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"""Tests for deepvariant .variant_labeler."""
from absl.testing import absltest
from absl.testing import parameterized
from third_party.nucleus.io import vcf
from third_party.nucleus.testing import test_utils
from third_party.nucleus.util import ranges
from deepvariant import testdata
from deepvariant.labeler import positional_labeler
def setUpModule():
testdata.init()
class PositionalVariantLabelerTest(parameterized.TestCase):
# Confident variants: SNP, deletion, and multi-allelic.
snp = test_utils.make_variant(start=10, alleles=['A', 'C'], gt=[0, 1])
deletion = test_utils.make_variant(start=20, alleles=['ACG', 'A'], gt=[1, 1])
multiallelic = test_utils.make_variant(
start=30, alleles=['ACT', 'ACTGT', 'A'], gt=[1, 2]
)
# Outside our confident regions.
non_confident = test_utils.make_variant(
start=200, alleles=['A', 'C'], gt=[0, 1]
)
filtered = test_utils.make_variant(start=40, filters='FAILED', gt=[0, 1])
variants = [snp, deletion, multiallelic, non_confident, filtered]
def _make_labeler(self, variants, confident_regions):
return positional_labeler.PositionalVariantLabeler(
truth_vcf_reader=vcf.InMemoryVcfReader(variants),
confident_regions=confident_regions,
)
@parameterized.parameters(
# Simple tests: we get back our matching variants in the confident regions
dict(candidate=snp, expected_confident=True, expected_truth=snp),
dict(
candidate=deletion, expected_confident=True, expected_truth=deletion
),
dict(
candidate=multiallelic,
expected_confident=True,
expected_truth=multiallelic,
),
# Test the behavior outside of our confident regions.
# If we provide a variant outside the confident regions (non_confident) we
# don't get back any expected_truth variants.
dict(
candidate=non_confident, expected_confident=False, expected_truth=None
),
# No matching variant, so we get a None as well as False.
dict(
candidate=test_utils.make_variant(start=300, alleles=['A', 'C']),
expected_confident=False,
expected_truth=None,
),
# This variant doesn't have any match but we're confident in it.
dict(
candidate=test_utils.make_variant(start=15, alleles=['C', 'A']),
expected_confident=True,
expected_genotype=(0, 0),
expected_truth=test_utils.make_variant(
start=15, alleles=['C', 'A'], gt=[0, 0]
),
),
# These variant start at our SNP but has a different allele. We are
# confident and we get back the true snp variant, despite having the
# different alleles. snp has alleles=['A', 'C'] and gt=[0, 1].
dict(
candidate=test_utils.make_variant(
start=snp.start, alleles=['A', 'G']
),
expected_confident=True,
expected_genotype=(0, 0),
expected_truth=snp,
),
dict(
candidate=test_utils.make_variant(
start=snp.start, alleles=['AC', 'C']
),
expected_confident=True,
expected_genotype=(0, 0),
expected_truth=snp,
),
dict(
candidate=test_utils.make_variant(
start=snp.start, alleles=['A', 'CA']
),
expected_confident=True,
expected_genotype=(0, 0),
expected_truth=snp,
),
# Checks that we don't match against the filtered truth variant in our
# database. This means that we return not the filtered variant but one
# with a (0, 0) genotype.
dict(
candidate=test_utils.make_variant(start=filtered.start),
expected_confident=True,
expected_genotype=(0, 0),
expected_truth=test_utils.make_variant(
start=filtered.start, gt=(0, 0)
),
),
)
def test_label_variants(
self,
candidate,
expected_confident,
expected_truth,
expected_genotype=None,
):
labeler = self._make_labeler(
self.variants,
ranges.RangeSet([ranges.make_range(self.snp.reference_name, 10, 100)]),
)
# Call _match so we can compare our expected truth with the actual one.
is_confident, truth_variant = labeler._match(candidate)
self.assertEqual(expected_truth, truth_variant)
self.assertEqual(is_confident, expected_confident)
# Now call label_variants to exercise the higher-level API.
if expected_genotype is None and expected_truth is not None:
expected_genotype = tuple(expected_truth.calls[0].genotype)
labels = list(labeler.label_variants([candidate]))
self.assertLen(labels, 1)
self.assertEqual(candidate, labels[0].variant)
self.assertEqual(expected_confident, labels[0].is_confident)
self.assertEqual(expected_genotype, labels[0].genotype)
def test_match_selects_variant_by_start(self):
# Tests that match() selects the variant at the same start even if that
# variant doesn't have the same alleles at candidate and there's an
# overlapping with the same alleles.
overlapping = [
test_utils.make_variant(start=20, alleles=['CC', 'A'], gt=[1, 1]),
test_utils.make_variant(start=21, alleles=['AAA', 'A'], gt=[0, 1]),
test_utils.make_variant(start=22, alleles=['AA', 'A'], gt=[1, 1]),
]
candidate = test_utils.make_variant(start=21, alleles=['CC', 'A'])
labeler = self._make_labeler(
overlapping,
ranges.RangeSet(
[ranges.make_range(overlapping[0].reference_name, 0, 100)]
),
)
is_confident, truth_variant = labeler._match(candidate)
self.assertEqual(is_confident, True)
self.assertEqual(truth_variant, overlapping[1])
@parameterized.parameters(
dict(
overlapping_variants=[
test_utils.make_variant(start=20, alleles=['A', 'CC'], gt=[1, 1]),
test_utils.make_variant(
start=20, alleles=['A', 'AAA'], gt=[0, 1]
),
test_utils.make_variant(start=20, alleles=['A', 'AA'], gt=[1, 1]),
],
candidate=test_utils.make_variant(start=20, alleles=['A', 'AAA']),
expected_confident=True,
truth_variant_idx=1,
),
# No candidate variant with matching alt, so use first candidate.
dict(
overlapping_variants=[
test_utils.make_variant(start=20, alleles=['A', 'CC'], gt=[1, 1]),
test_utils.make_variant(
start=20, alleles=['A', 'AAA'], gt=[0, 1]
),
test_utils.make_variant(start=20, alleles=['A', 'AA'], gt=[1, 1]),
],
candidate=test_utils.make_variant(start=20, alleles=['A', 'TT']),
expected_confident=True,
truth_variant_idx=0,
),
# GAAA->GAA is the same as GA->A (the second one in matches), but if we
# don't simplify the alleles before comparing, there will be no match and
# will incorrectly fall back to the first one.
dict(
overlapping_variants=[
test_utils.make_variant(
start=20, alleles=['GAA', 'G'], gt=[1, 1]
),
test_utils.make_variant(start=20, alleles=['GA', 'G'], gt=[0, 1]),
],
candidate=test_utils.make_variant(start=20, alleles=['GAAA', 'GAA']),
expected_confident=True,
truth_variant_idx=1,
),
)
def test_match_multiple_matches(
self,
overlapping_variants,
candidate,
expected_confident,
truth_variant_idx,
):
labeler = self._make_labeler(
overlapping_variants,
ranges.RangeSet(
[ranges.make_range(overlapping_variants[0].reference_name, 0, 100)]
),
)
is_confident, variant_match = labeler._match(candidate)
expected_variant = overlapping_variants[truth_variant_idx]
self.assertEqual(is_confident, expected_confident)
self.assertEqual(variant_match, expected_variant)
if __name__ == '__main__':
absltest.main()
