If I remember right, DNA sequence files are often very large. You could trade off cpu for memory by comparing hashes of each line instead of the line data itself. If a typical sequence file is 60 characters per line, that's 480 bits, so a 128bit MD5 digest would use significantly less memory, but more cpu. 
use warnings;
use strict;
use Digest::MD5 qw(md5);
my %SEEN;
while (<>) {
    chomp;
    my $digest=md5($_);
    if ($SEEN{$digest}++) {
       printf STDOUT "Dup: [%s] seen %d times\n",$_,$SEEN{$digest};
    }
}

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In reply to Re: Comparing each line of a file to itself by kschwab
in thread Comparing each line of a file to itself by Manju Moorthy

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