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 main():
options = get_options()
# build a graph of HPO terms, so we can trace paths between terms
hpo_ontology = Ontology(options.ontology)
hpo_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)
hpo_graph = ICSimilarity(hpo_by_proband, hpo_graph)
print("analysing similarity")
try:
analyse_genes(
hpo_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 a CalculateSimilarity object for unit tests
"""
path = os.path.join(os.path.dirname(__file__), "data", "obo.txt")
ontology = Ontology(path)
graph = ontology.get_graph()
self.hpo_terms = {
"person_01": ["HP:0000924"],
"person_02": ["HP:0000118", "HP:0002011"],
"person_03": ["HP:0000707", "HP:0002011"]
}
self.hpo_graph = CalculateSimilarity(self.hpo_terms, graph)
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)
class TestOntologyPy(unittest.TestCase):
""" test the Ontology class
"""
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)
def test_setup(self):
""" test that the Ontology class has loaded the test obo file correctly
"""
self.assertEqual(self.ontology.hpo_header, HEADER)
self.assertEqual(self.ontology.hpo_list, HPO_LIST)
def test_load_hpo_database(self):
""" check that load_hpo_database works (also in the class initialisation)
"""
path = os.path.join(os.path.dirname(__file__), "data", "obo.txt")
temp_header, temp_hpo = self.ontology.load_hpo_database(path)
self.assertEqual(temp_header, HEADER)
self.assertEqual(temp_hpo, HPO_LIST)
def test_add_hpo_attributes_to_node(self):
""" test that add_hpo_attributes_to_node works correctly
"""
# construct a node without any alternate IDs
node_id = "HP:0000118"
tags = {'comment': [Value('This is the root of the phenotypic abnormality subontology of the HPO.', None)], \
'synonym': [Value('Organ abnormality', ('EXACT []',))], \
'name': [Value('Phenotypic abnormality', None)], \
'is_a': [Value('HP:0000001', None)], \
'id': [Value('HP:0000118', None)], \
'def': [Value('A phenotypic abnormality.', ('[HPO:probinson]',))]}
graph = networkx.DiGraph()
graph.add_node(node_id)
self.ontology.add_hpo_attributes_to_node(graph, node_id, tags)
self.assertEqual(set(graph.node[node_id].keys()), \
set(["comment", "synonym", "name", "def", "is_a", "id"]))
self.assertEqual(graph.node[node_id]["comment"], \
"This is the root of the phenotypic abnormality subontology of the HPO.")
self.assertEqual(graph.node[node_id]["synonym"], "Organ abnormality")
self.assertEqual(graph.node[node_id]["name"], "Phenotypic abnormality")
self.assertEqual(graph.node[node_id]["def"], "A phenotypic abnormality.")
self.assertEqual(graph.node[node_id]["is_a"], "HP:0000001")
self.assertEqual(graph.node[node_id]["id"], "HP:0000118")
def test_track_alt_ids(self):
""" check that track_alt_ids works correctly
"""
# construct a node without any alternate IDs
node_id = "HP:0000118"
tags = {'comment': [Value('This is the root of the phenotypic abnormality subontology of the HPO.', None)], \
'synonym': [Value('Organ abnormality', ('EXACT []',))], \
'name': [Value('Phenotypic abnormality', None)], \
'is_a': [Value('HP:0000001', None)], \
'id': [Value('HP:0000118', None)], \
'def': [Value('A phenotypic abnormality.', ('[HPO:probinson]',))]}
# if we track the node, it shouldn't add anything to the empty ref_ids,
# or alt_ids
self.ontology.track_alt_ids(tags, node_id)
self.assertEqual(self.ontology.ref_ids, {})
self.assertEqual(self.ontology.alt_ids, {})
# construct a node with some alternate IDs
node_id = "HP:0000707"
tags = {'comment': [Value('The nervous system comprises the neuraxis (brain, spinal cord, and ventricles), the autonomic nervous system, the enteric nervous system, and the peripheral nervous system.', None)], \
'synonym': [Value('Neurologic abnormalities', ('EXACT []',)), \
Value('Neurological abnormality', ('EXACT []',))], \
'name': [Value('Abnormality of the nervous system', None)], \
'id': [Value('HP:0000707', None)], \
'is_a': [Value('HP:0000118', None)], \
'alt_id': [Value('HP:0001333', None), Value('HP:0006987', None)], \
'def': [Value('An abnormality of the `nervous system` (FMA:7157).', ('[HPO:probinson]',))]}
# now when we track the node, it should add in the alternate IDs
self.ontology.track_alt_ids(tags, node_id)
self.assertEqual(self.ontology.ref_ids, {node_id: ['HP:0001333', 'HP:0006987']})
self.assertEqual(self.ontology.alt_ids["HP:0001333"], node_id)
self.assertEqual(self.ontology.alt_ids["HP:0006987"], node_id)
def test_is_obsolete(self):
""" check that is_obsolete works correctly
"""
# check that some tags with a True is_obsolete entry is True
tags = {'is_obsolete': [Value('true', None)], \
'id': [Value('HP:0000489', None)], \
'name': [Value('Abnormality of globe location or size', None)]}
self.assertTrue(self.ontology.is_obsolete(tags))
# check that some tags with a False is_obsolete entry is False
tags = {'is_obsolete': [Value('false', None)], \
'id': [Value('HP:0000489', None)], \
'name': [Value('Abnormality of globe location or size', None)]}
self.assertFalse(self.ontology.is_obsolete(tags))
# check that some tags without an is_obsolete entry is False
tags = {'id': [Value('HP:0000707', None)], \
'name': [Value('Abnormality of the nervous system', None)]}
self.assertFalse(self.ontology.is_obsolete(tags))
def test_get_graph(self):
""" test that building a graph with get_graph works correctly
"""
graph = self.ontology.get_graph()
# 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(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(graph.edges('HP:0000924'), [])
# check that, as part of setting the graph up, we have constructed the
# correct set of obsolete IDs
self.assertEqual(self.ontology.obsolete_ids, set(["HP:0000489"]))
import json
from StringIO import StringIO
import pymongo
mongo_host='localhost'
mongo_port=27017
client = pymongo.MongoClient(host=mongo_host, port=int(mongo_port))
db=client['patients']
db.hpo.drop()
db.hpo.ensure_index('hp_id')
path = '/slms/UGI/vm_exports/vyp/phenotips/uclex_files/hp.obo'
ontology = Ontology(path)
hpo_graph = ontology.get_graph()
#print('\t'.join(['external_id','mode_of_inheritance','hpo_features','hpo_ancestors']))
for l in sys.stdin.readlines():
io = StringIO(l)
p=json.load(io)
external_id=p['external_id']
mode_of_inheritance= [i['id'] for i in p.get('global_mode_of_inheritance',[])]
hpo=[]
for f in p.get('features',[]):
if f['id'].startswith('MIM'):
hpo+=[x['hpo_term'] for x in phizz.query_disease([f['id']])]
else:
hpo+=[f['id']]
if hpo:
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)
class TestOntologyPy(unittest.TestCase):
""" test the Ontology class
"""
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)
def test_setup(self):
""" test that the Ontology class has loaded the test obo file correctly
"""
self.assertEqual(self.ontology.hpo_header, HEADER)
self.assertEqual(self.ontology.hpo_list, HPO_LIST)
def test_load_hpo_database(self):
""" check that load_hpo_database works (also in the class initialisation)
"""
path = os.path.join(os.path.dirname(__file__), "data", "obo.txt")
temp_header, temp_hpo = self.ontology.load_hpo_database(path)
self.assertEqual(temp_header, HEADER)
self.assertEqual(temp_hpo, HPO_LIST)
def test_add_hpo_attributes_to_node(self):
""" test that add_hpo_attributes_to_node works correctly
"""
# construct a node without any alternate IDs
node_id = "HP:0000118"
tags = {'comment': [Value('This is the root of the phenotypic abnormality subontology of the HPO.', None)], \
'synonym': [Value('Organ abnormality', ('EXACT []',))], \
'name': [Value('Phenotypic abnormality', None)], \
'is_a': [Value('HP:0000001', None)], \
'id': [Value('HP:0000118', None)], \
'def': [Value('A phenotypic abnormality.', ('[HPO:probinson]',))]}
graph = networkx.DiGraph()
graph.add_node(node_id)
self.ontology.add_hpo_attributes_to_node(graph, node_id, tags)
self.assertEqual(set(graph.node[node_id].keys()), \
set(["comment", "synonym", "name", "def", "is_a", "id"]))
self.assertEqual(graph.node[node_id]["comment"], \
"This is the root of the phenotypic abnormality subontology of the HPO.")
self.assertEqual(graph.node[node_id]["synonym"], "Organ abnormality")
self.assertEqual(graph.node[node_id]["name"], "Phenotypic abnormality")
self.assertEqual(graph.node[node_id]["def"],
"A phenotypic abnormality.")
self.assertEqual(graph.node[node_id]["is_a"], "HP:0000001")
self.assertEqual(graph.node[node_id]["id"], "HP:0000118")
def test_track_alt_ids(self):
""" check that track_alt_ids works correctly
"""
# construct a node without any alternate IDs
node_id = "HP:0000118"
tags = {'comment': [Value('This is the root of the phenotypic abnormality subontology of the HPO.', None)], \
'synonym': [Value('Organ abnormality', ('EXACT []',))], \
'name': [Value('Phenotypic abnormality', None)], \
'is_a': [Value('HP:0000001', None)], \
'id': [Value('HP:0000118', None)], \
'def': [Value('A phenotypic abnormality.', ('[HPO:probinson]',))]}
# if we track the node, it shouldn't add anything to the empty ref_ids,
# or alt_ids
self.ontology.track_alt_ids(tags, node_id)
self.assertEqual(self.ontology.ref_ids, {})
self.assertEqual(self.ontology.alt_ids, {})
# construct a node with some alternate IDs
node_id = "HP:0000707"
tags = {'comment': [Value('The nervous system comprises the neuraxis (brain, spinal cord, and ventricles), the autonomic nervous system, the enteric nervous system, and the peripheral nervous system.', None)], \
'synonym': [Value('Neurologic abnormalities', ('EXACT []',)), \
Value('Neurological abnormality', ('EXACT []',))], \
'name': [Value('Abnormality of the nervous system', None)], \
'id': [Value('HP:0000707', None)], \
'is_a': [Value('HP:0000118', None)], \
'alt_id': [Value('HP:0001333', None), Value('HP:0006987', None)], \
'def': [Value('An abnormality of the `nervous system` (FMA:7157).', ('[HPO:probinson]',))]}
# now when we track the node, it should add in the alternate IDs
self.ontology.track_alt_ids(tags, node_id)
self.assertEqual(self.ontology.ref_ids,
{node_id: ['HP:0001333', 'HP:0006987']})
self.assertEqual(self.ontology.alt_ids["HP:0001333"], node_id)
self.assertEqual(self.ontology.alt_ids["HP:0006987"], node_id)
def test_is_obsolete(self):
""" check that is_obsolete works correctly
"""
# check that some tags with a True is_obsolete entry is True
tags = {'is_obsolete': [Value('true', None)], \
'id': [Value('HP:0000489', None)], \
'name': [Value('Abnormality of globe location or size', None)]}
self.assertTrue(self.ontology.is_obsolete(tags))
# check that some tags with a False is_obsolete entry is False
tags = {'is_obsolete': [Value('false', None)], \
'id': [Value('HP:0000489', None)], \
'name': [Value('Abnormality of globe location or size', None)]}
self.assertFalse(self.ontology.is_obsolete(tags))
# check that some tags without an is_obsolete entry is False
tags = {'id': [Value('HP:0000707', None)], \
'name': [Value('Abnormality of the nervous system', None)]}
self.assertFalse(self.ontology.is_obsolete(tags))
def test_get_graph(self):
""" test that building a graph with get_graph works correctly
"""
graph = self.ontology.get_graph()
# 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(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(graph.edges('HP:0000924'), [])
# check that, as part of setting the graph up, we have constructed the
# correct set of obsolete IDs
self.assertEqual(self.ontology.obsolete_ids, set(["HP:0000489"]))
