use strict;
use warnings;
if (@ARGV != 2) {
    die "Usage:\n    perl $*0 sequence_file count_file\n";
}
my ($sequence_file, $count_file) = @ARGV;
open my $SEQ, '<', $sequence_file
    or die "Cannot open $sequence_file for input\n"; 
my $sequence = <$SEQ>;
close $SEQ;

my $total_pairs;
my %pair_counts;
for my $i (0..length($sequence)-2) {
    my $pair = substr $sequence, $i, 2;
    next if ($pair =~ /[^ABCDEFGHIJKLMNOPQRST]/);
    $pair_counts{$pair}++;
    $total_pairs++
}

print "Processed $total_pairs pairs\n";
open my $COUNTS, '>', $count_file
    or die "Cannot open $count_file for output\n";
foreach my $pair (sort keys %pair_counts) {
    print {$COUNTS}  $pair, ' ', $pair_counts{$pair}, "\n";
}