while(my $line = <$in>) {
  chomp $line;
  $line =~ s/^\s+//;      # strip leading whitespace
  next unless $line;      # skip blank lines
  next if ($line =~ /^#/; # skip comment line

  ...

}

##</code><code>##

my ($x, $y) = $sample =~ /(\d+)(.*)/;
$x = '?' unless $x;
$y = '?' unless $y;