while ($newline = <FILEHANDLE>){
   if ($newline = /^>/) {
     if ($i == $number) {
       #initialize a bunch of stuff and continue
       }
       else {
         $i++;
         #and then go back to whatever the last line that =~ /^>/ and go again
         }
     }
  $stuff = $newline;
  &play_with($stuff);
  }