I don't know exactly what your problem is, but perhaps this code could solve it? :)

#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;

my @lines;

while (<DATA>) {
    my %line;
    ++$line{$_} for split /\s+/;
    push @lines, { %line };
}

print Dumper \@lines;

__DATA__
one     two     three
three     one      two
one      one     three
[download]

it prints

$VAR1 = [
          {
            'three' => 1,
            'one' => 1,
            'two' => 1
          },
          {
            'three' => 1,
            'one' => 1,
            'two' => 1
          },
          {
            'three' => 1,
            'one' => 2
          }
        ];
[download]