def test_doesnt_give_a_flying_damn_about_spurious_filter_header(self):
chrom = "22"
variant = Variant(chrom, 11, "A", "C")
schema = Schema()
complex_filter_name = '.+-*\\/~@?!%^&><=\"\'(){}[]_|'
schema.set_filter(complex_filter_name, 'unusual characters')
gv_builder = VCFBuilder(join(self.work_dir, "genotype.vcf"),
schema=schema)
gv_builder.with_record_from_variant(variant,
filters={complex_filter_name})
gv_builder.build().index()
driver = SVCDriver(self)
dodgy_sample = "bobs_your_uncle"
driver.with_ref_sequence(
"ACGCCCCCTGCAAAAAAAAAA", chrom=chrom, pos_from=0).with_read(
"...........C.........",
n_fwd=5,
n_rev=5,
chrom=chrom,
sample_name=dodgy_sample).with_genotype_alleles(
gv_builder.compressed_filename)
expect = driver.call(expected_success=True)
expect .with_output_vcf()\
.has_record_for_variant(variant)\
.with_sample(dodgy_sample)\
.has_genotype("1/1")
def test_should_write_filter_in_expected_format(self):
mock_file = StringIO()
schema = Schema()
schema.set_filter('key', 'a filter')
writer = VCFWriter(mock_file)
writer.write_header(schema)
expected_file = '##fileformat=VCFv4.2\n' \
'##FILTER=<ID=key,Description="a filter">\n' \
'#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n'
self.assertEqual(expected_file, mock_file.getvalue())
def test_should_parse_valid_filter_header_fields(self):
lines = [
'##fileformat=VCFv4.2\n',
'##FILTER=<ID=key,Description="description">\n',
'#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n',
]
reader = VCFReader(iter(lines))
header = reader.read_header()
expected = Schema()
expected.set_filter('key', 'description')
self.assertEqual(expected, header)
def wecall_schema(file_date=None,
reference=None,
contigs=None,
add_ref_calls=True,
format='4.2'):
schema = Schema()
if file_date is not None:
schema.file_metadata['fileDate'] = file_date
if reference is not None:
schema.file_metadata['reference'] = reference
app_name = 'weCall'
version_number = '2.0.1'
app = {'4.1': None, '4.2': app_name}[format]
version = {'4.1': None, '4.2': version_number}[format]
schema.file_metadata[
'disclaimer'] = 'This software is in beta-testing. Results generated using the software are confidential and should only be used for research purposes in accordance with the legal agreement with Genomics plc.' # noqa
schema.file_metadata['source'] = '{application!s} v{version!s}'.format(
application=app_name, version=version_number) # noqa
schema.set_info_data(
'ABPV', 'A', 'Float',
'Allele bias P-value; probability that fraction of reads supporting alt allele (VC) amongst read depth (DP) is '
'more extreme than expected assuming a beta-binomial distribution.',
app, version) # noqa
schema.set_info_data(
'MQ', 'A', 'Float',
'Root mean square of mapping quality of reads supporting each alternative allele.',
app, version) # noqa
schema.set_info_data(
'PP', 'A', 'Integer',
'Posterior probability (phred scaled) that this variant does not segregate.',
app, version) # noqa
schema.set_info_data(
'SBPV', 'A', 'Float',
'Strand bias P-value; probability that the fraction of forward reads (VCF) amongst reads supporting alt allele '
'(VC) is more extreme than expected assuming a beta-binomial distribution.',
app, version) # noqa
schema.set_info_data('DP', '1', 'Integer',
'Total depth of read coverage at this locus.', app,
version)
schema.set_info_data(
'DPF', '1', 'Integer',
'Total probabilistic depth of forward read coverage at this locus (sum of probabilities of each read supporting '
'the variant).', app, version) # noqa
schema.set_info_data(
'DPR', '1', 'Integer',
'Total probabilistic depth of reverse read coverage at this locus (sum of probabilities of each read supporting '
'the variant).', app, version) # noqa
schema.set_info_data(
'VC', 'A', 'Integer',
'Total probabilistic number of reads supporting each alternative allele (sum of probabilities of each read '
'supporting the allele).', app, version) # noqa
schema.set_info_data(
'VCF', 'A', 'Integer',
'Total probabilistic number of forward reads supporting each alternative allele (sum of probabilities of '
'each read supporting the allele).', app, version) # noqa
schema.set_info_data(
'VCR', 'A', 'Integer',
'Total probabilistic number of reverse reads supporting each alternative allele (sum of probabilities of each '
'read supporting the allele).', app, version) # noqa
schema.set_info_data(
'QD', 'A', 'Float',
'Ratio of phred-scaled posterior probability (PP) to number of supporting reads for each allele (VC).',
app, version) # noqa
schema.set_info_data(
'BR', 'A', 'Float',
'The median of the per-read min base quality (within a interval of the locus) taken over reads supporting '
'each allele.', app, version) # noqa
schema.set_sample_data(
'GT', '1', 'String',
'Genotypes of reference and alternative alleles in order listed.')
if add_ref_calls:
schema.set_info_data('BEG', '1', 'Integer',
'Start position of reference call block.', app,
version)
schema.set_info_data(
'END', '1', 'Integer',
'End position of reference call block (inclusive).', app, version)
schema.set_info_data('LEN', '1', 'Integer',
'Length of reference call block.', app, version)
schema.set_sample_data(
'MIN_DP', '1', 'Integer',
'Minimum read coverage observed within the reference block.')
schema.set_sample_data(
'GQ', '1', 'Integer',
'Phred-scaled genotype quality (i.e. posterior probability that the genotype call is incorrect).'
) # noqa
schema.set_sample_data(
'PQ', '1', 'Integer',
'Phred-scaled phase quality (i.e. posterior probability that the phasing is incorrect).'
) # noqa
schema.set_sample_data('PS', '1', 'String', 'Phase set id.') # noqa
schema.set_sample_data(
'PL', 'G', 'Integer',
"Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification."
) # noqa
schema.set_sample_data(
'DP', '1', 'Integer',
'Number of reads overlapping the variant site (i.e. INFO::DP split out by sample). For reference calls the average depth (rounded to the nearest integer) over the region is reported.'
) # noqa
schema.set_sample_data(
'AD', '.', 'Integer',
'Probabilistic allelic depths for the ref and alt alleles in the order listed (i.e. INFO::VC split out by sample).'
) # noqa
schema.set_sample_data(
'VAF', 'A', 'Float',
'Probabilistic variant allelic frequencies for each alt allele (FORMAT::AD / FORMAT::DP).'
) # noqa
schema.set_filter(
'AB',
'Allele Bias: Indicates lower number of reads supporting variant than expected (any of INFO::ABPV < 0.009).'
) # noqa
schema.set_filter(
'SB',
'Strand Bias: Indicates imbalance between number of forward and reverse reads supporting variant (any of INFO::SBPV < 0.01).'
) # noqa
schema.set_filter(
'AB+SB',
'Allele + Strand Bias: Indicates that both the AB and SB filters are close to being triggered (any of INFO::ABPV + INFO::SBPV < 0.07).'
) # noqa
schema.set_filter(
'MQ',
'low Mapping Quality: Indicates presence of low mapping quality (any of INFO::MQ < 25).'
) # noqa
schema.set_filter(
'QD',
'Quality over Depth: Indicates low quality relative to number of supporting reads (any of INFO::QD < 3.5 for Indels or INFO::QD < 8 otherwise).'
) # noqa
schema.set_filter(
'BR',
'Bad Reads: Indicates low quality base pairs on reads in the vicinity of variant locus (any of INFO::BR < 0).'
) # noqa
schema.set_filter(
'NC',
'Not called: Indicates a variant that was not positively genotyped in any sample.'
) # noqa
schema.set_filter(
'LQ',
'Low Quality: Indicates a low variant quality (any of INFO::PP < 10).'
) # noqa
if contigs is not None:
for contig_name, contig_data in contigs.items():
schema.set_contig(contig_name, **contig_data)
return schema
