def input_y(a, b): try: return complex_ycost[letters.index(a), letters.index(b)] except: print('WTF ' + a + ' - ' + b + ' is not a real cost') sys.exit(1) return 0 if args.matrix: keys = list(fasta_sequences.keys()) keys.sort() res = numpy.zeros(shape=(len(keys),len(keys))) print(keys) for s1, s2 in list(permutations(keys,2)): if args.affine: res[keys.index(s1), keys.index(s2)] = AiBS.global_affine(fasta_sequences[s1], fasta_sequences[s2], input_y, 5, 5, False) else: res[keys.index(s1), keys.index(s2)] = AiBS.global_linear(fasta_sequences[s1], fasta_sequences[s2], input_y, 5, False) print(res) sys.exit() if args.affine: print(AiBS.global_affine(seq1, seq2, input_y, 5, 5, args.backtrack)) else: print(AiBS.global_linear(seq1, seq2, input_y, 5, args.backtrack))