bacteroidetes 2|976 100.0 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia 2|976|200643 100.0 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales 2|976|200643|171549 100.0 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae 2|976|200643|171549|815 100.0 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides 2|976|200643|171549|815|816 100.0 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_vulgatus 2|976|200643|171549|815|816|821 50.80292 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_dorei 2|976|200643|171549|815|816|357276 49.19708 |
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| b |
| b'@@ -0,0 +1,5000 @@\n+s__Bacteroides_dorei_read000001\t16\t357276|g__Bacteroides.s__Bacteroides_dorei|UniRef90_R7NX76|UniRef50_R5GDB8|927\t423\t11\t100M\t*\t0\t0\tTTTCGTATTAGTGGAGTATGGCATTGAAAGTACGGATGATGACACGTTGCGCAGGATAAACCGGGGACATACTTTTGCCGTTTCTGCAGAGGCTGTTCGG\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-12\tXS:i:-30\tXN:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tNM:i:2\tMD:Z:3T38A57\tYT:Z:UU\n+s__Bacteroides_dorei_read000002\t0\t357276|g__Bacteroides.s__Bacteroides_dorei|UniRef90_A6L5K0|UniRef50_A6L5K0|468\t88\t25\t100M\t*\t0\t0\tTTTACTGTAGTCGCCCTATTGGGATTACAGGATTCAGACTCTAACATAACCATCGGAAACAACTTCGAGAGCAAAAAGCTAGGTAAAAAAGGAATTTTCA\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-6\tXS:i:-42\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:96A3\tYT:Z:UU\n+s__Bacteroides_dorei_read000003\t16\t357276|g__Bacteroides.s__Bacteroides_dorei|UniRef90_A6L5D4|UniRef50_C6X591|1338\t1159\t0\t100M\t*\t0\t0\tAATACACGACAGGAAGATTATTCCGGCAAGAATTTTTCGGAGTTTGAACTGAGCGCTATGGAAAAACGTCATATTGCTAAAGTTCTGCAACATACTAAAG\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-24\tXS:i:-36\tXN:i:0\tXM:i:4\tXO:i:0\tXG:i:0\tNM:i:4\tMD:Z:5C28A16G0C47\tYT:Z:UU\n+s__Bacteroides_dorei_read000004\t16\t821|g__Bacteroides.s__Bacteroides_vulgatus|UniRef90_A6L7A5|UniRef50_R7NQK6|948\t802\t1\t100M\t*\t0\t0\tCAACACTCACGGGAAATCCCCTTCAATGAATTATGGGACAGAATGCTAAGAATCAGAAAAAACAATTATATACATCTTCCACTTTACCTAAAAATAAAGT\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-12\tXS:i:-12\tXN:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tNM:i:2\tMD:Z:85C0T13\tYT:Z:UU\n+s__Bacteroides_dorei_read000005\t0\t357276|g__Bacteroides.s__Bacteroides_dorei|UniRef90_A6L5C5|UniRef50_R6HHA5|1347\t637\t23\t100M\t*\t0\t0\tATAACATCCTTACATTCTGATGAAATTTGTTTCCGAGGTATGGAACATACTGGACCTCTTACATACGGTGAGGCCGAGAATTTTTTTGATAGCGGCATTG\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-24\tXN:i:0\tXM:i:4\tXO:i:0\tXG:i:0\tNM:i:4\tMD:Z:51C2A16A12A15\tYT:Z:UU\n+s__Bacteroides_dorei_read000006\t16\t357276|g__Bacteroides.s__Bacteroides_dorei|UniRef90_unknown|UniRef50_D5EYI2|2565\t184\t7\t100M\t*\t0\t0\tAATCCCGTTGCTTTATTGGAACGTTTGAGCTATGAAAAGCAGGAGGCATTAACCCAGGATAAGGTTATTGTAAAGCGCCTGAACGATGTATATGCTAAAT\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-18\tXS:i:-30\tXN:i:0\tXM:i:3\tXO:i:0\tXG:i:0\tNM:i:3\tMD:Z:40T24G12A21\tYT:Z:UU\n+s__Bacteroides_dorei_read000007\t16\t357276|g__Bacteroides.s__Bacteroides_dorei|UniRef90_R7P3C8|UniRef50_X5DCD9|1692\t629\t1\t100M\t*\t0\t0\tTGGCAGGAGAAGCCTATCTTCGGATGGGTATGCGTGATGCTTCCTAATTCAAGAAGGCGGAAGATGCGGTGACGCCTATTATACCAGGTGGCAAATATGA\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-18\tXS:i:-18\tXN:i:0\tXM:i:3\tXO:i:0\tXG:i:0\tNM:i:3\tMD:Z:46T36A7T8\tYT:Z:UU\n+s__Bacteroides_dorei_read000009\t0\t357276|g__Bacteroides.s__Bacteroides_dorei|UniRef90_unknown|UniRef50_R7DSH7|2871\t804\t2\t100M\t*\t0\t0\tAGGTACAGCCGGCTTTGCCTCCACCGAGAAAAAACCAGAAAAACCCTTTGCACAATGGATTCCCCGTATTCCCGAAACAGGAAAATATGCCGTCGATGTG\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-24\tXS:i:-30\tXN:i:0\tXM:i:4\tXO:i:0\tXG:i:0\tNM:i:4\tMD:Z:10C25G6G50T5\tYT:Z:UU\n+s__Bacteroides_dorei_read000012\t16\t357276|g__Bacteroides.s__Bacteroides_dorei|UniRef90_R6HWU5|UniRef50_R5JSB1|459\t11\t40\t100M\t*\t0\t0\tTATCTTATAAAATGTCCTACTATGCTTTATATGTCTGCTTTGCCGTTATTTTGGTAGTATTGGGCATGTTCTTCTTGGTAGGTTATAATAATCCGGTGGG\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-12\tXN:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tNM:i:2\tMD:Z:4A77A17\tYT:Z:UU\n+s__Bacteroides_dorei_read000013\t16\t357276|g__Bacteroides.s__Bacteroides_dorei|UniRef90_R6AN66|UniRef50_P9WQK2|1689\t1394\t12\t100M\t*\t0\t0\tTGGCACTGAAGGAAGAAGGCAACGTGCTGCTGCTGGACGAGCCTACCAATGATATTGACGTGAACTCGCTGCGCGCGCTGGAGGAAGGTCTGGACGATTT\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII'..b'I8WRK2|UniRef50_D6CZZ3|396\t242\t40\t100M\t*\t0\t0\tTCTTCGAGGATGAAATCATGCAGTGGATTGAACAGGGTGGAACATCGGGGACAGGCTGCGAGGAAGATTTCAACAGGCGGCTCGAAGCGTTGCGCAGCGG\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-12\tXN:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tNM:i:2\tMD:Z:37C18A43\tYT:Z:UU\n+s__Bacteroides_dorei_read006087\t16\t357276|g__Bacteroides.s__Bacteroides_dorei|UniRef90_I9F3X8|UniRef50_R6FQJ3|1026\t106\t40\t100M\t*\t0\t0\tGTTCCGGTAAACCTCACCGCCACGTGGGAGCGGGAATGGGAACGCAGCTACCAGACCGACTGGCAGTCCGTGTGGAACCCTGCATGGCCCCAACGCTATG\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-12\tXN:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tNM:i:2\tMD:Z:4A26A68\tYT:Z:UU\n+s__Bacteroides_dorei_read006089\t0\t357276|g__Bacteroides.s__Bacteroides_dorei|UniRef90_unknown|UniRef50_unknown|2841\t2127\t7\t100M\t*\t0\t0\tGGGCTCCGGTCTGGCTACAAGTTCTATTCTTGCATCGACTGTGCTGGGGGCAATCTCAGATTTTTGCGGGCTGAACTGGGATAAGAACGAGATATGTAAC\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-12\tXS:i:-24\tXN:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tNM:i:2\tMD:Z:14G42T42\tYT:Z:UU\n+s__Bacteroides_dorei_read006092\t16\t357276|g__Bacteroides.s__Bacteroides_dorei|UniRef90_A6KXU4|UniRef50_A6KXU4|1158\t387\t6\t100M\t*\t0\t0\tCCTGCTCATCTACCCATGCATTCATAAGCTTGTACGTGTCAATAAATCATTCATCGTGAAACGCGGCGTCAACATGCGGCAGAAACTGGAAGCATCTGCT\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-18\tXS:i:-24\tXN:i:0\tXM:i:3\tXO:i:0\tXG:i:0\tNM:i:3\tMD:Z:18G11G36C32\tYT:Z:UU\n+s__Bacteroides_dorei_read006093\t0\t357276|g__Bacteroides.s__Bacteroides_dorei|UniRef90_unknown|UniRef50_S0F6Q6|2250\t708\t23\t100M\t*\t0\t0\tCGTGAGTGCTACCGGACACCAACAACGTTTAGCGCGTGAAGGTATCGTGATGAAGAACGTTGTGGCTGCTACGGAGGATGCTGTCAGACAGGAACGGTTG\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-30\tXN:i:0\tXM:i:5\tXO:i:0\tXG:i:0\tNM:i:5\tMD:Z:27G17G13G7C2T29\tYT:Z:UU\n+s__Bacteroides_dorei_read006094\t0\t357276|g__Bacteroides.s__Bacteroides_dorei|UniRef90_A6KX21|UniRef50_A6KX21|1848\t788\t1\t100M\t*\t0\t0\tACAGAATTAGAATGATGAACAAAAAAAGAACCCGCACCACAGGGCATATCAAATATGCCTTGTCTGCACCGCTGACTGCTGCTCTACTCTTGGTCAGCAA\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-12\tXS:i:-12\tXN:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tNM:i:2\tMD:Z:9A53T36\tYT:Z:UU\n+s__Bacteroides_dorei_read006095\t16\t357276|g__Bacteroides.s__Bacteroides_dorei|UniRef90_R6HWC5|UniRef50_R6HYK5|1164\t333\t5\t100M\t*\t0\t0\tCGAAACTTTGATAAACGAGAAGGGTAGTCCTGTCTTGGGGTTGCATGTAGAAGGCCCTTACCTGAATTCGCAAAGCGCAGGTCAGCAGTTTGCCGGGAAA\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-30\tXS:i:-60\tXN:i:0\tXM:i:5\tXO:i:0\tXG:i:0\tNM:i:5\tMD:Z:12G10A46A4A6G17\tYT:Z:UU\n+s__Bacteroides_dorei_read006096\t16\t821|g__Bacteroides.s__Bacteroides_vulgatus|UniRef90_C3Q3D8|UniRef50_C3Q3D8|1362\t50\t1\t100M\t*\t0\t0\tCATATTTTTATCCTACAGCAGATATTAGGGTAATAAATAAGGAAACATATGATATATTATCGGCATTGAAAGAATATAAAGATATTCGTGAAGCCTTAGA\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-12\tXS:i:-12\tXN:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tNM:i:2\tMD:Z:6A80A12\tYT:Z:UU\n+s__Bacteroides_dorei_read006097\t0\t357276|g__Bacteroides.s__Bacteroides_dorei|UniRef90_A6L3W8|UniRef50_C6Y1M5|1341\t1021\t16\t100M\t*\t0\t0\tATTCTGGAGGATATCCGTGTAAGCAATATTGTGATGAGTAAAATCAAGAAAGAAGCTATTGTTCTCAATCTAAAATATAGCAAGATGCCTGCCGAACCGA\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-18\tXS:i:-48\tXN:i:0\tXM:i:3\tXO:i:0\tXG:i:0\tNM:i:3\tMD:Z:3G37T29G28\tYT:Z:UU\n+s__Bacteroides_dorei_read006098\t16\t357276|g__Bacteroides.s__Bacteroides_dorei|UniRef90_unknown|UniRef50_E6SR52|3096\t960\t32\t100M\t*\t0\t0\tCAATGAAGTAATTCCTGTCAAAGTAGGTTTCCGCAAGATTGAATTGAAAGGTGACCAGATCTTAGTTAACGGTAAAGCAGTCCTGTTCAAGGGGGCCGAC\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:0\tXS:i:-24\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:100\tYT:Z:UU\n' |
| b |
| diff -r 000000000000 -r 26ce946f4da9 test-data/demo_genefamilies.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demo_genefamilies.tsv Wed May 12 08:59:30 2021 +0000 |
| b |
| b'@@ -0,0 +1,866 @@\n+# Gene Family\thumann_Abundance-RPKs\n+UNMAPPED\t18900.0000000000\n+UniRef90_A0A174QBF2\t200.0000000000\n+UniRef90_A0A174QBF2|g__Bacteroides.s__Bacteroides_vulgatus\t200.0000000000\n+UniRef90_A0A078RDY6\t166.6666666667\n+UniRef90_A0A078RDY6|g__Bacteroides.s__Bacteroides_vulgatus\t166.6666666667\n+UniRef90_G1ULL9\t166.6666666667\n+UniRef90_G1ULL9|g__Bacteroides.s__Bacteroides_vulgatus\t166.6666666667\n+UniRef90_A0A015QIN1\t66.6666666667\n+UniRef90_A0A015QIN1|g__Bacteroides.s__Bacteroides_vulgatus\t66.6666666667\n+UniRef90_A0A069SBX4\t66.6666666667\n+UniRef90_A0A069SBX4|g__Bacteroides.s__Bacteroides_vulgatus\t66.6666666667\n+UniRef90_A0A069SHG5\t66.6666666667\n+UniRef90_A0A069SHG5|g__Bacteroides.s__Bacteroides_vulgatus\t66.6666666667\n+UniRef90_A0A078RD64\t66.6666666667\n+UniRef90_A0A078RD64|g__Bacteroides.s__Bacteroides_vulgatus\t66.6666666667\n+UniRef90_A0A174PVG2\t66.6666666667\n+UniRef90_A0A174PVG2|g__Bacteroides.s__Bacteroides_vulgatus\t66.6666666667\n+UniRef90_A0A173XK40\t56.3492063492\n+UniRef90_A0A173XK40|g__Bacteroides.s__Bacteroides_vulgatus\t56.3492063492\n+UniRef90_A0A078REY8\t55.5555555556\n+UniRef90_A0A078REY8|g__Bacteroides.s__Bacteroides_vulgatus\t55.5555555556\n+UniRef90_A0A174ILE1\t47.6190476190\n+UniRef90_A0A174ILE1|g__Bacteroides.s__Bacteroides_vulgatus\t47.6190476190\n+UniRef90_D4V7T1\t47.6190476190\n+UniRef90_D4V7T1|g__Bacteroides.s__Bacteroides_vulgatus\t47.6190476190\n+UniRef90_D4VBJ0\t47.6190476190\n+UniRef90_D4VBJ0|g__Bacteroides.s__Bacteroides_vulgatus\t47.6190476190\n+UniRef90_I3YNY4\t47.6190476190\n+UniRef90_I3YNY4|g__Bacteroides.s__Bacteroides_vulgatus\t47.6190476190\n+UniRef90_A0A078QZV1\t44.4444444444\n+UniRef90_A0A078QZV1|g__Bacteroides.s__Bacteroides_vulgatus\t44.4444444444\n+UniRef90_A0A078R670\t41.6666666667\n+UniRef90_A0A078R670|g__Bacteroides.s__Bacteroides_vulgatus\t41.6666666667\n+UniRef90_A0A078R6L3\t41.6666666667\n+UniRef90_A0A078R6L3|g__Bacteroides.s__Bacteroides_vulgatus\t41.6666666667\n+UniRef90_A0A078R911\t41.6666666667\n+UniRef90_A0A078R911|g__Bacteroides.s__Bacteroides_vulgatus\t41.6666666667\n+UniRef90_D4V4V0\t41.6666666667\n+UniRef90_D4V4V0|g__Bacteroides.s__Bacteroides_vulgatus\t41.6666666667\n+UniRef90_R9HIC6\t41.6666666667\n+UniRef90_R9HIC6|g__Bacteroides.s__Bacteroides_vulgatus\t41.6666666667\n+UniRef90_A0A078RFS7\t38.4615384615\n+UniRef90_A0A078RFS7|g__Bacteroides.s__Bacteroides_vulgatus\t38.4615384615\n+UniRef90_A7AE97\t37.0370370370\n+UniRef90_A7AE97|g__Bacteroides.s__Bacteroides_vulgatus\t37.0370370370\n+UniRef90_I9GA88\t36.3447559709\n+UniRef90_I9GA88|g__Bacteroides.s__Bacteroides_vulgatus\t36.3447559709\n+UniRef90_A0A078R120\t33.3333333333\n+UniRef90_A0A078R120|g__Bacteroides.s__Bacteroides_vulgatus\t33.3333333333\n+UniRef90_D4V9Q7\t33.3333333333\n+UniRef90_D4V9Q7|g__Bacteroides.s__Bacteroides_vulgatus\t33.3333333333\n+UniRef90_A0A3E4HP53\t31.2500000000\n+UniRef90_A0A3E4HP53|g__Bacteroides.s__Bacteroides_vulgatus\t31.2500000000\n+UniRef90_A0A069SKV1\t30.3030303030\n+UniRef90_A0A069SKV1|g__Bacteroides.s__Bacteroides_vulgatus\t30.3030303030\n+UniRef90_A0A173XQ94\t30.3030303030\n+UniRef90_A0A173XQ94|g__Bacteroides.s__Bacteroides_vulgatus\t30.3030303030\n+UniRef90_D4VA46\t30.3030303030\n+UniRef90_D4VA46|g__Bacteroides.s__Bacteroides_vulgatus\t30.3030303030\n+UniRef90_A0A078RD25\t28.5714285714\n+UniRef90_A0A078RD25|g__Bacteroides.s__Bacteroides_vulgatus\t28.5714285714\n+UniRef90_A0A069SV61\t27.7777777778\n+UniRef90_A0A069SV61|g__Bacteroides.s__Bacteroides_vulgatus\t27.7777777778\n+UniRef90_D4VC99\t27.7777777778\n+UniRef90_D4VC99|g__Bacteroides.s__Bacteroides_vulgatus\t27.7777777778\n+UniRef90_E5UU61\t26.1437908497\n+UniRef90_E5UU61|g__Bacteroides.s__Bacteroides_vulgatus\t26.1437908497\n+UniRef90_A0A078RDC9\t25.6410256410\n+UniRef90_A0A078RDC9|g__Bacteroides.s__Bacteroides_vulgatus\t25.6410256410\n+UniRef90_A0A174NIB7\t24.6913580247\n+UniRef90_A0A174NIB7|g__Bacteroides.s__Bacteroides_vulgatus\t24.6913580247\n+UniRef90_A0A078QYW1\t24.3902439024\n+UniRef90_A0A078QYW1|g__Bacteroides.s__Bacteroides_vulgatus\t24.3902439024\n+UniRef90_I0PXX6\t23.8095238095\n+UniRef90_I0PXX6|g__Bacteroides.s__Bacteroides_vulga'..b'Ref90_Q8A488|g__Bacteroides.s__Bacteroides_vulgatus\t6.5359477124\n+UniRef90_A0A0P0LLZ6\t6.5359477124\n+UniRef90_A0A0P0LLZ6|g__Bacteroides.s__Bacteroides_vulgatus\t6.5359477124\n+UniRef90_R7J8P5\t6.5146579805\n+UniRef90_R7J8P5|g__Bacteroides.s__Bacteroides_vulgatus\t6.5146579805\n+UniRef90_D4IQJ2\t6.4882400649\n+UniRef90_D4IQJ2|g__Bacteroides.s__Bacteroides_vulgatus\t6.4882400649\n+UniRef90_P94598\t6.4724919094\n+UniRef90_P94598|g__Bacteroides.s__Bacteroides_vulgatus\t6.4724919094\n+UniRef90_I8W803\t6.4279155188\n+UniRef90_I8W803|g__Bacteroides.s__Bacteroides_vulgatus\t6.4279155188\n+UniRef90_A0A081U579\t6.4214827788\n+UniRef90_A0A081U579|g__Bacteroides.s__Bacteroides_vulgatus\t6.4214827788\n+UniRef90_B5A7G1\t6.4102564103\n+UniRef90_B5A7G1|g__Bacteroides.s__Bacteroides_vulgatus\t6.4102564103\n+UniRef90_B6VTH0\t6.4102564103\n+UniRef90_B6VTH0|g__Bacteroides.s__Bacteroides_vulgatus\t6.4102564103\n+UniRef90_A0A076IVE7\t6.3291139241\n+UniRef90_A0A076IVE7|g__Bacteroides.s__Bacteroides_vulgatus\t6.3291139241\n+UniRef90_I9R4C5\t6.3168124393\n+UniRef90_I9R4C5|g__Bacteroides.s__Bacteroides_vulgatus\t6.3168124393\n+UniRef90_R6JK25\t6.3091482650\n+UniRef90_R6JK25|g__Bacteroides.s__Bacteroides_vulgatus\t6.3091482650\n+UniRef90_A0A0P0M475\t6.2893081761\n+UniRef90_A0A0P0M475|g__Bacteroides.s__Bacteroides_vulgatus\t6.2893081761\n+UniRef90_D1JXS4\t6.2695924765\n+UniRef90_D1JXS4|g__Bacteroides.s__Bacteroides_vulgatus\t6.2695924765\n+UniRef90_A6L3D5\t6.2597809077\n+UniRef90_A6L3D5|g__Bacteroides.s__Bacteroides_vulgatus\t6.2597809077\n+UniRef90_F7LXA9\t6.2597809077\n+UniRef90_F7LXA9|g__Bacteroides.s__Bacteroides_vulgatus\t6.2597809077\n+UniRef90_A0A0P0L9E5\t6.2500000000\n+UniRef90_A0A0P0L9E5|g__Bacteroides.s__Bacteroides_vulgatus\t6.2500000000\n+UniRef90_A0A1Y3ZKK1\t6.2111801242\n+UniRef90_A0A1Y3ZKK1|g__Bacteroides.s__Bacteroides_vulgatus\t6.2111801242\n+UniRef90_A0A076J5J6\t6.1919504644\n+UniRef90_A0A076J5J6|g__Bacteroides.s__Bacteroides_vulgatus\t6.1919504644\n+UniRef90_A6L1K4\t6.1892130858\n+UniRef90_A6L1K4|g__Bacteroides.s__Bacteroides_vulgatus\t6.1892130858\n+UniRef90_A0A076IIX7\t6.1871616396\n+UniRef90_A0A076IIX7|g__Bacteroides.s__Bacteroides_vulgatus\t6.1871616396\n+UniRef90_A0A076IUR5\t6.1728395062\n+UniRef90_A0A076IUR5|g__Bacteroides.s__Bacteroides_vulgatus\t6.1728395062\n+UniRef90_A0A0P0M3I1\t6.1728395062\n+UniRef90_A0A0P0M3I1|g__Bacteroides.s__Bacteroides_vulgatus\t6.1728395062\n+UniRef90_A6L3D0\t6.1349693252\n+UniRef90_A6L3D0|g__Bacteroides.s__Bacteroides_vulgatus\t6.1349693252\n+UniRef90_A0A0K2HGU4\t6.1162079511\n+UniRef90_A0A0K2HGU4|g__Bacteroides.s__Bacteroides_vulgatus\t6.1162079511\n+UniRef90_A0A076J0R4\t6.1162079511\n+UniRef90_A0A076J0R4|g__Bacteroides.s__Bacteroides_vulgatus\t6.1162079511\n+UniRef90_A0A076INL3\t6.0975609756\n+UniRef90_A0A076INL3|g__Bacteroides.s__Bacteroides_vulgatus\t6.0975609756\n+UniRef90_A0A0M1W2F8\t6.0882800609\n+UniRef90_A0A0M1W2F8|g__Bacteroides.s__Bacteroides_vulgatus\t6.0882800609\n+UniRef90_I8WL14\t6.0468631897\n+UniRef90_I8WL14|g__Bacteroides.s__Bacteroides_vulgatus\t6.0468631897\n+UniRef90_D4V591\t6.0122179883\n+UniRef90_D4V591|g__Bacteroides.s__Bacteroides_vulgatus\t6.0122179883\n+UniRef90_A0A0P0LFD2\t5.9880239521\n+UniRef90_A0A0P0LFD2|g__Bacteroides.s__Bacteroides_vulgatus\t5.9880239521\n+UniRef90_I8WHI1\t5.9523809524\n+UniRef90_I8WHI1|g__Bacteroides.s__Bacteroides_vulgatus\t5.9523809524\n+UniRef90_A6L013\t5.9259259259\n+UniRef90_A6L013|g__Bacteroides.s__Bacteroides_vulgatus\t5.9259259259\n+UniRef90_D4VC11\t5.9259259259\n+UniRef90_D4VC11|g__Bacteroides.s__Bacteroides_vulgatus\t5.9259259259\n+UniRef90_A0A3E4HLD6\t5.7870370370\n+UniRef90_A0A3E4HLD6|g__Bacteroides.s__Bacteroides_vulgatus\t5.7870370370\n+UniRef90_A0A0M1W7B1\t5.5741360089\n+UniRef90_A0A0M1W7B1|g__Bacteroides.s__Bacteroides_vulgatus\t5.5741360089\n+UniRef90_A6L100\t5.5248618785\n+UniRef90_A6L100|g__Bacteroides.s__Bacteroides_vulgatus\t5.5248618785\n+UniRef90_U6RK63\t5.4869684499\n+UniRef90_U6RK63|g__Bacteroides.s__Bacteroides_vulgatus\t5.4869684499\n+UniRef90_A0A174ILV5\t5.4137664346\n+UniRef90_A0A174ILV5|g__Bacteroides.s__Bacteroides_vulgatus\t5.4137664346\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 26ce946f4da9 test-data/demo_joined_pathabundance_pathcoverage.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demo_joined_pathabundance_pathcoverage.tsv Wed May 12 08:59:30 2021 +0000 |
| b |
| @@ -0,0 +1,8 @@ +# Pathway humann_Abundance humann_Coverage +UNMAPPED 9825.8289872883 1.0000000000 +UNINTEGRATED 3058.2089939573 1.0000000000 +UNINTEGRATED|unclassified 54.1292645042 1.0000000000 +PWY-4203: volatile benzenoid biosynthesis I (ester formation) 13.3772872602 0.8589609470 +PWY-4203: volatile benzenoid biosynthesis I (ester formation)|unclassified 13.3772872602 0.6438577695 +PWY-5423: oleoresin monoterpene volatiles biosynthesis 18.3746362785 0.9781854342 +PWY-5423: oleoresin monoterpene volatiles biosynthesis|unclassified 18.3746362785 0.9117549729 |
| b |
| diff -r 000000000000 -r 26ce946f4da9 test-data/demo_pathabundance.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demo_pathabundance.tsv Wed May 12 08:59:30 2021 +0000 |
| b |
| @@ -0,0 +1,8 @@ +# Pathway humann_Abundance +UNMAPPED 9825.8289872883 +UNINTEGRATED 3058.2089939573 +UNINTEGRATED|unclassified 54.1292645042 +PWY-5423: oleoresin monoterpene volatiles biosynthesis 18.3746362785 +PWY-5423: oleoresin monoterpene volatiles biosynthesis|unclassified 18.3746362785 +PWY-4203: volatile benzenoid biosynthesis I (ester formation) 13.3772872602 +PWY-4203: volatile benzenoid biosynthesis I (ester formation)|unclassified 13.3772872602 \ No newline at end of file |
| b |
| diff -r 000000000000 -r 26ce946f4da9 test-data/demo_pathcoverage.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demo_pathcoverage.tsv Wed May 12 08:59:30 2021 +0000 |
| b |
| @@ -0,0 +1,8 @@ +# Pathway humann_Coverage +UNMAPPED 1.0000000000 +UNINTEGRATED 1.0000000000 +UNINTEGRATED|unclassified 1.0000000000 +PWY-5423: oleoresin monoterpene volatiles biosynthesis 0.9781854342 +PWY-5423: oleoresin monoterpene volatiles biosynthesis|unclassified 0.9117549729 +PWY-4203: volatile benzenoid biosynthesis I (ester formation) 0.8589609470 +PWY-4203: volatile benzenoid biosynthesis I (ester formation)|unclassified 0.6438577695 \ No newline at end of file |
| b |
| diff -r 000000000000 -r 26ce946f4da9 test-data/genus-level-gene-families.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genus-level-gene-families.tsv Wed May 12 08:59:30 2021 +0000 |
| b |
| @@ -0,0 +1,2 @@ +# Gene Family humann_Abundance-RPKs +UNMAPPED 17559.0000000000 |
| b |
| diff -r 000000000000 -r 26ce946f4da9 test-data/hmp_pathabund.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hmp_pathabund.txt Wed May 12 08:59:30 2021 +0000 |
| b |
| b'@@ -0,0 +1,500 @@\n+FEATURE \\ SAMPLE\tSRS011084\tSRS011086\tSRS011090\tSRS011098\tSRS011111\tSRS011115\tSRS011126\tSRS011132\tSRS011134\tSRS011140\tSRS011144\tSRS011152\tSRS011239\tSRS011243\tSRS011247\tSRS011255\tSRS011263\tSRS011269\tSRS011302\tSRS011306\tSRS011310\tSRS011343\tSRS011355\tSRS011397\tSRS011405\tSRS011584\tSRS012273\tSRS012279\tSRS012281\tSRS012285\tSRS012291\tSRS012294\tSRS012663\tSRS012902\tSRS013155\tSRS013158\tSRS013164\tSRS013170\tSRS013215\tSRS013234\tSRS013239\tSRS013252\tSRS013269\tSRS013476\tSRS013502\tSRS013506\tSRS013521\tSRS013533\tSRS013542\tSRS013687\tSRS013705\tSRS013711\tSRS013723\tSRS013800\tSRS013818\tSRS013825\tSRS013836\tSRS013876\tSRS013879\tSRS013881\tSRS013945\tSRS013949\tSRS013951\tSRS013956\tSRS014124\tSRS014126\tSRS014235\tSRS014271\tSRS014287\tSRS014313\tSRS014343\tSRS014459\tSRS014464\tSRS014470\tSRS014472\tSRS014476\tSRS014494\tSRS014573\tSRS014575\tSRS014578\tSRS014613\tSRS014629\tSRS014682\tSRS014683\tSRS014684\tSRS014686\tSRS014690\tSRS014888\tSRS014890\tSRS014894\tSRS014901\tSRS014923\tSRS014979\tSRS015038\tSRS015040\tSRS015044\tSRS015051\tSRS015054\tSRS015133\tSRS015154\tSRS015158\tSRS015168\tSRS015174\tSRS015190\tSRS015209\tSRS015215\tSRS015217\tSRS015225\tSRS015264\tSRS015269\tSRS015272\tSRS015274\tSRS015278\tSRS015369\tSRS015374\tSRS015378\tSRS015395\tSRS015425\tSRS015430\tSRS015431\tSRS015434\tSRS015436\tSRS015440\tSRS015540\tSRS015574\tSRS015578\tSRS015640\tSRS015644\tSRS015646\tSRS015650\tSRS015663\tSRS015745\tSRS015752\tSRS015755\tSRS015762\tSRS015782\tSRS015890\tSRS015893\tSRS015895\tSRS015899\tSRS015937\tSRS015941\tSRS015960\tSRS015985\tSRS015989\tSRS015996\tSRS016002\tSRS016018\tSRS016033\tSRS016037\tSRS016039\tSRS016043\tSRS016056\tSRS016086\tSRS016092\tSRS016095\tSRS016111\tSRS016188\tSRS016191\tSRS016196\tSRS016200\tSRS016203\tSRS016225\tSRS016267\tSRS016292\tSRS016297\tSRS016319\tSRS016331\tSRS016335\tSRS016342\tSRS016349\tSRS016360\tSRS016434\tSRS016495\tSRS016501\tSRS016503\tSRS016513\tSRS016516\tSRS016541\tSRS016569\tSRS016575\tSRS016581\tSRS016600\tSRS016740\tSRS016746\tSRS016752\tSRS016753\tSRS016954\tSRS016989\tSRS017007\tSRS017013\tSRS017025\tSRS017044\tSRS017076\tSRS017080\tSRS017103\tSRS017120\tSRS017127\tSRS017139\tSRS017156\tSRS017191\tSRS017209\tSRS017215\tSRS017227\tSRS017244\tSRS017247\tSRS017304\tSRS017307\tSRS017433\tSRS017439\tSRS017441\tSRS017445\tSRS017451\tSRS017497\tSRS017520\tSRS017521\tSRS017687\tSRS017697\tSRS017700\tSRS017701\tSRS017713\tSRS017808\tSRS017810\tSRS017814\tSRS017820\tSRS017821\tSRS018133\tSRS018145\tSRS018149\tSRS018157\tSRS018300\tSRS018312\tSRS018313\tSRS018329\tSRS018337\tSRS018351\tSRS018357\tSRS018359\tSRS018369\tSRS018394\tSRS018427\tSRS018439\tSRS018463\tSRS018569\tSRS018573\tSRS018575\tSRS018585\tSRS018591\tSRS018656\tSRS018661\tSRS018665\tSRS018671\tSRS018739\tSRS018769\tSRS018774\tSRS018784\tSRS018791\tSRS018817\tSRS019215\tSRS019219\tSRS019221\tSRS019225\tSRS019245\tSRS019267\tSRS019327\tSRS019329\tSRS019333\tSRS019339\tSRS019379\tSRS019381\tSRS019386\tSRS019387\tSRS019389\tSRS019391\tSRS019397\tSRS019587\tSRS019591\tSRS019597\tSRS019600\tSRS019601\tSRS019607\tSRS019968\tSRS019974\tSRS019976\tSRS019980\tSRS019986\tSRS019989\tSRS020220\tSRS020222\tSRS020226\tSRS020232\tSRS020233\tSRS020328\tSRS020334\tSRS020336\tSRS020340\tSRS020349\tSRS020386\tSRS020856\tSRS020858\tSRS020862\tSRS020869\tSRS022137\tSRS022143\tSRS022145\tSRS022149\tSRS022158\tSRS022524\tSRS022530\tSRS022532\tSRS022536\tSRS022545\tSRS022713\tSRS023346\tSRS023352\tSRS023358\tSRS042428\tSRS042457\tSRS042643\tSRS043001\tSRS043239\tSRS043663\tSRS043755\tSRS044366\tSRS044373\tSRS045004\tSRS045049\tSRS045254\tSRS045262\tSRS045313\tSRS045713\tSRS046344\tSRS046973\tSRS047824\tSRS048164\tSRS049389\tSRS049712\tSRS049900\tSRS049959\tSRS050007\tSRS050025\tSRS050029\tSRS050184\tSRS050244\tSRS050628\tSRS050752\tSRS051244\tSRS051505\tSRS051613\tSRS051941\tSRS052227\tSRS052330\tSRS052590\tSRS052604\tSRS052697\tSRS052876\tSRS053335\tSRS053398\tSRS053437\tSRS053630\tSRS053854\tSRS054061\tSRS054590\tSRS054653\tSRS054687\tSRS054956\tSRS055118\tSRS055401\tSRS056323\tSRS056695\tSRS056796\tSRS056906\tSRS057539\tSRS057791\tSRS057807\tSRS058186\tSRS058213\tSRS058808\r\n+STSite\tStool\tTongue_dorsum\tBuccal_mucosa\tSupragingival_plaque\tPosterior_fornix\tTongue_dorsum\tSupragingival_plaque\tAnterior_nares\tStool\tTongue_dorsum\tBuccal_mucosa\tSupragingival_plaq'..b'5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.000110565\t0\t0\t0\t0\t0\t0\t0\t0\t0.000105739\t0\t0\t0\t0\t2.33738e-05\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t9.88647e-06\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1.39106e-05\t2.42838e-07\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.000295775\t0\t0\t0\t0\t0\t6.81845e-06\t0\t0\t0\t0\t8.23749e-05\t0\t0\t0\t4.76472e-06\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1.12389e-06\t0\t0\t3.645e-06\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+COA-PWY: coenzyme A biosynthesis I|g__Bulleidia.s__Bulleidia_extructa\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t5.73523e-07\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+COA-PWY: coenzyme A biosynthesis I|g__Campylobacter.s__Campylobacter_hominis\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t7.29465e-07\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3.14158e-06\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+COA-PWY: coenzyme A biosynthesis I|g__Capnocytophaga.s__Capnocytophaga_sp_CM59\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3.57568e-07\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t4.79523e-05\t0\t5.46675e-06\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3.45956e-05\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1.52358e-06\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1.65151e-05\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n+COA-PWY: coenzyme A biosynthesis I|g__Capnocytophaga.s__Capnocytophaga_sp_oral_taxon_338\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t5.52837e-07\t0\t0\t0\t1.86027e-06\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t9.5765e-07\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t9.11797e-07\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2.40718e-06\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t8.57993e-07\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1.324e-06\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t4.34332e-07\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1.88895e-06\t0\t0\t0\t0\t0\t4.18485e-07\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1.51934e-06\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2.32256e-06\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n' |
| b |
| diff -r 000000000000 -r 26ce946f4da9 test-data/humann_nucleotide_database.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/humann_nucleotide_database.loc Wed May 12 08:59:30 2021 +0000 |
| b |
| @@ -0,0 +1,6 @@ +# Tab separated with 4 columns: +# - db-build-version-date +# - db-name +# - build +# - /path/to/data +chocophlan-DEMO-20210421 Demo ChocoPhlAn for HUManN humann_nucleotide_database ${__HERE__}/test-db/nucleotide-db/ \ No newline at end of file |
| b |
| diff -r 000000000000 -r 26ce946f4da9 test-data/humann_protein_database.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/humann_protein_database.loc Wed May 12 08:59:30 2021 +0000 |
| b |
| @@ -0,0 +1,6 @@ +# Tab separated with 4 columns: +# - db-build-version-date +# - db-name +# - build +# - /path/to/data +uniref-DEMO_diamond-20210421 Demo UniRef for HUManN DEMO_diamond ${__HERE__}/test-db/protein-db/ \ No newline at end of file |
| b |
| diff -r 000000000000 -r 26ce946f4da9 test-data/humann_utility_mapping.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/humann_utility_mapping.loc Wed May 12 08:59:30 2021 +0000 |
| b |
| @@ -0,0 +1,7 @@ +# Tab separated with 4 columns: +# - db-build-version-date +# - db-name +# - build +# - /path/to/data +utility_mapping-full-map_uniref90_name-3.0.0-29042021 Full mapping: UniRef90 from protein names full-map_uniref90_name ${__HERE__}/test-db/utility_mapping/map_uniref90_name.txt +utility_mapping-full-map_go_uniref90-3.0.0-29042021 Full mapping: GO from UniRef90 full-map_go_uniref90 ${__HERE__}/test-db/utility_mapping/map_go_uniref90.txt \ No newline at end of file |
| b |
| diff -r 000000000000 -r 26ce946f4da9 test-data/metaphlan_database.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/metaphlan_database.loc Wed May 12 08:59:30 2021 +0000 |
| b |
| @@ -0,0 +1,6 @@ +# Tab separated with 4 columns: +# - db-build-version-date +# - db-name +# - build +# - /path/to/data +metaphlan-demo-db-20210421 MetaPhlan Test Database demo-db-v30 ${__HERE__}/test-db/metaphlan-db \ No newline at end of file |
| b |
| diff -r 000000000000 -r 26ce946f4da9 test-data/regrouped_gene_families_to_infogo1000.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/regrouped_gene_families_to_infogo1000.tsv Wed May 12 08:59:30 2021 +0000 |
| b |
| b'@@ -0,0 +1,1393 @@\n+# Gene Family\tdemo_Abundance-RPKs\n+UNMAPPED\t4531.0\n+UNGROUPED\t15490.72\n+UNGROUPED|g__Bacteroides.s__Bacteroides_dorei\t8949.382\n+UNGROUPED|g__Bacteroides.s__Bacteroides_vulgatus\t6476.05\n+UNGROUPED|unclassified\t65.288\n+GO:0000015\t4.177\n+GO:0000015|g__Bacteroides.s__Bacteroides_dorei\t2.506\n+GO:0000015|g__Bacteroides.s__Bacteroides_vulgatus\t1.671\n+GO:0000027\t7.937\n+GO:0000027|g__Bacteroides.s__Bacteroides_dorei\t7.937\n+GO:0000049\t29.232\n+GO:0000049|g__Bacteroides.s__Bacteroides_dorei\t7.205\n+GO:0000049|g__Bacteroides.s__Bacteroides_vulgatus\t22.027\n+GO:0000105\t22.302\n+GO:0000105|g__Bacteroides.s__Bacteroides_dorei\t9.093\n+GO:0000105|g__Bacteroides.s__Bacteroides_vulgatus\t13.209\n+GO:0000107\t5.077\n+GO:0000107|g__Bacteroides.s__Bacteroides_vulgatus\t5.077\n+GO:0000150\t29.481\n+GO:0000150|g__Bacteroides.s__Bacteroides_dorei\t14.86\n+GO:0000150|g__Bacteroides.s__Bacteroides_vulgatus\t14.62\n+GO:0000155\t98.896\n+GO:0000155|g__Bacteroides.s__Bacteroides_dorei\t45.55\n+GO:0000155|g__Bacteroides.s__Bacteroides_vulgatus\t53.346\n+GO:0000160\t71.811\n+GO:0000160|g__Bacteroides.s__Bacteroides_dorei\t43.683\n+GO:0000160|g__Bacteroides.s__Bacteroides_vulgatus\t28.128\n+GO:0000162\t6.418\n+GO:0000162|g__Bacteroides.s__Bacteroides_dorei\t1.115\n+GO:0000162|g__Bacteroides.s__Bacteroides_vulgatus\t5.303\n+GO:0000179\t5.376\n+GO:0000179|g__Bacteroides.s__Bacteroides_dorei\t2.688\n+GO:0000179|g__Bacteroides.s__Bacteroides_vulgatus\t2.688\n+GO:0000287\t144.517\n+GO:0000287|g__Bacteroides.s__Bacteroides_dorei\t69.932\n+GO:0000287|g__Bacteroides.s__Bacteroides_vulgatus\t60.803\n+GO:0000287|unclassified\t13.782\n+GO:0000453\t4.823\n+GO:0000453|g__Bacteroides.s__Bacteroides_dorei\t3.086\n+GO:0000453|g__Bacteroides.s__Bacteroides_vulgatus\t1.736\n+GO:0000723\t4.363\n+GO:0000723|g__Bacteroides.s__Bacteroides_dorei\t1.992\n+GO:0000723|g__Bacteroides.s__Bacteroides_vulgatus\t2.371\n+GO:0000917\t7.611\n+GO:0000917|g__Bacteroides.s__Bacteroides_dorei\t5.952\n+GO:0000917|g__Bacteroides.s__Bacteroides_vulgatus\t1.658\n+GO:0000967\t3.115\n+GO:0000967|g__Bacteroides.s__Bacteroides_vulgatus\t3.115\n+GO:0002094\t2.525\n+GO:0002094|g__Bacteroides.s__Bacteroides_vulgatus\t2.525\n+GO:0002100\t5.952\n+GO:0002100|g__Bacteroides.s__Bacteroides_vulgatus\t5.952\n+GO:0002161\t0.731\n+GO:0002161|g__Bacteroides.s__Bacteroides_vulgatus\t0.731\n+GO:0002935\t7.361\n+GO:0002935|g__Bacteroides.s__Bacteroides_dorei\t2.103\n+GO:0002935|g__Bacteroides.s__Bacteroides_vulgatus\t5.258\n+GO:0002949\t4.47\n+GO:0002949|g__Bacteroides.s__Bacteroides_dorei\t2.778\n+GO:0002949|g__Bacteroides.s__Bacteroides_vulgatus\t1.692\n+GO:0003684\t9.246\n+GO:0003684|g__Bacteroides.s__Bacteroides_dorei\t5.554\n+GO:0003684|g__Bacteroides.s__Bacteroides_vulgatus\t3.692\n+GO:0003697\t24.977\n+GO:0003697|g__Bacteroides.s__Bacteroides_dorei\t16.618\n+GO:0003697|g__Bacteroides.s__Bacteroides_vulgatus\t8.358\n+GO:0003725\t7.91\n+GO:0003725|g__Bacteroides.s__Bacteroides_dorei\t5.972\n+GO:0003725|g__Bacteroides.s__Bacteroides_vulgatus\t1.938\n+GO:0003727\t12.121\n+GO:0003727|g__Bacteroides.s__Bacteroides_dorei\t6.061\n+GO:0003727|g__Bacteroides.s__Bacteroides_vulgatus\t6.061\n+GO:0003729\t4.739\n+GO:0003729|g__Bacteroides.s__Bacteroides_vulgatus\t4.739\n+GO:0003735\t156.347\n+GO:0003735|g__Bacteroides.s__Bacteroides_dorei\t76.023\n+GO:0003735|g__Bacteroides.s__Bacteroides_vulgatus\t80.324\n+GO:0003743\t6.762\n+GO:0003743|g__Bacteroides.s__Bacteroides_dorei\t4.016\n+GO:0003743|g__Bacteroides.s__Bacteroides_vulgatus\t2.746\n+GO:0003746\t16.907\n+GO:0003746|g__Bacteroides.s__Bacteroides_dorei\t13.849\n+GO:0003746|g__Bacteroides.s__Bacteroides_vulgatus\t3.058\n+GO:0003755\t33.832\n+GO:0003755|g__Bacteroides.s__Bacteroides_dorei\t14.287\n+GO:0003755|g__Bacteroides.s__Bacteroides_vulgatus\t19.544\n+GO:0003796\t3.906\n+GO:0003796|g__Bacteroides.s__Bacteroides_dorei\t3.906\n+GO:0003848\t9.37\n+GO:0003848|g__Bacteroides.s__Bacteroides_vulgatus\t9.37\n+GO:0003852\t3.462\n+GO:0003852|g__Bacteroides.s__Bacteroides_dorei\t1.392\n+GO:0003852|g__Bacteroides.s__Bacteroides_vulgatus\t2.07\n+GO:0003856\t4.154\n+GO:0003856|g__Bacteroides.s__Bacteroides_dorei\t4.154\n+G'..b's__Bacteroides_vulgatus\t13.172\n+GO:0048472\t4.796\n+GO:0048472|g__Bacteroides.s__Bacteroides_dorei\t2.398\n+GO:0048472|g__Bacteroides.s__Bacteroides_vulgatus\t2.398\n+GO:0048500\t7.353\n+GO:0048500|g__Bacteroides.s__Bacteroides_dorei\t3.268\n+GO:0048500|g__Bacteroides.s__Bacteroides_vulgatus\t4.085\n+GO:0050380\t1.425\n+GO:0050380|g__Bacteroides.s__Bacteroides_dorei\t1.425\n+GO:0050480\t3.49\n+GO:0050480|g__Bacteroides.s__Bacteroides_vulgatus\t3.49\n+GO:0050511\t8.721\n+GO:0050511|g__Bacteroides.s__Bacteroides_dorei\t5.814\n+GO:0050511|g__Bacteroides.s__Bacteroides_vulgatus\t2.907\n+GO:0050570\t5.988\n+GO:0050570|g__Bacteroides.s__Bacteroides_dorei\t5.988\n+GO:0050577\t2.045\n+GO:0050577|g__Bacteroides.s__Bacteroides_vulgatus\t2.045\n+GO:0051073\t6.144\n+GO:0051073|g__Bacteroides.s__Bacteroides_dorei\t3.072\n+GO:0051073|g__Bacteroides.s__Bacteroides_vulgatus\t3.072\n+GO:0051205\t4.522\n+GO:0051205|g__Bacteroides.s__Bacteroides_dorei\t3.39\n+GO:0051205|g__Bacteroides.s__Bacteroides_vulgatus\t1.132\n+GO:0051537\t26.424\n+GO:0051537|g__Bacteroides.s__Bacteroides_dorei\t15.914\n+GO:0051537|g__Bacteroides.s__Bacteroides_vulgatus\t10.51\n+GO:0051539\t133.729\n+GO:0051539|g__Bacteroides.s__Bacteroides_dorei\t41.322\n+GO:0051539|g__Bacteroides.s__Bacteroides_vulgatus\t54.67\n+GO:0051539|unclassified\t37.738\n+GO:0051607\t2.165\n+GO:0051607|g__Bacteroides.s__Bacteroides_vulgatus\t2.165\n+GO:0051775\t3.623\n+GO:0051775|g__Bacteroides.s__Bacteroides_dorei\t3.623\n+GO:0051920\t25.421\n+GO:0051920|g__Bacteroides.s__Bacteroides_dorei\t12.187\n+GO:0051920|g__Bacteroides.s__Bacteroides_vulgatus\t13.234\n+GO:0051989\t7.465\n+GO:0051989|unclassified\t7.465\n+GO:0051991\t8.721\n+GO:0051991|g__Bacteroides.s__Bacteroides_dorei\t5.814\n+GO:0051991|g__Bacteroides.s__Bacteroides_vulgatus\t2.907\n+GO:0052381\t4.848\n+GO:0052381|g__Bacteroides.s__Bacteroides_dorei\t4.848\n+GO:0052692\t3.49\n+GO:0052692|g__Bacteroides.s__Bacteroides_dorei\t2.327\n+GO:0052692|g__Bacteroides.s__Bacteroides_vulgatus\t1.163\n+GO:0052717\t5.952\n+GO:0052717|g__Bacteroides.s__Bacteroides_vulgatus\t5.952\n+GO:0052865\t5.301\n+GO:0052865|g__Bacteroides.s__Bacteroides_dorei\t4.699\n+GO:0052865|g__Bacteroides.s__Bacteroides_vulgatus\t0.602\n+GO:0052908\t5.376\n+GO:0052908|g__Bacteroides.s__Bacteroides_dorei\t2.688\n+GO:0052908|g__Bacteroides.s__Bacteroides_vulgatus\t2.688\n+GO:0061711\t1.086\n+GO:0061711|g__Bacteroides.s__Bacteroides_dorei\t1.086\n+GO:0070006\t5.507\n+GO:0070006|g__Bacteroides.s__Bacteroides_vulgatus\t5.507\n+GO:0070040\t7.361\n+GO:0070040|g__Bacteroides.s__Bacteroides_dorei\t2.103\n+GO:0070040|g__Bacteroides.s__Bacteroides_vulgatus\t5.258\n+GO:0070084\t5.507\n+GO:0070084|g__Bacteroides.s__Bacteroides_vulgatus\t5.507\n+GO:0070181\t3.831\n+GO:0070181|g__Bacteroides.s__Bacteroides_dorei\t2.554\n+GO:0070181|g__Bacteroides.s__Bacteroides_vulgatus\t1.277\n+GO:0070204\t2.54\n+GO:0070204|g__Bacteroides.s__Bacteroides_vulgatus\t2.54\n+GO:0070401\t11.207\n+GO:0070401|g__Bacteroides.s__Bacteroides_dorei\t2.039\n+GO:0070401|g__Bacteroides.s__Bacteroides_vulgatus\t9.168\n+GO:0070402\t3.81\n+GO:0070402|g__Bacteroides.s__Bacteroides_dorei\t1.905\n+GO:0070402|g__Bacteroides.s__Bacteroides_vulgatus\t1.905\n+GO:0070403\t5.0\n+GO:0070403|g__Bacteroides.s__Bacteroides_vulgatus\t5.0\n+GO:0070475\t7.361\n+GO:0070475|g__Bacteroides.s__Bacteroides_dorei\t2.103\n+GO:0070475|g__Bacteroides.s__Bacteroides_vulgatus\t5.258\n+GO:0070626\t2.404\n+GO:0070626|g__Bacteroides.s__Bacteroides_dorei\t0.801\n+GO:0070626|g__Bacteroides.s__Bacteroides_vulgatus\t1.603\n+GO:0070677\t4.823\n+GO:0070677|g__Bacteroides.s__Bacteroides_dorei\t3.086\n+GO:0070677|g__Bacteroides.s__Bacteroides_vulgatus\t1.736\n+GO:0070814\t15.615\n+GO:0070814|g__Bacteroides.s__Bacteroides_dorei\t9.504\n+GO:0070814|g__Bacteroides.s__Bacteroides_vulgatus\t6.111\n+GO:0071436\t2.407\n+GO:0071436|g__Bacteroides.s__Bacteroides_vulgatus\t2.407\n+GO:0090071\t3.831\n+GO:0090071|g__Bacteroides.s__Bacteroides_dorei\t3.831\n+GO:0097264\t3.745\n+GO:0097264|g__Bacteroides.s__Bacteroides_dorei\t3.745\n+GO:1990077\t8.016\n+GO:1990077|g__Bacteroides.s__Bacteroides_dorei\t1.517\n+GO:1990077|g__Bacteroides.s__Bacteroides_vulgatus\t6.499\n' |
| b |
| diff -r 000000000000 -r 26ce946f4da9 test-data/relab_levelwise_renormalized_pathway_abundance.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/relab_levelwise_renormalized_pathway_abundance.tsv Wed May 12 08:59:30 2021 +0000 |
| b |
| @@ -0,0 +1,8 @@ +# Pathway humann_Abundance +UNMAPPED 0.760761 +UNINTEGRATED 0.236781 +UNINTEGRATED|unclassified 0.630281 +PWY-5423: oleoresin monoterpene volatiles biosynthesis 0.00142265 +PWY-5423: oleoresin monoterpene volatiles biosynthesis|unclassified 0.213954 +PWY-4203: volatile benzenoid biosynthesis I (ester formation) 0.00103573 +PWY-4203: volatile benzenoid biosynthesis I (ester formation)|unclassified 0.155765 |
| b |
| diff -r 000000000000 -r 26ce946f4da9 test-data/rna_dna_norm-dna.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rna_dna_norm-dna.txt Wed May 12 08:59:30 2021 +0000 |
| b |
| @@ -0,0 +1,7 @@ +# 1 2 +A 11 11 +A|1 10 10 +A|2 1 1 +D 5 10 +D|1 5 5 +D|2 0 5 |
| b |
| diff -r 000000000000 -r 26ce946f4da9 test-data/rna_dna_norm-rna.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rna_dna_norm-rna.txt Wed May 12 08:59:30 2021 +0000 |
| b |
| @@ -0,0 +1,7 @@ +# 1 2 +A 22 22 +A|1 20 20 +A|2 2 22 +R 10 20 +R|1 10 10 +R|2 0 10 |
| b |
| diff -r 000000000000 -r 26ce946f4da9 test-data/strain_profiler-input.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/strain_profiler-input.txt Wed May 12 08:59:30 2021 +0000 |
| b |
| @@ -0,0 +1,11 @@ +HEADERS 1 2 3 +A 10 10 10 +A|g1.s1 10 10 10 +A|g1.s2 0 10 10 +B 10 10 10 +B|g1.s1 10 10 10 +B|g1.s2 10 0 10 +C 10 10 10 +C|g1.s1 10 10 0 +C|g1.s2 10 10 0 +C|g1.s3 10 10 10 |
| b |
| diff -r 000000000000 -r 26ce946f4da9 test-data/test-db/metaphlan-db/demo-db-v30.1.bt2 |
| b |
| Binary file test-data/test-db/metaphlan-db/demo-db-v30.1.bt2 has changed |
| b |
| diff -r 000000000000 -r 26ce946f4da9 test-data/test-db/metaphlan-db/demo-db-v30.2.bt2 |
| b |
| Binary file test-data/test-db/metaphlan-db/demo-db-v30.2.bt2 has changed |
| b |
| diff -r 000000000000 -r 26ce946f4da9 test-data/test-db/metaphlan-db/demo-db-v30.3.bt2 |
| b |
| Binary file test-data/test-db/metaphlan-db/demo-db-v30.3.bt2 has changed |
| b |
| diff -r 000000000000 -r 26ce946f4da9 test-data/test-db/metaphlan-db/demo-db-v30.4.bt2 |
| b |
| Binary file test-data/test-db/metaphlan-db/demo-db-v30.4.bt2 has changed |
| b |
| diff -r 000000000000 -r 26ce946f4da9 test-data/test-db/metaphlan-db/demo-db-v30.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/metaphlan-db/demo-db-v30.fasta Wed May 12 08:59:30 2021 +0000 |
| b |
| b'@@ -0,0 +1,226 @@\n+>1262743__R5C054__BN727_01980 UniRef90_R5C054;k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_sp_CAG_598;GCA_000431055\n+TTGATACATCAGCATCACTTGGCTTTTAGCGGTGGTTCGGAAAACTCAAACTATCGAGCATCGTTCGGTTTTATGGATCATAATACAATTGTCAAAGTTAACGATTACCGAAATTTAGTGGTAAAACTTGATGCTACACAAAAGGCTTTCGATGGTCGCTTAGTTGGCGATTTTGGTGTATATGGCTACTCGTCAAAGATACACGACATTTTCGATACACGAATACTGTTTTACTCGGCAGCTGCACAGAATCCTACATATCCAGCAGGAACTGATGTTAATGGCAACTGGGTGAAGAACTCGGCTGCATCACACATCAACCACCCCGGAGCACTCCTCTATGAGAAAAATGACTCCGAAGAACGGAATTTCAATACACATTTGGGGCTGAAATTTAATATCCTTGACAATTTGATATTGTCGGCTTTCGGCTCTTATTCATATTCATCTACGGGAAATGCTCAATTTTGTCCTACATGGGTGTGGGCGCAAGGCAATGTTTATCGTGGAGAGTTCAAGGGTGAAGACTACTTTACAAATGTGTCCCTCTCATATAACAATGCTTGGGGAGACTCACACCTTGATGCTGTTGTTGGCGCAGAATATCTTAAACAGGTAAGGACTGGTTTATGGGTGCAGGCAAAAGGAATAACAACAAATGATTTCTCCTATAATAACATCGGAGCAACATCATCGCGTCCTTTCGGTGGTACGAGCAGTAGCTATGAAGACCCGTCACTTGCTTCAATAATGGGTAGTGTCACATATAGTTACAAGGATAGATATTCTATTGCGGCAGCACTCCGTGGAGATGGCTCTTCAATGGTAAGCGATAACAATACTTTCGGATTCTTCCCATCAGTATCACTGGGTTGGGATGTAAAAAAAGAAGGCTTCCTCTCTGATACTGACTTTATAACAATGTTGAAACTAAGAACCGGATATGGTCGGTCAGGAAATCTTGGAGGTATAACATCCTATACAACACTTAATACCGTAAAGGAGAATGGTATCGTATCCATCAACGGTGCACCTACCGTAACAATGGGAAGTATACGCAACACGAATCCGGACCTTAAGTGGGAGACTCGTTCAACATTTAATATCGGTTTTGACTTAGGTATATGGGATAATCGGTTGATGCTTACCTCGGAATTATATTACTCAAAGACAACGGATATGCTCTATGAGTATGATGTTCCCGTTCCGACCTTTGCGTTCGATAAACTGATGGCAAATATCGGCTCGATGTCTAACCAGGGTGTCGAACTAGGAATCTCGGTAGTTCCCATTCAACGAAAGGATATGGAGATGAATATCAACTTCAATATGTCCTACCAGAAGAATAAGTTACTTTCGCTTAGTGGAGAGTATAATGGTATGCATATGACAGCTTCAGATATTACTCCGATTGGCTCGCTTTATGGTGCAGGTCAGAACGGTGGAGACAATAATGTAGTATATCAGATTGTAGGTCAGCCATTGGGGGTATTCTATCTACCTCACTGCAAAGGGCTTAAAGAAAATGAACTTGGTGGCTACAGTTACGATATTGAAGATTTGAATGATGATGGCGAGATTGATTTTAGCGATGGCGGAGACAGGTATATAGCAGGTCAGGCAACCCCCAAGGTAACTATTGGATCAAACATCAGTTTCCGTTACAAGTCCTTTGATATTGCCATGCAGATAAATGGTGCTTTCGGTCATAAGATATTCAATGGCACGGGCTTGGCTTATACCAATATGTCTATATTCCCTGACTACAATGTATTGAAGGGTGCTCCTGAAAAAAATATTATTGATCAGAATGTTTCAGACTATTGGTTGGAAAAAGGTGACTATGTAAATATTGAACATATTACCATAGGCTACAATATTCCAATGAAATCCAAGGCTGTGAAGTCATTGCGTCTTTCGGCAGGCATTAGCAACCTTGCAACAATCACAGGCTATAGCGGTCTTACTCCAATGATAAACAGTTATGTAGTAAGCAACACTTTGGGCATTGACGACAAACGCACCTATCCTTTATATCGTACCTATTCGTTAGGTCTTAGTATTCAATTCTAA\n+>189722__E0NQU7__HMPREF0658_0548 UniRef90_E0NQU7;k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_marshii;GCA_000146675\n+ATGGAATCATCAATCAAGGACAAATACATCATCTTGGGCTTTGTCGGCTTCGCCATCGTCCTAATATCTTCCATTGCCACGCTGGTAATAGCGGACAGCTTCAACCAAGACAACTTTGTCAGGTGGATAGTATTCGTATGCTGTAACCTGTTGGGATGGTTGCTCTATCTCTCCTTTCAGACACTTATCTTTGATACATACGAAATCTACAAAATCAAGTTCGGCAAGAAAGAAACGATTGCCGAAGCCATAGAGGTGCAGGAAGAACTGTCACAAAATACACTTGAAGAAGCCACATCTGTGCCTGGACCTACATCAGTCCCTGAGCCTGTACCCGAATCATCCCCGACAAAAGAAGAGACACTTATCCAAACACAACCGATAGAGCTTACTATCGCCCCGGATCTTCACGAAAAGAACCGTGCCAATTACGCCAAGCAGAGAGCAACGGGAAAAGGAAGAGCGCATCCGCATGGTCATGGAGTATTGCCATTATTACCTGCCTCGCATTGCCGACCAAGAAACCGTGAACCACATCTGTACTGA\n+>357276__A0A076II57__GV66_07710 UniRef90_A0A076II57;k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_dorei;GCA_000738065\n+ATGGATACTAAAAAAGAGTTGAAAATCCTCTTTTGGATGATTGTGGTTTATGCAGCCGTATTTTTCATGCCACTCGGCAATGAGAGGTTCATGACGGCTGTCGATGCAACCCTCGACCTTGCTAAATGGTATGCGCAGGAACACGTTATGTTATGTCTGCTTCCCACCTTTTTCATCGCAGGTGTGATTGCCGTTTTCGTCAGTCAGGGTTCGGTTCTCAAATATTTCGGAGCAAATGCCAAGAAGTGGTTATCCTATACGGCAGCTGCTGTTTCGGGTAGTATATTGGCAGTCTGTTCCTGCACGATTCTGCCGTTGTTTACGAGTATTTACAAACGGGGCGCAGGGTTAGGCCCTGCTATAGCCTTTCTCTATTCCGGCCCAGCCATCAGTATTTTATCCATCATTTTGACAGCCCGTATTTTGGGTGTAGAGATGGGTGTTGCACGAACGGTTGGAGCTATCGGATTCTCCGTAGTGATAGCCTTGCTGTGGCATTTATTTTCCGTAAGGAAGAGAAAGCCAAACAAGAGGAACAGATGA\n+>357276__A0A076IN30__DXD47_09350 UniRef90_A0A076IN30;k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_dorei;GCA_003466465\n+ATGAATCAGGTCAAAATGGTATTAATTTTTGCCATATTATTATTTTTATTTTGTGTGAATGTAAGTGCCCAAGTAATAAAGGGAAGA'..b'GACTTATATTGCTGATATGGCAAAGGCAAGTTTCTCACTTGTTTCAGGTAATGCCGAAGATGCTAACAGCGATAAAGTATTCTATGCAGAAAAGGCTGATTCTAAAGCAGGAATTGTCAACTTCTATAAGGTAACTAATGCAGGAGGTAAATTTGTTGCTGATGATAAAGTGGTTATTGTAGGATTTGATGCATTGGTAGATGGTACTGACAAGACATTTGCTTCTGACTTGATTAAGGTTGAAGTTTCTGAGAAGAATGATATTGTAGTTACAGCTCAGAAGAGAATCACAGTAGATACAAATGTCGTTGTTCCTGTTAAGTTGACTGTAACTAATGCAGATGGCACAAATGCAACTGTATACGCTTCATTCACAGTAACAGTAAAAGCATACCCGATTCAGTAA\n+>821__R7P1Q7__M099_2990 UniRef90_R7P1Q7;k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_vulgatus;GCA_000699865\n+ATGAAACGTAAAAATAAAACAACTAAATATATTCTGGCCGGGTTATTTCTTTCTTCGATGATGGGAGTAACAACTGCATGTGATCCGTTAGGAATAGAACCTACAACAAAAGTGGATGAAGAACGCTTTTGGGAAAATCCTCAATTGGCTCGTTCTTATGTGAACAATTTCTATTTCATATCCCAATCGGCATCTGGTGACACCTTCCAGTCAGAACAGTGGTCAGATAACTGTCAGGGAAACTATGAACAGGACTGGGATACGTATCGACAGTACAATTTTAACAAACGTACTTATGATGAAAATAATGGTATCACTTGTTTCAGCGCCCCATGGAGTGGAGCTTATAAAAACATTCGTGCTGTAAATCTTGGAATTGAAAAAATTTCTTCCAGCAGCATATTGACAGAAGCTCAGAAGAACCAATTCTTGGGTGAATGTTACTTTTTCCGTGCTTTTATTTATTTTGACATGGAAAAGTTTTGGGGAAGCGTTCCTTATGTAGACAAAGCGTTAACGATTGAAGATGAAACCTATTTGCCTCGTACCAAACGCGAAACTATTTTCGACAATATTCTAGACGATTTGCAGAAATCCGTAGATTATTTTAAAGCTTATGGTGGAACGCATACGCTTGGTATGGTAAATGAAGATGTAGCTAACGCATACATTTCGCGCGTGGCTTTATATGCAGCCAATGCGGCCGATGCTTCAGCCAAAGGTCTATATTCGGATGACGCTGAAGGCTTGTTCAAGTTTGAGAAGAATGCAAATCATTATTATGAATTGGCTTATAATGCAGCTAAAGGATTGATAGGCAAGTACAGTTTGGAACCGAATTATGAGGATCTGTTCACAAAAACAGAGTCACATACAAGCGTTGAGTCAATTTGGCCGGTCATGTTTAAAGAAAACCAACGTAGTGGTTTCAATCCAACTGCAAAGAACGGACCTGACGGGAATTATTATGGAGCAACCGAAGATGCGACTTATTCTTACGGGCGTCGTTCAGGTTTATTTCCTACACAGGATTTGGTAGACTGTTATTTACAGAAAGATGACGCTGATGGCAAATGGAAAAATTGGTGGGAAACTTCACAGGCAAAAGCCATGGGAATCCATAGAAATGCAGAAGGAGAATTAGAAGGAGAATCTGCTAATTATCGCGATATGTTCAAGAATCGCGATAGCCGCTTCTATTCCACAGTTACTTACGATGGAGCATATATGGGACCGGAAGAAGAACGTTATATTATTCAAACTTGGATTGACAATACTACACTAGATGAAAAGACCTTAAAATACAGTGCTTTACATTCTGGGTATAGAGTGATGGAAAATTTAAATTCCGCACCAATCAACAGAGCTTCCGCACAAACAATAACTGGTTATTATTCAAGGAAGTACTCTCAGTTTAATAAAATCAATACGGACGGGACTTTGGATTTTGACACCCAGCGTCAGACTTGCTATTTCAATGTACGGTATGCGGAAGTGTTGCTGAATTGTGCCGAGGCAAGTATTAAACTAGGCAAGACCGATGCGGCAGGCTATATCAATGAAATCCGTAATCGTGCCGGATTGCCTAATTATGACGGCAATGATTTGTGGAATGAAATGAAACTGCAACGTCGTTTGGAATTTGCATTTGAATGTCCGGGCTTCCGTTATTTCGATTTATTGCGTTGGGGGGAAGCAGAAGGCAAAACGACTATTGAAGAGTTGAATACTCCTTCCAGAGGATTATGGATTTTCCGTAAAGGTATGGAAAGCGAAAAGGCTGGTGAGAATGGTTATCCTGTAGAGCCGGGTGGTGAAGGATATTTTACTCCTAAATTCCAGACTTTTGAGATGCCGTATTCTTATTATGAAAGAAAGTTTGATGATGCAAGATACTACTTTGTACCATTTTCACAGTCCATGTTGAGAGACTATACACAATTGCAACAGAATCCGGGATGGAAAAACTTCAACTATAACAATTAA\n+>821__U6RDC2__DXD46_15675 UniRef90_U6RDC2;k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_vulgatus;GCA_003437415\n+ATGGAAGAATGCAAAGCAGCTGATTATTCCAATATTCTGTACATCAGAATGCTGTGGAAAGATTTGGAACCCGAGGAGGGCAAATATGCATGGATTTACAATGAACGGTATAAATGGTATATACAAAAAGCCAAAGACAAAGGGCTTAAACTGGCCTTCAGGGTGTTCTTTCATGGTGTAGACGGAGTACCGTCCTATGTGTACGAAGCCGGAGCCACAGAAAGCCCAATAGACGATGAAGGCAAAACCCAGCCTTATTATGATAATCCAGTATTCCTTGAAAAGCTGGACAAGTTCATAGAGGCTTTTGCAAAGGAATATGACAATCCGGATGAGGTAGATTATATTGATGCATATGGATTGGGAAGATGGGGAGAAGGACATGGACTGGTACTCGAAAAGCAAGATAATCTGGAAAGCGTTATCCGACAGATAACCGAATCGTATGCAAGACACTTCAAAAAAGTGCTTACGGTAATGAATCTTTCGCAGAGCGACTACAGGTTTTCCAAGCCGCTAGTATATGACAAGCTGGGGTTTCTTCCTCGCAGGGATGGTATAGGCAGTTTTGGGTTTTCTAATGAAGAACGTGCGATGGTGCATGACGAACTTTTCCCAAAAAGAGCTCTTATTGGTGAGGGATGCTGGTGGTTTAACGCACAAGATGGTGATAACTCAAAATACAAGCATTTCCAAGGAGACAAACGTTTTGCCATGAACGATTTCAAAGAAGCTTTTACCGTTTCTGTGACTGATGCTTTGGACAGCCATTGTAACACGCTGGATTTGCGTATGCCTTTACAGTGCAAATTCTGGATAGAAGAGCTGCCGGACCAAGTTCAGCGTTTTATAACTTTAGGCGGTTATCGTCTTTATCCGGACTATATAAAGGTGGAGCAAGACCACAAAACGTTGACTTTGTTTCATTCATGGAAAAACTATGGTGTGGGTGTATTGCCTAATAATCATCCCAATTGGAATTATAAATATCAGGTTAGTTTTGTTTTGATGAATGAAAAAAAGGAAATTGTATTTCTTTATACAGAACCGGAAGCAGAACCTTCCGAATGGTTGAAGGGAATATCATACAATTATTTGAGTCGGTTTAATATTCCGGCAGAATTGCAGGGAAAGTATACCTTATGTGTCGGCTTGACTGACAAGACAAAAAATAACGAAGCGGCTATTGATCTGGCTGTGTCTGGGAATTTAAAAATAGGGAAATGGATATTTGTGGTTGAACTGGAGTTGTAA\n' |
| b |
| diff -r 000000000000 -r 26ce946f4da9 test-data/test-db/metaphlan-db/demo-db-v30.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/metaphlan-db/demo-db-v30.json Wed May 12 08:59:30 2021 +0000 |
| [ |
| b'@@ -0,0 +1,1 @@\n+{"markers": {"189722__E0NQU7__HMPREF0658_0548": {"clade": "s__Prevotella_marshii", "ext": ["GCA_002161435", "GCA_000598585", "GCA_000699765", "GCA_900445525", "GCA_000178195", "GCA_000273725", "GCA_002811025", "GCA_000598905", "GCA_000598245", "GCA_900114865", "GCA_000699705", "GCA_000157015", "GCA_000155815", "GCA_000601115", "GCA_002811085", "GCA_000699785", "GCA_002894165", "GCA_000185605", "GCA_000273035", "GCA_001405475", "GCA_001548195", "GCA_001693695", "GCA_000273095", "GCA_001274835", "GCA_000759305", "GCA_000307435", "GCA_002160605", "GCA_000598305", "GCA_003439865", "GCA_001405955", "GCA_000598185", "GCA_000273055", "GCA_002884635", "GCA_002529225", "GCA_002811035", "GCA_000273155", "GCA_000759045", "GCA_000273315", "GCA_001405935", "GCA_001682215", "GCA_900167355", "GCA_000599065", "GCA_000577955", "GCA_000177075", "GCA_001406015", "GCA_002161135", "GCA_000598745", "GCA_000598885", "GCA_001314995", "GCA_000598425", "GCA_002222615", "GCA_000598785", "GCA_003438465", "GCA_000403175", "GCA_000154205", "GCA_900102645", "GCA_001398115", "GCA_900129535", "GCA_900454945", "GCA_003515045", "GCA_000599245", "GCA_000210495", "GCA_000156075", "GCA_003439285", "GCA_002959625", "GCA_000710365", "GCA_003437875", "GCA_000759245", "GCA_002797185", "GCA_000144405", "GCA_001405055", "GCA_002959715", "GCA_001574405", "GCA_000599365", "GCA_000177355", "GCA_001412315", "GCA_000759315", "GCA_000068585", "GCA_000699725", "GCA_001406095", "GCA_001552775", "GCA_001398395", "GCA_900095495", "GCA_001578575", "GCA_003437415", "GCA_000177055", "GCA_000598325", "GCA_000599305", "GCA_001552765", "GCA_001398375", "GCA_003539055", "GCA_003438835", "GCA_000025985", "GCA_003526655", "GCA_000955645", "GCA_900454835", "GCA_000273275", "GCA_001406715", "GCA_001217505", "GCA_002763975", "GCA_000699865", "GCA_000598665", "GCA_003466465", "GCA_000218325", "GCA_000598805", "GCA_002762425", "GCA_000599225", "GCA_001953935", "GCA_000599345", "GCA_002871515", "GCA_002763745", "GCA_001546595", "GCA_000699845", "GCA_001406315", "GCA_000158335", "GCA_003438705", "GCA_002204405", "GCA_002763715", "GCA_000297735", "GCA_002529435", "GCA_002753835", "GCA_000273135", "GCA_002763575", "GCA_000178295", "GCA_003439685", "GCA_000599205", "GCA_000273215", "GCA_001406635", "GCA_000218345", "GCA_002810995", "GCA_003438235", "GCA_000382445", "GCA_001405735", "GCA_000599285", "GCA_003386475", "GCA_001553225", "GCA_000766005", "GCA_001405155", "GCA_003438895", "GCA_003437605", "GCA_003437205", "GCA_003438205", "GCA_000599105", "GCA_002160595", "GCA_003436935", "GCA_003436175", "GCA_000598545", "GCA_001405515", "GCA_000261025", "GCA_003363235", "GCA_000307455", "GCA_000598285", "GCA_003439415", "GCA_003503335", "GCA_000169015", "GCA_000598165", "GCA_003436085", "GCA_900107315", "GCA_000601055", "GCA_000273785", "GCA_003437005", "GCA_000210835", "GCA_000598825", "GCA_002959635", "GCA_000738045", "GCA_000297755", "GCA_002161115", "GCA_000759165", "GCA_000273115", "GCA_000403235", "GCA_003439505", "GCA_000185845", "GCA_003438765", "GCA_000193395", "GCA_000210075", "GCA_002797155", "GCA_002161715", "GCA_001699865", "GCA_000273295", "GCA_000026905", "GCA_000738065", "GCA_003265025", "GCA_003436855", "GCA_000273075", "GCA_002206325", "GCA_002763535", "GCA_002794335", "GCA_003437545", "GCA_000759185", "GCA_001546565", "GCA_000012825", "GCA_001406135", "GCA_000598925", "GCA_000699665", "GCA_900445515", "GCA_000068525", "GCA_000598445", "GCA_000577295", "GCA_000699885", "GCA_003201715", "GCA_000759265", "GCA_900107825", "GCA_900107475", "GCA_003466305", "GCA_900100465", "GCA_001404375", "GCA_000598565", "GCA_001405775", "GCA_000191765", "GCA_003439225", "GCA_000177315", "GCA_001404395", "GCA_000598505", "GCA_000699905", "GCA_001915605", "GCA_001580095", "GCA_000163035", "GCA_000154125", "GCA_001405595", "GCA_000178275", "GCA_003438645", "GCA_001953955", "GCA_000598985", "GCA_000012845", "GCA_000762405", "GCA_900109635", "GCA_003436285", "GCA_000598945", "GCA_000724815"'..b'oidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_xylanisolvens|t__GCA_000577295": ["2|976|200643|171549|815|816|371601", 6484037], "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_xylanisolvens|t__GCA_002161115": ["2|976|200643|171549|815|816|371601", 5692802], "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_xylanisolvens|t__GCA_000178215": ["2|976|200643|171549|815|816|371601", 6059812], "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_xylanisolvens|t__GCA_000577955": ["2|976|200643|171549|815|816|371601", 6228594], "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_xylanisolvens|t__GCA_000273315": ["2|976|200643|171549|815|816|371601", 6067695], "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_xylanisolvens|t__GCA_900107825": ["2|976|200643|171549|815|816|371601", 6131743], "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_xylanisolvens|t__GCA_000210075": ["2|976|200643|171549|815|816|371601", 5976145], "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_xylanisolvens|t__GCA_900114865": ["2|976|200643|171549|815|816|371601", 5867942], "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_salanitronis|t__GCA_000190575": ["2|976|200643|171549|815|816|376805", 4308663], "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_coprophilus|t__GCA_000157915": ["2|976|200643|171549|815|816|387090", 4041504], "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_sp_D2|t__GCA_000159075": ["2|976|200643|171549|815|816|556259", 6920457], "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_oleiciplenus|t__GCA_001915515": ["2|976|200643|171549|815|816|626931", 6012549], "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_oleiciplenus|t__GCA_000315485": ["2|976|200643|171549|815|816|626931", 7087734], "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_oleiciplenus|t__GCA_003438445": ["2|976|200643|171549|815|816|626931", 6457077], "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_sartorii|t__GCA_000403195": ["2|976|200643|171549|815|816|671267", 5464209], "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_reticulotermitis|t__GCA_000517545": ["2|976|200643|171549|815|816|1133319", 5365278], "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_caecimuris|t__GCA_002221665": ["2|976|200643|171549|815|816|1796613", 4800416], "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_caecimuris|t__GCA_001688725": ["2|976|200643|171549|815|816|1796613", 4839927], "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_sp_43_108|t__GCA_001915545": ["2|976|200643|171549|815|816|1896974", 5012994], "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_sp_OM05_12|t__GCA_003438995": ["2|976|200643|171549|815|816|2292283", 4475735], "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenella|s__Rikenella_microfusus|t__GCA_900455755": ["2|976|200643|171549|171550|28138|28139", 2945869]}, "merged_taxon": {}}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 26ce946f4da9 test-data/test-db/metaphlan-db/demo-db-v30.pkl |
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| Binary file test-data/test-db/metaphlan-db/demo-db-v30.pkl has changed |
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| diff -r 000000000000 -r 26ce946f4da9 test-data/test-db/metaphlan-db/demo-db-v30.rev.1.bt2 |
| b |
| Binary file test-data/test-db/metaphlan-db/demo-db-v30.rev.1.bt2 has changed |
| b |
| diff -r 000000000000 -r 26ce946f4da9 test-data/test-db/metaphlan-db/demo-db-v30.rev.2.bt2 |
| b |
| Binary file test-data/test-db/metaphlan-db/demo-db-v30.rev.2.bt2 has changed |
| b |
| diff -r 000000000000 -r 26ce946f4da9 test-data/test-db/metaphlan-db/humann_markers.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/metaphlan-db/humann_markers.tabular Wed May 12 08:59:30 2021 +0000 |
| b |
| @@ -0,0 +1,113 @@ +1262743__R5C054__BN727_01980 +189722__E0NQU7__HMPREF0658_0548 +357276__A0A076II57__GV66_07710 +357276__A0A076IN30__DXD47_09350 +357276__A0A076INK2__BSEG_04225 +357276__A0A076INR8__EL88_12300 +357276__A0A076IRX4__ABI39_13585 +357276__A0A076IS46__BACDOR_03265 +357276__A0A076IS73__GV66_00410 +357276__A0A076ITH2__BSEG_03273 +357276__A0A076IXE0__HMPREF1064_04364 +357276__A0A076IYE6__IY41_04275 +357276__A0A076J726__IY41_15030 +357276__A0A076J8D4__HMPREF1064_00553 +357276__A0A076J9V8__BACDOR_01395 +357276__A0A0K2HF58__IY41_03550 +357276__A0A0K2HFA1__HMPREF1065_02962 +357276__A0A0K2HG61__BACDOR_02028 +357276__A0A0K2HGB7__HMPREF1064_01580 +357276__A0A0K2HHN3__GV66_08845 +357276__A0A0K2HI25__DXD47_04465 +357276__A0A0K2HI42__ABI39_06975 +357276__A0A0K2HJA6__DXD47_07320 +357276__A0A0K2HMX2__HMPREF1063_03979 +357276__A0A0K2HNG3__HMPREF1064_03004 +357276__A0A0K2HP62__HMPREF1063_01560 +357276__A0A0M1VXQ9__BSEG_00942 +357276__A0A0M1VYB8__HMPREF1063_02104 +357276__A0A0M1W1I8__ABI39_13620 +357276__A0A0M1W657__HMPREF1064_04629 +357276__A0A0M1W6X7__HMPREF1065_03898 +357276__A0A0M1W9N4__GV66_05135 +357276__A0A174L570__GV66_05720 +357276__A0A1Y3Z6X3__GV66_07715 +357276__A0A3E4JJ65__HMPREF1064_00497 +357276__B6VVS0__HMPREF1064_03951 +357276__B6VXX7__HMPREF1063_02683 +357276__B6VYT9__HMPREF1063_05030 +357276__B6W1J2__BACDOR_03380 +357276__B6W1Y1__BSEG_03960 +357276__B6W1Y5__IY41_11405 +357276__B6W5Q7__DXD47_13945 +357276__B6W5Q9__HMPREF1063_03125 +357276__C3R9Y0__HMPREF1064_01889 +357276__C3RA36__HMPREF1065_03270 +357276__C3RDQ5__HMPREF1065_03827 +357276__C3REQ8__GV66_09740 +357276__D1JY58__BACDOR_04277 +357276__D1JYA0__EL88_06560 +357276__D1JZM4__HMPREF1065_01278 +357276__D1K3K9__EL88_23995 +357276__D1K526__GV66_17250 +357276__E5UTL1__HMPREF1065_03551 +357276__I8VN48__ABI39_07855 +357276__I8VQA2__HMPREF1065_04183 +357276__I8WBQ9__HMPREF1065_03212 +357276__I8WDF1__B5F00_02455 +357276__I8WFU9__BACDOR_02006 +357276__I9F327__DXD47_22495 +357276__I9FGI3__EL88_12385 +357276__I9FRW5__B5F95_21685 +357276__I9FU68__HMPREF1063_00557 +357276__I9QBT4__GV66_09000 +357276__I9QBT7__BSEG_03340 +357276__I9QPN0__B5F95_09195 +357276__I9QXD4__IY41_00345 +357276__I9R1V6__DXD47_04125 +357276__I9R201__B5F00_01910 +357276__I9R994__BACDOR_04044 +357276__I9RAC4__BSEG_00561 +357276__I9RCD3__IY41_15070 +671267__R9I8L9__C802_02304 +671267__R9IB12__C802_00696 +821__A0A0N7J7X2__SAMN04487923_101621 +821__A0A0P0L8F8__ERS852509_03705 +821__A0A0P0LFP6__C5Z04_13890 +821__A0A0P0LH09__ERS852457_03390 +821__A0A0P0LJ37__DXB82_14270 +821__A0A0P0LKG6__HMPREF1058_02188 +821__A0A0P0M2J4__DXD46_10295 +821__A0A0P0M3U7__DXB90_14325 +821__A0A0P0M405__DXC02_15075 +821__A0A0P0M4G3__M099_3092 +821__A0A173XDD3__DXB82_17180 +821__A0A174ALF2__BvMPK_3016 +821__A0A174AYT0__DXC02_03530 +821__A0A174JYD3__ERS852457_02610 +821__A0A174MBW9__SAMN04487923_10272 +821__A0A174NM17__lacZ_6 +821__A0A174NSU0__BVU_3144 +821__A0A174NVL6__NCTC10583_01782 +821__A0A174T998__DXB82_10860 +821__A0A395UNT8__DXD64_15275 +821__A0A395VIK7__BVU_1225 +821__A0A395VLM8__BvMPK_3650 +821__A0A396ER29__ERS852457_02298 +821__A0A396F1N0__M099_1553 +821__A0A396F598__CUU_3259 +821__A0A396F9T7__M097_3427 +821__A0A3E4HP25__SAMN04487923_102450 +821__A0A3E4KIM1__M097_3660 +821__A0A3E4WAR6__DXD64_10735 +821__A0A3E4XY72__NCTC10583_01067 +821__A6L0C7__ERS852556_03520 +821__C3RB94__DXC03_15585 +821__C6ZAA5__ERS852556_00403 +821__D4V4X2__DXC16_18525 +821__D4VC51__M099_1508 +821__D4VD59__BHV80_04260 +821__E5UPR6__SAMN04487923_101768 +821__I9R3W6__DXC16_12455 +821__R7P1Q7__M099_2990 +821__U6RDC2__DXD46_15675 |
| b |
| diff -r 000000000000 -r 26ce946f4da9 test-data/test-db/nucleotide-db/g__Bacteroides.s__Bacteroides_dorei.centroids.v296_201901b.ffn.gz |
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| Binary file test-data/test-db/nucleotide-db/g__Bacteroides.s__Bacteroides_dorei.centroids.v296_201901b.ffn.gz has changed |
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| diff -r 000000000000 -r 26ce946f4da9 test-data/test-db/nucleotide-db/g__Bacteroides.s__Bacteroides_vulgatus.centroids.v296_201901b.ffn.gz |
| b |
| Binary file test-data/test-db/nucleotide-db/g__Bacteroides.s__Bacteroides_vulgatus.centroids.v296_201901b.ffn.gz has changed |
| b |
| diff -r 000000000000 -r 26ce946f4da9 test-data/test-db/protein-db/uniref90_demo_prots_v201901b.dmnd |
| b |
| Binary file test-data/test-db/protein-db/uniref90_demo_prots_v201901b.dmnd has changed |
| b |
| diff -r 000000000000 -r 26ce946f4da9 test-data/test-db/protein-db/uniref90_demo_prots_v201901b.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/protein-db/uniref90_demo_prots_v201901b.fasta Wed May 12 08:59:30 2021 +0000 |
| b |
| b'@@ -0,0 +1,88 @@\n+>UniRef90_W7T1N9|1098\n+MPYKCQCPSQRIKTHNLKVRSMFKACDGRGTTKIFLSIIYTKIPHQICQHSQHSTPICRSGKCEIHRKCSLMSSLALTPFKAGLFVGKSIIVTGGGTGLGYAIAKELVSLGAKVVIAARRIEVLEAAASEMNKSSQRGGKIYVCQCNVRNEDDIQKLVTFALETMGGIDGLVNNAGGQFVSPVENISARGFKAVVETNLLSCFMLSKEIYNRWWSQQEDRKRSGSIVNIILANKNGFPMMAHSGAARAGVENLTKSMALEWIGRGVRVNCVAPGIIYTESGFANYGEMAGAFLSSVLPCIPAHRCGTAEEVSSLVVFLLSDAAVYITGQNMGVDGGMGQGTIPLRPQDHGASLLPVYGELPMKARL\n+>UniRef90_U3KI10|2454\n+MRTDSNNENSVPKDFETIDNSNFAPRTQRQKPQSELVKKPLSKQKEHLRKKLEEERMKENLLLGKNSNEVVQFSDPLGKNSSSSNTLKEIDRFPTEHLLQKLEISSPEVKYEQPPKCEVTGKEAISAMSRAKSPQCRQEIADVYCQHKLGTLMPEQVTRFCALEGKANTNVQWDEDSVEFMPAQPVRIAFVLVVHGRASRQLQRMFKAIYHKDHFYYIHVDKRSNYLHRQVLQFASQYPNVRVTSWRMATIWGGASLLTTYLQTMKDLMEMSDWPWDFFINLSAADYPIRTNEQLVAFLSRYRDMNFLKSHGRDNARFIRKQGLDRLFLECDTHMWRLGDRKIPEGITVDGGSDWFLLNRKFVEYVTFSNDDLVTKMKRFYSYTLLPAESFFHTVLENSPFCDSMVDNNLRITNWNRKLGCKCQYKHIVDWCGCSPNDFKPADFHRFQQTARPTFFARKFEAVVNQEIIGQLDYHLYGNYPPGTPGLRSYWENVWEEPDGLGALSDAALTLFHSFSRLGLRRAQSALHAAGDSCRYYPMGHPVSIHLYFLADRFQGFLIRHHATNLAGSKLETLETWVMPKKVFKIASPPSDFGRLQFSEIGTEWDAKERLFRNFGGLLGPTDEPVGMQKWGKGPNVTVTVIWVDPINVIAATYDILIESSAEFTHYKPPLNLPLRPGVWTIKILHHWVQVAETKFLVTPLAFSNQQPIKQEDAIKLHSGPPKNAYMEQSFQGLNPVLNMPVSAARAEQARRNAALVGPRLDAWVDSLAGGVWSAVEVCSVGPSGCPALQGCAQTAWSSLSPDPKAELGPVKPDGRLR\n+>UniRef90_Z9JLB1|1683\n+MSQTRPWLQHYPSGIPTEIDADAFRTIVDVFNTSVIKYRDCPAYTNFGKTLTYGEIDLLTKQFASYLLNELKLKKGERIALMMLNCLQYPVATFGALRAGLTVVNVNPLYTARELKHQLVDAGASVLVVIDNFCTTVQHIIADTSVKQVITTGLGDLLGFPKRSLVNFAVKHIKKLVPEYRLPGSIRFREALARGGKHAMPPIHIASDDLAFLQYTGGTTGTAKGAMLTHRNMVANMQQTSHWLNNNLKESCETVITALPLYHIFALTANNLLFMKIGGCNHLITNPRDIPGFVKELKRVRFTAITGVNTLFNKLLNTPGVAEIDFSSLKIALGGGMAVQRSVAERWKQVTHVPLIEAYGLTEASPGVCINPLDLKEYNGSIGLPIPSTDVCIKDDTDTPLPTGEIGELCIKGPQVMKGYWQHPEETSNVFDADGWLHTGDIAKMDEQGFFYIIDRKKEIILVSGFNVYPNEIEEVIAMMPGVDEVAAFGVPDEKYGEVVKVVIVKKDPMLTAEEVKAHASANLTRYKLPRIIEFRTKLPKTDVGKILRHELRHAAPTSTT\n+>UniRef90_Z9JRB3|1773\n+MQTHTYDVVIVGAGGAGMRAALESSKRARTAVLTKLYPTRSHTGAAQGGMCAALANVEEDNWEWHTYDTVKGGDYLVDQDAAEVMAKEAIDAVLDLEKMGLPFNRTPEGKIDQRRFGGHTREHGEAPVRRSCYAADRTGHMILQTLYQNCVKQNVEFFNEFYVLDVLMTGDPRDEAEVRASGVVAYELATGEVHIFRAKSVVFASGGFGKMFKTTSNAHTLTGDGPAMALRRGIPLEDMEFFQFHPTGLAGLGILLSEAARGEGGILRNAQMERFMERYAPTLKDLAPRDVVARAMANEVREGRGCGPNKDYVLLDLTHLEPAHIDAKLPDITEFARTYLGVEPYTEPVPVFPTAHYGMGGMPTNIKGEVLRNETDVVPGLYAAGEVACVSVHGGNRLGTNSLLDINVFGRRAGIYAAEHAAGVELAEIEPGLEAPTVELLERLRDRPATTDRIADIRRDLQETMDANVQVFRTEETCRTALADIHQLKKRYETVAVQDKGRRYNLDLLEAVELGFLLDLAEVVTVGALNRKESRGGHFREDFEKRDDVNYLWHTMAYRTREGEEGFEGTDIRLGTKPVVITRYEPKERTF\n+>UniRef90_X8JRH1|978\n+MSTANGATGQKGFLASPKTIAIVGCPFSGGQPKAGVDRGPIHLINAGLEDQLSGLGWKVKFDGHHQFEEIDAQNDTPLGILKRPRLVSQVCEAVAKVVGDHARNGELPLTLGGDHSLAMGTISGVLSAHPEACVVWVDAHADINTPSTSTSGNIHGMPLSFLLGIAGEVPQAEFGPQPFSWIKPTLRPERLVYIGLRDIDDGERKILREHGIRAYSMHEVDRYGIGRVVELALAHVNPDGKRPIHLSFDVDALDPTVAPSTGTPVRGGLTFREGHYICEAIAETGLLVGLDIMEVNPSLGSTDADVSATVAVGCSLARSALGETLL\n+>UniRef90_Q8GT21|1368\n+MAHDQSLSFEVCRRKPELIRPAKQTPHEFKKLSDVEDQEGLRFQIPVIQFYKHNNESMQERDPVQVIREGIARALVYYYPFAGRLREVDGRKLVVECTGEGVMFIEADADVTLEQFGDALQPPFPCFDQLLFDVPGSGGILDSPLLLIQVTRLKCGSFIFALRLNHTMADAAGIVLFMKAVGEMARGAATPSTLPVWDRHILNARVPPQVTFNHREYEEVKGTIFTPFDDLAHRSFFFGSTEISAMRKQIPPHLRSCSTTIEVLTACLWRCRTLAIKPNPDEEVRMICIVNARSKFNPPLPDGYYGNAFAIPAAVTTAGKLCNNPLGFALELIRKAKREVTEEYMHSVADLMVATGRPHFTVVNTYLVSDVTRAGFGEVDFGWGEAVYGGPAKGGVGVIPGVTSFYIPLRNRQGEKGIVLPICLPSAAMEIFAEALNNTLNGKEIEIAKHFTQSSL\n+>UniRef90_X6L320|957\n+MSLEDAKRQIDHAFTRDDLKGPSFENVFAGAASFLRRKYTKDLTGVDIAVTGLPFDQAVTNRPGTRLGPRAIREASLLQTMDKPYGWDFDVLSDFAIADYGDMAFDYAMPSAVPARIEEHVRGILDAGAACVALGGDHSVTLGALRAHAAVHGPLSVIQFDAHTDTWADDDPGRVDHGTFLYTAAKEGIVVPERSVQIGIRTDNPDTMGFHILDAREVHAAGPERIAEQVHQIVGRSACYITFDIDALDPAFAPGTGTPVWGGLTSHQAAVMLRRLAGVNMVGGDVVEVSPPFDTTGATAIAAAHVATELLSIWASTRR\n+>UniRef90_W7DVV5|549\n+MPIGGGKGGSDFDPKGKSDAEIMRFCQSFMSELAMHIGPDTDVPAGDIGVSGREIGYLFGQYKKMTGRFDAGTITGKGLTYGGSLTRTEATGYGLVYFTKEMLAATNQSLKNKTVVVSGSGNVAIYAIEKAEELGAKVVACSDSSGYIFDQEGINLKTLKQIKEVERRRIHTYLEKHPTAEIF\n+>UniRef90_W8YTG4|1614\n+MAYEMPWTADTSKLNKMELWKIEKDGLDVIRTIIEKYALEGYDSIPEDDMNRFKWAGVYEQKPRDGYFMMRIRINSGVMTTAQARALASIGRDYGRDLIDVTTRQAIQYHWLRIENMPDIFKRLEEVGLYSYESCGDCPRT'..b'SGADLYKVEMPLFGKGSRKELLCASQKLNDHIAMPWVILSSGVDEKLFPRAVRVAMEAGASGFLAGRAVWSSVIGLPDTEMMLRDISVPKLHRLGEIVDEVMARR\n+>UniRef90_Z9JUT2|1308\n+MTASPAPADLCAPLEESTVSSPRERRALPRPYDAILLASFGGPEREEDVLPFLRNVTRGRGIPDERLEEVGAHYRALGGRSPINDQNRALIRALRAELDERGIDLPIHWGNRNWQPTMAEAVRGLHADGHREVLAIATSAYSSYSSCRQYREDFGRALVETGLLGTVRLDKVRPYFSHPGFLAPMADGILDALAQLQEEGHDGARVRILFSTHSIPTAMADASGPAEERTGGPARWYVRQHEAACRYLMDAVAQRRAAEGAGTELPGWELVYQSRSGAPHTPWLEPDVNDVIARIAEEGEHDAVVVVPVGFVSDHVEVIWDLDTEARESAEQHSLAFRRVATPGTDPRFVAALADLVEERIRPDAPRRAVTEFGPTADVCGTACCVSGSPRARIVPTTSALDSGEDLRAARTqaardegGSTRPAGAGTTGEAGGR\n+>UniRef90_U3KP22|1143\n+MFPSRRKAAQLPWEDGRRDTIPYLSPPPsprpekeprgrgRLCRASSLPRPLAGLASAPVRRKPppqddGGSRLLPSGLSRKCSVFHLFVACLLLGFFPLLWLQLSCSGDVARTAGGQGQETPGPPRACPPEPPPELWEEDASWGPHRLAVLVPFRERFEELLVFVPHMHRFLSRKKIQHHIYVLNQVDHFRFNRAALINVGFLESSNSTDYIAMHDVDLLPLNEELDYGFPEAGPFHVASPELHPLYHYKTYVGGILLLSKQHYQLCNGMSNRFWGWGREDDEFYRRIKGAGLQLFRPSGITTGYKTFRHLHDPAWRKRDQKRIAAQKQEQFKVDREGGLSTVRYRVDSRTALSVAGAPCTVLNIMLDCDKAATPWCTFS\n+>UniRef90_Z9JWW5|1404\n+MADTSTDQSYDVVILGGGSGGYAAALRGAQLGLKIALVEKDKLGGTCLHRGCVPTKALLHVGEVADSAAEGAEMGVKMSLEGIDIATTLEFKDKIIGRLYKGLQGLVKSRKVEYVEGFGRLTGKNTVSvetsegvreltgknvvlaSGSYSKTLPGLELGGRILDSEAALQLPEVPKNPIILGGGVIGVEFASVWKSFGAESVTIVEGLPHLAANEDESLSKALERSFKKRGIKFSLGTFFEKAVQTDTGVTVTLVDGTTFEGDYLLVAVGRGPATAGLGYEEQGITMDRGFVLADKNTLETNVPGIYAVGDIVPGLQLAHRGFQQGILVAERIAGQDPAPIVESGIPRVTYCDPQLGSVGITEKQAKEQFGEDGVETYEYNLGGNGKSQILGTTGFIKLVREKNGPIVGVHMIGRNLAEQIGEAQLIVNWEAYPEDVASLVHAHPTQNEAIGEAALALAGKPLHAHA\n+>UniRef90_Q9VTG7|1437\n+MKGGNYTSLGTCSGINVSGNVAGTRKMSLGKSIKMYLTIFILTTCIYMALYQYHISREPFAASEVVKHQEKSSSYIASYLWSPISLLMAnsssntnnnstttstttttapttptttttttvgsvgQKLGASSISSIRMVSLAATIPSFKSTLSESRSVSLGGHQKTATVKTSTtittrttasglattklsattrttaktsaklsaattpTASHMENGYKTRPTFVAASLPPPLYIITPTYRRPEQLAELTRLGYTLKHVVNLLWLVIEDANKTNPLVGHTLDRIGVPYEYMVAPMPEKYKQTKKAKPRGVSNRNRGLEYLREHATEGVLYFADDDNTYDISIFEQMRYISKVAMWPVGLVTKTGVSSPIIQAGKLVGYYDGWIGGRKYPVDMAGFAVSVKFLKERPNAQMPFKPGYEEDGFLRSLAPLDDAEIELLADECRDILTWHTQTKKNAPAQALNRTRYKNTNLEHIDRLLVRP\n+>UniRef90_X7F2P9|852\n+MSESDESVSRAKRVDIGKVGVGNDRPLALIAGPCQLENLDHARMLAHRIAEAADAAGLPWIFKASYDKANRSSLSGRRGLGIDEGLGILARIREEFGVPVLTDVHAPDQCARAAEAVDVLQIPAFLSRQTDLLLAAGETGAAINVKKGQFLAPWDMANVADKIASTGNARILLCERGASFGYNMLVSDMRSLPIMARTGWPVVFDATHSVQLPGGQGGSSGGQREFVEPLARAAVAVGCAAVFIETHEAPDTAPSDGPNMVPIDRLPALLDGLAALDRLTKGRG\n+>UniRef90_X8DN03|1056\n+MPPSRPGGPACATPCWLRWPTSSPPAARSTCAGQAPTLPPRSCRDSSVAASACARPSHCWAGCAGRCRAAALRAAASLELLHAFALLQDDVMDDSPVRRGRASAHVQFACWHRDRGLSGSSSRFGESAAMLLGDLCLVWAEQMLRGSGLARDALDRAWPRYDTMRTELAVGQLGDIVVDAASLPSLVEVLDVARRKSGNYTVRWPLEIGAVLAGCDDDVLTLLSGYGEAVGEAFQMRDDLLGIYGSPRVTGKPAGADLSERKATTVVVAAYQLADNGLRRRLSELMGSAELDQSAVDQWRTLIAATGAVELIEQMIAERVAAALELLSSDRIDHGVRDALADMAVACSQRAA\n+>UniRef90_Z9JWA2|2748\n+MTAHETPSPIGINLPSHAQDPDPEETREWLDSLDQLVDERGDERATAIVQNVIQRARDKKLHLPDSLTTDYVNTIDVESQPEYPGDLELEKEIRNALRWNAAMVVHRAQRPGVGVGGHLSSYASISTMYEVGFNHFFRGREHPGGGDHvffqghaspgiyarafmqgrlSQEDLDGFRQEFSSEHGMPSYPHPRAMPDFWEFPTVSMGIGPVNAIEQASFDKYLHNRGIKDTSDQHTWAFLGDGEMDEVESRGALHIAAKEHLDNLTFVVNCNLQRLDGPVRGNGKIVQELESQFRGAGWNVIKVIWGSGWDPLFAADSDGALIDLMNATPDGDFQTYRTENGGFIRDNFFGRDPRTKALVEDMSDDDIWWKLNRGGHDTKKIYAAFKAAMEHKGQPTVILAHTIKGYRLGKNFAGRNATHQMKKFTPEDLKALRDTLQIPISDEVLESSSVYDAPFYVPDADSPAMRYFHERRSELGGQVPSRSREHKPLNLPGEEAYKVVKKGSGKQEIATTMALVRLLKDLMRDKETGKLWVPIIPDEARTFGMDSLFPTAKIYNPDGQNYISVDRDLLLAYKESTSGQIKHMGINEISSTSAFTAAGTSYATHGQPMIPLYIFYSMFGFQRTGDFFWAAGDQLAKGFVIGATAGKTTLAGEGLQHMDGHSPILAYTNPGAVIYDPAYGYEIGHIMRDGLQRMYGADEKRLQEVFYYITVYNEPMVQPAEPENLDVEGLLKGMYLLAPAPEGEGPEVQLMASGVGVPWALHAQKLLAEDWGVRGAVWSVTSWTEMRKDALEAEKDAFLHPEQEARVPFISERLQGVEGPFIATSDYDFLVPDLIRPWIPGPYGVLGADGWGFSDTRPAARRHLHIDAHSMAVKALQMLARDGRVDASLPAQAVKKYDLLNPNAGQSGSFGGDS\n+>UniRef90_X5M7Z0|1134\n+MVTDRIKDFLRTTRSDEPFVVVDLDVVRDNYNRLARALPESRVYYAVKANPAPEILALLAKLGSSFDAASIAEVEMVLAAGASADRISFGNTIKKERDIARAYTLGVRMFAVDCPEEVEKVARVAPASRVFCRILTDGVGAEWPLSRKFGCVPDMASNVLRHAHDLGLEAHGVSFHVGSQQPDTGAWDRALEDASTIFRTLADQGIHLKMVNLGGGFPTRYLKEVPTSEDYGKAIFGALRRHFGNQIPETIIEPGRGLVGDAGVIRAEVVLVSRKTQEPDADRWVYLDIGKFGGLAETMDEAIRYPIRTPHDGERTTPCVVAGPTCDSADVLYEKTPYDLPVSLTIGDEILIEATGAYTTTYASNGFNGFAPLKSYII\n' |
| b |
| diff -r 000000000000 -r 26ce946f4da9 test-data/test-db/utility_mapping/map_go_uniref90.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/utility_mapping/map_go_uniref90.txt Wed May 12 08:59:30 2021 +0000 |
| b |
| b'@@ -0,0 +1,326 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|
| b |
| diff -r 000000000000 -r 26ce946f4da9 test-data/test-db/utility_mapping/map_uniref90_name.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/utility_mapping/map_uniref90_name.txt Wed May 12 08:59:30 2021 +0000 |
| b |
| @@ -0,0 +1,8 @@ +UniRef90_A0A0K2HIA2 Acetyltransferase +UniRef90_Q8GT21 Benzyl alcohol O-benzoyltransferase +UniRef90_Q9ZUH4 Tricyclene synthase, chloroplastic +UniRef90_U5FT06 Hexosyltransferase +UniRef90_W7DVV5 Glutamate dehydrogenase +UniRef90_W8YTG4 Ferredoxin--nitrite reductase +UniRef90_Z9JRB3 Succinate dehydrogenase flavoprotein subunit +UniRef90_Z9JUT2 Ferrochelatase |
| b |
| diff -r 000000000000 -r 26ce946f4da9 tool-data/humann_nucleotide_database.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/humann_nucleotide_database.loc.sample Wed May 12 08:59:30 2021 +0000 |
| b |
| @@ -0,0 +1,8 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of metagenomics files. +#file has this format (white space characters are TAB characters) +# - db-build-version-date +# - db-name +# - build +# - /path/to/data +#02_16_2014 ChocoPhlAn chocophlan /path/to/data \ No newline at end of file |
| b |
| diff -r 000000000000 -r 26ce946f4da9 tool-data/humann_protein_database.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/humann_protein_database.loc.sample Wed May 12 08:59:30 2021 +0000 |
| b |
| @@ -0,0 +1,8 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of metagenomics files. +#file has this format (white space characters are TAB characters) +# - db-build-version-date +# - db-name +# - build +# - /path/to/data +#02_16_2014 EC-filtered UniRef90 uniref90_ec_filtered_diamond /path/to/data \ No newline at end of file |
| b |
| diff -r 000000000000 -r 26ce946f4da9 tool-data/humann_utility_mapping.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/humann_utility_mapping.loc.sample Wed May 12 08:59:30 2021 +0000 |
| b |
| @@ -0,0 +1,9 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of metagenomics files. +#file has this format (white space characters are TAB characters) +# Tab separated with 4 columns: +# - db-build-version-date +# - db-name +# - build +# - /path/to/data +#utility_mapping-full-20210421 Full mapping full /path/to/data \ No newline at end of file |
| b |
| diff -r 000000000000 -r 26ce946f4da9 tool-data/metaphlan_database.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/metaphlan_database.loc.sample Wed May 12 08:59:30 2021 +0000 |
| b |
| @@ -0,0 +1,8 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of metagenomics files. +#file has this format (white space characters are TAB characters) +# - db-build-version-date +# - db-name +# - build +# - /path/to/data +#02_16_2014 MetaPhlAn2 clade-specific marker genes db_v20 /path/to/data \ No newline at end of file |
| b |
| diff -r 000000000000 -r 26ce946f4da9 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Wed May 12 08:59:30 2021 +0000 |
| b |
| @@ -0,0 +1,18 @@ +<tables> + <table name="metaphlan_database" comment_char="#"> + <columns>value, name, dbkey, path</columns> + <file path="tool-data/metaphlan_database.loc" /> + </table> + <table name="humann_nucleotide_database" comment_char="#"> + <columns>value, name, dbkey, path</columns> + <file path="tool-data/humann_nucleotide_database.loc" /> + </table> + <table name="humann_protein_database" comment_char="#"> + <columns>value, name, dbkey, path</columns> + <file path="tool-data/humann_protein_database.loc" /> + </table> + <table name="humann_utility_mapping" comment_char="#"> + <columns>value, name, dbkey, path</columns> + <file path="tool-data/humann_utility_mapping.loc" /> + </table> +</tables> |
| b |
| diff -r 000000000000 -r 26ce946f4da9 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Wed May 12 08:59:30 2021 +0000 |
| b |
| @@ -0,0 +1,18 @@ +<tables> + <table name="metaphlan_database" comment_char="#"> + <columns>value, name, dbkey, path</columns> + <file path="${__HERE__}/test-data/metaphlan_database.loc" /> + </table> + <table name="humann_nucleotide_database" comment_char="#"> + <columns>value, name, dbkey, path</columns> + <file path="${__HERE__}/test-data/humann_nucleotide_database.loc" /> + </table> + <table name="humann_protein_database" comment_char="#"> + <columns>value, name, dbkey, path</columns> + <file path="${__HERE__}/test-data/humann_protein_database.loc" /> + </table> + <table name="humann_utility_mapping" comment_char="#"> + <columns>value, name, dbkey, path</columns> + <file path="${__HERE__}/test-data/humann_utility_mapping.loc" /> + </table> +</tables> \ No newline at end of file |
| b |
| diff -r 000000000000 -r 26ce946f4da9 transform_json_to_pkl.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/transform_json_to_pkl.py Wed May 12 08:59:30 2021 +0000 |
| [ |
| @@ -0,0 +1,30 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- + +import argparse +import bz2 +import cPickle as pickle +import json + + +def transform_json_to_pkl(args): + with open(args.json_input, 'r') as json_file: + json_str = json_file.read() + metadata = json.loads(json_str) + + for marker in metadata["markers"]: + a_set = set(metadata["markers"][marker]["ext"]) + metadata["markers"][marker]["ext"] = a_set + + pkl_output = bz2.BZ2File(args.pkl_output, 'w') + pickle.dump(metadata, pkl_output, pickle.HIGHEST_PROTOCOL) + pkl_output.close() + + +if __name__ == '__main__': + parser = argparse.ArgumentParser() + parser.add_argument('--json_input', required=True) + parser.add_argument('--pkl_output', required=True) + args = parser.parse_args() + + transform_json_to_pkl(args) |
