my %hoh;

while (<DATA>) {
    chomp;
    my ($c1, $c2, $c3) = split;
    
    $hoh{$c1}{count}++;
    $hoh{$c1}{$c2}{count}++;
    push @{$hoh{$c1}{$c2}{values}}, $c3;
}

__DATA__
A	B	n1
A	B	n2
A	C	n1
D	E	n2
D	E	n4
D	F	n1