def create_vcf_for_annotation_all_samples(out_dir):
out_vcf = '%s/%s.vcf' % (out_dir, 'all_samples')
vcf_header = "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tALL\n"
hotspot_vars = hotspot_mongo.get_hotspot_vars()
with open(out_vcf, "w") as out_file:
out_file.write(vcf_header)
client, db = mongo.get_connection()
for var in hotspot_vars:
chrom, pos, ref, alt = var['CHROM'], var['POS'], var['REF'], var['ALT']
if not hotspot_mongo.has_annotation(chrom, pos, ref, alt, db):
chrom, pos, ref, alt = str(chrom), str(pos), ref, ",".join(alt)
gt = './.'
if gt is None:
gt = './.'
list_entry = [chrom, pos, '.', str(ref), str(alt)]
variant = list_entry + ['.', '.', '.', 'GT', gt]
out_file.write("\t".join([str(val) for val in variant]) + "\n")
client.close()
return out_vcf
def create_vcf_for_annotation(sample, type, out_dir):
sample_vars = variants_mongo.get_sample_vars(sample, type)
out_vcf = '%s/%s.vcf' % (out_dir, sample)
with open(out_vcf, "w") as out_file:
vcf_header = "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t%s\n" % sample
out_file.write(vcf_header)
client, db = mongo.get_connection()
for var in sample_vars:
chrom, pos, ref, alt = var['CHROM'], var['POS'], var['REF'], var['ALT']
if not hotspot_mongo.has_annotation(chrom, pos, ref, alt, db):
chrom, pos, ref, alt = str(chrom), str(pos), ref, ",".join(alt)
gt = var['GT_orig']
if gt is None:
gt = './.'
list_entry = [chrom, pos, '.', str(ref), str(alt)]
variant = list_entry + ['.', '.', 'DP=%s' % var['READ_DEPTH'], 'GT', gt]
out_file.write("\t".join([str(val) for val in variant]) + "\n")
client.close()
return out_vcf