You'll want references to hashes, and a loop.

use strict;
use warnings;
use Data::Dumper;

my $hashref = {};

my $hashrefTemp = $hashref;

$hashrefTemp = ($hashrefTemp->{a} ||= {}); 
$hashrefTemp = ($hashrefTemp->{b} ||= {});
$hashrefTemp->{e} = 'd';

print Dumper $hashref;
[download]

$VAR1 = {
          'a' => {
                   'b' => {
                            'e' => 'd'
                          }
                 }
        };
[download]

Looping and I/O is left as an exercise for the reader.

Dealing with input where an endpoint coexists with a non-endpoint is also left as an exercise for the reader. (Eg: [['a','b'] ['a','b','c']])