Bioperl-guts: Notification: incoming/203

James Gilbert jgrg@sanger.ac.uk
Thu, 6 Apr 2000 19:25:58 +0100 (BST)


On Thu, 6 Apr 2000, Ewan Birney wrote:

> On Thu, 6 Apr 2000, kevin richard thornton wrote:
> 
> > This makes sense.  I used the next_primary_string() as suggested by Ewan,
> > and it did cut memory use down, but only to about 200MB (I killed the
> > process then and don't know if would have gotten bigger).  Before I
> > started using bioperl, I was reading FASTA sequences with a memory use of
> > 1MB per megabase, which makes sense, so it probably is the use of arrays
> > that's causing trouble.  Admittedly, this isn't a big problem on the
> > machines I'm using, but it will be quite serious when people start dealing
> > with whole human sequences later this year.
> 
> James - you are planning to fix this on the main trunk and the branch
> right? It would be great if you could do so...

	Fixed.  James

> -----------------------------------------------------------------
> Ewan Birney. Mobile: +44 (0)7970 151230
> <birney@ebi.ac.uk>
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James G.R. Gilbert
The Sanger Centre
Wellcome Trust Genome Campus
Hinxton
Cambridge                        Tel: 01223 494906
CB10 1SA                         Fax: 01223 494919

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