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
|
#!/usr/bin/python3
"""
For each interval in `bed1` count the number of intersecting regions in `bed2`.
usage: %prog bed1 bed2
"""
import sys
from bx.intervals import (
Intersecter,
Interval,
)
bed1, bed2 = sys.argv[1:3]
ranges = {}
for line in open(bed2):
fields = line.strip().split()
chrom = fields[0]
start = int(fields[1])
end = int(fields[2])
if chrom not in ranges:
ranges[chrom] = Intersecter()
ranges[chrom].add_interval(Interval(start, end))
for line in open(bed1):
fields = line.strip().split()
chrom, start, end = fields[0], int(fields[1]), int(fields[2])
other = " ".join(fields[3:])
out = " ".join(fields[:3] + [other])
if chrom in ranges:
print(out, len(ranges[chrom].find(start, end)))
else:
print(out, 0)
|
