def test_merge_predictions_simplifies_alleles(self):
"""Checks that merge_predictions simplifies alleles."""
ref, alts = 'CCA', ['CA', 'C']
inputs = [
_create_call_variants_output(ref=ref,
indices=[0],
probabilities=[0.0, 1.0, 0.0],
alts=alts),
_create_call_variants_output(ref=ref,
indices=[1],
probabilities=[1.0, 0.0, 0.0],
alts=alts),
_create_call_variants_output(ref=ref,
indices=[0, 1],
probabilities=[0.0, 1.0, 0.0],
alts=alts),
]
for permuted_inputs in itertools.permutations(inputs):
# qual_filter=2 is needed so we remove our middle 'C' allele.
variant, probs = postprocess_variants.merge_predictions(
permuted_inputs, qual_filter=2)
np.testing.assert_almost_equal(probs, [0.0, 1.0, 0.0])
self.assertEqual(variant.reference_bases, 'CC')
self.assertEqual(variant.alternate_bases, ['C'])
def test_merge_predictions(self, inputs, expected_unnormalized_probs):
denominator = sum(expected_unnormalized_probs)
for permuted_inputs in itertools.permutations(inputs):
_, predictions = postprocess_variants.merge_predictions(
permuted_inputs)
np.testing.assert_almost_equal(
predictions,
[x / denominator for x in expected_unnormalized_probs])
def test_merge_predictions_simplifies_alleles(self):
"""Checks that merge_predictions simplifies alleles."""
ref, alts = 'CCA', ['CA', 'C']
inputs = [
_create_call_variants_output(
ref=ref, indices=[0], probabilities=[0.0, 1.0, 0.0], alts=alts),
_create_call_variants_output(
ref=ref, indices=[1], probabilities=[1.0, 0.0, 0.0], alts=alts),
_create_call_variants_output(
ref=ref, indices=[0, 1], probabilities=[0.0, 1.0, 0.0], alts=alts),
]
for permuted_inputs in itertools.permutations(inputs):
# qual_filter=2 is needed so we remove our middle 'C' allele.
variant, probs = postprocess_variants.merge_predictions(
permuted_inputs, qual_filter=2)
np.testing.assert_almost_equal(probs, [0.0, 1.0, 0.0])
self.assertEqual(variant.reference_bases, 'CC')
self.assertEqual(variant.alternate_bases, ['C'])
def test_exception_merge_predictions(self, inputs, text):
with self.assertRaisesRegexp(ValueError, text):
postprocess_variants.merge_predictions(inputs)
def test_exception_merge_predictions(self, inputs, text):
with self.assertRaisesRegexp(ValueError, text):
postprocess_variants.merge_predictions(inputs)
def test_merge_predictions(self, inputs, expected_unnormalized_probs):
denominator = sum(expected_unnormalized_probs)
for permuted_inputs in itertools.permutations(inputs):
_, predictions = postprocess_variants.merge_predictions(permuted_inputs)
np.testing.assert_almost_equal(
predictions, [x / denominator for x in expected_unnormalized_probs])