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))
