-
Notifications
You must be signed in to change notification settings - Fork 0
/
sim4.py
43 lines (39 loc) · 1.16 KB
/
sim4.py
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
37
38
39
40
41
42
43
import random as R
def padding(x):
alphabet = ['A', 'C', 'G', 'T']
return ''.join([R.choice(alphabet) for _ in range(x)])
# Load sequences and LCS from file
f = open("genomes/sars_cov_2/sars_cov_2_ref_NC_045512.fasta", "r")
covid_seq = ''.join([x[:-1] for x in f.readlines()[1:]])
f.close()
f = open("genomes/RaTG13_MN996532.fasta", "r")
ratg13_seq = ''.join([x[:-1] for x in f.readlines()[1:]])
f.close()
f = open('lcs.txt', 'r')
lcs = f.read()
# Fill in missing characters.
covid_pos = 0
rat_pos = 0
new_rat = ''
for ch in lcs:
while covid_seq[covid_pos] != ch and ratg13_seq[rat_pos] != ch:
new_rat += ratg13_seq[rat_pos]
covid_pos += 1
rat_pos += 1
if covid_seq[covid_pos] == ch and ratg13_seq[rat_pos] == ch:
new_rat += ch
covid_pos += 1
rat_pos += 1
continue
while covid_seq[covid_pos] != ch:
new_rat += covid_seq[covid_pos]
covid_pos += 1
while ratg13_seq[rat_pos] != ch:
# new_rat += R.choice(['A', 'C', 'G', 'T'])
rat_pos += 1
new_rat += ch
covid_pos += 1
rat_pos += 1
# Pad new_rat
new_rat += padding(len(covid_seq) - len(new_rat))
#then mutate.