def make_vcf_writer(outfile, contigs, samples, filters, round_qualities=False):
"""Creates a VcfWriter.
Args:
outfile: str. A path where we'll write our VCF file.
contigs: Iterable of learning.genomics.deepvariant.core.ContigInfo protobufs
used to populate the contigs info in the VCF header.
samples: Iterable of str. The name of the samples we will be writing to this
VCF file. The order of samples provided here must be the same as the order
of VariantCall elements in any Variant written to this writer.
filters: Iterable of learning.genomics.deepvariant.core.VcfFilterInfo
protos. Description of the filter fields that may occur in Variant protos
written to this writer. Filters can include filter descriptions that never
occur in any Variant proto, but all filter field values among all of the
written Variant protos must be provided here.
round_qualities: bool. If True, the QUAL field is rounded to one point past
the decimal.
Returns:
vcf_writer.VcfWriter.
"""
writer_options = core_pb2.VcfWriterOptions(
contigs=contigs,
sample_names=samples,
filters=filters,
round_qual_values=round_qualities)
return vcf_writer.VcfWriter.to_file(outfile, writer_options)
def test_round_trip_vcf(self, test_datum_name):
# Round-trip variants through writing and reading:
# 1. Read variants v1 from VcfReader;
# 2. Write v1 to vcf using our VcfWriter;
# 3. Read back in using VcfReader -- v2;
# 4. compare v1 and v2.
in_file = test_utils.genomics_core_testdata(test_datum_name)
out_file = test_utils.test_tmpfile('output_' + test_datum_name)
v1_reader = genomics_io.make_vcf_reader(in_file, use_index=False)
v1_records = list(v1_reader.iterate())
self.assertTrue(v1_records, 'Reader failed to find records')
writer_options = core_pb2.VcfWriterOptions(
contigs=v1_reader.contigs,
sample_names=v1_reader.samples,
filters=v1_reader.filters)
with vcf_writer.VcfWriter.to_file(out_file, writer_options) as writer:
for record in v1_records:
writer.write(record)
v2_reader = genomics_io.make_vcf_reader(out_file, use_index=False)
v2_records = list(v2_reader.iterate())
self.assertEqual(v1_records, v2_records,
'Round-tripped variants not as expected')
def setUp(self):
self.out_fname = test_utils.test_tmpfile('output.vcf')
self.options = core_pb2.VcfWriterOptions(
contigs=[
core_pb2.ContigInfo(name='Chr1', n_bases=50, pos_in_fasta=0),
core_pb2.ContigInfo(name='Chr2', n_bases=25, pos_in_fasta=1),
],
sample_names=['Fido', 'Spot'],
filters=[])
self.writer = vcf_writer.VcfWriter.to_file(self.out_fname, self.options)
self.variant = test_utils.make_variant(
chrom='Chr1', start=10, alleles=['A', 'C'])
self.variant.calls.add(genotype=[0, 0], call_set_name='Fido')
self.variant.calls.add(genotype=[0, 1], call_set_name='Spot')
def test_writing_canned_variants(self):
"""Tests writing all the variants that are 'canned' in our tfrecord file."""
# This file is in the TF record format
tfrecord_file = test_utils.genomics_core_testdata(
'test_samples.vcf.golden.tfrecord')
writer_options = core_pb2.VcfWriterOptions(
contigs=[
core_pb2.ContigInfo(name='chr1', n_bases=248956422),
core_pb2.ContigInfo(name='chr2', n_bases=242193529),
core_pb2.ContigInfo(name='chr3', n_bases=198295559),
core_pb2.ContigInfo(name='chrX', n_bases=156040895)
],
sample_names=['NA12878_18_99'],
filters=[
core_pb2.VcfFilterInfo(id='LowQual'),
core_pb2.VcfFilterInfo(id='VQSRTrancheINDEL95.00to96.00'),
core_pb2.VcfFilterInfo(id='VQSRTrancheINDEL96.00to97.00'),
core_pb2.VcfFilterInfo(id='VQSRTrancheINDEL97.00to99.00'),
core_pb2.VcfFilterInfo(id='VQSRTrancheINDEL99.00to99.50'),
core_pb2.VcfFilterInfo(id='VQSRTrancheINDEL99.50to99.90'),
core_pb2.VcfFilterInfo(id='VQSRTrancheINDEL99.90to99.95'),
core_pb2.VcfFilterInfo(id='VQSRTrancheINDEL99.95to100.00+'),
core_pb2.VcfFilterInfo(id='VQSRTrancheINDEL99.95to100.00'),
core_pb2.VcfFilterInfo(id='VQSRTrancheSNP99.50to99.60'),
core_pb2.VcfFilterInfo(id='VQSRTrancheSNP99.60to99.80'),
core_pb2.VcfFilterInfo(id='VQSRTrancheSNP99.80to99.90'),
core_pb2.VcfFilterInfo(id='VQSRTrancheSNP99.90to99.95'),
core_pb2.VcfFilterInfo(id='VQSRTrancheSNP99.95to100.00+'),
core_pb2.VcfFilterInfo(id='VQSRTrancheSNP99.95to100.00'),
])
variant_records = list(
io_utils.read_tfrecords(tfrecord_file, proto=variants_pb2.Variant))
out_fname = test_utils.test_tmpfile('output.vcf')
with vcf_writer.VcfWriter.to_file(out_fname, writer_options) as writer:
for record in variant_records[:5]:
writer.write(record)
# Check: are the variants written as expected?
# pylint: disable=line-too-long
expected_vcf_content = [
'##fileformat=VCFv4.2\n',
'##FILTER=<ID=PASS,Description="All filters passed">\n',
'##FILTER=<ID=LowQual,Description="">\n',
'##FILTER=<ID=VQSRTrancheINDEL95.00to96.00,Description="">\n',
'##FILTER=<ID=VQSRTrancheINDEL96.00to97.00,Description="">\n',
'##FILTER=<ID=VQSRTrancheINDEL97.00to99.00,Description="">\n',
'##FILTER=<ID=VQSRTrancheINDEL99.00to99.50,Description="">\n',
'##FILTER=<ID=VQSRTrancheINDEL99.50to99.90,Description="">\n',
'##FILTER=<ID=VQSRTrancheINDEL99.90to99.95,Description="">\n',
'##FILTER=<ID=VQSRTrancheINDEL99.95to100.00+,Description="">\n',
'##FILTER=<ID=VQSRTrancheINDEL99.95to100.00,Description="">\n',
'##FILTER=<ID=VQSRTrancheSNP99.50to99.60,Description="">\n',
'##FILTER=<ID=VQSRTrancheSNP99.60to99.80,Description="">\n',
'##FILTER=<ID=VQSRTrancheSNP99.80to99.90,Description="">\n',
'##FILTER=<ID=VQSRTrancheSNP99.90to99.95,Description="">\n',
'##FILTER=<ID=VQSRTrancheSNP99.95to100.00+,Description="">\n',
'##FILTER=<ID=VQSRTrancheSNP99.95to100.00,Description="">\n',
'##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n',
'##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n',
'##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth of all '
'passing filters reads.">\n',
'##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth of all '
'passing filters reads for each allele.">\n',
'##FORMAT=<ID=VAF,Number=A,Type=Float,Description=\"Variant allele '
'fractions.">\n',
'##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype '
'likelihoods, log10 encoded">\n',
'##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Genotype '
'likelihoods, Phred encoded">\n',
'##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of '
'the interval">\n', '##contig=<ID=chr1,length=248956422>\n',
'##contig=<ID=chr2,length=242193529>\n',
'##contig=<ID=chr3,length=198295559>\n',
'##contig=<ID=chrX,length=156040895>\n',
'#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNA12878_18_99\n',
'chr1\t13613\t.\tT\tA\t39.88\tVQSRTrancheSNP99.90to99.95\t.\tGT:GQ:DP:AD:PL\t0/1:16:4:1,3:68,0,16\n',
'chr1\t13813\t.\tT\tG\t90.28\tPASS\t.\tGT:GQ:DP:AD:PL\t1/1:9:3:0,3:118,9,0\n',
'chr1\t13838\trs28428499\tC\tT\t62.74\tPASS\t.\tGT:GQ:DP:AD:PL\t1/1:6:2:0,2:90,6,0\n',
'chr1\t14397\trs756427959\tCTGT\tC\t37.73\tPASS\t.\tGT:GQ:DP:AD:PL\t0/1:75:5:3,2:75,0,152\n',
'chr1\t14522\t.\tG\tA\t49.77\tVQSRTrancheSNP99.60to99.80\t.\tGT:GQ:DP:AD:PL\t0/1:78:10:6,4:78,0,118\n'
]
# pylint: enable=line-too-long
with tf.gfile.GFile(out_fname, 'r') as f:
self.assertEqual(f.readlines(), expected_vcf_content)