If I understand what you want correctly, this (not very elegant) script should work (provided your values are in ascending order of contig start site (column 3)): 

#!/usr/bin/perl 
use strict;
use warnings;

my $dataFile = $ARGV[0];
my $get = 1;
my @array = ();
my $col1 = 0;
my $col2 = 0;
my $low = 0;
my $high = 0; 

open (FILE, "<", $dataFile);
while (<FILE>)
    {
        next unless $_ =~ /[0-9]/;
        @array = split(" ", $_);
        
        if ($get == 1)
            {
                if (($array[2] > $high) && ($high > 0))
                    {
                        print STDOUT "$col1\t$col2\t$low\t$high\n";
                        $low = $array[2];
                        $high = $array[3];
                    }
                $col1 = $array[0];
                $col2 = $array[1]; 
                $low = $array[2] if (($array[2] < $low) || ($low == 0)
+);
                $high = $array[3] if (($array[3] > $high) || ($high ==
+ 0));; 

                $get = 0;
            }

        if ($array[2] <= $high)
            {
                $high = $array[3] if $array[3] > $high;
            }
                
        if (($array[2] > $high) || (eof(FILE)))
            {
                print STDOUT "$col1\t$col2\t$low\t$high\n";

                $low = $array[2];
                $high = $array[3];
                $get = 1;
            }
    }

[download]

If the chromosome changes during your large file, it would need to be modified to account for that.

There's probably a much prettier way of doing it though...

Michael

In reply to Re: Finding Overlapping Regions on Genome by mtmcc
in thread Finding Overlapping Regions on Genome by oxydeepu

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