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 = vcf.VcfReader(in_file) v1_records = list(v1_reader.iterate()) self.assertTrue(v1_records, 'Reader failed to find records') header = copy.deepcopy(v1_reader.header) writer_options = variants_pb2.VcfWriterOptions() with vcf_writer.VcfWriter.to_file(out_file, header, writer_options) as writer: for record in v1_records: writer.write(record) v2_reader = vcf.VcfReader(out_file) 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.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 __init__(self, output_path, header=None, round_qualities=False, excluded_info_fields=None, excluded_format_fields=None): """Initializer for NativeVcfWriter. Args: output_path: str. The path to which to write the VCF file. header: nucleus.genomics.v1.VcfHeader. The header that defines all information germane to the constituent variants. This includes contigs, FILTER fields, INFO fields, FORMAT fields, samples, and all other structured and unstructured header lines. round_qualities: bool. If True, the QUAL field is rounded to one point past the decimal. excluded_info_fields: list(str). A list of INFO field IDs that should not be written to the output. If None, all INFO fields are included. excluded_format_fields: list(str). A list of FORMAT field IDs that should not be written to the output. If None, all FORMAT fields are included. """ super(NativeVcfWriter, self).__init__() if header is None: header = variants_pb2.VcfHeader() writer_options = variants_pb2.VcfWriterOptions( round_qual_values=round_qualities, excluded_info_fields=excluded_info_fields, excluded_format_fields=excluded_format_fields, ) self._writer = vcf_writer.VcfWriter.to_file(output_path, header, writer_options) self.field_access_cache = VcfHeaderCache(header)
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)