[Bioperl-l] bioperl-db

[Ewan Birney]

On Wed, 13 Mar 2002, Elia Stupka wrote:

> I've been thinking that if we want to start using bioperl-db seriously
> over here we will be loading a lot of data, and data loading still seems
> relatively slow (talking about annotated files). Do you guys think there
> is room for improvement somewhere? The bioperl side of it? (parsers?) The
> biosql part of it (for fresh loads of data is it maybe too paranoyed at
> the moment?)

Most of the time is in the parsers. I looked at the parsers (are you using
main trunk?) and sliced off about 50% of the time. Now the time is
distributed around alot of areas. I suspect you can remove another chunk
somewhere, but it is going to take time no matter how you look at it.


Heikki is I believe going to being looked into profiling Rec::Descent
which maybe faster (we effectively have a hand-coded LLR parser in
embl/genbank and I can't believe we've done a good job).





> 
> Elia
> 
> 
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