def test_genotype_from_matched_truth_no_call_truth_variant_raises(self):
with six.assertRaisesRegex(self, ValueError,
'Expected exactly one VariantCal'):
variant_labeler._genotype_from_matched_truth(self.snp,
test_utils.make_variant(
start=10,
alleles=['A', 'C'],
))
def test_genotype_from_matched_truth_no_gt_truth_variant_raises(self):
with six.assertRaisesRegex(self, ValueError,
'truth_variant needs genotypes'):
variant_labeler._genotype_from_matched_truth(self.snp,
test_utils.make_variant(
start=10,
alleles=['A', 'C'],
gt=[-1, -1],
))
def test_genotype_from_matched_truth(self, variant_alleles, alt_alleles,
truth_alleles, truth_gt,
expected_genotype, expected_label):
variant = test_utils.make_variant(start=10, alleles=variant_alleles)
truth_variant = test_utils.make_variant(
start=10, alleles=truth_alleles, gt=truth_gt)
self.assertEqual(expected_genotype,
variant_labeler._genotype_from_matched_truth(
variant, truth_variant))
labeled = variant_labeler.VariantLabel(
is_confident=True,
variant=variant,
genotype=expected_genotype)
indices = [variant_alleles.index(alt) - 1 for alt in alt_alleles]
self.assertEqual(labeled.label_for_alt_alleles(indices), expected_label)
def test_genotype_from_matched_truth_none_variant_raises(self):
with six.assertRaisesRegex(self, ValueError, 'variant cannot be None'):
variant_labeler._genotype_from_matched_truth(None, self.snp)
def test_genotype_from_matched_truth_none_truth_variant_raises(self):
with self.assertRaisesRegexp(ValueError,
'truth_variant cannot be None'):
variant_labeler._genotype_from_matched_truth(self.snp, None)
