def setUp(self):
""" construct a ICSimilarity object and terms per proband for unit tests
"""
path = os.path.join(os.path.dirname(__file__), "data", "obo.txt")
self.hpo_graph, _, _ = open_ontology(path)
self.hpo_terms = {
"person_01": ["HP:0000924"],
"person_02": ["HP:0000118", "HP:0002011"],
"person_03": ["HP:0000707", "HP:0002011"]
}
self.hpo_graph.tally_hpo_terms(self.hpo_terms)
def test_get_graph(self):
""" test that building a graph with get_graph works correctly
"""
graph, alt_ids, obsolete = open_ontology(self.path)
# check that all the nodes (aside from the obsolete node) have been
# included
self.assertEqual(set(graph.nodes()), \
set(['HP:0000001', 'HP:0000118', 'HP:0000707', 'HP:0000924', 'HP:0002011',]))
# check that the graph info is set correctly from the HPO header
self.assertEqual(graph.graph, HEADER)
# check that the edges match what is expected foir each node
self.assertEqual(list(graph.edges('HP:0000001')),
[("HP:0000001", "HP:0000118")])
self.assertEqual(set(graph.edges('HP:0000118')), \
set([("HP:0000118", "HP:0000707"), ("HP:0000118", "HP:0000924")]))
self.assertEqual(list(graph.edges('HP:0000924')), [])
# check that, as part of setting the graph up, we have constructed the
# correct set of obsolete IDs
self.assertEqual(obsolete, set(["HP:0000489"]))
def main():
options = get_options()
# build a graph of HPO terms, so we can trace paths between terms
graph, alt_ids, obsolete = open_ontology(options.ontology)
# 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_ids, obsolete)
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.")