ok, maybe way off here but I'll give it a try

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

my $datafile = "test.dat";
my %finalQ = ();

open(FH, "<$datafile") || die ;

my %combined = ();

while( <FH> ){
  chomp;
  my ($key,$value) = sort (split(/\t/,$_));
  $combined{$key}=$value;
}

my %count = ();
my %reverse = reverse(%combined);

foreach my $key (sort %combined) {
        print "$key => $combined{$key}\n";
        if ( exists $reverse{$key} ) {
                $count{"$key\t$reverse{$key}"}+=2;
                print "$key => $reverse{$key} :: match\n";
        } else {
                $count{"$key\t$combined{$key}"}++;
        }
}

print Dumper(%count);
[download]

output

$VAR1 = '       ';
$VAR2 = 4;
$VAR3 = 'NP_05  NP_04';
$VAR4 = 2;
$VAR5 = 'YP_01  NP_03';
$VAR6 = 2;
$VAR7 = 'NP_03  NP_02';
$VAR8 = 4;
$VAR9 = 'NP_02  NP_03';
$VAR10 = 1;
$VAR11 = 'NP_04 NP_05';
$VAR12 = 1;