def main():
options = get_options()
# build a graph of HPO terms, so we can trace paths between terms
hpo_ontology = Ontology(options.ontology)
graph = hpo_ontology.get_graph()
alt_node_ids = hpo_ontology.get_alt_ids()
obsolete_ids = hpo_ontology.get_obsolete_ids()
# load HPO terms and probands for each gene
print("loading HPO terms and probands by gene")
hpo_by_proband = load_participants_hpo_terms(options.phenotypes_path, \
alt_node_ids, obsolete_ids)
probands_by_gene = load_genes(options.genes_path)
if options.permute:
probands_by_gene = permute_probands(probands_by_gene)
graph.tally_hpo_terms(hpo_by_proband)
print("analysing similarity")
try:
analyse_genes(graph, hpo_by_proband, probands_by_gene, \
options.output, options.iterations, options.score_type)
except KeyboardInterrupt:
sys.exit("HPO similarity exited.")
def setUp(self):
""" construct a CalculateSimilarity object for unit tests
"""
path = os.path.join(os.path.dirname(__file__), "data", "obo.txt")
ontology = Ontology(path)
self.graph = ontology.get_graph()
self.hpo_terms = {
"person_01": ["HP:0000924"],
"person_02": ["HP:0000118", "HP:0002011"],
"person_03": ["HP:0000707", "HP:0002011"]
}
self.graph.tally_hpo_terms(self.hpo_terms)
def setUp(self):
""" construct an Ontology object for unit tests
"""
path = os.path.join(os.path.dirname(__file__), "data", "obo.txt")
self.ontology = Ontology(path)
