LICENSE
MANIFEST.in
history.md
readme.md
setup.cfg
setup.py
examples/demo.fasta
examples/demo.fastq
examples/demo.m8
examples/demo.sam
humann2/__init__.py
humann2/check.py
humann2/config.py
humann2/humann2.cfg
humann2/humann2.py
humann2/store.py
humann2/utilities.py
humann2.egg-info/PKG-INFO
humann2.egg-info/SOURCES.txt
humann2.egg-info/dependency_links.txt
humann2.egg-info/entry_points.txt
humann2.egg-info/not-zip-safe
humann2.egg-info/top_level.txt
humann2/data/chocophlan_DEMO/g__Bacteroides.s__Bacteroides_dorei.centroids.v0.1.1.ffn.gz
humann2/data/chocophlan_DEMO/g__Bacteroides.s__Bacteroides_vulgatus.centroids.v0.1.1.ffn.gz
humann2/data/misc/KeggOrgId2OrgNameTable.txt
humann2/data/misc/README.txt
humann2/data/misc/map_eggnog_name.txt.gz
humann2/data/misc/map_go_name.txt.gz
humann2/data/misc/map_kegg-mdl_name.txt.gz
humann2/data/misc/map_kegg-pwy_name.txt.gz
humann2/data/misc/map_ko_name.txt.gz
humann2/data/misc/map_level4ec_name.txt.gz
humann2/data/misc/map_metacyc-pwy_name.txt.gz
humann2/data/misc/map_metacyc-rxn_name.txt.gz
humann2/data/misc/map_pfam_name.txt.gz
humann2/data/misc/map_transporter_uniref50.txt.gz
humann2/data/misc/map_uniref50_name.txt.bz2
humann2/data/pathways/metacyc_pathways
humann2/data/pathways/metacyc_pathways_structured
humann2/data/pathways/metacyc_pathways_structured_filtered
humann2/data/pathways/metacyc_pathways_to_organisms
humann2/data/pathways/metacyc_reactions_level4ec_only.uniref.bz2
humann2/data/pathways/unipathway_pathways
humann2/data/pathways/unipathway_uniprots.uniref.bz2
humann2/data/uniref_DEMO/uniref90_demo_prots.dmnd
humann2/data/uniref_DEMO/uniref90_demo_prots.faa
humann2/maintenance/Build_mapping_Pathways_Uniprot.py
humann2/maintenance/Build_mapping_Uniref_Citations.py
humann2/maintenance/Map_Pathway_Or_Reaction_To_Organism_from_Extract.py
humann2/maintenance/Map_Pathway_To_Organism.py
humann2/maintenance/README.md
humann2/maintenance/Reaction_to_Uniref5090.py
humann2/maintenance/ReadSwissprot.py
humann2/maintenance/ReadUniref.py
humann2/maintenance/UniProt_mapping.py
humann2/maintenance/__init__.py
humann2/maintenance/chocophlan_hardlen.py
humann2/maintenance/create_metacyc_structured_pathways_database.py
humann2/maintenance/create_uniref_database.py
humann2/maintenance/filter_pathways.py
humann2/maintenance/filter_uniref_ec_list.py
humann2/maintenance/make_map_ec_name.py
humann2/maintenance/make_map_eggnog_name.py
humann2/maintenance/make_map_go_name.py
humann2/maintenance/make_map_ko_name.py
humann2/maintenance/make_map_metacyc-pwy_name.py
humann2/maintenance/make_map_metacyc-pwy_taxonomy.py
humann2/maintenance/make_map_pfam_name.py
humann2/maintenance/make_map_transporter_uniref50.py
humann2/maintenance/make_map_uniprot_name.py
humann2/maintenance/make_map_uniref50_go.py
humann2/maintenance/make_uniref-tol-lca.py
humann2/maintenance/make_utility_mapping.py
humann2/maintenance/map_ECs_to_Uniref50_90.py
humann2/maintenance/map_reactions_to_uniprot.py
humann2/maintenance/metacyc2mcpc.py
humann2/maintenance/metacyc_swissprot_trembl_reference_databases.md
humann2/quantify/MinPath12hmp.py
humann2/quantify/__init__.py
humann2/quantify/chi2cdf.py
humann2/quantify/families.py
humann2/quantify/modules.py
humann2/quantify/xipe.py
humann2/search/__init__.py
humann2/search/blastx_coverage.py
humann2/search/nucleotide.py
humann2/search/pick_frames.py
humann2/search/prescreen.py
humann2/search/translated.py
humann2/tests/__init__.py
humann2/tests/advanced_tests_blastx_coverage.py
humann2/tests/advanced_tests_nucleotide_search.py
humann2/tests/advanced_tests_quantify_families.py
humann2/tests/advanced_tests_quantify_modules.py
humann2/tests/advanced_tests_store.py
humann2/tests/advanced_tests_translated_search.py
humann2/tests/advanced_tests_utilities.py
humann2/tests/basic_tests_nucleotide_search.py
humann2/tests/basic_tests_quantify_modules.py
humann2/tests/basic_tests_store.py
humann2/tests/basic_tests_utilities.py
humann2/tests/cfg.py
humann2/tests/functional_tests_biom_humann2.py
humann2/tests/functional_tests_biom_tools.py
humann2/tests/functional_tests_humann2.py
humann2/tests/functional_tests_tools.py
humann2/tests/humann2_test.py
humann2/tests/utils.py
humann2/tests/data/2_aligned_3_unaligned.sam
humann2/tests/data/annotations.m8
humann2/tests/data/annotations.sam
humann2/tests/data/convert_file.fasta
humann2/tests/data/convert_file.fastq
humann2/tests/data/convert_file_at_character.fastq
humann2/tests/data/convert_file_multiline.fasta
humann2/tests/data/convert_file_pick_frames.fasta
humann2/tests/data/demo.fasta
humann2/tests/data/demo.fastq
humann2/tests/data/demo.m8
humann2/tests/data/demo.sam
humann2/tests/data/demo_genefamilies.biom
humann2/tests/data/demo_genefamilies.tsv
humann2/tests/data/demo_genefamilies_with_names.tsv
humann2/tests/data/demo_metaphlan_bugs_list.tsv
humann2/tests/data/demo_pathabundance_with_names.tsv
humann2/tests/data/demo_pathcoverage_with_names.tsv
humann2/tests/data/file.bam
humann2/tests/data/file.fasta
humann2/tests/data/file.fastq
humann2/tests/data/file_no_space_identifier.fastq
humann2/tests/data/file_single_line_sequences.fasta
humann2/tests/data/file_space_identifier.fastq
humann2/tests/data/file_with_header.sam
humann2/tests/data/file_without_header.sam
humann2/tests/data/file_without_header_with_tags.sam
humann2/tests/data/gene_families.tsv
humann2/tests/data/gene_families_uniref50_with_names.tsv
humann2/tests/data/genefamilies.biom
humann2/tests/data/genefamilies_biom_match.tsv
humann2/tests/data/id_mapping.tsv
humann2/tests/data/id_mapping_coverage_filter.tsv
humann2/tests/data/id_mapping_gene_table.tsv
humann2/tests/data/multi_sample_biom_genefamilies_sample1.biom
humann2/tests/data/multi_sample_biom_genefamilies_sample2.biom
humann2/tests/data/multi_sample_genefamilies.biom
humann2/tests/data/multi_sample_genefamilies.tsv
humann2/tests/data/multi_sample_genefamilies_sample1.tsv
humann2/tests/data/multi_sample_genefamilies_sample2.tsv
humann2/tests/data/rapsearch2_output_with_header.m8
humann2/tests/data/rapsearch2_output_with_header_no_log.m8
humann2/tests/data/rapsearch2_output_without_header.m8
humann2/tests/data/rapsearch2_output_without_header_coverage_filter.m8
humann2/tests/data/rapsearch2_output_without_header_coverage_filter_chocophlan_annotation.m8
humann2/tests/data/rapsearch2_output_without_header_coverage_filter_custom_annotation.m8
humann2/tests/data/reactions.tsv
humann2/tests/data/small_map_uniref50_name.txt.gz
humann2/tests/data/test_pathways.dat
humann2/tests/data/test_pathways_flat.tsv
humann2/tests/data/test_pathways_results.tsv
humann2/tests/data/usearch_output.tsv
humann2/tests/data/usearch_with_uniref50_output.tsv
humann2/tests/data/tooltest-infer_taxonomy/genes.tsv
humann2/tests/data/tooltest-infer_taxonomy/genes_inferred.tsv
humann2/tests/data/tooltest-infer_taxonomy/infer_taxonomy-command.sh
humann2/tests/data/tooltest-merge_abundance_tables/demo_genefamilies.tsv
humann2/tests/data/tooltest-merge_abundance_tables/demo_pathabundance.tsv
humann2/tests/data/tooltest-merge_abundance_tables/merge_abundance-command.sh
humann2/tests/data/tooltest-merge_abundance_tables/merge_output.tsv
humann2/tests/data/tooltest-merge_abundance_tables/merge_output_remove_taxonomy.tsv
humann2/tests/data/tooltest-regroup_table/regroup_table-builtin_command.sh
humann2/tests/data/tooltest-regroup_table/regroup_table-builtin_input.biom
humann2/tests/data/tooltest-regroup_table/regroup_table-builtin_input.txt
humann2/tests/data/tooltest-regroup_table/regroup_table-builtin_uniref50_ec_output.txt
humann2/tests/data/tooltest-regroup_table/regroup_table-builtin_uniref50_go_output.txt
humann2/tests/data/tooltest-regroup_table/regroup_table-builtin_uniref50_ko_output.txt
humann2/tests/data/tooltest-regroup_table/regroup_table-builtin_uniref50_rxn_mean_output.txt
humann2/tests/data/tooltest-regroup_table/regroup_table-builtin_uniref50_rxn_output.txt
humann2/tests/data/tooltest-regroup_table/regroup_table-custom_command.sh
humann2/tests/data/tooltest-regroup_table/regroup_table-custom_groups.txt
humann2/tests/data/tooltest-regroup_table/regroup_table-custom_input.txt
humann2/tests/data/tooltest-regroup_table/regroup_table-custom_output.txt
humann2/tests/data/tooltest-rename_table/pathabundance_without_names.txt
humann2/tests/data/tooltest-rename_table/rename_table-builtin_command.sh
humann2/tests/data/tooltest-rename_table/rename_table-builtin_ec_output.txt
humann2/tests/data/tooltest-rename_table/rename_table-builtin_ko_output.txt
humann2/tests/data/tooltest-rename_table/rename_table-builtin_output.txt
humann2/tests/data/tooltest-rename_table/rename_table-builtin_pathways_output.txt
humann2/tests/data/tooltest-rename_table/rename_table-builtin_rxn_output.txt
humann2/tests/data/tooltest-rename_table/rename_table-custom.sh
humann2/tests/data/tooltest-rename_table/rename_table-custom.txt.gz
humann2/tests/data/tooltest-rename_table/rename_table-custom_command.sh
humann2/tests/data/tooltest-rename_table/rename_table-custom_output.txt
humann2/tests/data/tooltest-rename_table/rename_table-input.biom
humann2/tests/data/tooltest-rename_table/rename_table-input.txt
humann2/tests/data/tooltest-rename_table/rename_table-input_ec.txt
humann2/tests/data/tooltest-rename_table/rename_table-input_ko.txt
humann2/tests/data/tooltest-rename_table/rename_table-input_rxn.txt
humann2/tests/data/tooltest-renorm_table/renorm_table-command.sh
humann2/tests/data/tooltest-renorm_table/renorm_table-cpm_output.biom
humann2/tests/data/tooltest-renorm_table/renorm_table-cpm_output.txt
humann2/tests/data/tooltest-renorm_table/renorm_table-input.biom
humann2/tests/data/tooltest-renorm_table/renorm_table-input.txt
humann2/tests/data/tooltest-renorm_table/renorm_table-relab_output.txt
humann2/tests/data/tooltest-rna_dna_norm/rna_dna_norm-command.sh
humann2/tests/data/tooltest-rna_dna_norm/rna_dna_norm-dna.txt
humann2/tests/data/tooltest-rna_dna_norm/rna_dna_norm-laplace-relative_expression.tsv
humann2/tests/data/tooltest-rna_dna_norm/rna_dna_norm-laplace-smoothed_dna.tsv
humann2/tests/data/tooltest-rna_dna_norm/rna_dna_norm-laplace-smoothed_rna.tsv
humann2/tests/data/tooltest-rna_dna_norm/rna_dna_norm-log-10-relative_expression.tsv
humann2/tests/data/tooltest-rna_dna_norm/rna_dna_norm-log-10-smoothed_dna.tsv
humann2/tests/data/tooltest-rna_dna_norm/rna_dna_norm-log-10-smoothed_rna.tsv
humann2/tests/data/tooltest-rna_dna_norm/rna_dna_norm-log-relative_expression.tsv
humann2/tests/data/tooltest-rna_dna_norm/rna_dna_norm-log-smoothed_dna.tsv
humann2/tests/data/tooltest-rna_dna_norm/rna_dna_norm-log-smoothed_rna.tsv
humann2/tests/data/tooltest-rna_dna_norm/rna_dna_norm-rna.txt
humann2/tests/data/tooltest-rna_dna_norm/rna_dna_norm-witten-bell-relative_expression.tsv
humann2/tests/data/tooltest-rna_dna_norm/rna_dna_norm-witten-bell-smoothed_dna.tsv
humann2/tests/data/tooltest-rna_dna_norm/rna_dna_norm-witten-bell-smoothed_rna.tsv
humann2/tests/data/tooltest-strain_profiler/s1-strain_profile.tsv
humann2/tests/data/tooltest-strain_profiler/s2-strain_profile.tsv
humann2/tests/data/tooltest-strain_profiler/strain_profiler-command.sh
humann2/tests/data/tooltest-strain_profiler/strain_profiler-input.txt
humann2/tools/__init__.py
humann2/tools/build_custom_database.py
humann2/tools/genefamilies_genus_level.py
humann2/tools/humann2_associate.py
humann2/tools/humann2_barplot.py
humann2/tools/humann2_benchmark.py
humann2/tools/humann2_config.py
humann2/tools/humann2_databases.py
humann2/tools/humann2_expand_results_taxonomy.py
humann2/tools/humann2_humann1_kegg.py
humann2/tools/infer_taxonomy.py
humann2/tools/join_tables.py
humann2/tools/merge_abundance.py
humann2/tools/reduce_table.py
humann2/tools/regroup_table.py
humann2/tools/rename_table.py
humann2/tools/renorm_table.py
humann2/tools/rna_dna_norm.py
humann2/tools/split_stratified_table.py
humann2/tools/split_table.py
humann2/tools/strain_profiler.py
humann2/tools/util.py