def test_no_variance(self):
ci = HPOSet([self.ontology[1]])
assert ci.variance() == (0, 0, 0, [])
class SetMetricsTests(unittest.TestCase):
def setUp(self):
self.ontology = mo.make_ontology()
self.ci = HPOSet([term for term in self.ontology])
def test_variance(self):
with patch.object(HPOTerm,
'path_to_other',
side_effect=[(1, None), (1, None), (1, None),
(1, None), (1, None), (1, None),
(2, None), (2, None), (2, None),
(2, None), (2, None), (3, None),
(3, None), (3, None), (3, None),
(4, None), (4, None), (4, None),
(5, None), (5, None),
(6, None)]) as mock_pto:
res = self.ci.variance()
assert len(res) == 4, len(res)
assert 1 < res[0] < 7, res[0]
assert res[1] == 1
assert res[2] == 6, res[2]
assert len(res[3]) == 6 + 5 + 4 + 3 + 2 + 1, len(res[3])
calls = [
call(self.ci._list[1]),
call(self.ci._list[2]),
call(self.ci._list[3]),
call(self.ci._list[4]),
call(self.ci._list[5]),
call(self.ci._list[6]),
call(self.ci._list[2]),
call(self.ci._list[3]),
call(self.ci._list[4]),
call(self.ci._list[5]),
call(self.ci._list[6]),
call(self.ci._list[3]),
call(self.ci._list[4]),
call(self.ci._list[5]),
call(self.ci._list[6]),
call(self.ci._list[4]),
call(self.ci._list[5]),
call(self.ci._list[6]),
call(self.ci._list[5]),
call(self.ci._list[6]),
call(self.ci._list[6])
]
mock_pto.assert_has_calls(calls)
def test_no_variance(self):
ci = HPOSet([self.ontology[1]])
assert ci.variance() == (0, 0, 0, [])
def test_information_content(self):
i = 0
for term in self.ci:
term.information_content.omim = i
term.information_content.gene = i * 2
i += 1
res = self.ci.information_content()
assert res['mean'] == 3.0
assert res['total'] == 21
assert res['max'] == 6
assert res['all'] == [0, 1, 2, 3, 4, 5, 6]
# checking default value
assert self.ci.information_content() == res
res = self.ci.information_content('gene')
assert res['mean'] == 6.0
assert res['total'] == 42
assert res['max'] == 12
assert res['all'] == [0, 2, 4, 6, 8, 10, 12]