Consolidating genomic elements by ID relationship

consolidate.py

#!/usr/bin/env python

import sys, copy

def sampleInput():
    return '''gain_765	chr15	9681969	9685418	chr15	9660912	9712719	loss_1136
gain_766	chr15	9706682	9852347	chr15	9660912	9712719	loss_1136
gain_766	chr15	9706682	9852347	chr15	9765125	9863990	loss_765
gain_780	chr20	9706682	9852347	chr20	9765125	9863990	loss_769
gain_760	chr15	9706682	9852347	chr15	9660912	9712719	loss_1137
gain_760	chr15	9706682	9852347	chr15	9765125	9863990	loss_763'''

class Range:
    """Defines a generic genomic range"""
    def __init__(self, chr, start, stop):
        self.chr = str(chr)
        self.start = int(start)
        self.stop = int(stop)
    def __str__(self):
        return "[" + str(self.chr) + ":" + str(self.start) + "-" + str(self.stop) + "]"

class Entity:
    """Defines an entity"""
    def __init__(self, name, range):
        self.name = name
        self.range = range
    def __str__(self):
        return self.name + " " + str(self.range)

def main():
    ranges = dict()
    rels = dict()

    for line in sampleInput().split('\n'):
        elems = line.split('\t')
        enA = Entity(elems[0], Range(elems[1], elems[2], elems[3]))
        enB = Entity(elems[7], Range(elems[4], elems[5], elems[6]))

        ranges[enA.name] = enA.range
        ranges[enB.name] = enB.range

        if len(rels) > 0:
            if enA.name in rels:
                rels[enA.name].add(enB.name)
                if enB.name in rels:
                    rels[enB.name].add(enA.name)
                else:
                    rels[enB.name] = set([enA.name])
            elif enB.name in rels:
                rels[enB.name].add(enA.name)
                if enA.name in rels:
                    rels[enA.name].add(enB.name)
                else:
                    rels[enA.name] = set([enB.name])
            else:
                rels[enA.name] = set([enB.name])
                rels[enB.name] = set([enA.name])

        else:
            rels[enA.name] = set([enB.name])
            rels[enB.name] = set([enA.name])

    for k in rels:
        s = rels[k]
        ns = copy.deepcopy(s)
        for e in s:
            if e in rels:
                os = rels[e]
                ns = ns.union(os)
        rels[k] = ns

    nrels = dict()
    for k in rels:
        s = rels[k]
        for e in s:
            if e != k:
                rels[e] = set()
            elif len(rels[e]) > 0:
                nrels[e] = s

    for nk in nrels:
        s = nrels[nk]
        chr = ""
        min = sys.maxint
        max = -sys.maxint - 1
        for r in s:
            chr = ranges[r].chr
            if ranges[r].start < min:
                min = ranges[r].start
            if ranges[r].stop > max:
                max = ranges[r].stop
        print '\t'.join([chr, str(min), str(max), str(s)])
            
if __name__ == "__main__":
    main()

$ ./consolidate.py | sort-bed -
chr15   9660912 9863990 set(['gain_765', 'loss_1136', 'gain_766', 'loss_765'])
chr15   9660912 9863990 set(['loss_1137', 'loss_763', 'gain_760'])
chr20   9706682 9863990 set(['loss_769', 'gain_780'])