def _parse_read_barcode(self, read):
for barcode in self.barcodes:
barcode_len = len(barcode)
read_barcode = read[1][0:barcode_len]
if seq_match(barcode, read_barcode, mismatches=self.mismatches):
if self.write_to_header:
read[0] += " bcd:%s desc:%s" % (barcode,
self.barcodes[barcode])
read[1] = read[1][barcode_len:]
read[3] = read[3][barcode_len:]
self.writer.write((barcode, read))
def __call__(self):
for barcode in self.barcodes:
barcode_len = len(barcode)
read_barcode = self.read[1][0:barcode_len]
if seq_match(barcode, read_barcode, mismatches=self.mismatches):
if self.write_to_header:
self.read[0] += " bcd:%s desc:%s" % (
barcode, str(self.barcodes[barcode]))
self.read[1] = self.read[1][barcode_len:]
self.read[3] = self.read[3][barcode_len:]
return (barcode, self.read)
return (None, self.read)
def _parse_read_barcode(self, read):
for barcode in self.barcodes:
barcode_len = len(barcode)
read_barcode = read[1][0:barcode_len]
if seq_match(barcode, read_barcode, mismatches=self.mismatches):
if self.write_to_header:
read[0] += " bcd:%s desc:%s" % (
barcode,
self.barcodes[barcode]
)
read[1] = read[1][barcode_len:]
read[3] = read[3][barcode_len:]
self.writer.write((barcode, read))
def __call__(self):
for barcode in self.barcodes:
barcode_len = len(barcode)
read_barcode = self.read[1][0:barcode_len]
if seq_match(barcode, read_barcode, mismatches=self.mismatches):
if self.write_to_header:
self.read[0] += " bcd:%s desc:%s" % (
barcode,
str(self.barcodes[barcode])
)
self.read[1] = self.read[1][barcode_len:]
self.read[3] = self.read[3][barcode_len:]
return (barcode, self.read)
return (None, self.read)