code: def combinealleles(self, alleles):
          
          printtime('Creating combined core allele file', self.start)
          if not os.path.isfile(os.path.join(self.coregenelocation, 'core_combined.tfa')):
              with open(os.path.join(self.coregenelocation, 'core_combined.tfa'), 'w') as combinedfile:
                  # Open each allele file
                  for allele in sorted(alleles):
                      for record in SeqIO.parse(open(allele, "rU"), "fasta"):
                          # Extract the sequence record from each entry in the multifasta
                          # Remove and dashes or 'N's from the sequence data - makeblastdb can't handle sequences
                          # with gaps
                          # noinspection PyProtectedMember
                          record.seq._data = record.seq._data.replace('-', '').replace('N', '')
                          # Clear the name and description attributes of the record
                          record.name = ''
                          record.description = ''
                          # Write each record to the combined file
                          SeqIO.write(record, combinedfile, 'fasta')
docs: Creates a large multi-fasta file from all core genes in the analysis
          :param alleles: .fasta file for each core gene