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
|
#!/usr/bin/python3
"""
Match up intersecting intervals from two files. This performs a "full join",
any pair of intervals with any basewise overlap will be printed side-by-side.
usage: %prog bed1 bed2
"""
import sys
import bx.intervals.intersection
import bx.intervals.io
def main():
intersecters = {}
# Read second set into intersecter
for interval in bx.intervals.io.GenomicIntervalReader(open(sys.argv[2])):
if interval.chrom not in intersecters:
intersecters[interval.chrom] = bx.intervals.Intersecter()
intersecters[interval.chrom].add_interval(interval)
# Join with first set
for interval in bx.intervals.io.GenomicIntervalReader(open(sys.argv[1])):
if interval.chrom in intersecters:
intersection = intersecters[interval.chrom].find(interval.start, interval.end)
for interval2 in intersection:
print("\t".join([str(interval), str(interval2)]))
if __name__ == "__main__":
main()
|
