use strict;
use warnings;

my %pairs;

while (<DATA>) {
    chomp;
    next if ! length;

    my @pair = sort split;
    ++$pairs{$pair[0]}{$pair[1]};
}

my $totalHits = 0;
my %seconds;

for my $first (sort keys %pairs) {
    for my $second (sort keys %{$pairs{$first}}) {
        next if $pairs{$first}{$second} <= 1;
        ++$totalHits;

        my $previous =
            grep {exists $pairs{$_}{$first} && exists $pairs{$_}{$seco
+nd}}
            keys %{$seconds{$first}};

        ++$seconds{$second}{$first};
        next if $previous;
        print "$first $second\n";
    }
}

print "$totalHits\n";

__DATA__
NP_01 NP_02
NP_02 NP_01
NP_01 NP_03
NP_03 NP_01
NP_02 NP_03
NP_03 NP_02
NP_04 NP_05
[download]

Prints:

NP_01 NP_02
NP_01 NP_03
3
[download]

Note that I changed YP_01 to NP_01 to avoid inconsistencies between your reported results and the actual results.

This is awesome! Thank you so much GrandFather. I tried with the following data:

 __DATA__
NP_01 NP_02
NP_02 NP_01
NP_01 NP_03
NP_03 NP_01
NP_02 NP_03
NP_03 NP_02
NP_04 NP_05
NP_06 NP_07
NP_07 NP_06

This prints:
NP_01 NP_02
NP_01 NP_03
NP_06 NP_07
4
[download]

I want the output to be like this instead:

NP_01 NP_02
NP_01 NP_03
3
NP_06 NP_07
1
[download]

3 for the presence of all three NP_01-NP_02, NP_01-NP_03, NP_02-NP_03 possible pairs in the file. Lets say, if NP_02-NP_03 combination was not present in the file then the number should become 2 showing that NP_02-NP_03 combo does not exist in the file. Any suggestion how can I get this from your code.

Example in case when NP_02-NP_03 reciprocal pair does not exist in the file and the required output

 __DATA__
NP_01 NP_02
NP_02 NP_01
NP_01 NP_03
NP_03 NP_01
NP_04 NP_05
NP_06 NP_07
NP_07 NP_06

prints:
NP_01 NP_02
NP_01 NP_03
 2 [not present in NP_02 NP_03]

NP_06 NP_07
1
[download]

That makes it more interesting. If you discover any more interesting cases however you'd better tell us what the application actually is and give us the bigger picture.

use strict;
use warnings;

my %pairs;

while (<DATA>) {
    chomp;
    next if ! length;

    my @pair = sort split;
    ++$pairs{$pair[0]}{$pair[1]};
}

for my $first (sort keys %pairs) {
    my @hits;
    my $count = 0;
    my @implied;

    for my $second (keys %{$pairs{$first}}) {
        next if $pairs{$first}{$second} < 2;

        push @implied, $second;
        ++$count;

        if (exists $pairs{$second}{$first}) {
            delete $pairs{$second}{$first};
            ++$count;
        }

        print "$first $second\n";
    }

    next if ! $count;

    @implied = sort @implied;
    if (@implied == 2 && $pairs{$implied[0]}{$implied[1]}) {
        ++$count;
        delete $pairs{$implied[0]}{$implied[1]};
        @implied = ();
    }

    print "$count";
    print " [not present in @implied]" if @implied == 2;
    print "\n\n"
}

__DATA__
AP_01 AP_02
AP_02 AP_01
AP_01 AP_03
AP_03 AP_01
NP_01 NP_02
NP_02 NP_01
NP_01 NP_03
NP_03 NP_01
NP_02 NP_03
NP_03 NP_02
NP_04 NP_05
NP_06 NP_07
NP_07 NP_06
[download]

Prints:

AP_01 AP_02
AP_01 AP_03
2 [not present in AP_02 AP_03]

NP_01 NP_03
NP_01 NP_02
3

NP_06 NP_07
1
[download]

I added the AP_dd set to make it clearer which groups were which and to provide data to demonstrate the third case.

---

True laziness is hard work

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;

A B
B C
C D
D A
B D
[download]