def setUp(self):
self.t0 = c.Entity('number', 'GO:testing')
self.t1 = c.Entity('amount', 'GO:testing')
self.t2 = c.Entity('size', 'GO:testing')
self.t3 = c.Entity('count', 'GO:testing')
self.c0 = c.Cluster(self.t0, {self.t0, self.t1})
self.c1 = c.Cluster(self.t2, {self.t2, self.t3})
def test_simplity(self):
self.t0 = c.Entity('vitamin C', 'GO:000')
self.t1 = c.Entity('ascorbic acid', 'GO:000')
self.t2 = c.Entity('ascorbate', 'GO:000')
self.c0 = c.Cluster(self.t0, {self.t0, self.t1, self.t2})
self.t3 = c.Entity('vitamin C', 'GO:111')
self.t4 = c.Entity('L-ascorbic acid', 'GO:111')
self.t5 = c.Entity('L-ascorbate', 'GO:111')
self.c1 = c.Cluster(self.t3, {self.t3, self.t4, self.t5})
self.t6 = c.Entity('vitamin B12', 'GO:222')
self.t7 = c.Entity('cobalamin', 'GO:222')
self.c2 = c.Cluster(self.t6, {self.t6, self.t7})
cb = self.cb
cb.add(self.c0)
cb.add(self.c1)
cb.add(self.c2)
result = cb.simplify(0.2)
self.assertNotEqual(cb.preferred_term(self.t1),
cb.preferred_term(self.t3))
self.assertNotEqual(cb.preferred_term(self.t1),
cb.preferred_term(self.t6))
self.assertEqual(result.preferred_term(self.t1),
result.preferred_term(self.t3))
self.assertNotEqual(result.preferred_term(self.t1),
result.preferred_term(self.t6))
def setUp(self):
self.t0 = c.Entity('vitamin C', 'GO:000')
self.t1 = c.Entity('ascorbic acid', 'GO:000')
self.t2 = c.Entity('ascorbate', 'GO:000')
self.c0 = c.Cluster(self.t0, {self.t0, self.t1, self.t2})
self.t3 = c.Entity('vitamin C', 'GO:111')
self.t4 = c.Entity('L-ascorbic acid', 'GO:111')
self.t5 = c.Entity('L-ascorbate', 'GO:111')
self.c1 = c.Cluster(self.t3, {self.t3, self.t4, self.t5})
self.t6 = c.Entity('vitamin B12', 'GO:222')
self.t7 = c.Entity('cobalamin', 'GO:222')
self.c2 = c.Cluster(self.t6, {self.t6, self.t7})
def test_evidence_split(self):
regex_in = gopattern.PatternManager.from_definition(
PATTERN_PATH).regex_in()
goid = 'GO:testing'
label = 'upregulation of gene slicing via miRNA'
trunk = self.main_trunk
t1 = c.Pattern('positregulate', 'annotator')
e1 = c.Evidence(t1, 'upregulation', 0, len('upregulation'))
t2 = c.Entity('gene slicing', 'GO:testing')
e2 = c.Evidence(t2, 'gene slicing', self.label.index('gene slicing'),
len(trunk.text))
t3 = c.Constraint('miRNA', 'GO:testing')
e3 = c.Evidence(t3, 'miRNA', self.label.index('miRNA'),
len(self.label))
result = c.evidence_split(goid, label, regex_in)
wanted = [e1, e2, e3]
self.assertEqual(result, wanted)
def setUp(self):
self.t0 = c.Entity('number', 'GO:testing')
self.t1 = c.Entity('amount', 'GO:testing')
self.c0 = c.Cluster(self.t0, {self.t0, self.t1})
self.t2 = c.Entity('size', 'GO:testing')
self.t3 = c.Entity('count', 'GO:testing')
self.c1 = c.Cluster(self.t2, {self.t2, self.t3})
self.t4 = c.Entity('teacher', 'GO:testing')
self.t5 = c.Entity('tutor', 'GO:testing')
self.c2 = c.Cluster(self.t4, {self.t4, self.t5})
self.cb = c.ClusterBook()