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 write_variant_to_tempfile(self, variant): output_path = test_utils.test_tmpfile('test.vcf') header = variants_pb2.VcfHeader( contigs=[reference_pb2.ContigInfo(name='20')], sample_names=[call.call_set_name for call in variant.calls], formats=[ variants_pb2.VcfFormatInfo( id='DP', number='1', type='Integer', description='Read depth'), variants_pb2.VcfFormatInfo( id='AD', number='R', type='Integer', description='Read depth for each allele') ]) writer = vcf.VcfWriter(output_path, header=header) with writer: writer.write(variant) return output_path
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 = variants_pb2.VcfWriterOptions() header = variants_pb2.VcfHeader( contigs=[ reference_pb2.ContigInfo(name='chr1', n_bases=248956422), reference_pb2.ContigInfo(name='chr2', n_bases=242193529), reference_pb2.ContigInfo(name='chr3', n_bases=198295559), reference_pb2.ContigInfo(name='chrX', n_bases=156040895) ], sample_names=['NA12878_18_99'], filters=[ variants_pb2.VcfFilterInfo( id='PASS', description='All filters passed'), variants_pb2.VcfFilterInfo(id='LowQual', description=''), variants_pb2.VcfFilterInfo(id='VQSRTrancheINDEL95.00to96.00'), variants_pb2.VcfFilterInfo(id='VQSRTrancheINDEL96.00to97.00'), variants_pb2.VcfFilterInfo(id='VQSRTrancheINDEL97.00to99.00'), variants_pb2.VcfFilterInfo(id='VQSRTrancheINDEL99.00to99.50'), variants_pb2.VcfFilterInfo(id='VQSRTrancheINDEL99.50to99.90'), variants_pb2.VcfFilterInfo(id='VQSRTrancheINDEL99.90to99.95'), variants_pb2.VcfFilterInfo(id='VQSRTrancheINDEL99.95to100.00+'), variants_pb2.VcfFilterInfo(id='VQSRTrancheINDEL99.95to100.00'), variants_pb2.VcfFilterInfo(id='VQSRTrancheSNP99.50to99.60'), variants_pb2.VcfFilterInfo(id='VQSRTrancheSNP99.60to99.80'), variants_pb2.VcfFilterInfo(id='VQSRTrancheSNP99.80to99.90'), variants_pb2.VcfFilterInfo(id='VQSRTrancheSNP99.90to99.95'), variants_pb2.VcfFilterInfo(id='VQSRTrancheSNP99.95to100.00+'), variants_pb2.VcfFilterInfo(id='VQSRTrancheSNP99.95to100.00'), ], infos=[ variants_pb2.VcfInfo( id='END', number='1', type='Integer', description='Stop position of the interval') ], formats=[ variants_pb2.VcfFormatInfo( id='GT', number='1', type='String', description='Genotype'), variants_pb2.VcfFormatInfo( id='GQ', number='1', type='Integer', description='Genotype Quality'), variants_pb2.VcfFormatInfo( id='DP', number='1', type='Integer', description='Read depth of all passing filters reads.'), variants_pb2.VcfFormatInfo( id='MIN_DP', number='1', type='Integer', description='Minimum DP observed within the GVCF block.'), variants_pb2.VcfFormatInfo( id='AD', number='R', type='Integer', description= 'Read depth of all passing filters reads for each allele.'), variants_pb2.VcfFormatInfo( id='VAF', number='A', type='Float', description='Variant allele fractions.'), variants_pb2.VcfFormatInfo( id='PL', number='G', type='Integer', description='Genotype likelihoods, Phred encoded'), ], ) 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, header, 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', '##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of ' 'the interval">\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=MIN_DP,Number=1,Type=Integer,Description="Minimum DP ' 'observed within the GVCF block.">\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=PL,Number=G,Type=Integer,Description="Genotype ' 'likelihoods, Phred encoded">\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 gfile.GFile(out_fname, 'r') as f: self.assertEqual(f.readlines(), expected_vcf_content)
id='VALIDATED', number='0', type=FLAG_TYPE, description='Validated by follow-up experiment'), variants_pb2.VcfInfo( id='1000G', number='0', type=FLAG_TYPE, description='1000 Genomes membership'), ] # Reserved FORMAT field definitions, as per the VCF 4.3 spec. RESERVED_FORMAT_FIELDS = [ variants_pb2.VcfFormatInfo( id='AD', number='R', type=INTEGER_TYPE, description='Read depth for each allele'), variants_pb2.VcfFormatInfo( id='ADF', number='R', type=INTEGER_TYPE, description='Read depth for each allele on the ' 'forward strand'), variants_pb2.VcfFormatInfo( id='ADR', number='R', type=INTEGER_TYPE, description='Read depth for each allele on the ' 'reverse strand'), variants_pb2.VcfFormatInfo(