def filter_out_seq_from_files(self, final_paths):
"""Filter out a sequence"""
pattern = self.options.new_parser_filter_out_seq
for path in final_paths:
if path.lower().endswith('.gz'):
f, out = gzip.open(path, 'rb'), gzip.open(path + '.temp', 'wb')
else:
f, out = open(path, 'r'), open(path + '.temp', 'w')
for rec in barcode_splitter.read_fastq(f):
rec['seq'], rec['qual'] = self.filter_out_from_seq(
pattern, rec['seq'], rec['qual'])
if rec['seq']:
#Don't write out a record if we've filtered the whole read
out.write(barcode_splitter.fastq_string(rec))
f.close()
out.close()
shutil.move(path + '.temp', path)
def filter_out_seq_from_files(self, final_paths):
"""Filter out a sequence"""
pattern = self.options.new_parser_filter_out_seq
for path in final_paths:
if path.lower().endswith('.gz'):
f, out = gzip.open(path, 'rb'), gzip.open(path + '.temp', 'wb')
else:
f, out = open(path, 'r'), open(path + '.temp', 'w')
for rec in barcode_splitter.read_fastq(f):
rec['seq'], rec['qual'] = self.filter_out_from_seq(
pattern, rec['seq'], rec['qual'])
if rec['seq']:
#Don't write out a record if we've filtered the whole read
out.write(barcode_splitter.fastq_string(rec))
f.close()
out.close()
shutil.move(path + '.temp', path)