def test_lin_zero(self):
self.simscore.register('lin', d.Lin)
terms = make_terms()
terms[0].information_content.omim = 0
terms[1].information_content.omim = 0
res = self.simscore(terms[0], terms[1], method='lin')
assert res == 0.0, res
def test_jc2(self):
self.simscore.register('jc2', d.JC2)
terms = make_terms()
terms[0].information_content.omim = 0.5
terms[1].information_content.omim = 0.7
# 1 - (0.5 + 0.7 - 1.8)
res = self.simscore(terms[0], terms[1], method='jc2')
assert res == 1.6, res
def test_lin(self):
self.simscore.register('lin', d.Lin)
terms = make_terms()
terms[0].information_content.omim = 0.5
terms[1].information_content.omim = 0.7
# 1.8 / (0.5+0.7) = 1.5
res = self.simscore(terms[0], terms[1], method='lin')
assert res == 1.5, res
def test_jc(self):
self.simscore.register('jc', d.JC)
terms = make_terms()
terms[0].information_content.omim = 0.5
terms[1].information_content.omim = 0.7
# -1 / ((1 + 1.8) - 0.5 - 0.7)
res = self.simscore(terms[0], terms[1], method='jc')
assert res == -0.625, res
def test_resnik(self):
self.simscore.register('resnik', d.Resnik)
terms = make_terms()
t1 = MagicMock()
t1.common_ancestors = MagicMock(return_value=terms[0:3])
terms[0].information_content.omim = 0.5
terms[1].information_content.omim = 0.7
terms[2].information_content.omim = 0.6
res = self.simscore(t1, {}, method='resnik')
assert res == 0.7
def setUp(self):
items = make_terms()
self.root = items[0]
self.child_1_1 = items[1]
self.child_1_2 = items[2]
self.child_2_1 = items[3]
self.child_3 = items[4]
self.terms = Ontology(from_obo_file=False)
self.terms._append(self.root)
self.terms._append(self.child_1_1)
self.terms._append(self.child_1_2)
self.terms._append(self.child_2_1)
self.terms._append(self.child_3)
self.terms._connect_all()
def test_graphic(self):
self.simscore.register('graphic', d.GraphIC)
terms = make_terms()
t1 = MagicMock()
t1.common_ancestors = MagicMock(return_value=terms[2:4])
t1.all_parents = set(terms[0:4])
t2 = MagicMock()
t2.all_parents = set(terms[3:5])
terms[0].information_content.omim = 0.5
terms[1].information_content.omim = 0.7
terms[2].information_content.omim = 0.6
terms[3].information_content.omim = 0.2
terms[4].information_content.omim = 0.1
# common: 0.6 + 0.2 => 0.8
# union: (0.5 + 0.7 + 0.6 + 0.2) + 0.1 => 2.1
res = self.simscore(t1, t2, method='graphic')
assert int(res * 10_000) == 3809, res
def setUp(self):
self.terms = mo.make_terms()