refineGEMs package

Here is an overview on all functions.

For an alphabetically ordered list, see the Index.

Subpackages

• analysis
  • comparison module
    • plot_venn()
    • sbo_terms()
  • core_pan module
    • collect_reacs_from_model()
    • compare_to_core_pan()
    • extract_reactions_ids()
    • find_core_reaction_ids()
    • find_pan_reactions()
    • generate_core_pan_model()
  • growth module
    • find_additives_to_enable_growth()
    • find_growth_enhancing_exchanges()
    • find_growth_essential_exchanges()
    • get_essential_exchanges_via_bounds()
    • get_essential_reactions_via_single_knockout()
    • get_metabs_essential_for_growth_wrapper()
    • get_production()
    • get_secretion()
    • get_uptake()
    • growth_analysis()
    • growth_sim_multi()
    • growth_sim_single()
    • model_minimal_medium()
    • set_bounds_to_default()
    • test_auxotrophies()
    • test_growth_with_source()
  • investigate module
    • get_mass_charge_unbalanced()
    • get_metabs_with_one_cvterm()
    • get_orphans_deadends_disconnected()
    • get_reac_with_gpr()
    • get_reactions_per_sbo()
• classes
  • egcs module
    • DISSIPATION_RXNS
    • EGCSolver
    • EGC_SCORING_MATRIX
    • GreedyEGCSolver
  • gapfill module
    • BioCycGapFiller
    • GapFiller
    • GeneGapFiller
    • KEGGapFiller
    • cobra_gapfill_wrapper()
    • map_biocyc_to_reac()
    • map_ec_to_reac()
    • multiple_cobra_gapfill()
    • single_cobra_gapfill()
  • medium module
    • ALLOWED_DATABASE_LINKS
    • FLOAT_REGEX
    • INTEGER_REGEX
    • Medium
    • REQUIRED_SUBSTANCE_ATTRIBUTES
    • add_subset_to_db()
    • enter_db_single_entry()
    • enter_m2s_row()
    • enter_medium_into_db()
    • enter_s2db_row()
    • enter_substance_row()
    • extract_medium_info_from_model_bigg()
    • generate_docs_for_subset()
    • generate_insert_query()
    • generate_update_query()
    • get_last_idx_table()
    • load_external_medium()
    • load_media()
    • load_medium_from_db()
    • medium_to_model()
    • read_from_cobra_model()
    • read_substances_from_file()
    • update_db_entry_single()
    • update_db_multi()
    • updated_db_to_schema()
  • reports module
    • AuxotrophySimulationReport
    • CorePanAnalysisReport
    • GapFillerReport
    • GrowthSimulationReport
    • KEGGPathwayAnalysisReport
    • KEGG_GLOBAL_PATHWAY
    • KEGG_METABOLISM_PATHWAY
    • KEGG_METABOLISM_PATHWAY_DATE
    • KEGG_OVERVIEW_PATHWAY
    • ModelInfoReport
    • MultiModelInfoReport
    • MultiSBOTermReport
    • Report
    • SBOTermReport
    • SingleGrowthSimulationReport
    • SourceTestReport
• curation
  • biomass module
    • check_normalise_biomass()
  • charges module
    • correct_charges_from_db()
    • correct_charges_modelseed()
  • curate module
    • NH_PATTERN
    • add_compartment_structure_specs()
    • check_direction()
    • extend_gp_annots_via_KEGG()
    • extend_gp_annots_via_mapping_table()
    • extend_metab_reac_annots_via_id()
    • extend_metab_reac_annots_via_notes()
    • polish_entity_conditions()
    • polish_model()
    • polish_model_units()
    • resolve_duplicate_metabolites()
    • resolve_duplicate_reactions()
    • resolve_duplicates()
    • set_initial_amount_metabs()
    • set_model_default_units()
    • set_units_of_parameters()
    • update_annotations_from_others()
  • pathways module
    • add_kegg_pathways()
    • create_pathway_groups()
    • find_kegg_pathways()
    • kegg_pathway_analysis()
    • load_model_enable_groups()
    • set_kegg_pathways()
  • polish module
• developement
  • decorators module
    • debug()
    • deprecate()
    • implement()
    • template()
• utility
  • connection module
    • adjust_BOF()
    • filter_DIAMOND_blastp_results()
    • get_memote_score()
    • perform_mcc()
    • run_DIAMOND_blastp()
    • run_SBOannotator()
    • run_memote()
  • cvterms module
    • DB2PREFIX_GENES
    • DB2PREFIX_METABS
    • DB2PREFIX_PATHWAYS
    • DB2PREFIX_REACS
    • MIRIAM
    • OLD_MIRIAM
    • PREFIX2DB_GENES
    • PREFIX2DB_METABS
    • PREFIX2DB_PATHWAYS
    • PREFIX2DB_REACS
    • _add_annotations_from_dict_cobra()
    • add_cv_term_genes()
    • add_cv_term_metabolites()
    • add_cv_term_pathways()
    • add_cv_term_pathways_to_entity()
    • add_cv_term_reactions()
    • add_cv_term_units()
    • generate_cvterm()
    • get_id_from_cv_term()
    • print_cvterm()
  • databases module
    • PATH_TO_DB
    • PATH_TO_DB_FOLDER
    • VERSION_FILE
    • VERSION_URL
    • ValidationCodes
    • create_media_database()
    • get_latest_bigg_databases()
    • get_modelseed_compounds_database()
    • initialise_database()
    • is_valid_database()
    • reset_database()
    • update_bigg_db()
    • update_mnx_namespaces()
  • db_access module
    • ALL_BIGG_COMPARTMENTS_ONE_LETTER
    • ALL_BIGG_COMPARTMENTS_TWO_LETTER
    • BIGG_METABOLITES_URL
    • BIOCYC_TIER1_DATABASES_PREFIXES
    • _add_annotations_from_bigg_reac_row()
    • _search_ncbi_for_gp()
    • add_annotations_from_BiGG_metabs()
    • add_info_from_ChEBI_BiGG()
    • compare_model_modelseed()
    • compare_to_modelseed()
    • get_BiGG_metabs_annot_via_dbid()
    • get_charge_mismatch()
    • get_compared_formulae()
    • get_ec_from_ncbi()
    • get_ec_via_swissprot()
    • get_formula_mismatch()
    • get_kegg_genes()
    • get_model_charges()
    • get_modelseed_charges()
    • get_modelseed_compounds()
    • kegg_reaction_parser()
    • map_dmnd_res_to_sp_ec_brenda()
    • map_to_homologs()
    • parse_KEGG_ec()
    • parse_KEGG_gene()
  • entities module
    • REF_COL_GF_GENE_MAP
    • are_compartment_names_valid()
    • build_metabolite_bigg()
    • build_metabolite_kegg()
    • build_metabolite_mnx()
    • build_metabolite_xxx()
    • build_reaction()
    • build_reaction_bigg()
    • build_reaction_kegg()
    • build_reaction_mnx()
    • build_reaction_xxx()
    • compare_gene_lists()
    • create_fba_units()
    • create_gp()
    • create_gpr()
    • create_random_id()
    • create_reaction()
    • create_species()
    • create_unit()
    • create_unit_definition()
    • get_gpid_mapping()
    • get_model_reacs_or_metabs()
    • get_reaction_annotation_dict()
    • get_reversible()
    • isreaction_complete()
    • match_id_to_namespace()
    • parse_reac_str()
    • print_UnitDefinitions()
    • reaction_equation_to_dict()
    • remove_non_essential_genes()
    • resolve_compartment_names()
    • validate_reaction_compartment_bigg()
  • io module
    • create_missing_genes_protein_fasta()
    • load_a_table_from_database()
    • load_document_libsbml()
    • load_model()
    • load_subset_from_db()
    • load_substance_table_from_db()
    • parse_dict_to_dataframe()
    • parse_gbff_for_cds()
    • parse_gff_for_cds()
    • search_sbo_label()
    • validate_libsbml_model()
    • write_model_to_file()
  • set_up module
    • PATH_MEDIA_CONFIG
    • download_config()
    • download_url()
  • util module
    • COMP_MAPPING
    • DB2REGEX
    • MIN_GROWTH_THRESHOLD
    • SBO_BIOCHEM_TERMS
    • SBO_TRANSPORT_TERMS
    • VALID_COMPARTMENTS
    • is_stoichiometric_factor()
    • reannotate_sbo_memote()
    • sum_biomass_weight()
    • test_biomass_consistency()
    • test_biomass_presence()

refineGEMs.cmd_access module

Entry points to the code from the command line.

refinegems.cmd_access.analyse()

Analyse a model by testing for auxotrophies and growth on different media along with finding EGCs and looking at overall model statistics.

refinegems.cmd_access.annot()

Add annotations to your model.

refinegems.cmd_access.curate()

Curate a model

refinegems.cmd_access.database()

Access, curate, etc. the in-build database.

refinegems.cmd_access.growth()

Analyse the growth under different conditions.

refinegems.cmd_access.initialise()

Initialise or update the database.

refinegems.cmd_access.media()

Access the media part of the database.

refinegems.cmd_access.refine()

Refine a model. Includes steps like biomass, charges, SBO annotation, reaction direction correction and addition of Pathways and further gene product annotations.

refinegems.cmd_access.reset()

Reset the database by removing additionally downloaded tables.

refinegems.cmd_access.setup()

Set-up tools, folder structure and more for running the program.

More information:

• Command line access points
  • General Options
  • refinegems analyse
    • refinegems analyse growth
  • refinegems database
  • refinegems gaps
  • refinegems media
  • refinegems polish
  • refinegems refine
    • refinegems refine annot
  • refinegems setup