def test_set_feature_float(self):
"""can set and retrieve values"""
rr = Representation()
rr.set("abc", 1)
self.assertEqual(rr.get("abc"), 1.0)
self.assertTrue(type(rr.get("abc")) is float)
def test_impute_fromseeds_highfirst(self):
"""imputing values from manually-specified seeds."""
rr = Representation(dict())
# specify data for two children, DOID:4 is higher in tree, so should gain
rr.set("DOID:0014667", 0.4)
rr.set("DOID:0080015", 0.3)
rr.impute(self.obo,
self.obodef,
seeds=["DOID:0014667", "DOID:0080015"])
self.assertAlmostEqual(rr.get("DOID:0014667"),
0.4,
msg="should remain")
self.assertAlmostEqual(rr.get("DOID:0080015"),
0.3,
msg="should remain")
self.assertAlmostEqual(
rr.get("DOID:4"),
1 - ((1 - 0.4) * (1 - 0.3) * (1 - 0.2)),
msg="ancestor gains from two children (and prior)")
self.assertAlmostEqual(rr.get("DOID:655"),
0.2,
msg="remain; new DOID:4")
def test_impute_fromseeds_lowfirst(self):
"""imputing values from manually-specified seeds."""
rr = Representation(dict())
## specify an inconsistent set of values, DOID:4 is higher in tree, so cannot
## have a lower value than DOID:0014667
rr.set("DOID:0014667", 0.4).set("DOID:4", 0.1)
rr.impute(self.obo, self.obodef, seeds=["DOID:4", "DOID:0014667"])
self.assertEqual(rr.get("DOID:0080015"), 0.1, "child of DOID:4")
self.assertEqual(rr.get("DOID:655"), 0.1, "child of DOID:4")
def test_copy(self):
"""can copy a representation into a new object."""
r1 = Representation(self.defaults, name="hello")
r1.set("abc", 0.5)
result = r1.copy()
self.assertEqual(r1.name, result.name)
self.assertEqual(r1.get("abc"), result.get("abc"))
result.set("abc", 0.75)
self.assertEqual(r1.get("abc"), 0.5)
self.assertEqual(result.get("abc"), 0.75)
def test_general_representation_get(self):
"""setting and getting from a generic representation."""
rr = Representation(dict(xyz=0.2))
rr.set("bob", 0.4)
rr.set("xyz", 0.3)
rr.defaults(self.defaults)
self.assertEqual(rr.get("bob"), 0.4,
"value should come from manual input")
self.assertEqual(rr.get("abc"), 0.1,
"value should come from defaults dict")
self.assertEqual(rr.get("xyz"), 0.3,
"value should come from manual override")
def test_general_representation_get2(self):
"""setting and getting from a generic representation."""
# Similar to previous, but setting defaults before the specifics
rr = Representation(dict(abc=0.1, xyz=0.2))
rr.defaults(self.defaults)
rr.set("bob", 0.4)
rr.set("xyz", 0.3)
self.assertEqual(rr.get("bob"), 0.4,
"value should come from manual input")
self.assertEqual(rr.get("abc"), 0.1,
"value should come from defaults dict")
self.assertEqual(rr.get("xyz"), 0.3,
"value should come from manual override")
def test_impute_up_avoid_doubles(self):
"""updating values in representation via positive evidence in DAG"""
rr = Representation(dict())
# DOID:11044 in test ontology has two paths to root (DOID:4)
# one is direct (a shortcut)
# another path is through 0080015
rr.set("DOID:11044", 0.4)
rr.impute(self.obo, self.obodef)
self.assertGreater(rr.get("DOID:0080015"), 0.2,
"ancestor should increase")
self.assertAlmostEqual(
rr.get("DOID:0080015"),
rr.get("DOID:4"),
msg="4 should get bumped once, despite two paths from 11044")
def test_impute_down(self):
"""updating values in representation via negative evidence."""
rr = Representation(dict())
rr.set("unrelated", 0.8)
rr.set("DOID:0014667", 0.05)
rr.impute(self.obo, self.obodef)
self.assertAlmostEqual(rr.get("unrelated"), 0.8,
"out-of-ontology terms remain")
self.assertAlmostEqual(rr.get("DOID:0014667"), 0.05,
"set value should remain")
self.assertAlmostEqual(rr.get("DOID:4"), 0.2,
"ancestors should remain")
self.assertAlmostEqual(rr.get("DOID:0080015"), 0.2,
"unrelated terms get default")
self.assertAlmostEqual(rr.get("DOID:655"), 0.05,
"children are unaffected")
def test_impute_up_always_increases(self):
"""updating values in representation via positive evidence."""
rr = Representation(dict())
rr.set("DOID:3650", 0.25)
defaults = self.obodef.copy()
defaults["DOID:0014667"] = 0.5
defaults["DOID:4"] = 1
rr.impute(self.obo, defaults)
self.assertEqual(rr.get("DOID:3650"), 0.25, "set value should remain")
self.assertGreater(rr.get("DOID:0060158"), 0.25,
"ancestors should receive greater score")
self.assertEqual(rr.get("DOID:655"), 0.2,
"unrelated should stay at default")
# ancestor that has already a higher score than what is propagated
self.assertGreater(
rr.get("DOID:0014667"), 0.5,
"ancestor should receive score greater than its prior")
def test_impute_up(self):
"""updating values in representation via positive evidence."""
rr = Representation(dict())
rr.set("unrelated", 0.8)
rr.set("DOID:0014667", 0.4)
rr.impute(self.obo, self.obodef)
self.assertEqual(rr.get("unrelated"),
0.8,
msg="out-of-ontology terms remain")
self.assertEqual(rr.get("DOID:0014667"),
0.4,
msg="set value should remain")
self.assertGreater(rr.get("DOID:4"),
0.4,
msg="ancestors should receive greater score")
self.assertEqual(rr.get("DOID:0080015"),
0.2,
msg="unrelated terms get default")
self.assertEqual(rr.get("DOID:655"),
0.2,
msg="children are unaffected")
def make_target_reference(reference, oomap, oo_median=None):
"""convert a single representation from one ontology to another."""
result = Representation(name=reference.name)
result.title = reference.title
for phenotype, value in reference.data.items():
for oo_phenotype, oo_score in oomap[phenotype]:
# perhaps compute a rescaled oo value
newvalue = value
if oo_median is not None:
newvalue = value * tanh(oo_score / oo_median)
# always take the larger value if previously set
if result.has(oo_phenotype):
newvalue = max(newvalue, result.get(oo_phenotype))
result.set(oo_phenotype, newvalue)
return result
def test_init_float(self):
"""initializing with a dict ensure float values"""
rr = Representation(dict(abc=1), name="rr")
self.assertEqual(rr.get("abc"), 1.0)
self.assertTrue(type(rr.get("abc")) is float)
def test_set_feature(self):
"""can set and retrieve values"""
rr = Representation()
rr.set("abc", 0.2)
self.assertEqual(rr.get("abc"), 0.2)