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#!/usr/bin/python3
"""
Read two lists of intervals (with chromosomes) and count the number of entries
in the second set that intersect any entry in the first set.
TODO: This could use bitsets rather than the intervals package, would it be
faster?
usage: %prog bed1 bed2 > out
"""
import sys
from bx import (
intervals,
misc,
)
def main():
intersecters = {}
# Read ranges
for chr, start, end in read_intervals(misc.open_compressed(sys.argv[1])):
if chr not in intersecters:
intersecters[chr] = intervals.Intersecter()
intersecters[chr].add_interval(intervals.Interval(start, end))
# Count intersection
total = 0
for chr, start, end in read_intervals(misc.open_compressed(sys.argv[2])):
if chr in intersecters:
intersection = intersecters[chr].find(start, end)
if intersection:
total += 1
print(total)
def read_intervals(input):
for line in input:
fields = line.split()
yield fields[0], int(fields[1]), int(fields[2])
main()
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