Bioperl: manipulating long strings (genomes) in PERL

[Ian Korf]

Is it possible you have code that does something like this?

my $seq = "";
while (<FH>) {
	chomp;
	$seq .= $_
}

If so, you may be causing reallocations as Perl keeps the scalar contiguous.
Here's an approach that should work better.

my $seq;
LOCAL_BLOCK: {
	my @seq = <FH>;
	chomp @seq;
	$seq = join("", @seq);
}

Now you only have to allocate the scalar once. The local block there is
just forcing garbage collection of @seq;

-Ian
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