def single_entry_handling(gene, genomicHGVS):
check_file_status()
vcf_utils.validate_gene(gene, genes_set)
variants_list = [[gene, genomicHGVS]]
output_file = os.path.join(
json_data['output'],
''.join(['{}-{}'.format(gene, genomicHGVS), '.vcf']))
process_variants(variants_list, output_file)
def test_validate_gene(self):
test_genes = {
"correct": ["ALK", "BRCA1"],
"incorrect": ["POLOP", "GHOSH"]
}
for gene in test_genes["correct"]:
self.assertFalse(vcf_utils.validate_gene(gene, genes_set))
for gene in test_genes["incorrect"]:
self.assertTrue(vcf_utils.validate_gene(gene, genes_set))
def create_non_substitution_entries(output, others):
for variant in others:
ENTRY = copy.deepcopy(json_data['vcf_entry'])
gene, gHGVS = [variant[0], variant[1]]
isGeneInvalid = vcf_utils.validate_gene(gene, genes_set)
if isGeneInvalid:
print(messages['error_messages']['INVALID_GENE'].format(gene))
print(messages['error_messages']['VARIANT_SKIPPED'].format(
gene, gHGVS))
continue
chrom = vcf_utils.get_chromosome(gene, gene_chrom_dict)
if 'delins' in gHGVS:
(pos, ref,
alt) = variant_functions.delins_handling(gHGVS, chrom, genome)
elif 'dup' in gHGVS:
(pos, ref, alt) = variant_functions.duplication_handling(
gHGVS, chrom, genome)
elif 'del' in gHGVS and 'ins' not in gHGVS:
(pos, ref,
alt) = variant_functions.deletion_handling(gHGVS, chrom, genome)
else:
(pos, ref,
alt) = variant_functions.insertion_handling(gHGVS, chrom, genome)
ENTRY['#CHROM'] = chrom
ENTRY['POS'] = pos
ENTRY['REF'] = ref
ENTRY['ALT'] = alt
field_values = [str(ENTRY[i]) for i in json_data['vcf_header']]
output.write(sep.join(field_values))
output.write('\n')
def create_substitution_entries(output, subs):
for variant in subs:
ENTRY = copy.deepcopy(json_data['vcf_entry'])
gene, gHGVS = variant.values()
isGeneInvalid = vcf_utils.validate_gene(gene, genes_set)
if isGeneInvalid:
print(messages['error_messages']['INVALID_GENE'].format(gene))
print(messages['error_messages']['VARIANT_SKIPPED'].format(
gene, gHGVS))
continue
ref_alt = re.findall(r'[A-Z]', gHGVS)
position = ''.join(re.findall(r'[0-9]+', gHGVS))
ref, alt = [ref_alt[0], ref_alt[1]]
chromosome = vcf_utils.get_chromosome(gene, gene_chrom_dict)
(isPositionInvalid, actual_ref) = vcf_utils.validate_position(
{
"chrom": chromosome,
"pos": position,
"ref": ref
}, genome)
if isPositionInvalid:
print(messages['error_messages']['INVALID_GENOMIC_HGVS'].format(
gHGVS))
print(messages['error_messages']['REF_MISMATCH'].format(
position, ref, actual_ref))
print(messages['error_messages']['VARIANT_SKIPPED'].format(
gene, gHGVS))
continue
ENTRY['#CHROM'] = chromosome
ENTRY['POS'] = position
ENTRY['REF'] = ref
ENTRY['ALT'] = alt
field_values = [ENTRY[i] for i in json_data['vcf_header']]
output.write(sep.join(field_values))
output.write('\n')