-
Notifications
You must be signed in to change notification settings - Fork 57
/
3rd-gc.py
62 lines (43 loc) · 1.28 KB
/
3rd-gc.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
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
import csv
def read_csv(filename):
records = []
with open(filename, 'rt') as fp:
reader = csv.reader(fp, delimiter=',')
for ii, row in enumerate(reader):
if ii > 0:
records.append(row)
return records
codons = read_csv('codon-table-grouped.csv')
#print(codons)
c2s= {}
for c in codons:
c2s[c[1]] = c[0]
print(c2s)
virvac = read_csv("side-by-side.csv")
#print(virvac)
matches = 0
for element in virvac:
vir = element[1]
vac = element[2]
print(f'{vir} v {vac}, amino: {c2s[vir]} == {c2s[vac]}.')
our = vir
if vir[2] == 'G' or vir[2] == 'C':
print('codon ended on G or C already, not doing anything')
else:
prop = vir[:2]+"G"
print(f'Attempting G substution, new candidate {prop}')
if c2s[vir] == c2s[prop]:
print('amino acid still the same, done!')
our = prop
else:
print(f'Oops, maino acid changed. Trying C, new candidate {prop}')
prop = vir[:2] + "C"
if c2s[vir] == c2s[prop]:
print('Amino acid still the same, done!')
our = prop
if vac == our:
print('Matched the vaccine!')
matches +=1
else:
print('No Match.')
print(100*matches / len(virvac))