def _match_one_allele(true_allele):
if true_allele == truth_variant.reference_bases:
return 0
else:
simplifed_true_allele = variant_utils.simplify_alleles(
truth_variant.reference_bases, true_allele)
for alt_index, alt_allele in enumerate(candidate_variant.alternate_bases):
simplifed_alt_allele = variant_utils.simplify_alleles(
candidate_variant.reference_bases, alt_allele)
if simplifed_true_allele == simplifed_alt_allele:
return alt_index + 1
# If nothing matched, we don't have this alt, so the alt allele index for
# should be 0 (i.e., not any alt).
return 0
def _match_one_allele(true_allele):
if true_allele == truth_variant.reference_bases:
return 0
else:
simplified_true_allele = variant_utils.simplify_alleles(
truth_variant.reference_bases, true_allele)
for alt_index, alt_allele in enumerate(candidate_variant.alternate_bases):
simplified_alt_allele = variant_utils.simplify_alleles(
candidate_variant.reference_bases, alt_allele)
if simplified_true_allele == simplified_alt_allele:
return alt_index + 1
# If nothing matched, we don't have this alt, so the alt allele index for
# should be 0 (i.e., not any alt).
return 0
def simplify_alleles(variant):
"""Replaces the alleles in variants with their simplified versions.
This function takes a variant and replaces its ref and alt alleles with those
produced by a call to variant_utils.simplify_alleles() to remove common
postfix bases in the alleles that may be present due to pruning away alleles.
Args:
variant: learning.genomics.genomics.Variant proto we want to simplify.
Returns:
variant with its ref and alt alleles replaced with their simplified
equivalents.
"""
simplified_alleles = variant_utils.simplify_alleles(
variant.reference_bases, *variant.alternate_bases)
variant.reference_bases = simplified_alleles[0]
variant.alternate_bases[:] = simplified_alleles[1:]
variant.end = variant.start + len(variant.reference_bases)
return variant
def simplify_alleles(variant):
"""Replaces the alleles in variants with their simplified versions.
This function takes a variant and replaces its ref and alt alleles with those
produced by a call to variant_utils.simplify_alleles() to remove common
postfix bases in the alleles that may be present due to pruning away alleles.
Args:
variant: learning.genomics.genomics.Variant proto we want to simplify.
Returns:
variant with its ref and alt alleles replaced with their simplified
equivalents.
"""
simplified_alleles = variant_utils.simplify_alleles(variant.reference_bases,
*variant.alternate_bases)
variant.reference_bases = simplified_alleles[0]
variant.alternate_bases[:] = simplified_alleles[1:]
variant.end = variant.start + len(variant.reference_bases)
return variant
def test_simplify_alleles(self, alleles, expected):
self.assertEqual(variant_utils.simplify_alleles(*alleles), tuple(expected))
self.assertEqual(
variant_utils.simplify_alleles(*reversed(alleles)),
tuple(reversed(expected)))
def test_simplify_alleles(self, alleles, expected):
self.assertEqual(variant_utils.simplify_alleles(*alleles), tuple(expected))
self.assertEqual(
variant_utils.simplify_alleles(*reversed(alleles)),
tuple(reversed(expected)))
