Is there a reason you are using hashes and not arrays? I ask because your keys are only numbers, and nearly sequential numbers at that - this would seem to be the classic example of when to use arrays.

But, assuming you want to do this with hashes, you would first iterate over a sorted key list (see the FAQ How do I sort a hash (optionally by value instead of key)?) and then iterate over that list and output your desired result (How do I process an entire hash?). Something like:

#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;

my %hash1 = ("1", "20",
             "2", "20",
             "4", "19",
             "5", "20",
             "6", "18");
my %hash2 = ("1", "19",
             "2", "20",
             "4", "16",
             "5", "19",
             "6", "20");

my %differences;
for my $key ( sort {$a <=> $b} keys %hash1) {
    $differences{$key} = $hash1{$key} - $hash2{$key};
    print "$key ($hash1{$key} - $hash2{$key}) = $differences{$key}\n";
}

print "\n", Dumper \%differences;
__END__
1 (20 - 19) = 1
2 (20 - 20) = 0
4 (19 - 16) = 3
5 (20 - 19) = 1
6 (18 - 20) = -2

$VAR1 = {
          '6' => -2,
          '4' => 3,
          '1' => 1,
          '2' => 0,
          '5' => 1
        };
[download]

and using arrays instead:

#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;

my @array1 = (undef,20,20,19,20,undef,18);
my @array2 = (undef,19,20,16,19,undef,20);

my @differences;
for my $i (0 .. $#array1) {
    next unless defined $array1[$i];
    
    $differences[$i] = $array1[$i] - $array2[$i];
    print "$i ($array1[$i] - $array2[$i]) = $differences[$i]\n";
}

print "\n", Dumper \@differences;
__END__
1 (20 - 19) = 1
2 (20 - 20) = 0
4 (19 - 16) = 3
5 (20 - 19) = 1
6 (18 - 20) = -2

$VAR1 = [
          undef,
          1,
          0,
          3,
          1,
          undef,
          -2
        ];
[download]

Update: Added storage of differences

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