Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U _ __authors__ (in module microbetag) __cite__ (in module microbetag) __license__ (in module microbetag) __RANKS__ (in module microbetag.build_mtg_cx2) __version__ (in module microbetag) A a_modules_maps() (in module microbetag.pathway_complementarity) AbdTableHandler (class in microbetag.helpers) all_alternatives() (in module microbetag.pathway_complementarity) all_complements() (in module microbetag.pathway_complementarity) alt_genome_prefix() (in module microbetag.db) apply_layout() (in module microbetag.build_mtg_cx2) B bigg_to_seed_mapping_df() (in module microbetag.seed_complementarity) bin_kos_to_file() (in module microbetag.utils) BinsHandler (class in microbetag.helpers) build_base_graph() (in module microbetag.networks) build_complement_queries() (in module microbetag.db) build_cx2() (in module microbetag.build_mtg_cx2) build_genres() (in module microbetag.wrappers) build_kegg_url() (in module microbetag.pathway_complementarity) build_kegg_urls() (in module microbetag.db) build_pairs_complements() (in module microbetag.db) build_url_with_seed_complements() (in module microbetag.seed_complementarity) C carve_reconstructions() (microbetag.genres.GEMSReconstruction method) check_if_all_in_one_par() (in module parse_module_definitions) Config (class in microbetag.config) convert_to_json_serializable() (in module microbetag.utils) create_final_regular_dictionary() (in module parse_module_definitions) D DB_CREDENTIALS (in module microbetag.db) default() (microbetag.utils.SetEncoder method) definition (in module parse_module_definitions) detect_separator() (in module microbetag.utils) dnngior_gapfill() (in module microbetag.genres) E Emojis (class in microbetag.helpers) emojis (in module microbetag.helpers) ensure_flashweave_format() (in module microbetag.utils) ensure_same_namespace_after_fw() (in module microbetag.utils) execute() (in module microbetag.db) execute_in_a_pool() (in module microbetag.db) export_pathway_complementarities() (in module microbetag.pathway_complementarity) export_to_log() (microbetag.config.Config method) ExportSeedComplementarities (class in microbetag.seed_complementarity) extend_complements() (in module microbetag.utils) extend_faprotax() (in module microbetag.utils) F Faprotax (class in microbetag.helpers) fgs_annotate_genomes() (microbetag.genres.GEMSReconstruction method) file_exists_and_nonzero() (in module microbetag.utils) find_three_column_format() (in module microbetag.utils) flatten() (in module microbetag.utils) (in module parse_module_definitions) flatten_list() (in module microbetag.utils) G gapfill() (in module microbetag.msgenre) gc_unify() (in module microbetag.db) GEMSReconstruction (class in microbetag.genres) generate_fixed_pairwise_comparisons() (in module microbetag.seed_complementarity) get_coloured_complements() (in module microbetag.db) get_compl_maps() (in module microbetag.build_mtg_cx2) get_complement_ids() (in module microbetag.db) get_edgelist() (in module microbetag.networks) get_files_with_suffixes() (in module microbetag.utils) get_genomes_for_ncbi_tax_id() (in module microbetag.db) get_independent_step_alternatives() (in module parse_module_definitions) get_kegg_module_related() (in module microbetag.seed_complementarity) get_kofam_db_path() (microbetag.helpers.PathwayComplementarity method) get_library_version() (in module microbetag.utils) get_ncbi_tax_id_for_genome() (in module microbetag.db) get_node_attributes() (in module microbetag.build_mtg_cx2) get_path_compls_for_ncbi_ids() (in module microbetag.db) get_path_compls_otf() (in module microbetag.db) get_phen_traits() (microbetag.db.GetPhenotrexTraits method) get_phendb_traits() (microbetag.db.GetPhenotrexTraits method) get_scores_and_compls() (microbetag.seed_complementarity.ExportSeedComplementarities method) get_sets() (microbetag.seed_complementarity.ExportSeedComplementarities method) get_tool_location() (in module microbetag.utils) get_value() (in module microbetag.config) GetPhenotrexTraits (class in microbetag.db) H handle_missing_kofam_db() (microbetag.helpers.PathwayComplementarity method) hmmsearch() (in module microbetag.tools) I init_connection_pool() (in module microbetag.db) init_nodes_and_edges() (in module microbetag.build_mtg_cx2) initialize() (microbetag.helpers.PathwayComplementarity method) is_any_nan() (in module microbetag.utils) K kegg_annotation() (in module microbetag.tools) kegg_module_related_intersect() (in module microbetag.seed_complementarity) ko_list_parser() (in module microbetag.utils) L load_abundance() (in module microbetag.config) load_abundance_table() (microbetag.helpers.AbdTableHandler method) load_confidence() (in module microbetag.seed_complementarity) load_config() (in module microbetag.config) load_merged_ko_file() (in module microbetag.utils) load_metadata_file() (microbetag.helpers.AbdTableHandler method) load_nonseeds() (in module microbetag.seed_complementarity) load_otf_seq_map() (in module microbetag.build_mtg_cx2) load_phenotypic_traits() (in module microbetag.utils) load_seed_complement_files() (in module microbetag.seed_complementarity) logger (in module microbetag.microbetag) (in module microbetag.pathway_complementarity) M main() (in module microbetag.microbetag) (in module microbetag.msgenre) manta_input_net() (in module microbetag.helpers) many_to_one_files() (in module microbetag.utils) map_queries_to_pairs() (in module microbetag.db) MappingPaths (class in microbetag.helpers) merge_ko() (in module microbetag.utils) microbetag module microbetag.build_mtg_cx2 module microbetag.config module microbetag.db module microbetag.genres module microbetag.helpers module microbetag.microbetag module microbetag.msgenre module microbetag.networks module microbetag.pathway_complementarity module microbetag.seed_complementarity module microbetag.tools module microbetag.utils module microbetag.wrappers module modelseed_reconstructions() (microbetag.genres.GEMSReconstruction method) module microbetag microbetag.build_mtg_cx2 microbetag.config microbetag.db microbetag.genres microbetag.helpers microbetag.microbetag microbetag.msgenre microbetag.networks microbetag.pathway_complementarity microbetag.seed_complementarity microbetag.tools microbetag.utils microbetag.wrappers parse_module_definitions module (in module parse_module_definitions) module_components_raw (in module parse_module_definitions) module_steps_parsed (in module parse_module_definitions) modules (in module parse_module_definitions) ms_reconstruct() (in module microbetag.genres) mtg_annotate_network() (in module microbetag.build_mtg_cx2) mtg_logger() (in module microbetag.utils) N NetworkHandler (class in microbetag.helpers) O otf_seqid_ncbi_gtdb_map() (in module microbetag.helpers) output_dirs() (microbetag.helpers.PathwayComplementarity method) P P (in module parse_module_definitions) parse() (in module parse_module_definitions) parse_commas_on_pre_and_post_character() (in module parse_module_definitions) parse_hmmout() (in module microbetag.utils) parse_module_definitions module parse_regular_module_dictionary() (in module parse_module_definitions) pathway_complement_edge() (in module microbetag.build_mtg_cx2) pathway_complements() (in module microbetag.build_mtg_cx2) PathwayComplementarity (class in microbetag.helpers) patric_from_gc_list() (in module microbetag.db) phen_query() (microbetag.db.GetPhenotrexTraits static method) phenotrex_genotype() (in module microbetag.tools) phenotrex_predict() (in module microbetag.tools) process_network() (microbetag.helpers.NetworkHandler method) process_sbml() (microbetag.seed_complementarity.ExportSeedComplementarities method) progress_tracker() (in module microbetag.seed_complementarity) Q q (in module parse_module_definitions) query_for_getting_compl_ids() (in module microbetag.db) R rast_annotate_a_genome() (microbetag.genres.GEMSReconstruction method) rast_annotate_genomes() (microbetag.genres.GEMSReconstruction method) read_cyjson() (in module microbetag.networks) reconstrucion_paths() (microbetag.helpers.SeedComplementarityHandler method) reconstruct() (in module microbetag.msgenre) remove_nan_from_list() (in module microbetag.utils) resolve_file_path() (in module microbetag.utils) resolve_relative_path() (in module microbetag.utils) run_carve() (in module microbetag.genres) run_faprotax() (in module microbetag.tools) run_flashweave() (in module microbetag.tools) run_kegg_annotate() (in module microbetag.wrappers) run_manta() (in module microbetag.tools) run_microbetag() (in module microbetag.microbetag) run_otf_prodigal() (in module microbetag.wrappers) run_prodigal() (in module microbetag.tools) run_seed_complementarity() (in module microbetag.tools) run_until_done() (in module microbetag.utils) S safe_literal_eval() (in module microbetag.utils) seed_complement_edge() (in module microbetag.build_mtg_cx2) seed_complements() (in module microbetag.build_mtg_cx2) SeedComplementarityHandler (class in microbetag.helpers) seeds_paths() (microbetag.helpers.SeedComplementarityHandler method) SetEncoder (class in microbetag.utils) setup_kegg_annotations() (microbetag.helpers.PathwayComplementarity method) species_scores_compls() (microbetag.seed_complementarity.ExportSeedComplementarities method) split_list() (in module microbetag.utils) split_to_independent_chunks() (in module parse_module_definitions) structurals (in module parse_module_definitions) T taxon_kos_per_module() (in module microbetag.pathway_complementarity) taxonomy_levels_sa() (in module microbetag.build_mtg_cx2) to_csv() (microbetag.db.GetPhenotrexTraits static method) U update_for_patric() (in module microbetag.db) update_with_faprotax_traits() (in module microbetag.build_mtg_cx2) update_with_manta() (in module microbetag.build_mtg_cx2) update_with_phen_traits() (in module microbetag.build_mtg_cx2)