[Bioperl-l] Blast temporary open files not closed

Hilmar Lapp hlapp at gmx.net
Mon Sep 11 08:10:34 EDT 2006


On Sep 11, 2006, at 7:46 AM, ende wrote:

> BioPerl ought to convert the content of the result to local memory  
> vars and close and delete any /tmp/temporary files before returning!!


Well that's what I meant by Bioperl needs to serve a variety of  
requirement. Your suggestion will probably work great on your machine  
and your number of sequences but will fail completely on a machine  
with limited memory and a query of 10,000 sequences.

I agree with you that the fact that temporary files will accumulate  
along with storing the report objects should be documented (I haven't  
checked - maybe it even is but not conspicuous enough?).

Also, I believe that at some point it was being discussed to have the  
option of reading everything into memory. I'm not sure where that  
went in terms of implementation.

	-hilmar

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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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