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.

True laziness is hard work

In reply to Re: help needed in modifying the code for counting possible combinations by GrandFather
in thread help needed in modifying the code for counting possible combinations by BhariD

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