def fixGeneral(self):
# main logic here
bases = re.compile('G|A|T|C')
# find boundaries
match_obj = bases.search(self.alignedRecords[0].seq.tostring())
start_index = match_obj.start()
cdr_len = len(bases.findall(self.alignedRecords[0].seq.tostring()))
# copy in original cdr
localFixedRecord = ''.join([
self.alignedRecords[1].seq.tostring()[0:start_index],
self.alignedRecords[0].seq.tostring()[(start_index):(start_index+cdr_len)],
self.alignedRecords[1].seq.tostring()[(start_index+cdr_len):]
])
# remove any '-' from sequence. Possible if alignment created '-' in CDR
localFixedRecord = SeqRecord(Seq(localFixedRecord.replace('-',''),DNAAlphabet),id="fixedSequence")
if not (localFixedRecord.seq.tostring() == self.fixedRecord.seq.tostring()):
self.reportHandle.write('Using alignment between CDR and sequence:\n')
self.reportHandle.write(self.alignedRecords[0].seq.tostring())
self.reportHandle.write('\n')
self.reportHandle.write(self.alignedRecords[1].seq.tostring())
self.reportHandle.write('\n')
self.reportHandle.write('The sequence was corrected to be:\n')
self.reportHandle.write(localFixedRecord.seq.tostring())
self.reportHandle.write('\n')
self.cdrModifications = True
self.fixedRecord = localFixedRecord
