Here is some code which does what you want:
use Modern::Perl;
use List::Compare;

# Make two arrays with fake data
my @left  = map {'AA' . int(rand (5000000) + 1000000)} (1 ... 5000000)
+;
my @right = map {'AA' . int(rand (5000000) + 1000000)} (1 ... 5000000)
+;

my $start = time;
my $lc = List::Compare->new('-u', \@left, \@right);

{
    open my $OUT_INTER, '>', './intersection.txt';
    say $OUT_INTER $_ for $lc->get_intersection;
}
{
    open my $OUT_DIFF, '>', './difference.txt';
    say $OUT_DIFF $_ for $lc->get_symmetric_difference;
}
my $duration = time - $start;

say "Duration: $duration seconds.";

[download]
However, on my small laptop (only 2 GByte RAM and running a lot of other programs and services) I get an "Out of memory" error, so two lists of 5 million proteins is too big for it. YMMV if you have a more performant machine. It runs fine and fast for 500,000 proteins (15 seconds), 1,000,000 proteins (52 seconds) and 2,000,000 proteins (185 seconds).

CountZero

A program should be light and agile, its subroutines connected like a string of pearls. The spirit and intent of the program should be retained throughout. There should be neither too little or too much, neither needless loops nor useless variables, neither lack of structure nor overwhelming rigidity." - The Tao of Programming, 4.1 - Geoffrey James

In reply to Re^5: Is there a way to compare strings without using an array? by CountZero
in thread Is there a way to compare strings without using an array? by Jeri

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