use Data::Dumper;
my %pairs = ();
while (<>) {
    chomp;
    my @found = split;
    for my $k1 ( @found );
        for my $k2 ( @found ) {
            if ( $k2 gt $k1 ) { # ensuring each pair is counted once only for the line
                $pairs{ $k1 }{ $k2 }++;
            }
        }
    }
} 
print Dumper \%pairs;