Untested code illustrating the algorithm described in my post above: 
# opening file 1
# ...
my %hash;
while (my $line1=<TR>)
{
    chomp($line1);
    my @ar = split(/\t/,$line1);
    $hash{$ar[1]} = $ar[3];
}
close TR;

open my $SC, "<", $file2 or die "Error blah blah... $!";
while (my $line2 = <$SC>) 
{
    my ($id, $val) = split /\t/, $line2;
    my $val_file1 = $hash{$id};
    if ( $val > $val_file1 - $margin and $val < $val_file1 + $margin) 
+{
        # print out something
    }
}
close $SC;

[download]
BTW, I basically kept your syntax almost unchanged for the first part and tried to improve it in accordance to good practices in the second part. Take a look at the differences.

In reply to Re: Sliding window perl program by Laurent_R
in thread Sliding window perl program by genome

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.