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)
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))
parser.add_argument('seq1', type=str, help='Sequence 1')
parser.add_argument('seq2', type=str, help='Sequence 2')
parser.add_argument('seq3', type=str, help='Sequence 3')
parser.add_argument('--backtrack', dest='backtrack', action='store_true')
parser.set_defaults(backtrack=False)
args = parser.parse_args()
fasta_sequences = SeqIO.to_dict(SeqIO.parse(open(args.fasta),'fasta'))
seq1 = str(fasta_sequences[args.seq1].seq).lower()
seq2 = str(fasta_sequences[args.seq2].seq).lower()
seq3 = str(fasta_sequences[args.seq3].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
print(AiBS.exact_3(seq1, seq2, seq3, input_y, 5, args.backtrack))
parser = argparse.ArgumentParser(description='Genome Sequence Analyzor')
parser.add_argument('cost', type=str, help='Cost file to read')
parser.add_argument('--backtrack', dest='backtrack', action='store_true')
parser.add_argument('fastas', type=str, nargs='+', help='Fasta')
args = parser.parse_args()
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
print("#len\texact\tapprox")
for fasta in args.fastas:
fasta_sequences = SeqIO.to_dict(SeqIO.parse(open(fasta),'fasta'))
seq1 = str(list(fasta_sequences.values())[0].seq).lower()
seq2 = str(list(fasta_sequences.values())[1].seq).lower()
seq3 = str(list(fasta_sequences.values())[2].seq).lower()
with open(args.cost, 'r') as cost_file:
letters = cost_file.readline().lower()
complex_ycost = numpy.matrix(cost_file.read())
print(str(len(seq1)) + "\t" + str(AiBS.exact_3(seq1, seq2, seq3, input_y, 5, args.backtrack)) + "\t" + str(AiBS.approx_score(input_y, 5, seq1, seq2, seq3)))
