tooluniverse.enrichr_tool module¶

class tooluniverse.enrichr_tool.EnrichrTool[source]¶

Tool to perform gene enrichment analysis using Enrichr.

get_official_gene_name(gene_name)[source]¶

Retrieve the official gene symbol for a given gene name or synonym using the MyGene.info API.

Parameters: gene_name (str): The gene name or synonym to query.
Returns: str: The official gene symbol if found; otherwise, raises an Exception.

submit_gene_list(gene_list)[source]¶

Submit the gene list to Enrichr and return the user list ID.

get_enrichment_results(user_list_id, library)[source]¶

Fetch enrichment results for a specific library.

Parameters: user_list_id (str): The user list ID from Enrichr. library (str): The name of the enrichment library.
Returns: dict: The enrichment results.

build_graph(genes, enrichment_results)[source]¶

Initialize and build the graph with gene nodes and enriched terms.

Parameters: genes (list): List of gene names. enrichment_results (dict): Dictionary of enrichment results by library.
Returns: networkx.Graph: The constructed graph.

rank_paths_by_weight(G, source, target)[source]¶

Find and rank paths between source and target based on total edge weight.

Parameters: G (networkx.Graph): The graph to search. source (str): The source node. target (str): The target node.
Returns: list: List of tuples (path, weight) sorted by weight descending.

rank_paths_to_term(G, gene, term)[source]¶

Find and rank paths from each gene to a specified term based on total edge weight.

Parameters: G (networkx.Graph): The graph to search. gene (str): The source gene. term (str): The target term.
Returns: list or None: List of tuples (path, weight) sorted by weight descending, or None if no paths.

enrichr_api(genes, libs)[source]¶

Main API function to perform gene enrichment analysis.

Parameters: genes (list): List of gene names. libs (list): List of enrichment libraries to use.
Returns: tuple: (connected_path, connections) dictionaries.