[Bioperl-l] Blast temporary open files not closed
hlapp at gmx.net
Mon Sep 11 12:10:34 UTC 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 Lapp -:- Durham, NC -:- hlapp at gmx dot net :
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