# write the chr\tpos\t... line
combined_f.write(vcf_list[0].header)
# Write the variants
for v_key in combined_variants:
callers_indexes = variant_to_vcf_dict[v_key]
callers_names = [callers[i] for i in callers_indexes]
info_dict = OrderedDict()
for i in callers_indexes:
# Combine the selected information in the dictionary
info_dict.update(vcf_list[i].variants[v_key].info)
i = callers_indexes[0]
combined_variant = Variant.combine_info(
vcf_list[i].variants[v_key], columns_to_keep, callers_names,
info_dict)
combined_f.write(Variant.write(combined_variant))
else:
# Process each vcf and extract the information from the selected columns
vcf_list = [
NormalisedVcf(vcf).process_somatic_vcf(columns_to_keep, normal_id,
tumor_id) for vcf in vcf_in
]
# Combine the variants into a list
combined_variants, variant_to_vcf_dict = [], dd(list)
callers = [vcf.caller for vcf in vcf_list]
if args.priority:
if set(callers) != set(args.priority):
# Write the header lines
if line.startswith('##'):
f_vcf_out.write(line)
elif line.startswith('#'):
for new_line in BAM_STATS_LINES:
f_vcf_out.write(new_line)
f_vcf_out.write(line)
# Calcualte bam stats for variants
else:
variant = Variant().read_variant(line)
mpileup = mpileup_dict.get(
'\t'.join([variant.chr, variant.pos]), '')
bam_stats = variant.cal_bam_stats(mpileup)
variant = variant.add_bam_stats(bam_stats)
f_vcf_out.write(variant.write())
else:
normal_mpileup_dict = create_mpileup_dict(normal_mpileup)
tumor_mpileup_dict = create_mpileup_dict(tumor_mpileup)
with open(vcf_in, 'r') as vcf_i, open(vcf_out, 'w') as vcf_o:
for line in vcf_i:
if line.startswith('#'):
if line.startswith('##'):
vcf_o.write(line)
else:
for new_line in BAM_STATS_LINES:
vcf_o.write(new_line)
line = line.split()
with open(args.input, "r") as f_vcf, open(args.output, "w") as f_vcf_out:
for line in f_vcf:
# Write the header lines
if line.startswith("##"):
f_vcf_out.write(line)
elif line.startswith("#"):
f_vcf_out.write(AF_HEADER_LINE)
f_vcf_out.write(line)
# Calcualte AF for strelka variants
else:
variant = Variant().read_variant(line)
if "DP" in variant.format.keys():
if variant.format["DP"] == "0":
variant.format["AF"] = "."
else:
variant.format["AF"] = ",".join([
str(round(float(i) / float(variant.format["DP"]), 2))
for i in variant.format["AD"].split(",")[1:]
])
else:
variant.format["DP"] = variant.format["DPI"]
if variant.format["DPI"] == "0":
variant.format["AF"] = "."
else:
variant.format["AF"] = ",".join([
str(round(float(i) / float(variant.format["DPI"]), 2))
for i in variant.format["AD"].split(",")[1:]
])
f_vcf_out.write(variant.write())
