def test_baddata(self):
"""inference should raise when input is bad"""
rs = ReferenceSet(dict(refA=0.5, refB=0.5), ids=["a", "b", "c"])
rs.prep()
with self.assertRaises(Exception) as e:
rs.inference(5)
def test_scores_bad_input(self):
"""inference function should raise with bad input."""
# model is empty
rs = ReferenceSet(dict(refA=0.5, refB=0.5), ids=obo.ids())
with self.assertRaises(Exception):
rs.inference("refA")
def test_between2(self):
"""inference when model equally similar to two refs"""
# let ref universe have two annotations
rs = ReferenceSet(dict(refA=0.5, refB=0.5), ids=self.obo.ids(),
row_priors=self.obodefaults)
rs.add(self.refA).add(self.refB)
rs.learn_obo(self.obo)
rs.prep()
inf = rs.inference(self.y3model)
self.assertAlmostEqual(inf["refA"], inf["refB"], msg="equally likely")
def test_between_refs_and_null(self):
"""inference when model is similar to two refs and a there is a null"""
# let ref universe have two annotations and one null
rs = ReferenceSet(dict(null=0.8, refA=0.15, refB=0.15),
ids=self.obo.ids(), row_priors=self.obodefaults)
rs.add(self.refA).add(self.refB)
rs.learn_obo(self.obo)
rs.prep()
inf = rs.inference(self.y3model)
self.assertAlmostEqual(inf["refA"], inf["refB"],
msg="equally likely")
def test_model_nodata(self):
"""inference when references are unequal but model has no data"""
model = Representation(name="nodata")
# let ref universe have two annotations and one null
rs = ReferenceSet(dict(null=0.8, refA=0.1, refB=0.1),
ids=self.obo.ids(), row_priors=self.obodefaults)
rs.add(self.refA).add(self.refB)
rs.learn_obo(self.obo)
rs.prep()
inf = rs.inference(model)
self.assertAlmostEqual(inf["refA"], inf["refB"],
msg="equally likely")
def test_difference_in_priors(self):
"""inference when model matches two references,
but have different priors"""
# let ref universe have two annotations and one null
rs = ReferenceSet(dict(null=0.85, refA=0.05, refB=0.1),
ids=self.obo.ids(), row_priors=self.obodefaults)
rs.add(self.refA).add(self.refB)
rs.learn_obo(self.obo)
rs.prep()
inf = rs.inference(self.y3model)
self.assertLess(inf["refA"], inf["refB"],
msg="equal match, but A has weaker prior")
def test_underflow(self):
"""attempt to get underflow in individual p."""
# let model have very sure values
model = Representation(name="underflow")
model.set("Y:007", 0.00001).set("Y:004", 1).set("Y:003", 1)
# let ref universe have two annotations and one null
refA = Representation(name="refA").set("Y:003", 1)
refB = Representation(name="refB").set("Y:003", 1)
rs = ReferenceSet(dict(null=0.98, refA=0.001, refB=0.001),
ids=self.obo.ids())
rs.add(refA).add(refB)
rs.learn_obo(self.obo)
rs.prep()
result = rs.inference(model, verbose=True)
self.assertGreaterEqual(result["refA"], 0,
msg="must always be a number, even if zero")
self.assertGreaterEqual(result["refB"], 0,
msg="must always be a number, even if zero")
self.assertGreaterEqual(result["refB"], 0,
msg="must always be a number, even if zero")
