Utils

This module contains miscellaneous methods.

compath.utils.log = <Logger compath.utils (WARNING)>

General utils

compath.utils.dict_to_pandas_df(d)

Transform pandas df into a dict.

Parameters

d (dict) –

Return type

pandas.DataFrame

Returns

pandas dataframe

compath.utils.process_form_gene_set(text)

Process the string containing gene symbols and returns a gene set.

Parameters

text (str) – string to be processed

Return type

set[str]

Returns

gene set

compath.utils.calculate_relative_enrichments(results, total_pathways_by_resource)

Calculate relative enrichment of pathways (enriched pathways/total pathways).

Parameters

• results (dict) – result enrichment

• total_pathways_by_resource (dict) – resource to number of pathways

Return type

dict

compath.utils.count_genes_in_pathway(pathways_gene_sets, genes)

Calculate how many of the genes are associated to each pathway gene set.

Parameters

• pathways_gene_sets (dict) – pathways and their gene sets

• genes (set) – genes queried

Return type

dict

compath.utils.apply_filter(results, threshold)

Run one simulation with a given threshold.

Parameters

• results (dict) – resource with pathways

• threshold (int) – necessary genes to enrich a pathway

Return type

dict

compath.utils.simulate_pathway_enrichment(resource_gene_sets, gene_set_query, runs=200)

Simulate pathway enrichment.

Parameters

• resource_gene_sets – resource and their gene sets

• gene_set_query – shared genes between all resources

• runs – number of simulation

Return type

dict[list[tuple]]

compath.utils.get_genes_without_assigned_pathways(enrichment_results, genes_query)

Return the genes without any known pathway assigned.

Parameters

• gene_set (dict) – list of managers

• genes_query (set[str]) – gene set queried

Returns

compath.utils.get_enriched_pathways(manager_list, gene_set)

Return the results of the queries for every registered manager.

Parameters

• Manager] manager_list (dict[str,) – list of managers

• gene_set (set[str]) – gene set queried

Return type

dict[str,dict[str,dict]]

compath.utils.get_gene_pathways(manager_list, gene)

Return the pathways associated with a gene for every registered manager.

Parameters

• Manager] manager_list (dict[str,) – list of managers

• gene (str) – HGNC symbol

Return type

dict[str,dict[str,dict]]

compath.utils.get_mappings(compath_manager, only_accepted=True)

Return a pandas dataframe with mappings information as an excel sheet file.

Parameters

• compath_manager (compath.manager.Manager) – ComPath Manager

• only_accepted (bool) – only accepted (True) or all (False)

compath.utils.get_pathway_model_by_name(manager_dict, resource, pathway_name)

Return the pathway object from the resource manager.

Parameters

• manager_dict (dict) – manager name to manager instances dictionary

• resource (str) – name of the manager

• pathway_name (str) – pathway name

Return type

Optional[Pathway]

Returns

pathway if exists

compath.utils.get_pathway_model_by_id(app, resource, pathway_id)

Return the pathway object from the resource manager.

Parameters

• app (flask.Flask) – current app

• resource (str) – name of the manager

• pathway_id (str) – pathway id

Return type

Optional[Pathway]

Returns

pathway if exists

compath.utils.get_gene_sets_from_pathway_names(app, pathways)

Return the gene sets for a given pathway/resource tuple.

Parameters

• app (flask.Flask) – current app

• pathways (list[tuple[str,str]) – pathway/resource tuples

Return type

tuple[dict[str,set[str]],dict[str,str]]

Returns

gene sets

compath.utils.get_pathway_info(app, pathways)

Return the gene sets for a given pathway/resource tuple.

Parameters

• app (flask.Flask) – current app

• pathways (list[tuple[str,str]) – pathway/resource tuples

Return type

list

Returns

pathway info

compath.utils.get_last_action_in_module(module_name, action)

Return the info about the last action in the given module.

Parameters

module_name (str) –

Returns

compath.utils.perform_hypergeometric_test(gene_set, manager_pathways_dict, gene_universe, apply_threshold=False, threshold=0.05)

Perform hypergeometric tests.

Parameters

• gene_set (set[str]) – gene set to test against pathway

• manager_pathways_dict (dict[str,dict[str,dict]]) – manager to pathways

• gene_universe (int) – number of HGNC symbols

• apply_threshold (Optional[bool]) – return only significant pathways

• threshold (Optional[float]) – significance threshold (by default 0.05)

Return type

dict[str,dict[str,dict]]

Returns

manager_pathways_dict with p value info

compath.utils.calculate_szymkiewicz_simpson_coefficient(set_1, set_2)

Calculate Szymkiewicz-Simpson coefficient between two sets.

Parameters

• set_1 (set) – set 1

• set_2 (set) – set 2

Returns

similarity of the two sets

Return type

float

compath.utils.calculate_similarity(name_1, name_2)

Calculate the string based similarity between two names.

Parameters

• name_1 (str) – name 1

• name_2 (str) – name 2

Return type

float

Returns

Levenshtein similarity

compath.utils.get_top_matches(matches, top)

Order list of tuples by second value and returns top values.

Parameters

• matches (list[tuple[str,float]]) – list of tuples

• top (int) – top values to return

compath.utils.filter_results(results, threshold)

Filter a tuple based iterator given a threshold.

Parameters

• results (list[tuple[str,float]]) – list of tuples

• threshold (float) – thresholding

compath.utils.get_most_similar_names(reference_name, names, threshold=0.4, top=5)

Return the most similar names based on string matching.

Parameters

• reference_name (str) –

• names (list[str]) –

• threshold (optional[float]) –

• top (optional[int]) –

Returns

compath.utils.to_csv(triplets, file=None, sep='\t')

Writs triplets as a tab-separated.

Parameters

• triplets (iterable[tuple[str,str,str]]) – iterable of triplets

• file (file) – A writable file or file-like. Defaults to stdout.

• sep (str) – The separator. Defaults to tab.