def test_variant_position_and_range(self):
v1 = test_utils.make_variant(chrom='1', alleles=['A', 'C'], start=10)
v2 = test_utils.make_variant(chrom='1', alleles=['AGCT', 'C'], start=10)
pos = ranges.make_range('1', 10, 11)
range_ = ranges.make_range('1', 10, 14)
v1_range_tuple = ('1', 10, 11)
v2_range_tuple = ('1', 10, 14)
self.assertEqual(pos, variant_utils.variant_position(v1))
self.assertEqual(pos, variant_utils.variant_position(v2))
self.assertEqual(pos, variant_utils.variant_range(v1))
self.assertEqual(range_, variant_utils.variant_range(v2))
self.assertEqual(v1_range_tuple, variant_utils.variant_range_tuple(v1))
self.assertEqual(v2_range_tuple, variant_utils.variant_range_tuple(v2))
def test_variant_position_and_range(self):
v1 = test_utils.make_variant(chrom='1', alleles=['A', 'C'], start=10)
v2 = test_utils.make_variant(chrom='1', alleles=['AGCT', 'C'], start=10)
pos = ranges.make_range('1', 10, 11)
range_ = ranges.make_range('1', 10, 14)
v1_range_tuple = ('1', 10, 11)
v2_range_tuple = ('1', 10, 14)
self.assertEqual(pos, variant_utils.variant_position(v1))
self.assertEqual(pos, variant_utils.variant_position(v2))
self.assertEqual(pos, variant_utils.variant_range(v1))
self.assertEqual(range_, variant_utils.variant_range(v2))
self.assertEqual(v1_range_tuple, variant_utils.variant_range_tuple(v1))
self.assertEqual(v2_range_tuple, variant_utils.variant_range_tuple(v2))
def _find_matching_variant_in_reader(self, variant):
"""Finds a variant in vcf_reader compatible with variant, if one exists."""
region = variant_utils.variant_position(variant)
matches = [
variant_utils.simplify_variant_alleles(truth_variant)
for truth_variant in self._get_truth_variants(region)
if variant.start == truth_variant.start
]
if not matches:
return None
best_match = None
for match in matches:
if (match.alternate_bases == variant.alternate_bases
and match.reference_bases == variant.reference_bases):
best_match = match
if best_match is None:
logging.info(
'Multiple matches detected; no good match found. Fall back '
'to first. variant: %s: matches: %s', variant, matches)
# redacted
# likely not the best. Think about what to do for different use cases.
best_match = matches[0]
return best_match
def _find_matching_variant_in_reader(self, variant):
"""Finds a variant in vcf_reader compatible with variant, if one exists."""
region = variant_utils.variant_position(variant)
matches = [
truth_variant for truth_variant in self._get_truth_variants(region)
if variant.start == truth_variant.start
]
if not matches:
return None
elif len(matches) > 1:
logging.warning(
'Multiple matches detected, keeping first, for variant %s: %s',
variant, matches)
return matches[0]
def _find_matching_variant_in_reader(self, variant):
"""Finds a variant in vcf_reader compatible with variant, if one exists."""
region = variant_utils.variant_position(variant)
matches = [
truth_variant for truth_variant in self._get_truth_variants(region)
if variant.start == truth_variant.start
]
if not matches:
return None
elif len(matches) > 1:
logging.warning(
'Multiple matches detected, keeping first, for variant %s: %s',
variant, matches)
return matches[0]
def _find_matching_variant_in_reader(self, variant):
"""Finds a variant in vcf_reader compatible with variant, if one exists."""
region = variant_utils.variant_position(variant)
matches = [
truth_variant for truth_variant in self._get_truth_variants(region)
if variant.start == truth_variant.start
]
if not matches:
return None
elif len(matches) > 1:
logging.info('Multiple matches detected for variant %s: %s', variant,
matches)
best_match = matches[0]
for match in matches:
if match.alternate_bases == variant.alternate_bases:
best_match = match
return best_match