Index

A

a_modules_maps() (in module microbetag.pathway_complementarity) AbdTableHandler (class in microbetag.helpers) add_edge_pathway_complements() (in module microbetag.build_mtg_cx2)

add_edge_seed_complements() (in module microbetag.build_mtg_cx2) add_seed_edge_attributes() (in module microbetag.build_mtg_cx2) all_alternatives() (in module microbetag.pathway_complementarity) all_complements() (in module microbetag.pathway_complementarity)

B

bin_kos_to_file() (in module microbetag.utils) BinsHandler (class in microbetag.helpers) build_a_base_node() (in module microbetag.networks) build_base_graph() (in module microbetag.networks) build_cx() (microbetag.build_mtg_cx2.UpdateCX2Netork method) build_edge_list() (in module microbetag.networks)

build_kegg_url() (in module microbetag.pathway_complementarity) build_mtg_edges() (in module microbetag.build_mtg_cx2) build_mtg_nodes() (in module microbetag.build_mtg_cx2) build_ndex2_net() (in module microbetag.build_mtg_cx2) build_pseudo_cx() (in module microbetag.build_mtg_cx2) 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

default() (microbetag.utils.SetEncoder method)

definition (in module parse_module_definitions) detect_separator() (in module microbetag.utils)

E

Emojis (class in microbetag.helpers) ensure_flashweave_format() (in module microbetag.utils) ensure_same_namespace_after_fw() (in module microbetag.utils) export_pathway_complementarities() (in module microbetag.pathway_complementarity)

export_seed_complements() (microbetag.seed_complementarity.ExportSeedComplementarities method) 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)

fire_microbetag() (in module microbetag.genres) flatten() (in module microbetag.utils) (in module parse_module_definitions) flatten_list() (in module microbetag.utils)

G

GEMSReconstruction (class in microbetag.genres) get_edgelist() (in module microbetag.networks) get_edges() (microbetag.build_mtg_cx2.UpdateCX2Netork method) get_files_with_suffixes() (in module microbetag.utils)

get_independent_step_alternatives() (in module parse_module_definitions) get_kofam_db_path() (microbetag.helpers.PathwayComplementarity method) get_library_version() (in module microbetag.utils) get_nodes() (microbetag.build_mtg_cx2.UpdateCX2Netork method) get_tool_location() (in module microbetag.utils)

H

handle_missing_kofam_db() (microbetag.helpers.PathwayComplementarity method)

hmmsearch() (in module microbetag.tools)

I

initialize() (microbetag.helpers.PathwayComplementarity method)

K

kegg_annotation() (in module microbetag.tools) KEGG_MODULES_TO_MAPS (in module microbetag)

KEGG_TERMS_PER_MODULE (in module microbetag) ko_list_parser() (in module microbetag.utils)

L

load_abundance() (in module microbetag.config) load_abundance_table() (microbetag.helpers.AbdTableHandler method) load_merged_ko_file() (in module microbetag.utils)

load_metadata_file() (microbetag.helpers.AbdTableHandler method) load_phenotypic_traits() (in module microbetag.utils) load_seed_complement_files() (in module microbetag.seed_complementarity) local_seed_url() (in module microbetag.helpers)

M

manta_input_net() (in module microbetag.helpers) many_to_one_files() (in module microbetag.utils) map_carveme_seeds() (microbetag.seed_complementarity.ExportSeedComplementarities method) MappingPaths (class in microbetag.helpers) merge_ko() (in module microbetag.utils) microbetag module microbetag.build_mtg_cx2 module microbetag.config module microbetag.genres module microbetag.helpers module microbetag.networks module microbetag.pathway_complementarity module microbetag.seed_complementarity module microbetag.tools module

microbetag.utils module modelseed_reconstructions() (microbetag.genres.GEMSReconstruction method) module microbetag microbetag.build_mtg_cx2 microbetag.config microbetag.genres microbetag.helpers microbetag.networks microbetag.pathway_complementarity microbetag.seed_complementarity microbetag.tools microbetag.utils parse_module_definitions module (in module parse_module_definitions) module_components_raw (in module parse_module_definitions) MODULE_DEFINITION_MAP (in module microbetag) module_related_seeds() (microbetag.seed_complementarity.ExportSeedComplementarities method) module_steps_parsed (in module parse_module_definitions) modules (in module parse_module_definitions)

N

NetworkHandler (class in microbetag.helpers)

O

order_seed_complements() (in module microbetag.seed_complementarity)

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) PathwayComplementarity (class in microbetag.helpers) phenotrex_genotype() (in module microbetag.tools) phenotrex_predict() (in module microbetag.tools) process_network() (microbetag.helpers.NetworkHandler method) process_seeds() (in module microbetag.seed_complementarity)

Q

q (in module parse_module_definitions)

R

rast_annotate_a_genome() (microbetag.genres.GEMSReconstruction method) rast_annotate_genomes() (microbetag.genres.GEMSReconstruction method) read_cyjson() (in module microbetag.networks) reconstruct_a_model() (microbetag.genres.GEMSReconstruction method) recursive_build() (microbetag.genres.GEMSReconstruction method) resolve_file_path() (in module microbetag.utils) resolve_relative_path() (in module microbetag.utils)

run_carve() (microbetag.genres.GEMSReconstruction method) run_faprotax() (in module microbetag.tools) run_flashweave() (in module microbetag.tools) run_manta() (in module microbetag.tools) run_phylomint() (in module microbetag.tools) run_prodigal() (in module microbetag.tools) run_until_done() (in module microbetag.utils)

S

SeedComplementarityHandler (class in microbetag.helpers) seeds_paths() (microbetag.helpers.SeedComplementarityHandler method) seqId_faprotax_functions_assignment() (in module microbetag.build_mtg_cx2) SetEncoder (class in microbetag.utils)

setup_kegg_annotations() (microbetag.helpers.PathwayComplementarity method) setup_ko_merged() (microbetag.helpers.PathwayComplementarity 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)

U

update() (microbetag.seed_complementarity.ExportSeedComplementarities method)

UpdateCX2Netork (class in microbetag.build_mtg_cx2)