Hi all,

I am so sorry. I wont repeat the mistake. I do understand the policy.

The question is

how to get the overlapping coordinates pairs if there any? If yes take the smallest start position and largest stop position from overlapping coordinates and if no overlap for a pair, report as it is?

The example I gave was a small part of a huge file. I was manually doing it, that is why I missed some overlapping coordinates.

I did write a code for it.

here is the code which I wrote, 


open $fh,"genome_pred_exons.bed";

use List::Util qw( min max );

while(<$fh>)
{
        chomp;
        @lh = split /\t/,$_;
        $ph{$lh[0]."\t".$lh[1]."\t".$lh[2]} .= $lh[3]."\t".$lh[4]."NNN
+NNN";
}

close($fh);

foreach $k(sort keys %ph)
{
        @c =  sort { $a <=> $b } split ("NNNNNN",$ph{$k});
        @g = ();
        foreach $m(@c)
        {
            @r = split /\t/,$m;
            if (@g == 0)
            {
                push @g, [$r[0]+0, $r[1]+0];
                next;
            }
            else
            {
                for ($i = 0;$i <= $#g;$i++)
                {
                    if(($r[0] + 0) <= ($g[$i][1] + 1))
                    {
                        $g[$i][0] = min($g[$i][0]+0, $r[0]+0);
                        $g[$i][1] = max($g[$i][1]+0, $r[1]+0);
                        last;
                    }
                    elsif ( $i == $#g )
                    {
                        push @g, [$r[0]+0, $r[1]+0];
                        last;
                    }
                } 
            }
        }
}

print Dumper \@g;

[download]

This was an adapted script from internet. I changed it, but it did not give me any output.

I hope this is a better way to ask than the last one.

thank you, Deepak

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

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.