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
|
#!/usr/bin/python3
"""
Read a set of ranges and a nib file, print portions of nib overlapping
those ranges to stdout
usage: %prog range_file nib_file
"""
import bx.seq.nib
from bx.cookbook import doc_optparse
def __main__():
options, args = doc_optparse.parse(__doc__)
try:
range_file = open(args[0])
nib_file = open(args[1])
except Exception:
doc_optparse.exit()
nib = bx.seq.nib.NibFile(nib_file)
for line in range_file:
fields = line.split()
start, end = int(fields[0]), int(fields[1])
print(">", start, end)
print_wrapped(nib.get(start, end - start))
def print_wrapped(s):
l = len(s)
c = 0
while c < l:
b = min(c + 50, l)
print(s[c:b])
c = b
if __name__ == "__main__":
__main__()
|
