def setUp(self):
self.out_fname = test_utils.test_tmpfile('output.vcf')
self.header = variants_pb2.VcfHeader(
contigs=[
reference_pb2.ContigInfo(name='Chr1',
n_bases=50,
pos_in_fasta=0),
reference_pb2.ContigInfo(name='Chr2',
n_bases=25,
pos_in_fasta=1),
],
sample_names=['Fido', 'Spot'],
formats=[
variants_pb2.VcfFormatInfo(id='GT',
number='1',
type='String',
description='Genotype'),
variants_pb2.VcfFormatInfo(id='GQ',
number='1',
type='Float',
description='Genotype Quality')
],
)
self.options = variants_pb2.VcfWriterOptions()
self.writer = vcf_writer.VcfWriter.to_file(self.out_fname, self.header,
self.options)
self.variant = test_utils.make_variant(
chrom='Chr1',
start=10,
alleles=['A', 'C'],
)
self.variant.calls.extend([
variants_pb2.VariantCall(genotype=[0, 0], call_set_name='Fido'),
variants_pb2.VariantCall(genotype=[0, 1], call_set_name='Spot'),
])
def _create_variant_with_alleles(ref=None, alts=None, start=0):
"""Creates a Variant record with specified alternate_bases."""
return variants_pb2.Variant(
reference_bases=ref,
alternate_bases=alts,
start=start,
calls=[variants_pb2.VariantCall(call_set_name=_DEFAULT_SAMPLE_NAME)])
def test_reserved_format_field_get_fn(self):
info = variants_pb2.VariantCall().info
expected = [0.2, 0.5, 0.3]
struct_utils.set_number_field(info, 'GP', expected[:])
get_fn = vcf_constants.reserved_format_field_get_fn('GP')
actual = get_fn(info, 'GP')
self.assertEqual(actual, expected)
def test_add_call_to_variant(self, probs, expected):
raw_variant = variants_pb2.Variant(
reference_name=expected.reference_name,
reference_bases=expected.reference_bases,
alternate_bases=expected.alternate_bases,
start=expected.start,
end=expected.end,
calls=[variants_pb2.VariantCall(call_set_name=_DEFAULT_SAMPLE_NAME)])
variant = postprocess_variants.add_call_to_variant(
variant=raw_variant,
predictions=probs,
sample_name=_DEFAULT_SAMPLE_NAME)
self.assertEqual(variant.reference_bases, expected.reference_bases)
self.assertEqual(variant.alternate_bases, expected.alternate_bases)
self.assertEqual(variant.reference_name, expected.reference_name)
self.assertEqual(variant.start, expected.start)
self.assertEqual(variant.end, expected.end)
self.assertAlmostEquals(variant.quality, expected.quality, places=6)
self.assertEqual(variant.filter, expected.filter)
self.assertEqual(len(variant.calls), 1)
self.assertEqual(len(expected.calls), 1)
self.assertEqual(variant.calls[0].genotype, expected.calls[0].genotype)
self.assertEqual(variant.calls[0].info['GQ'], expected.calls[0].info['GQ'])
for gl, expected_gl in zip(variant.calls[0].genotype_likelihood,
expected.calls[0].genotype_likelihood):
self.assertAlmostEquals(gl, expected_gl, places=6)
def test_exception_extract_single_variant_name(self, names):
variant_calls = [
variants_pb2.VariantCall(call_set_name=name) for name in names
]
variant = variants_pb2.Variant(calls=variant_calls)
record = deepvariant_pb2.CallVariantsOutput(variant=variant)
with self.assertRaisesRegexp(ValueError, 'Expected exactly one VariantCal'):
postprocess_variants._extract_single_sample_name(record)
def test_invalid_only_call(self, num_calls):
calls = [
variants_pb2.VariantCall(call_set_name=str(x)) for x in range(num_calls)
]
variant = variants_pb2.Variant(calls=calls)
with self.assertRaisesRegexp(ValueError,
'Expected exactly one VariantCall'):
variant_utils.only_call(variant)
def test_modify_only_call(self): variant = variants_pb2.Variant(calls=[variants_pb2.VariantCall()]) call = variant_utils.only_call(variant) call.call_set_name = 'name' call.genotype[:] = [0, 1] self.assertLen(variant.calls, 1) self.assertEqual(variant.calls[0].call_set_name, 'name') self.assertEqual(variant.calls[0].genotype, [0, 1])
def test_set_format(self, field_name, value, reader, expected):
if reader is not None:
reader = mock.Mock()
reader.field_access_cache.format_field_set_fn.return_value = (
struct_utils.set_string_field)
call = variants_pb2.VariantCall()
variantcall_utils.set_format(call, field_name, value, reader)
actual = call.info[field_name].values
self._assert_struct_lists_equal(actual, expected)
def test_variantcall_format_roundtrip(self, field_name, setter, getter,
values):
vc = variants_pb2.VariantCall()
self.assertNotIn(field_name, vc.info)
for value in values:
setter(vc, value)
if field_name not in ['GT', 'GL']:
self.assertIn(field_name, vc.info)
actual = getter(vc)
self.assertEqual(actual, value)
def _make_synthetic_hom_ref(self, variant):
"""Creates a version of variant with a hom-ref genotype.
Args:
variant: Our candidate third_party.nucleus.protos.Variant variant.
Returns:
A new Variant with the same position and alleles as variant but with a
hom-ref genotype.
"""
return variants_pb2.Variant(
reference_name=variant.reference_name,
start=variant.start,
end=variant.end,
reference_bases=variant.reference_bases,
alternate_bases=variant.alternate_bases,
calls=[variants_pb2.VariantCall(genotype=[0, 0])])
def test_get_format(self, field_name, reader, expected):
if reader is not None:
reader = mock.Mock()
reader.field_access_cache.format_field_get_fn.return_value = (
functools.partial(struct_utils.get_string_field,
is_single_field=True))
call = variants_pb2.VariantCall()
variantcall_utils.set_format(call, 'GP', [.1, .2, .7])
variantcall_utils.set_format(call, 'AD', [55, 3])
variantcall_utils.set_format(call, 'DP', 58)
variantcall_utils.set_format(call, 'GL', [-1, -3, -5.5])
variantcall_utils.set_format(call, 'GT', [0, 1])
variantcall_utils.set_format(call, 'FT', ['LowQual'])
actual = variantcall_utils.get_format(call,
field_name,
vcf_object=reader)
self.assertEqual(actual, expected)
def make_gvcfs(self, allele_count_summaries):
"""Primary interface function for computing gVCF confidence at a site.
Looks at the counts in the provided list of AlleleCountSummary protos and
returns properly-formatted Variant protos containing gVCF reference
blocks for all sites in allele_count_summaries. The returned Variant has
reference_name, start, end are set and contains a single VariantCall in the
calls field with call_set_name of options.sample_name, genotypes set to 0/0
(diploid reference), a GQ value bound in the info field appropriate to the
data in allele_count, and a MIN_DP value which is the minimum read coverage
seen in the block.
The provided allele count must have either a canonical DNA sequence base (
A, C, G, T) or be "N".
Args:
allele_count_summaries: iterable of AlleleCountSummary protos in
coordinate-sorted order. Each proto is used to get the read counts for
reference and alternate alleles, the reference position, and reference
base.
Yields:
third_party.nucleus.protos.Variant proto in
coordinate-sorted order containing gVCF records.
"""
def with_gq_and_likelihoods(summary_counts):
"""Returns summary_counts along with GQ and genotype likelihoods.
If the reference base is not in CANONICAL_DNA_BASES, both GQ and genotype
likelihoods are set to None.
Args:
summary_counts: A single AlleleCountSummary.
Returns:
A tuple of summary_counts, quantized GQ, raw GQ, and genotype
likelihoods for summary_counts where raw GQ and genotype_likelihood are
calculated by self.reference_confidence.
Raises:
ValueError: The reference base is not a valid DNA or IUPAC base.
"""
if summary_counts.ref_base not in CANONICAL_DNA_BASES:
if summary_counts.ref_base in EXTENDED_IUPAC_CODES:
# Skip calculating gq and likelihoods, since this is an ambiguous
# reference base.
quantized_gq, raw_gq, likelihoods = None, None, None
n_total = summary_counts.total_read_count
else:
raise ValueError(
'Invalid reference base={} found during gvcf '
'calculation'.format(summary_counts.ref_base))
else:
n_ref = summary_counts.ref_supporting_read_count
n_total = summary_counts.total_read_count
raw_gq, likelihoods = self.reference_confidence(n_ref, n_total)
quantized_gq = _quantize_gq(raw_gq, self.options.gq_resolution)
return _GVCF(summary_counts=summary_counts,
quantized_gq=quantized_gq,
raw_gq=raw_gq,
likelihoods=likelihoods,
read_depth=n_total)
# Combines contiguous, compatible single-bp blocks into larger gVCF blocks,
# respecting non-reference variants interspersed among them. Yields each
# combined gVCF Variant proto, in order. Compatible right now means that the
# blocks to be merged have the same non-None GQ value.
for key, combinable in itertools.groupby(
(with_gq_and_likelihoods(sc) for sc in allele_count_summaries),
key=operator.attrgetter('quantized_gq')):
if key is None:
# A None key indicates that a non-DNA reference base was encountered, so
# skip this group.
continue
combinable = list(combinable)
min_gq = min(elt.raw_gq for elt in combinable)
min_dp = min(elt.read_depth for elt in combinable)
first_record, last_record = combinable[0], combinable[-1]
call = variants_pb2.VariantCall(
call_set_name=self.options.sample_name,
genotype=[0, 0],
genotype_likelihood=first_record.likelihoods)
variantcall_utils.set_gq(call, min_gq)
variantcall_utils.set_min_dp(call, min_dp)
yield variants_pb2.Variant(
reference_name=first_record.summary_counts.reference_name,
reference_bases=first_record.summary_counts.ref_base,
alternate_bases=[vcf_constants.GVCF_ALT_ALLELE],
start=first_record.summary_counts.position,
end=last_record.summary_counts.position + 1,
calls=[call])
def test_ploidy(self, genotype, expected):
call = variants_pb2.VariantCall(genotype=genotype)
actual = variantcall_utils.ploidy(call)
self.assertEqual(actual, expected)
def test_only_call(self): expected = variants_pb2.VariantCall(call_set_name='name', genotype=[0, 1]) variant = variants_pb2.Variant(calls=[expected]) actual = variant_utils.only_call(variant) self.assertEqual(actual, expected)
class VariantUtilsTests(parameterized.TestCase):
def test_only_call(self):
expected = variants_pb2.VariantCall(call_set_name='name', genotype=[0, 1])
variant = variants_pb2.Variant(calls=[expected])
actual = variant_utils.only_call(variant)
self.assertEqual(actual, expected)
@parameterized.parameters(
0,
2,
3,
)
def test_invalid_only_call(self, num_calls):
calls = [
variants_pb2.VariantCall(call_set_name=str(x)) for x in range(num_calls)
]
variant = variants_pb2.Variant(calls=calls)
with self.assertRaisesRegexp(ValueError,
'Expected exactly one VariantCall'):
variant_utils.only_call(variant)
def test_modify_only_call(self):
variant = variants_pb2.Variant(calls=[variants_pb2.VariantCall()])
call = variant_utils.only_call(variant)
call.call_set_name = 'name'
call.genotype[:] = [0, 1]
self.assertLen(variant.calls, 1)
self.assertEqual(variant.calls[0].call_set_name, 'name')
self.assertEqual(variant.calls[0].genotype, [0, 1])
def test_decode_variants(self):
variants = [
test_utils.make_variant(start=1),
test_utils.make_variant(start=2)
]
encoded = [variant.SerializeToString() for variant in variants]
actual = variant_utils.decode_variants(encoded)
# We have an iterable, so actual isn't equal to variants.
self.assertNotEqual(actual, variants)
# Making actual a list now makes it equal.
self.assertEqual(list(actual), variants)
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))
@parameterized.parameters(
(test_utils.make_variant(alleles=['A', 'C']), 'A/C'),
(test_utils.make_variant(alleles=['A', 'C', 'T']), 'A/C,T'),
(test_utils.make_variant(alleles=['A', 'AT']), 'A/AT'),
(test_utils.make_variant(alleles=['AT', 'A']), 'AT/A'),
(test_utils.make_variant(alleles=['AT', 'A', 'CT']), 'AT/A,CT'),
)
def test_format_alleles(self, variant, expected):
self.assertEqual(variant_utils.format_alleles(variant), expected)
@parameterized.parameters(
(None, '.'),
(['.'], '.'),
(['PASS'], 'PASS'),
(['FILTER1', 'FILTER2'], 'FILTER1,FILTER2'),
(['FILTER1', 'FILTER2', 'FILTER3'], 'FILTER1,FILTER2,FILTER3'),
)
def test_format_filters(self, filters, expected):
variant = test_utils.make_variant(filters=filters)
if filters is None:
variant.ClearField('filter')
self.assertEqual(variant_utils.format_filters(variant), expected)
@parameterized.parameters(
# variant => status if we require non_ref genotype / status if we don't.
(test_utils.make_variant(alleles=['A', 'C']), True, True),
(test_utils.make_variant(alleles=['A', 'C'], gt=None), True, True),
(test_utils.make_variant(alleles=['A', 'C', 'AT']), True, True),
(test_utils.make_variant(alleles=['A']), False, False),
(test_utils.make_variant(filters=['FAIL']), False, False),
(test_utils.make_variant(gt=[-1, -1]), False, True),
(test_utils.make_variant(gt=[0, 0]), False, True),
(test_utils.make_variant(gt=[0, 1]), True, True),
(test_utils.make_variant(gt=[1, 1]), True, True),
)
def test_is_variant_call(self, variant, expected_req_non_ref,
expected_any_genotype):
# Check that default call checks for genotypes.
self.assertEqual(
variant_utils.is_variant_call(variant), expected_req_non_ref)
# Ask explicitly for genotypes to be included.
self.assertEqual(
variant_utils.is_variant_call(variant, require_non_ref_genotype=True),
expected_req_non_ref)
# Don't require non_ref genotypes.
self.assertEqual(
variant_utils.is_variant_call(variant, require_non_ref_genotype=False),
expected_any_genotype)
with self.assertRaises(Exception):
variant_utils.is_variant_call(None)
def test_is_variant_call_no_calls_are_variant(self):
def check_is_variant(variant, expected, **kwargs):
self.assertEqual(
variant_utils.is_variant_call(variant, **kwargs), expected)
no_call = test_utils.make_variant(gt=[-1, -1])
hom_ref = test_utils.make_variant(gt=[0, 0])
het = test_utils.make_variant(gt=[0, 1])
hom_var = test_utils.make_variant(gt=[1, 1])
check_is_variant(no_call, False, no_calls_are_variant=False)
check_is_variant(no_call, True, no_calls_are_variant=True)
check_is_variant(hom_ref, False, no_calls_are_variant=False)
check_is_variant(hom_ref, False, no_calls_are_variant=True)
check_is_variant(het, True, no_calls_are_variant=False)
check_is_variant(het, True, no_calls_are_variant=True)
check_is_variant(hom_var, True, no_calls_are_variant=False)
check_is_variant(hom_var, True, no_calls_are_variant=True)
@parameterized.parameters(
(test_utils.make_variant(filters=None), False),
(test_utils.make_variant(filters=['.']), False),
(test_utils.make_variant(filters=['PASS']), False),
(test_utils.make_variant(filters=['FAIL']), True),
(test_utils.make_variant(filters=['FAIL1', 'FAIL2']), True),
# These two are not allowed in VCF, but worth testing our
# code's behavior
(test_utils.make_variant(filters=['FAIL1', 'PASS']), True),
(test_utils.make_variant(filters=['FAIL1', '.']), True),
)
def test_is_filtered(self, variant, expected):
self.assertEqual(variant_utils.is_filtered(variant), expected)
@parameterized.parameters(
(test_utils.make_variant(alleles=['A', 'C']),
variant_utils.VariantType.snp),
(test_utils.make_variant(alleles=['A', 'C', 'T']),
variant_utils.VariantType.snp),
(test_utils.make_variant(alleles=['A']), variant_utils.VariantType.ref),
(test_utils.make_variant(alleles=['A', '.']),
variant_utils.VariantType.ref),
(test_utils.make_variant(alleles=['A', 'AC']),
variant_utils.VariantType.indel),
(test_utils.make_variant(alleles=['AC', 'A']),
variant_utils.VariantType.indel),
(test_utils.make_variant(alleles=['A', 'AC', 'ACC']),
variant_utils.VariantType.indel),
(test_utils.make_variant(alleles=['ACC', 'AC', 'A']),
variant_utils.VariantType.indel),
)
def test_variant_type(self, variant, expected):
self.assertEqual(variant_utils.variant_type(variant), expected)
@parameterized.parameters(
(test_utils.make_variant('chr1', 10), 'chr1:11'),
(test_utils.make_variant('chr2', 100), 'chr2:101'),
)
def test_format_position(self, variant, expected):
self.assertEqual(variant_utils.format_position(variant), expected)
@parameterized.parameters(
(test_utils.make_variant(alleles=['A', 'C']), True),
(test_utils.make_variant(alleles=['A', 'C', 'T']), True),
(test_utils.make_variant(alleles=['A', 'AT']), False),
(test_utils.make_variant(alleles=['AT', 'A']), False),
(test_utils.make_variant(alleles=['AT', 'A', 'CT']), False),
(test_utils.make_variant(alleles=['A', 'C', 'AT']), False),
(test_utils.make_variant(alleles=['A']), False),
(test_utils.make_variant(alleles=['A', '.']), False),
)
def test_is_snp(self, variant, expected):
self.assertEqual(variant_utils.is_snp(variant), expected)
@parameterized.parameters(
(test_utils.make_variant(alleles=['A', 'C']), False),
(test_utils.make_variant(alleles=['A', 'C', 'T']), False),
(test_utils.make_variant(alleles=['A', 'AT']), True),
(test_utils.make_variant(alleles=['AT', 'A']), True),
(test_utils.make_variant(alleles=['AT', 'A', 'CT']), True),
(test_utils.make_variant(alleles=['A', 'C', 'AT']), True),
(test_utils.make_variant(alleles=['A']), False),
(test_utils.make_variant(alleles=['A', '.']), False),
)
def test_is_indel(self, variant, expected):
self.assertEqual(variant_utils.is_indel(variant), expected)
@parameterized.parameters(
(test_utils.make_variant(alleles=['A', 'C']), False),
(test_utils.make_variant(alleles=['A', 'C', 'T']), True),
(test_utils.make_variant(alleles=['A', 'AT']), False),
(test_utils.make_variant(alleles=['AT', 'A']), False),
(test_utils.make_variant(alleles=['AT', 'A', 'CT']), True),
(test_utils.make_variant(alleles=['A', 'C', 'AT']), True),
)
def test_is_multiallelic(self, variant, expected):
self.assertEqual(variant_utils.is_multiallelic(variant), expected)
@parameterized.parameters(
(test_utils.make_variant(alleles=['A', 'C']), True),
(test_utils.make_variant(alleles=['A', 'C', 'T']), False),
(test_utils.make_variant(alleles=['A', 'AT']), True),
(test_utils.make_variant(alleles=['AT', 'A']), True),
(test_utils.make_variant(alleles=['AT', 'A', 'CT']), False),
(test_utils.make_variant(alleles=['AT']), False),
)
def test_is_biallelic(self, variant, expected):
self.assertEqual(variant_utils.is_biallelic(variant), expected)
@parameterized.parameters(
(['A', 'C'], ['A', 'C']),
(['AA', 'CA'], ['A', 'C']),
(['AAG', 'CAG'], ['A', 'C']),
(['AAGAG', 'CAGAG'], ['A', 'C']),
(['AACAG', 'CAGAG'], ['AAC', 'CAG']),
(['AACAC', 'CAGAG'], ['AACAC', 'CAGAG']),
(['ACT', 'A'], ['ACT', 'A']),
(['ACTCT', 'ACT'], ['ACT', 'A']),
(['ACTCT', 'A'], ['ACTCT', 'A']),
(['CAG', 'GAG'], ['C', 'G']),
# Make sure we don't reduce an allele to nothing.
(['AT', 'ATAT'], ['A', 'ATA']),
# Tests for multi-allelics.
# There's one extra T here.
(['ATT', 'AT', 'ATTT'], ['AT', 'A', 'ATT']),
# Another single base postfix where we can remove a 'G'.
(['CAG', 'GAG', 'TCG'], ['CA', 'GA', 'TC']),
# There are two extra Ts to remove.
(['ATTT', 'ATT', 'ATTTT'], ['AT', 'A', 'ATT']),
# One pair can simplify, but not the other, so nothing can reduce.
(['CAG', 'GAG', 'TCA'], ['CAG', 'GAG', 'TCA']),
# Example from b/64022627.
(['CGGCGG', 'CGG', 'CAACGG'], ['CGGC', 'C', 'CAAC']),
)
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)))
@parameterized.parameters(
(['A', 'C'], ['A', 'C'], NO_MISMATCH),
(['A', 'AC'], ['A', 'AC'], NO_MISMATCH),
(['AC', 'A'], ['AC', 'A'], NO_MISMATCH),
(['AC', 'A', 'ACT'], ['AC', 'A', 'ACT'], NO_MISMATCH),
(['AC', 'A', 'ACT'], ['AC', 'ACT', 'A'], NO_MISMATCH),
# Alleles are incompatible, so we have mismatches in both directions.
(['A', 'C'], ['A', 'T'], {TRUE_MISS, EVAL_MISS}),
(['A', 'C'], ['G', 'C'], {TRUE_MISS, EVAL_MISS}),
# Missing alts specific to eval and truth.
(['A', 'C', 'G'], ['A', 'C'], {EVAL_MISS}),
(['A', 'C'], ['A', 'C', 'G'], {TRUE_MISS}),
# Duplicate alleles.
(['A', 'C', 'C'], ['A', 'C'], {EVAL_DUP}),
(['A', 'C'], ['A', 'C', 'C'], {TRUE_DUP}),
(['A', 'C', 'C'], ['A', 'C', 'C'], {EVAL_DUP, TRUE_DUP}),
# Dups in truth, discordant alleles.
(['A', 'C'], ['A', 'G', 'G'], {TRUE_DUP, EVAL_MISS, TRUE_MISS}),
# Simplification of alleles does the right matching.
(['A', 'C'], ['AA', 'CA'], NO_MISMATCH), # trailing A.
# preceding A, doesn't simplify so it's a mismatch.
(['A', 'C'], ['AA', 'AC'], {EVAL_MISS, TRUE_MISS}),
# both training preceding A, doesn't simplify, so mismatches
(['A', 'C'], ['AAA', 'ACA'], {EVAL_MISS, TRUE_MISS}),
# # Eval has 1 of the two alt alleles, so no eval mismatch.
(['ACT', 'A'], ['ACTCT', 'ACT', 'A'], {TRUE_MISS}),
# Eval has extra unmatched alleles, so it's got a mismatch.
(['ACTCT', 'ACT', 'A'], ['ACT', 'A'], {EVAL_MISS}),
)
def test_allele_mismatch(self, a1, a2, expected):
v1 = test_utils.make_variant(alleles=a1)
v2 = test_utils.make_variant(alleles=a2)
self.assertEqual(variant_utils.allele_mismatches(v1, v2), expected)
@parameterized.parameters(
(['A', 'C'], False),
(['A', 'G'], True),
(['A', 'T'], False),
(['C', 'G'], False),
(['C', 'T'], True),
(['G', 'T'], False),
)
def test_is_transition(self, ordered_alleles, expected):
for alleles in [ordered_alleles, reversed(ordered_alleles)]:
self.assertEqual(variant_utils.is_transition(*alleles), expected)
def test_is_transition_raises_with_bad_args(self):
with self.assertRaises(ValueError):
variant_utils.is_transition('A', 'A')
with self.assertRaises(ValueError):
variant_utils.is_transition('A', 'AA')
with self.assertRaises(ValueError):
variant_utils.is_transition('AA', 'A')
@parameterized.parameters(
# alleles followed by is_insertion and is_deletion expectation
(['A', 'C'], False, False),
(['A', 'AT'], True, False),
(['A', 'ATT'], True, False),
(['AT', 'A'], False, True),
(['ATT', 'A'], False, True),
(['CAT', 'TCA'], False, False),
# These are examples where ref is not simplified, such as could occur
# a multi-allelic record, such as the following:
# alleles = AT, A, ATT, CT (1 deletion, 1 insertion, 1 SNP)
(['AT', 'A'], False, True),
(['AT', 'ATT'], True, False),
(['AT', 'CT'], False, False),
)
def test_is_insertion_deletion(self, alleles, is_insertion, is_deletion):
self.assertEqual(variant_utils.is_insertion(*alleles), is_insertion)
self.assertEqual(variant_utils.is_deletion(*alleles), is_deletion)
@parameterized.parameters(
(test_utils.make_variant(alleles=['A', 'C']), False, False),
(test_utils.make_variant(alleles=['A', 'C', 'T']), False, False),
(test_utils.make_variant(alleles=['A', 'AT']), True, False),
(test_utils.make_variant(alleles=['AT', 'A']), False, True),
(test_utils.make_variant(alleles=['AT', 'A', 'ATT']), True, True),
(test_utils.make_variant(alleles=['AT', 'A', 'CT']), False, True),
(test_utils.make_variant(alleles=['A', 'C', 'AT']), True, False),
(test_utils.make_variant(alleles=['A']), False, False),
(test_utils.make_variant(alleles=['A', '.']), False, False),
)
def test_has_insertion_deletion(self, variant, has_insertion, has_deletion):
self.assertEqual(variant_utils.has_insertion(variant), has_insertion)
self.assertEqual(variant_utils.has_deletion(variant), has_deletion)
@parameterized.parameters(
(test_utils.make_variant(gt=None), False),
(test_utils.make_variant(gt=[0, 0]), True),
(test_utils.make_variant(gt=[0, 1]), True),
(test_utils.make_variant(gt=[1, 1]), True),
(test_utils.make_variant(gt=[-1, -1]), True),
(variants_pb2.Variant(calls=[]), False),
(variants_pb2.Variant(
calls=[variants_pb2.VariantCall(call_set_name='no_geno')]), True),
(variants_pb2.Variant(calls=[
variants_pb2.VariantCall(call_set_name='no_geno'),
variants_pb2.VariantCall(call_set_name='no_geno2'),
]), True),
)
def test_has_calls(self, variant, expected):
self.assertEqual(variant_utils.has_calls(variant), expected)
def test_has_calls_raises_with_bad_inputs(self):
with self.assertRaises(Exception):
variant_utils.has_calls(None)
@parameterized.parameters(
(test_utils.make_variant(gt=None), variant_utils.GenotypeType.no_call),
(test_utils.make_variant(gt=[-1, -1]),
variant_utils.GenotypeType.no_call),
(test_utils.make_variant(gt=[0, 0]), variant_utils.GenotypeType.hom_ref),
(test_utils.make_variant(gt=[0, 1]), variant_utils.GenotypeType.het),
(test_utils.make_variant(gt=[1, 0]), variant_utils.GenotypeType.het),
(test_utils.make_variant(gt=[0, 2]), variant_utils.GenotypeType.het),
(test_utils.make_variant(gt=[2, 0]), variant_utils.GenotypeType.het),
(test_utils.make_variant(gt=[1, 1]), variant_utils.GenotypeType.hom_var),
(test_utils.make_variant(gt=[1, 2]), variant_utils.GenotypeType.het),
)
def test_genotype_type(self, variant, expected):
self.assertEqual(variant_utils.genotype_type(variant), expected)
def test_genotype_type_raises_with_bad_args(self):
with self.assertRaises(Exception):
variant_utils.genotype_type(None)
@parameterized.parameters(
(test_utils.make_variant(alleles=['A', 'C'], gt=[0, 0]), ['A', 'A']),
(test_utils.make_variant(alleles=['A', 'C'], gt=[0, 1]), ['A', 'C']),
(test_utils.make_variant(alleles=['A', 'C'], gt=[1, 0]), ['C', 'A']),
(test_utils.make_variant(alleles=['A', 'C'], gt=[1, 1]), ['C', 'C']),
(test_utils.make_variant(alleles=['A', 'C', 'T'], gt=[0, 0]), ['A', 'A']),
(test_utils.make_variant(alleles=['A', 'C', 'T'], gt=[0, 1]), ['A', 'C']),
(test_utils.make_variant(alleles=['A', 'C', 'T'], gt=[0, 2]), ['A', 'T']),
(test_utils.make_variant(alleles=['A', 'C', 'T'], gt=[1, 2]), ['C', 'T']),
(test_utils.make_variant(alleles=['A', 'C', 'T'], gt=[2, 1]), ['T', 'C']),
(test_utils.make_variant(alleles=['A', 'C', 'T'], gt=[1, 1]), ['C', 'C']),
(test_utils.make_variant(alleles=['A', 'C', 'T'], gt=[2, 2]), ['T', 'T']),
(test_utils.make_variant(alleles=['A', 'C'], gt=[-1, -1]), ['.', '.']),
)
def test_genotype_as_alleles(self, variant, expected):
self.assertEqual(variant_utils.genotype_as_alleles(variant), expected)
def test_genotype_as_alleles_raises_with_bad_inputs(self):
with self.assertRaises(Exception):
variant_utils.genotype_as_alleles(None)
with self.assertRaises(Exception):
variant_utils.genotype_as_alleles(test_utils.make_variant(gt=None))
with self.assertRaises(Exception):
variant_utils.genotype_as_alleles(
test_utils.make_variant(alleles=['A', 'C'], gt=[0, 0]), call_ix=1)
with self.assertRaises(Exception):
variant_utils.genotype_type(None)
@parameterized.parameters(
# Ref without an alt isn't gVCF.
(test_utils.make_variant(alleles=['A']), False),
# SNPs and indels aren't gVCF records.
(test_utils.make_variant(alleles=['A', 'T']), False),
(test_utils.make_variant(alleles=['A', 'AT']), False),
(test_utils.make_variant(alleles=['AT', 'T']), False),
# These are gVCF records.
(test_utils.make_variant(alleles=['A', '<*>']), True),
(test_utils.make_variant(alleles=['A', '<*>'], filters='PASS'), True),
(test_utils.make_variant(alleles=['A', '<*>'], filters='FAIL'), True),
# These are close but not exactly gVCFs.
(test_utils.make_variant(alleles=['A', '<*>', 'C']), False),
(test_utils.make_variant(alleles=['A', '<*F>']), False),
(test_utils.make_variant(alleles=['A', '<CNV>']), False),
)
def test_is_gvcf(self, variant, expected):
self.assertEqual(variant_utils.is_gvcf(variant), expected)
@parameterized.parameters(
# Variants with one ref and one alt allele.
(test_utils.make_variant(alleles=['A', 'C']), [(0, 0, 'A', 'A'),
(0, 1, 'A', 'C'),
(1, 1, 'C', 'C')]),
# Variants with one ref and two alt alleles.
(test_utils.make_variant(alleles=['A', 'C', 'G']), [(0, 0, 'A', 'A'),
(0, 1, 'A', 'C'),
(1, 1, 'C', 'C'),
(0, 2, 'A', 'G'),
(1, 2, 'C', 'G'),
(2, 2, 'G', 'G')]),
# Variants with one ref and three alt alleles.
(test_utils.make_variant(alleles=['A', 'C', 'G', 'T']),
[(0, 0, 'A', 'A'), (0, 1, 'A', 'C'), (1, 1, 'C', 'C'), (0, 2, 'A', 'G'),
(1, 2, 'C', 'G'), (2, 2, 'G', 'G'), (0, 3, 'A', 'T'), (1, 3, 'C', 'T'),
(2, 3, 'G', 'T'), (3, 3, 'T', 'T')]),
)
def test_genotype_ordering_in_likelihoods(self, variant, expected):
self.assertEqual(
list(variant_utils.genotype_ordering_in_likelihoods(variant)), expected)
@parameterized.parameters(
# Haploid.
dict(gls=[0.], allele_indices=[0], expected=0.),
dict(gls=[-1, -2], allele_indices=[1], expected=-2),
dict(gls=[-1, -2, -3], allele_indices=[2], expected=-3),
# Diploid.
dict(gls=[0.], allele_indices=[0, 0], expected=0.),
dict(gls=[-1, -2, -3], allele_indices=[0, 0], expected=-1),
dict(gls=[-1, -2, -3], allele_indices=[0, 1], expected=-2),
dict(gls=[-1, -2, -3], allele_indices=[1, 0], expected=-2),
dict(gls=[-1, -2, -3], allele_indices=[1, 1], expected=-3),
dict(gls=[-1, -2, -3, -4, -5, -6], allele_indices=[0, 0], expected=-1),
dict(gls=[-1, -2, -3, -4, -5, -6], allele_indices=[0, 1], expected=-2),
dict(gls=[-1, -2, -3, -4, -5, -6], allele_indices=[1, 0], expected=-2),
dict(gls=[-1, -2, -3, -4, -5, -6], allele_indices=[1, 1], expected=-3),
dict(gls=[-1, -2, -3, -4, -5, -6], allele_indices=[0, 2], expected=-4),
dict(gls=[-1, -2, -3, -4, -5, -6], allele_indices=[2, 0], expected=-4),
dict(gls=[-1, -2, -3, -4, -5, -6], allele_indices=[1, 2], expected=-5),
dict(gls=[-1, -2, -3, -4, -5, -6], allele_indices=[2, 1], expected=-5),
dict(gls=[-1, -2, -3, -4, -5, -6], allele_indices=[2, 2], expected=-6),
dict(gls=range(10), allele_indices=[0, 3], expected=6),
dict(gls=range(10), allele_indices=[1, 3], expected=7),
dict(gls=range(10), allele_indices=[2, 3], expected=8),
dict(gls=range(10), allele_indices=[3, 3], expected=9),
)
def test_genotype_likelihood(self, gls, allele_indices, expected):
variantcall = variants_pb2.VariantCall(genotype_likelihood=gls)
actual = variant_utils.genotype_likelihood(variantcall, allele_indices)
self.assertEqual(actual, expected)
def test_unsupported_genotype_likelihood(self):
variantcall = variants_pb2.VariantCall(genotype_likelihood=[-1, -2, -3])
with self.assertRaisesRegexp(NotImplementedError,
'only supports haploid and diploid'):
variant_utils.genotype_likelihood(variantcall, [0, 1, 1])
def test_haploid_allele_indices_for_genotype_likelihood_index(self):
for aix in six.moves.xrange(20):
allele_indices = (aix,)
ix = variant_utils.genotype_likelihood_index(allele_indices)
actual = variant_utils.allele_indices_for_genotype_likelihood_index(
ix, ploidy=1)
self.assertEqual(actual, aix)
def test_diploid_allele_indices_for_genotype_likelihood_index(self):
for aix in range(20):
for bix in range(20):
allele_indices = (aix, bix)
expected = tuple(sorted(allele_indices))
ix = variant_utils.genotype_likelihood_index(allele_indices)
actual = variant_utils.allele_indices_for_genotype_likelihood_index(
ix, ploidy=2)
self.assertEqual(actual, expected)
@parameterized.parameters(
dict(ploidy=-1),
dict(ploidy=0),
dict(ploidy=3),
)
def test_unsupported_allele_indices_for_genotype_likelihood_index(
self, ploidy):
with self.assertRaisesRegexp(NotImplementedError,
'only supported for haploid and diploid'):
variant_utils.allele_indices_for_genotype_likelihood_index(0, ploidy)
@parameterized.parameters(
dict(alt_bases=[], num_alts=0, expected=[(0, 0)]),
dict(alt_bases=['A'], num_alts=0, expected=[(0, 0)]),
dict(alt_bases=['A'], num_alts=1, expected=[(0, 1)]),
dict(alt_bases=['A'], num_alts=2, expected=[(1, 1)]),
dict(alt_bases=['A', 'C'], num_alts=0, expected=[(0, 0)]),
dict(alt_bases=['A', 'C'], num_alts=1, expected=[(0, 1), (0, 2)]),
dict(alt_bases=['A', 'C'], num_alts=2, expected=[(1, 1), (1, 2), (2, 2)]),
)
def test_allele_indices_with_num_alts(self, alt_bases, num_alts, expected):
variant = variants_pb2.Variant(alternate_bases=alt_bases)
actual = variant_utils.allele_indices_with_num_alts(
variant, num_alts, ploidy=2)
self.assertEqual(actual, expected)
@parameterized.parameters(
dict(alt_bases=['A'], num_alts=0, ploidy=1),
dict(alt_bases=['A'], num_alts=0, ploidy=3),
dict(alt_bases=['A'], num_alts=-1, ploidy=2),
dict(alt_bases=['A'], num_alts=3, ploidy=2),
)
def test_invalid_allele_indices_with_num_alts(self, alt_bases, num_alts,
ploidy):
variant = variants_pb2.Variant(alternate_bases=alt_bases)
with self.assertRaises((NotImplementedError, ValueError)):
variant_utils.allele_indices_with_num_alts(variant, num_alts, ploidy)
def test_variants_overlap(self):
v1 = test_utils.make_variant(chrom='1', alleles=['A', 'C'], start=10)
v2 = test_utils.make_variant(chrom='1', alleles=['A', 'C'], start=20)
with mock.patch.object(ranges, 'ranges_overlap') as mock_overlap:
mock_overlap.return_value = 'SENTINEL'
self.assertEqual(variant_utils.variants_overlap(v1, v2), 'SENTINEL')
mock_overlap.assert_called_once_with(
variant_utils.variant_range(v1), variant_utils.variant_range(v2))
@parameterized.parameters(
# Degenerate cases - no and one variant.
dict(sorted_variants=[],),
dict(sorted_variants=[
test_utils.make_variant(chrom='1', start=10),
],),
# Two variants on the same chromosome.
dict(
sorted_variants=[
test_utils.make_variant(chrom='1', start=10),
test_utils.make_variant(chrom='1', start=15),
],),
# The first variant has start > the second, but it's on a later chrom.
dict(
sorted_variants=[
test_utils.make_variant(chrom='1', start=15),
test_utils.make_variant(chrom='2', start=10),
],),
# Make sure the end is respected.
dict(
sorted_variants=[
test_utils.make_variant(chrom='1', start=10),
test_utils.make_variant(chrom='1', start=15),
test_utils.make_variant(chrom='1', alleles=['AA', 'A'], start=15),
],),
# Complex example with multiple chromosomes, ends, etc.
dict(
sorted_variants=[
test_utils.make_variant(chrom='1', start=10),
test_utils.make_variant(chrom='2', start=5),
test_utils.make_variant(chrom='2', alleles=['AA', 'A'], start=5),
test_utils.make_variant(chrom='2', start=6),
test_utils.make_variant(chrom='2', start=10),
test_utils.make_variant(chrom='3', start=2),
],),
)
def test_sorted_variants(self, sorted_variants):
for permutation in itertools.permutations(
sorted_variants, r=len(sorted_variants)):
# Check that sorting the permutations produced sorted.
self.assertEqual(
variant_utils.sorted_variants(permutation), sorted_variants)
# Check that variants_are_sorted() is correct, which we detect if
# the range_tuples of permutation == the range_tuples of sorted_variants.
def _range_tuples(variants):
return [variant_utils.variant_range_tuple(v) for v in variants]
self.assertEqual(
variant_utils.variants_are_sorted(permutation),
_range_tuples(permutation) == _range_tuples(sorted_variants))
@parameterized.parameters(
dict(
variant=test_utils.make_variant(
chrom='1', start=10, alleles=['A', 'C']),
expected_key='1:11:A->C'),
dict(
variant=test_utils.make_variant(
chrom='1', start=10, alleles=['A', 'G', 'C']),
sort_alleles=True,
expected_key='1:11:A->C/G'),
dict(
variant=test_utils.make_variant(
chrom='1', start=10, alleles=['A', 'G', 'C']),
sort_alleles=False,
expected_key='1:11:A->G/C'),
)
def test_variant_key(self, variant, expected_key, sort_alleles=True):
self.assertEqual(
variant_utils.variant_key(variant, sort_alleles=sort_alleles),
expected_key)
@parameterized.parameters(
dict(
field_name='AD',
value=[23, 25],
reader=None,
expected=[
struct_pb2.Value(int_value=23),
struct_pb2.Value(int_value=25)
],
),
dict(
field_name='AA',
value='C',
reader=True,
expected=[struct_pb2.Value(string_value='C')],
),
)
def test_set_info(self, field_name, value, reader, expected):
if reader is not None:
reader = mock.Mock()
reader.field_access_cache.info_field_set_fn.return_value = (
struct_utils.set_string_field)
variant = variants_pb2.Variant()
variant_utils.set_info(variant, field_name, value, reader)
actual = variant.info[field_name].values
self.assertEqual(len(actual), len(expected))
for actual_elem, expected_elem in zip(actual, expected):
self.assertEqual(actual_elem, expected_elem)
@parameterized.parameters(
dict(field_name='AD', reader=None, expected=[23, 25]),
dict(field_name='AA', reader=True, expected='C'),
dict(field_name='1000G', reader=None, expected=True),
)
def test_get_info(self, field_name, reader, expected):
if reader is not None:
reader = mock.Mock()
reader.field_access_cache.info_field_get_fn.return_value = (
functools.partial(
struct_utils.get_string_field, is_single_field=True))
variant = variants_pb2.Variant()
variant_utils.set_info(variant, 'AD', [23, 25])
variant_utils.set_info(variant, 'AA', 'C')
variant_utils.set_info(variant, '1000G', True)
variant_utils.set_info(variant, 'DB', False)
actual = variant_utils.get_info(variant, field_name, vcf_object=reader)
self.assertEqual(actual, expected)
@parameterized.parameters(
dict(alt_bases=['A', 'T'], calls=[[0, 0], [0, 1], [1, 2]],
expected=[2, 1]),
dict(alt_bases=['C'], calls=[[0, 0], [0, 0]], expected=[0]),
dict(alt_bases=[], calls=[[0, 0], [0, 0], [0, 0]], expected=[]),
)
def test_calc_ac(self, alt_bases, calls, expected):
variant = variants_pb2.Variant()
variant.alternate_bases[:] = alt_bases
for gt in calls:
variant.calls.add().genotype[:] = gt
self.assertEqual(variant_utils.calc_ac(variant), expected)
@parameterized.parameters(
dict(calls=[[0, 0], [0, 1], [1, 2]], expected=6),
dict(calls=[[0, 0], [0, 0]], expected=4),
dict(calls=[[0, 0], [-1, -1], [0, -1]], expected=3),
)
def test_calc_an(self, calls, expected):
variant = variants_pb2.Variant()
for gt in calls:
variant.calls.add().genotype[:] = gt
self.assertEqual(variant_utils.calc_an(variant), expected)
def test_unsupported_genotype_likelihood(self):
variantcall = variants_pb2.VariantCall(genotype_likelihood=[-1, -2, -3])
with self.assertRaisesRegexp(NotImplementedError,
'only supports haploid and diploid'):
variant_utils.genotype_likelihood(variantcall, [0, 1, 1])
def test_genotype_likelihood(self, gls, allele_indices, expected): variantcall = variants_pb2.VariantCall(genotype_likelihood=gls) actual = variant_utils.genotype_likelihood(variantcall, allele_indices) self.assertEqual(actual, expected)
def test_has_variation(self, genotype, expected):
call = variants_pb2.VariantCall(genotype=genotype)
actual = variantcall_utils.has_variation(call)
self.assertEqual(actual, expected)
def _simplify_variant_call(call):
"""Returns a new VariantCall with the basic fields of call."""
return variants_pb2.VariantCall(
call_set_name=call.call_set_name,
genotype=call.genotype,
info=dict(call.info)) # dict() is necessary to actually set info.
def test_is_heterozygous(self, genotype, expected):
call = variants_pb2.VariantCall(genotype=genotype)
actual = variantcall_utils.is_heterozygous(call)
self.assertEqual(actual, expected)
