[Fwd: Bioperl: manipulating long strings (genomes) in PERL]

[Matthew Pocock]

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Date: Tue, 30 Mar 1999 11:11:01 +0100
From: Matthew Pocock <mrp@sanger.ac.uk>
Organization: The Sanger Center
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To: Ian Korf <ikorf@sapiens.wustl.edu>
Subject: Re: Bioperl: manipulating long strings (genomes) in PERL
References: <199903291901.NAA02346@genotype.wustl.edu>
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Or even

my $seq = join "", grep { chomp } <FH>;

which also avoids some re-alocation issues

Ian Korf wrote:

> 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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