my $file = '/path/to/file.txt';
open(IN,"<$file") || die $!;
read IN, my $html, -s $file;
close(IN);
$html =~ s/<!-- Begin -->(.*?)<!-- End -->/$1/s;

##</code><code>##

my $flag = 0;
while (<FILE>) {
    $flag = 1 if (/<!-- Begin -->/);
    $flag = 0 if (/<!-- End -->/);

    process_line($_) if ($flag);
}