parser.set_defaults(permutations=False)
parser.add_argument('seqs', type=str, nargs='+', help='Sequences')
args = parser.parse_args()
fasta_sequences = SeqIO.to_dict(SeqIO.parse(open(args.fasta), 'fasta'))
seqs = []
for seq in args.seqs:
seqs.append(str(fasta_sequences[seq].seq).lower())
with open(args.cost, 'r') as cost_file:
letters = cost_file.readline().lower()
complex_ycost = numpy.matrix(cost_file.read())
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.permutations:
AiBS.multi_approx(input_y, 5, *seqs)
else:
alignment = AiBS.approx(input_y, 5, *seqs)
for (i, r) in enumerate(alignment):
print(">seq" + str(i+1))
print(r)
