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)
class TestCalculateSimilarityPy(unittest.TestCase):
""" class to test CalculateSimilarity
"""
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 test_setup(self):
""" test that the class initialised correctly.
Mainly I want to check that when the class initialised, it ran
tally_hpo_terms() correctly. Check that the counts of the HPO terms
used in the probands match what is expected.
"""
self.assertEqual(self.hpo_graph.total_freq, 5)
self.assertEqual(self.hpo_graph.hpo_counts["HP:0002011"], 2)
self.assertEqual(self.hpo_graph.hpo_counts["HP:0000118"], 1)
# Check that we get an error if we look for counts of a term that was
# not used in the probands.
with self.assertRaises(KeyError):
self.assertEqual(self.hpo_graph.hpo_counts["HP:0000001"])
def test_add_hpo(self):
""" check that HPO counting works correctly
"""
# check the baseline count for a term
self.assertEqual(self.hpo_graph.hpo_counts["HP:0002011"], 2)
# add a term, and check that the count for the term increases, along
# with the total number of terms used
self.hpo_graph.add_hpo("HP:0002011")
self.assertEqual(self.hpo_graph.hpo_counts["HP:0002011"], 3)
self.assertEqual(self.hpo_graph.total_freq, 6)
# check that if we try to add a term that isn't in the HPO ontology, we
# don't increment any counts
self.hpo_graph.add_hpo("unknown_term")
self.assertEqual(self.hpo_graph.total_freq, 6)
# Check that if we add a term that currently doesn't have a tallied
# count then the term getes inserted correctly, and the counts increment
# appropriately.
with self.assertRaises(KeyError):
self.assertEqual(self.hpo_graph.hpo_counts["HP:0000001"])
self.hpo_graph.add_hpo("HP:0000001")
self.assertEqual(self.hpo_graph.hpo_counts["HP:0000001"], 1)
self.assertEqual(self.hpo_graph.total_freq, 7)
def test_get_descendants(self):
""" check that get_descendants works correctly
"""
# check that a high-level node returns the expected set of nodes
self.assertEqual(self.hpo_graph.get_descendants("HP:0000118"), \
set(['HP:0000707', 'HP:0002011', 'HP:0000924']))
# check that a terminal node doesn't have any descendants
self.assertEqual(self.hpo_graph.get_descendants("HP:0000924"), \
set([]))
def test_get_ancestors(self):
""" check that get_ancestors works correctly
"""
# check that we get an appropriate set of ancestor tersm for a termina
# node
self.assertEqual(self.hpo_graph.get_ancestors("HP:0000924"), \
set(['HP:0000001', 'HP:0000118', 'HP:0000924']))
# check that even the top node returns itself as a ancestor node
self.assertEqual(self.hpo_graph.get_ancestors("HP:0000001"), \
set(['HP:0000001']))
def test_find_common_ancestors(self):
""" check that find_common_ancestors works correctly
"""
# check that two terms on different arms only return their common
# ancestors
self.assertEqual(self.hpo_graph.find_common_ancestors('HP:0000924', \
'HP:0000707'), set(["HP:0000001", "HP:0000118"]))
# check that two identical terms return their list of ancestors
self.assertEqual(self.hpo_graph.find_common_ancestors('HP:0000707', \
'HP:0000707'), set(["HP:0000001", "HP:0000118", "HP:0000707"]))
# check that if one of the two terms is not in the HPO graqph, then we
# return an empty set
self.assertEqual(self.hpo_graph.find_common_ancestors('HP:9999999', \
'HP:0000707'), set([]))
