TCT.TCT_pathfinder

TCT.TCT_pathfinder.build_query_graph(start_node_id, end_node_id, start_node_categories=None, end_node_categories=None, constraints_path=None)

start_node_categories and end_node_categories are lists of categories.

TCT.TCT_pathfinder.format_pathfinder_query(node1_id, node1_category, node2_id, node2_category)

TCT.TCT_pathfinder.format_query_json_for_pathfinder_with_constraints(subject_ids, object_ids=None, subject_categories=None, object_categories=None, predicates=None, constraints=None)

format user’s input into a query json for pathfinder pipeline with constraints on the intermediate node categories.

Parameters:

subject_idsstr

a curie id for the subject node

object_idsstr

a curie id for the object node

subject_categorieslist

a list of categories for the subject node

object_categorieslist

a list of categories for the object node

predicateslist

a list of predicates for the edge between subject and object nodes

constraintslist

a list of intermediate categories for the pathfinder pipeline, currently only one intermediate category is allowed in the constraints list.

Returns:

query_json_tempdict

a query json for pathfinder pipeline

Examples

>>> query_json_temp = format_query_json_for_pathfinder_with_constraints(
    subject_ids='NCBIGene:6774',
    object_ids='NCBIGene:4170',
    subject_categories=['biolink:Gene'],
    object_categories=['biolink:Gene'],
    predicates=['biolink:related_to'],
    constraints=['biolink:Protein'])

TCT.TCT_pathfinder.generate_score_results(results, method='infores')

Generates a score dict, and a list of “analyses”. method can be ‘infores’ or ‘edges’

TCT.TCT_pathfinder.parse_results_for_pathfinder(start_node_id: str, end_node_id: str, result1: dict, result2: dict, start_node_categories=None, end_node_categories=None, get_node_info=True, scoring_method='infores')

Converts the results of two TRAPI queries into the same general json format as the other pathfinder APIs. scoring_method is how the node scores are generated, and could be ‘infores’ or ‘edges’.

TCT.TCT_pathfinder.pathfinder(input_node1_id: str, input_node2_id: str, intermediate_categories: list, APInames, metaKG, API_predicates, scoring_method='infores')

Returns a Pathfinder output for the given pair of nodes. scoring_method could be ‘infores’ or ‘edges’.