dictionary[key] = valuelist[0:10] from pprint import pprint fielddict_file = open("global.dict", "w") pprint(dictionary, fielddict_file) fielddict_file.close() reference = [] for i, j in dictionary.iteritems(): n = 0 combined_seq = MultipleSeqAlignment([ SeqRecord(Seq('', generic_dna), id="hg19"), SeqRecord(Seq('', generic_dna), id="panTro4"), SeqRecord(Seq('', generic_dna), id="gorGor3"), SeqRecord(Seq('', generic_dna), id="rheMac3"), SeqRecord(Seq('', generic_dna), id="ponAbe2") ]) combined_seq.sort() for ref in j: n = n + 1 seq_records = AlignIO.read(ref, 'fasta') seq_records.description = "" seq_records.sort() combined_seq = combined_seq + seq_records combined_seq.description = "" with open('%s.ref' % i, 'w') as write_file: AlignIO.write(combined_seq, write_file, 'fasta') referencelist = open('reference.list', 'a') referencelist.write('%s\t%i\n' % (i, n))