-
Notifications
You must be signed in to change notification settings - Fork 1
/
qver.py
executable file
·39 lines (35 loc) · 1.02 KB
/
qver.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
#!/usr/bin/python
import sys
from collections import defaultdict
corr=defaultdict(lambda:0)
miss=defaultdict(lambda:0)
for fn in sys.argv[1:]:
f=file(fn)
while f:
try:
name=f.next()
pos=f.next()
query=f.next()
match=f.next()
sbjct=f.next()
except StopIteration:
break
[_, start, _, end, _, outof] = pos.split(' ')[:6]
if (int(end)-int(start)) / float(outof[:-1]) < .95:
continue
if len(query)!=len(sbjct):
print 'Length mismatch %s %s (%d vs %d)' % (fn, name, len(query), len(sbjct))
continue
quality=file(fn.replace('.align','.q')).read()
qi=int(start)
for i in range(len(query)):
if query[i]=='-':
continue
if match[i]=='|':
corr[quality[qi]]+=1
else:
miss[quality[qi]]+=1
qi+=1
for i in range(30):
c=chr(i+33)
print '%d, %d, %d' % (i, corr[c], miss[c])