your solution is missing some possibilities.
Well, I implemented (on purpose) exactly the list the OP asked for. It can of course be extended, if so desired:
my @cnt = qw(A2G G2A C2T T2C A2T A2C G2T G2C ...);
Alternatively, simply compute the full matrix of count routines:
#!/usr/bin/perl -w
use strict;
my %cnt;
my @c = qw(A T C G);
for my $c1 (@c) {
for my $c2 (@c) {
next if $c1 eq $c2;
(my $t = $c2) =~ tr/ATCG/HRDZ/;
my $x = $c1 ^ $t;
$cnt{$c1."2".$c2} = eval "sub { \$_[0] =~ tr/$x/$x/ }";
}
}
my $seq1 = 'AAAACCCCGGGGTTTT';
my $seq2 = 'ACGTACGTACGTACGT';
(my $tmp = $seq2) =~ tr/ATCG/HRDZ/;
my $diff = $seq1 ^ $tmp;
print join("; ", map { $_."=".$cnt{$_}->($diff) } sort keys %cnt ), ".
+";
__END__
A2C=1; A2G=1; A2T=1; C2A=1; C2G=1; C2T=1; G2A=1; G2C=1; G2T=1; T2A=1;
+T2C=1; T2G=1.
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