#!/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