open(OUT,">$outfile");
open(F1, "<$infile")   or die "Could not open $infile for reading!\n";
$/ = "#";
while (<F1>) {
      print OUT "$_\n";
}

##</code><code>##

while ($line1 =<F1> || $line2= <F2>){
  foo($line1,$line2);
}