1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
|
#!/usr/bin/env python3
"""
Mutate nucleotides in a FASTA or FASTQ file
The modified sequences are written to standard output.
"""
import sys
import random
from sqt import HelpfulArgumentParser
from sqt.io.fasta import FastaReader, FastaWriter
from sqt.dna import mutate
__author__ = "Marcel Martin"
def main():
parser = HelpfulArgumentParser(description=__doc__)
parser.add_argument("--rate", type=float, default=0.03,
help="Substitution rate (default: %(default)s)")
parser.add_argument("--indel-rate", type=float, default=0.0005,
help="Indel rate (default: %(default)s)")
parser.add_argument("--seed", type=int, default=None,
help="Set random seed for reproducible runs (default: use different seed each run)")
parser.add_argument("fasta", metavar='FASTA-file', help="Input FASTA file")
args = parser.parse_args()
if args.seed is not None:
random.seed(args.seed)
fasta_output = FastaWriter(sys.stdout, line_length=80)
for record in FastaReader(args.fasta):
mutated, n_sub, n_indel = mutate(record.sequence, rate=args.rate, alphabet='ACGT', indel_rate=args.indel_rate, counts=True)
fasta_output.write(record.name + '-sub{}-indel{}'.format(n_sub, n_indel), mutated)
if __name__ == '__main__':
main()
|
