open ($input, $ARGV[0]) or die ("Could not open input file $ARGV[0].\n"); 
open ($output, '>output.txt') or die ("Could not open input file output.txt.\n"); 

while ($line = <$input>) { 
 chomp($line);
 unless ($line =~ m/>/) { 
  $line = uc($line);
  $seq .= $line;
  }
 }

$orf1 = $seq;
$orf2 = substr($seq, 1);
$orf3 = substr($seq, 2);