Python snippet: mimic the command `bedtools merge`

merge_intervals.py

#!/usr/bin/env python

"""merge_intervals.py

Merge tab-delimited intervals:

    cat tissue1.txt 
    chr1,1-2
    chr1,3-4
    chr1,5-6
    chr1,6-7
    chr1,7-8
    chr1,9-10
    chr2,52,53
    chr2,40-50

    cat tissue2.txt 
    chr1,11-15
    chr1,20-23
    chr2,53,57
    chr2,40-50

    python merge_intervals.py <(cat tissue?.txt | tr ,- '\t')
    chr2    40  50
    chr2    52  57
    chr1    1   2
    chr1    3   4
    chr1    5   8
    chr1    9   10
    chr1    11  15
    chr1    20  23
"""

import fileinput
from bx.intervals.cluster import ClusterTree
from collections import defaultdict

# ClusterTree arguments:
# Intervals this far apart are combined into a cluster.
# Number of overlapping intervals needed to make a cluster.
trees = defaultdict(lambda: ClusterTree(0, 1))

for n, line in enumerate(fileinput.input()):
    chrom, beg, end = line.split('\t')[:3]
    trees[chrom].insert(int(beg), int(end), n)

for chrom, tree in trees.iteritems():
    # Tuples like: (beg, end, [sorted list of interval ids in the cluster])
    for beg, end, ns in trees[chrom].getregions():
        print chrom, '\t', beg, '\t', end

Check out:

• bx-python: https://bitbucket.org/james_taylor/bx-python/wiki/Home
• bedtools: http://bedtools.readthedocs.org/en/latest/