def execute(self):
counter = 0
for vcf_file_name in self.vcf_file_names:
# TODO This is very similar to what we do in vcfpaste
# Should abstract out in both cases so there's less repeated code
input_stream = None
if vcf_file_name.endswith('.gz'):
input_stream = gzip.open(vcf_file_name, 'rb')
else:
input_stream = open(vcf_file_name, 'r')
samples = l_bp.parse_vcf(input_stream,
self.vcf_lines,
self.vcf_headers,
include_ref=self.include_ref)
for sample in samples:
self.vcf_headers.append("##SAMPLE=<ID=" + sample + ">\n")
self.has_genotypes = True
counter += 1
if counter > self.batchsize:
self.vcf_lines.sort(key=l_bp.vcf_line_key)
self.write_temp_file()
counter = 0
# no need to write the final batch to file
# FIXME Replace this with a new VCF class with the headers all added
self.write_header()
self.vcf_lines.sort(key=l_bp.vcf_line_key)
iterables = self.temp_files + [self.vcf_lines]
self.output_handle.writelines(merge(*iterables))
self.close_tempfiles()
def execute(self):
counter = 0
samples_name_list = [] # Avoid same sample lines -D
for vcf_file_name in self.vcf_file_names:
input_stream = InputStream(vcf_file_name, self.tempdir)
samples = l_bp.parse_vcf(input_stream,
self.vcf_lines,
self.vcf_headers,
include_ref=self.include_ref)
for sample in samples:
if sample not in samples_name_list and sample != 'VARIOUS':
self.vcf_headers.append("##SAMPLE=<ID=" + sample + ">\n")
samples_name_list.append(sample)
self.has_genotypes = True
else:
self.has_genotypes = True
counter += 1
if counter > self.batchsize:
self.vcf_lines.sort(key=l_bp.vcf_line_key)
self.write_temp_file()
counter = 0
# no need to write the final batch to file
# FIXME Replace this with a new VCF class with the headers all added
self.write_header()
self.vcf_lines.sort(key=l_bp.vcf_line_key)
iterables = self.temp_files + [self.vcf_lines]
self.output_handle.writelines(merge(*iterables))
self.close_tempfiles()
def execute(self):
counter = 0
for vcf_file_name in self.vcf_file_names:
# TODO This is very similar to what we do in vcfpaste
# Should abstract out in both cases so there's less repeated code
input_stream = None
if vcf_file_name.endswith('.gz'):
input_stream = gzip.open(vcf_file_name, 'rb')
else:
input_stream = open(vcf_file_name, 'r')
samples = l_bp.parse_vcf(input_stream, self.vcf_lines, self.vcf_headers, include_ref=self.include_ref)
for sample in samples:
self.vcf_headers.append("##SAMPLE=<ID=" + sample + ">\n")
self.has_genotypes = True
counter += 1
if counter > self.batchsize:
self.vcf_lines.sort(key=l_bp.vcf_line_key)
self.write_temp_file()
counter = 0
# no need to write the final batch to file
# FIXME Replace this with a new VCF class with the headers all added
self.write_header()
self.vcf_lines.sort(key=l_bp.vcf_line_key)
iterables = self.temp_files + [self.vcf_lines]
self.output_handle.writelines(merge(*iterables))
self.close_tempfiles()
def execute(self):
counter = 0
for vcf_file_name in self.vcf_file_names:
samples = l_bp.parse_vcf(vcf_file_name, self.vcf_lines, self.vcf_headers)
for sample in samples:
self.vcf_headers.append("##SAMPLE=<ID=" + sample + ">\n")
counter += 1
if counter > self.batchsize:
self.vcf_lines.sort(key=l_bp.vcf_line_key)
self.write_temp_file()
counter = 0
# no need to write the final batch to file
self.write_header()
self.vcf_lines.sort(key=l_bp.vcf_line_key)
iterables = self.temp_files + [self.vcf_lines]
sys.stdout.writelines(merge(*iterables))
def execute(self):
counter = 0
for vcf_file_name in self.vcf_file_names:
samples = l_bp.parse_vcf(vcf_file_name, self.vcf_lines, self.vcf_headers)
for sample in samples:
self.vcf_headers.append("##SAMPLE=<ID=" + sample + ">\n")
counter += 1
if counter > self.batchsize:
self.vcf_lines.sort(key=l_bp.vcf_line_key)
self.write_temp_file()
counter = 0
# no need to write the final batch to file
self.write_header()
self.vcf_lines.sort(key=l_bp.vcf_line_key)
iterables = self.temp_files + [self.vcf_lines]
self.output_handle.writelines(merge(*iterables))
self.close_tempfiles()
