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
63
64
65
66
67
68
69
70
71
72
73
|
# cf https://www.evernote.com/l/ARUGTnFwaO9Kf7CO5fYJhYXh4T20R54V6eU
'''
Transforms the phased alleles from kissreads to a K2000 input format: (https://github.com/Malfoy/BWISE/blob/master/src/K2000/K2000.py)
#comments blabla toto
-1064h;-917l;1880l; => 2
...
becomes
#comments blabla toto
-2128;-1835;3761;
Moreover, K2000 is not able to deal with long range interactions (non overlaping). Thus pairend variants are forgotten:
-1064h;-917l;1880l; 24h;1l => 2
becomes:
-2128;-1835;3761;
48;3;
'''
import sys
if len(sys.argv)>1:
file = open(sys.argv[1])
else:
file=sys.stdin
def f(variant):
'''
sVp
* s='-' or nothing
* V=int value
* p='h' or 'l' (path)
f(sVp)=s2V+g(p) with g(p)=0 if p='h' and 1 if p='l'
'''
s=''
if variant[0]=='-':
s='-'
V=int(variant[1:-1])
else:
V=int(variant[:-1])
p=variant[-1]
odd=0
if p=='l':
odd=1
res=(V*2)+odd
return s+str(res)
for line in file:
#-1064h;-917l;1880l; => 2
# or
#-1064h;-917l;1880l; 24h;1l => 2
if line[0]=='#':
# print(line,end='')
continue
line=line.strip().rstrip().split(" ")
if int(line[-1])<1:
continue
for variant in line[0].split(';')[:-1]:
print (f(variant)+';', end='')
print ()
if len(line)==4: # not paired
for variant in line[1].split(';'):
print (f(variant)+';', end='')
print ()
|
