Something similar to this should do it. The trick is not to update $lastline until you don't have a match. As a side note, in the past I have successfully loaded around 100K lines into an array. You may be surprised at what Perl can handle.
open (IN, "$input_file");
open (OUT, ">$output_file");
my $lastline = <IN>;
print OUT $lastline;
while(<IN>){
my $line = $_;
if ($line eq $lastline){
next;
}
print OUT $line;
$lastline = $line;
}
update: corrected typo
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