I tired this first and am running into an error. I am very new at Perl so may be missing how the subroutine is set up. I run my script witht he following (my actual arrays have many more words than that in my sample):

my @sets = (\@array1, \@array2, \@array3, \@array4 );
for my $h (0..$#sets) {
    for my $j ($h+1..$#sets) {
        compute_stuff($sets[$h], $sets[$j]);
     }
}

Sub union_intersection {
    my ($set1, $set2) = @_;
    my (%union, %intersect);
        foreach my $e (@$set1, @$set2) {
            $union{$e}++ && $intersect{$e}++
        }
    my @intersect = sort keys %intersect;
    #print FILEOUT "@intersect\n";
    print FILEOUT scalar @intersect;
    print FILEOUT "\n";
}
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I get a syntax error on 2 lines. One on this line: my (%union, %intersect); The other near the last line (with '}'). Not sure why. In you example you did't have the semi-colon at the end and added it but that wasn't it. Also, don't I need to call the subroutine somewhere for it to work. Not sure if this an error on my part (e.g. not sure what compute_stuff should be doing). Thanks for the help-