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
|
import sys, random
from pbsuite.utils.FileHandlers import FastaFile, revComp, wrap
def getRandomSeq(length):
return "".join([random.choice(['A', 'T', 'C', 'G']) for i in xrange(length)])
if __name__ == '__main__':
fasta = FastaFile(sys.argv[1])
key = fasta.keys()[0]
ref = list(fasta[key])
#800bp insertion in the sample (deletion in the reference)
ref[5000:5800] = ""
#5000 Insertion
#Inversion in the sample (inversion in the reference) tails
ref[9000:12000] = list("".join(ref[10000:13000]).translate(revComp)[::-1])
#9000-12000 - INversion
#1kb deletion in sample (insert into the reference) tails
seq = getRandomSeq(1000)
ref[20000:20000] = list(seq)
#20000-21000 -- Deletion
#100bp insertion in sample (deletion in the reference) spots
ref[30000:30100] = ""
#30000 - Insertion
#200bp deletion in sample (insert into the reference) spots
seq = getRandomSeq(200)
ref[35000:35000] = list(seq)
#35000 - 35200 -- Deletion
print ">%s\n%s" % (key, wrap("".join(ref)))
|
