This should do the trick:

my $r;
...
while( <> ) {
    chomp;
    $r = insert($r, split /[-_.]/, $_);
}

sub insert {
    my $r = shift;
    my $last = \$r;
    $last = \$$last->{$_} for @_;
    $$last ||= 1;
    $r;
}
[download]

edit: fixed up call to insert()