Hi monks i have 2 files 
file1
contig1 10037203    10038203    blah
contig1    10037203    10038203    blah
contig1    10037203    10038203    blah

[download]
file2

contig1    997329    938329    blab11
contig1    10037329    10038329    blah11
contig1    10037329    10038329    blah11

[download]
i want to get my output as below 
contig1 10037203    10038203    blah
contig1    10037203    10038203    blah
contig1    10037203    10038203    blah
contig1    10037329    10038329    blah11
contig1    10037329    10038329    blah11

[download]
i,e., if the overlap exists first output all the overlapping ones of file1 and then of file2 i was able to read each line by line and then compare but that is not what i want. here is what i was doing 
open FILE1,"file1" or die "can't open file 1";
open FILE2,"file2" or die "can't open file 2";
open(w1,">output");
while ((my $line1 = <FILE1>) && (my $line2 = <FILE2>)) {
    chomp $line1;
    chomp $line2;
    my @cond1 = split("\t" , $line1);
    my @cond2 = split("\t" , $line2);
    if(($cond1[1] >= $cond2[1]) && ($cond1[2] <= $cond2[2]))
    {
        print w1 "$line1\t$line2\n";
    }
}
close FILE1;
close FILE2;
close w1;

[download]

In reply to output the overlapping regions to new file by Anonymous Monk

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.