def process_vcf(self, cols):
"""Build object from vcf
"""
vcf = open(self.name, 'r')
info_dict, format_dict = {}, {}
# Read the meta-information lines from the vcf
for i, line in enumerate(vcf):
# Handle exceptions: the AF will be calcualted regardless;
if line.startswith('##FORMAT=<ID=AF'):
pass
# Select the INFO/FORMAT lines
elif line.startswith('##FORMAT'):
vcf_header = VcfHeader(line)
format_dict.update({vcf_header.meta_id: vcf_header})
elif line.startswith('##INFO'):
vcf_header = VcfHeader(line)
info_dict.update({vcf_header.meta_id: vcf_header})
# Keep other meta-info lines
elif line.startswith('##'):
if line.startswith('##source='):
self.caller = line.replace('##source=', '').strip()
self.meta_info.append(line)
else:
break
# Only extract the (filtered) DP in the format
if "DP" in info_dict.keys() and format_dict.keys():
info_dict.pop("DP", None)
if not self.caller:
sys.exit("Cannot identify caller from file {}\nPlease add caller \
identify line '##source=(caller name)' to vcf header"
.format(self.name))
# When user specify the AF and vcf does not have, try to calculate that
# for the user
if ('AF' in cols) and ('AF' not in info_dict.keys()):
vcf_header = VcfHeader(AF_LINE)
info_dict.update({vcf_header.meta_id: vcf_header})
# Select the columns from INFO/FORMAT
info_cols, format_cols = extract_cols(info_dict, format_dict, cols)
# Add the INFO line (with caller) / FORMAT (unchanged) to header_list
self.meta_info += [VcfHeader.write(VcfHeader.add_caller(v,
self.caller)) for k, v in info_cols.items()]
self.meta_info += [VcfHeader.write(v) for k, v in format_cols.items()]
self.header = line
# Continue to read the file, this time the variants
for j, line in enumerate(vcf):
variant = Variant().process_variant(line, caller=self.caller)
if variant.alt == '*':
print("Warning: Vcf {} line {} has variant with alt=*".format(self.caller, str(i+j+1)))
cleaned_variant = Variant.select_info(variant, info_cols, format_cols)
# The dictionary is query by chr\tpos\tref\talt
self.variants.update({cleaned_variant.variant_key: cleaned_variant})
return self
def process_somatic_vcf(self, cols, nid, tid):
"""Process somatic vcf, with normal and tumor sample id provided
"""
vcf = open(self.name, 'r')
info_dict, format_dict = od(), od()
# Read the meta-information lines from the vcf
for i, line in enumerate(vcf):
# Handle exceptions: skip the AF and DP in INFO
if (line.startswith('##INFO=<ID=DP') or
line.startswith('##INFO=<ID=AF')):
pass
# Select the INFO/FORMAT lines
elif line.startswith('##FORMAT'):
vcf_header = VcfHeader(line)
format_dict.update({vcf_header.meta_id: vcf_header})
elif line.startswith('##INFO'):
vcf_header = VcfHeader(line)
info_dict.update({vcf_header.meta_id: vcf_header})
# Keep other meta-info lines
elif line.startswith('##'):
if line.startswith('##source='):
self.caller = line.replace('##source=', '').strip()
self.meta_info.append(line)
else:
break
if not self.caller:
sys.exit("Cannot locate caller from file {}\nPlease add caller \
identify line '##source=(caller name)' to vcf header"
.format(self.name))
# Select the columns from INFO/FORMAT
info_cols, format_cols = extract_cols_somatic(info_dict, format_dict,
cols)
# Add the INFO line (with caller) / FORMAT (unchanged) to header_list
self.meta_info += [VcfHeader.write(VcfHeader.add_caller(v,
self.caller)) for k, v in info_cols.items()]
self.meta_info += [VcfHeader.write(v) for k, v in format_cols.items()]
self.header = line
# find the location of normal / tumor column index
if self.caller == 'strelka':
normal_index, tumor_index = (self.header.split().index('NORMAL'),
self.header.split().index('TUMOR'))
elif (self.header.split()[9] == nid) and \
(self.header.split()[10] == tid):
normal_index, tumor_index = 9, 10
elif (self.header.split()[10] == nid) and \
(self.header.split()[9] == tid):
normal_index, tumor_index = 10, 9
else:
sys.exit("Normal sample id [{}] or tumor sample id [{}] didn't match with file {}: [{}], [{}]"
.format(nid, tid, self.name, self.header.split()[9], self.header.split()[10]))
# Continue to read the file, this time the variants
for j, line in enumerate(vcf):
variant = Variant().process_somatic_variant(
line, self.caller, normal_index, tumor_index)
if variant.alt == '*':
print("Warning: Line {} contains variant with alt=*".format(str(i+j+1)))
cleaned_variant = Variant.select_info(variant, info_cols, format_cols,
caller=self.caller, somatic=True)
# The dictionary is query by chr\tpos\tref\talt
self.variants.update({cleaned_variant.variant_key: cleaned_variant})
return self
