( A => { count => 3,
         B => { count => 2, values => ["n1", "n2"] },
         C => { count => 1, values => ["n1"      ] } },
  D => { count => 3,
         E => { count => 2, values => ["n2", "n4"] },
         F => { count => 1, values => ["n1"      ] } } )

##</code><code>##

my %hoh = ( A => { B => [ "n1", "n2" ],
                   C => [ "n1"       ] },
            D => { E => [ "n2", "n4" ],
                   F => [ "n1"       ] }, );

foreach my $col1 (keys %hoh) {
    my $count1 = 0;
    
    foreach my $col2 (keys %{$hoh{$col1}}) {
        my $count2 = scalar @{$hoh{$col1}{$col2}};
        
        $hoh{$col1}{$col2} = { count => $count2,
                               values => $hoh{$col1}{$col2} };
        
        $count1 += $count2;
    }
    
    $hoh{$col1}{count} = $count1;
}

##</code><code>##

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