Bioperl-guts: Notification: incoming/203

Ewan Birney birney@ebi.ac.uk
Thu, 6 Apr 2000 16:02:47 +0100 (GMT)


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...

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Ewan Birney. Mobile: +44 (0)7970 151230
<birney@ebi.ac.uk>
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