X => { count => n, [ ... ] }

##</code><code>##

    X => { count => n, values => [ ... ] }

##</code><code>##

#!/usr/bin/env perl -l

use strict;
use warnings;
use autodie;

use Text::CSV;

my $csv = Text::CSV::->new({sep_char => "\t"});
my %data;

while (my $row = $csv->getline(\*DATA)) {
    ++$data{$row->[0]}{count};
    ++$data{$row->[0]}{values}{$row->[1]}{count};
    push @{$data{$row->[0]}{values}{$row->[1]}{values}}, $row->[2];
}

use Data::Dump;
dd \%data;

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

##</code><code>##

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