Index

Symbols

1→0 / 1→1 / 1→n outcomes

_

_add_mapping_column() (in module idtrack._external_mappers._utils) _as_list() (in module idtrack._external_mappers._utils) _atexit_cleanup() (ConnectionBridge static method) _attach_included_forms() (TheGraph method) _biomart_dataset_for_species() (in module idtrack._external_mappers._backend_pybiomart) _bm_list_attribute_names() (in module idtrack._external_mappers._backend_pybiomart) _bm_list_filter_names() (in module idtrack._external_mappers._backend_pybiomart) _bm_pick_attribute() (in module idtrack._external_mappers._backend_pybiomart) _bm_pick_filter() (in module idtrack._external_mappers._backend_pybiomart) _build_metadata_column() (in module idtrack._external_mappers._backend_gprofiler) _calculate_node_scores_helper (Track property) _canonical_from_alias() (in module idtrack._external_mappers._ortholog) _choose_relevant_synonym_helper() (Track method) _chunker() (in module idtrack._external_mappers._utils) _combined_edges() (TheGraph static method) _combined_edges_genes_helper() (TheGraph static method) _create_priority_list_ensembl() (Track method) _create_relation_helper() (DatabaseManager method) _determine_usecols_ids() (DatabaseManager static method) _download_table_from_ftp() (DatabaseManager method) _emit() (ConnectionBridge method) _emit_global() (ConnectionBridge class method) _empty_result() (in module idtrack._external_mappers._utils) _ensembl_archive_host_for_release() (in module idtrack._external_mappers._backend_pybiomart) _ensure_all_inputs() (in module idtrack._external_mappers._utils) _ensure_assembly_priority_cache() (Track method) _external_entrance_placeholder (Track attribute) _external_entrance_placeholders (Track attribute) _extract_namespace_tokens() (in module idtrack._external_mappers._backend_gprofiler) _final_conversion() (Track method) _final_conversion_dict_prepare() (Track static method) _force_disable_bridge() (ConnectionBridge class method) _format_history_travel_testing_report() (TrackTests method) _format_history_travel_testing_report_header() (TrackTests method) _format_proxy_url() (ConnectionBridge static method) _ftp_db_dir_url() (DatabaseManager method)

_ftp_find_core_db_dir() (DatabaseManager class method) _ftp_mysql_root_candidates() (DatabaseManager class method) _ftp_schema_for_sql_url() (DatabaseManager class method) _ftp_schema_url() (DatabaseManager method) _get_active_ranges_of_id() (TheGraph method) _get_blosum62() (in module idtrack._external_mappers._ortholog) _get_core_db_index() (DatabaseManager class method) _get_core_db_index_from_ftp() (DatabaseManager class method) _gget_extract() (in module idtrack._external_mappers._backend_gget) _gp_target_candidates() (in module idtrack._external_mappers._backend_gprofiler) _initialize() (HarmonizeFeatures method) _initialize_idt() (HarmonizeFeatures method) _is_bare_numeric() (in module idtrack._external_mappers._utils) _is_retryable_http_read_error() (DatabaseManager class method) _iter_exception_chain() (DatabaseManager static method) _json() (in module idtrack._external_mappers._utils) _mg_extract() (in module idtrack._external_mappers._backend_mygene) _minimum_assembly_jumps_helper() (Track static method) _node_trios() (TheGraph method) _normalize_biomart_host() (in module idtrack._external_mappers._backend_pybiomart) _open_decompressed_http_text() (DatabaseManager static method) _parse_apache_dir_listing_dirs() (DatabaseManager static method) _parse_apache_dir_listing_files() (DatabaseManager static method) _path_score_sorter_all_targets() (Track method) _path_score_sorter_single_target() (Track static method) _probe_mysql_core_schemas_by_port() (DatabaseManager class method) _process_gprofiler_response() (in module idtrack._external_mappers._backend_gprofiler) _recursive_synonymous() (Track method) _refresh_core_db_index_mysql() (DatabaseManager class method) _require_ortholog_deps() (in module idtrack._external_mappers._ortholog) _require_pysocks() (ConnectionBridge static method) _require_track() (API method) _restore_socks_default_proxy() (ConnectionBridge static method) _species_for_mygene() (in module idtrack._external_mappers._utils) _species_to_genus_species() (in module idtrack._external_mappers._ortholog) _suppress_stdout_stderr() (in module idtrack._external_mappers._utils) _unique_not_null() (in module idtrack._external_mappers._utils)

A

align_ortholog_pair_with_features() (in module idtrack._external_mappers._ortholog) AlignmentScores (class in idtrack._external_mappers._ortholog) all_assemblies (DB attribute) alternative_versions (DB attribute) API (class in idtrack._api) Assembly assembly_mysqlport_priority (DB attribute) available_external_databases (TheGraph property)

available_external_databases_assembly (TheGraph property) available_genome_assemblies (TheGraph property) available_releases (DatabaseManager property) available_releases_all_assemblies (DatabaseManager property) available_releases_given_database_assembly (TheGraph property) available_releases_no_save (DatabaseManager property) available_releases_versions() (DatabaseManager method) available_tables_mysql() (DatabaseManager method)

B

Backbone namespace

backbone_form (DB attribute) build_graph() (API method)

C

calculate_caches() (TheGraph method) calculate_graph_caches() (API method) calculate_node_scores() (Track method) calculate_score_and_select() (Track method) canonical_db() (in module idtrack._external_mappers._utils) canonical_species() (in module idtrack._external_mappers._utils) change_assembly() (DatabaseManager method) change_form() (DatabaseManager method) change_release() (DatabaseManager method) change_release_auto_assembly() (DatabaseManager method) check_if_change_assembly_works() (DatabaseManager method) check_optional_dependencies() (in module idtrack._external_mappers) (in module idtrack._external_mappers._utils) check_version_info() (DatabaseManager method) choose_relevant_synonym() (Track method) classify_multiple_conversion() (API method) combined_edges (TheGraph property) combined_edges_assembly_specific_genes (TheGraph property) combined_edges_genes (TheGraph property) compact_ranges() (TheGraph static method) compute_alignment_scores() (in module idtrack._external_mappers._ortholog) compute_embedding_features() (in module idtrack._external_mappers._ortholog) configure_logger() (API method) conn_dict_str_ensembl_base (DB attribute) connection_dict (DB attribute) connection_timeout (DB attribute)

ConnectionBridge (class in idtrack._connection_bridge) construct_graph() (GraphMaker method) construct_graph_form() (GraphMaker method) conversion_failed_but_consistent_identifiers (HarmonizeFeatures property) conversion_failed_identifiers (HarmonizeFeatures property) convert() (Track method) convert_identifier() (API method) convert_identifier_multiple() (API method) convert_ids() (in module idtrack._external_mappers) (in module idtrack._external_mappers._convert) convert_optimized_multiple() (Track method) create_available_databases() (DatabaseManager method) create_database_content() (DatabaseManager method) create_dataset_conversion_dataframe() (HarmonizeFeatures method) create_external_all() (DatabaseManager method) create_external_db() (DatabaseManager method) create_file_name() (GraphMaker method) create_id_history() (DatabaseManager method) create_id_history_fixed() (DatabaseManager method) create_ids() (DatabaseManager method) create_intersection_column_values() (HarmonizeFeatures method) create_multiple_ensembl_dict() (HarmonizeFeatures method) create_relation_archive() (DatabaseManager method) create_relation_current() (DatabaseManager method) create_release_id() (DatabaseManager method) create_template_yaml() (ExternalDatabases method) create_version_info() (DatabaseManager method)

D

DatabaseManager (class in idtrack._database_manager) datataset_conversion_dataframe_issues (HarmonizeFeatures property)

DB (class in idtrack._db) dict_1_to_not_1 (HarmonizeFeatures property) download_table() (DatabaseManager method)

E

edge_key_orientor() (Track method) EmbeddingFeatures (class in idtrack._external_mappers._ortholog) Ensembl release ensembl_ftp_base (DB attribute) Explainability payload export_disk() (GraphMaker method) External namespace

External YAML external_database_connection_form (TheGraph property) external_database_forms() (API method) external_inst (DatabaseManager property) external_search_settings (DB attribute) ExternalDatabases (class in idtrack._external_databases) extract_source_identifiers_from_anndata() (HarmonizeFeatures method)

F

feature_harmonizer() (HarmonizeFeatures method) fetch_aa_sequence() (in module idtrack._external_mappers._ortholog) fetch_organism_and_latest_release() (VerifyOrganism method) file_name() (DatabaseManager method)

file_name_modified_yaml() (ExternalDatabases method) file_name_template_yaml() (ExternalDatabases method) first_version (DB attribute) forms_in_order (DB attribute)

G

get_active_ranges_of_base_id_alternative() (TheGraph method) get_active_ranges_of_id (TheGraph property) get_active_ranges_of_id_ensembl_all_inclusive() (TheGraph method) get_database_manager() (API method) get_db() (DatabaseManager method) get_external_database_nodes() (TheGraph method) get_formal_name() (VerifyOrganism method) get_from_release_and_reverse_vars() (Track static method) get_graph() (GraphMaker method) get_id_list() (TheGraph method) get_idtrack_matchings_for_all_datasets() (HarmonizeFeatures method) get_intersecting_ranges() (TheGraph static method) get_latest_release() (VerifyOrganism method)

get_next_edge_releases() (TheGraph method) get_next_edges() (Track method) get_ortholog_ids_for_species() (in module idtrack._external_mappers._ortholog) get_ortholog_table() (in module idtrack._external_mappers._ortholog) get_possible_paths() (Track method) get_protein_embedding() (in module idtrack._external_mappers._ortholog) get_release_date() (DatabaseManager method) get_table() (DatabaseManager method) get_two_nodes_coinciding_releases() (TheGraph method) give_list_for_case() (ExternalDatabases method) graph (Track attribute) Graph snapshot GraphMaker (class in idtrack._graph_maker)

H

HarmonizeFeatures (class in idtrack._harmonize_features) history_travel_testing() (TrackTests method) history_travel_testing_random() (TrackTests method) history_travel_testing_random_arguments_generator() (TrackTests method)

how_many_corresponding_path_ensembl() (TrackTests method) Hyperconnected node hyperconnecting_threshold (DB attribute) hyperconnective_nodes (TheGraph property)

I

id_ver_delimiter (DB attribute) id_ver_from_df() (DatabaseManager method) Identifier drift identify_source() (Track method) idt (HarmonizeFeatures attribute) idtrack._api module idtrack._connection_bridge module idtrack._database_manager module idtrack._db module idtrack._external_databases module idtrack._external_mappers module idtrack._external_mappers._backend_gget module idtrack._external_mappers._backend_gprofiler module idtrack._external_mappers._backend_mygene module idtrack._external_mappers._backend_pybiomart module idtrack._external_mappers._constants module idtrack._external_mappers._convert module

idtrack._external_mappers._ortholog module idtrack._external_mappers._utils module idtrack._graph_maker module idtrack._harmonize_features module idtrack._the_graph module idtrack._track module idtrack._track_tests module idtrack._verify_organism module infer_identifier_source() (API method) initialize_downloads() (GraphMaker method) is_active (ConnectionBridge property) is_base_is_range_correct() (TrackTests method) is_combined_edges_dicts_overlapping_and_complete() (TrackTests method) is_edge_with_same_nts_only_at_backbone_nodes() (TrackTests method) is_final_external_conversion_robust() (TrackTests method) is_id_functions_consistent_ensembl() (TrackTests method) is_id_functions_consistent_ensembl_2() (TrackTests method) is_id_functions_consistent_external() (TrackTests method) is_node_consistency_robust() (TrackTests method) is_point_in_range() (TheGraph static method) is_range_functions_robust() (TrackTests method)

K

kept_conversion_failed_identifiers (HarmonizeFeatures attribute)

L

list_ensembl_releases() (API method) list_external_databases() (API method) list_external_databases_by_assembly() (API method) list_genome_assemblies() (API method) list_to_ranges() (TheGraph static method) load_modified_yaml() (ExternalDatabases method)

Local repository (cache directory) local_repository (API attribute) log (API attribute) (ConnectionBridge attribute) logger_configured (API attribute) lower_chars_graph (TheGraph property)

M

main_assembly (DB attribute) map_with_gget() (in module idtrack._external_mappers._backend_gget) map_with_gprofiler() (in module idtrack._external_mappers._backend_gprofiler) map_with_mygene() (in module idtrack._external_mappers._backend_mygene) map_with_pybiomart() (in module idtrack._external_mappers._backend_pybiomart) minimum_assembly_jumps() (Track method) module idtrack._api idtrack._connection_bridge idtrack._database_manager idtrack._db idtrack._external_databases idtrack._external_mappers idtrack._external_mappers._backend_gget idtrack._external_mappers._backend_gprofiler idtrack._external_mappers._backend_mygene idtrack._external_mappers._backend_pybiomart idtrack._external_mappers._constants idtrack._external_mappers._convert idtrack._external_mappers._ortholog idtrack._external_mappers._utils idtrack._graph_maker idtrack._harmonize_features idtrack._the_graph idtrack._track idtrack._track_tests idtrack._verify_organism

multiple_ensembl_dict (HarmonizeFeatures attribute) myqsl_user (DB attribute) mysql_database (DatabaseManager property) mysql_host (DB attribute) mysql_port_min_release (DB attribute) mysql_togo (DB attribute)

N

n_to_1_within_individual_dataset() (HarmonizeFeatures method) no_new_node_id (DB attribute) no_old_node_id (DB attribute) node_dict_maker() (DatabaseManager static method) node_name_alternatives() (TheGraph method) node_name_maker() (DatabaseManager static method) node_trios (TheGraph property) node_type_str (DB attribute)

nts_assembly (DB attribute) nts_assembly_gene (DB attribute) nts_assembly_reverse (DB attribute) nts_base_ensembl (DB attribute) nts_base_ensembl_reverse (DB attribute) nts_bidirectional_synonymous_search (DB attribute) nts_ensembl (DB attribute) nts_ensembl_reverse (DB attribute) nts_external (DB attribute)

P

parse_clustal_alignment() (in module idtrack._external_mappers._ortholog) path_search() (Track method) path_step_possible_assembly_jumps() (Track method) pick_ortholog_for_species() (in module idtrack._external_mappers._ortholog)

placeholder_na (DB attribute) print_binned_conversion() (API method) proxy_host (ConnectionBridge attribute) proxy_port (ConnectionBridge attribute)

R

raise_missing_dependency() (in module idtrack._external_mappers._utils) random_dataset_source_generator() (TrackTests method) ranges_to_list() (TheGraph method) read_exported() (GraphMaker static method) reading_timeout (DB attribute) remove_non_gene_trees() (GraphMaker static method) removed_conversion_failed_identifiers (HarmonizeFeatures attribute) removed_inconsistent_identifier_matching (HarmonizeFeatures attribute)

reporter_dict_creator() (HarmonizeFeatures method) reporter_dict_creator_helper_reason_finder() (HarmonizeFeatures method) resolve_organism() (API method) rest_server_api (DB attribute) rest_server_ext (DB attribute) rev (TheGraph property) run_idtrack_for_single_dataset() (HarmonizeFeatures method) run_muscle_pairwise() (in module idtrack._external_mappers._ortholog)

S

set_env_proxy (ConnectionBridge attribute) should_graph_reversed() (Track method) Snapshot release (snapshot boundary) split_id() (GraphMaker static method) start() (ConnectionBridge method)

stop() (ConnectionBridge method) Strategy (best vs all) strip_version() (in module idtrack._external_mappers._utils) synonym_id_nodes_prefix (DB attribute) synonymous_nodes() (Track method)

T

tables_in_disk() (DatabaseManager method) test_connection() (ConnectionBridge method) TheGraph (class in idtrack._the_graph)

track (API attribute) Track (class in idtrack._track) TrackTests (class in idtrack._track_tests)

U

unified_matching_dict (HarmonizeFeatures property) unify_multiple_anndatas() (HarmonizeFeatures method)

update_graph_with_the_new_release() (GraphMaker method) UTF8 (DB attribute) UTF8_STR (DB attribute)

V

validate_yaml_file_up_to_date() (ExternalDatabases method) VerifyOrganism (class in idtrack._verify_organism) version_fix() (DatabaseManager method)

version_fix_incomplete() (DatabaseManager method) version_info (Track attribute) version_uniformize() (DatabaseManager method)