[BioPython] Precompute database information

[Peter]

Fernando wrote:
> Hi everybody,
> 
> I am thinking in including some algorithms that I work with into biopython.
> My first concern is that I'm using a local image of the Gene Ontology
> database to perform several operations. In order to avoid such database
> accesses I could precompute the information I need and load it once the
> module is called. How should I do it? Is there a guideline style to load
> external variables or something like that? Any other ideas/suggestions?

I think you need to go into more detail.

How big would your pre-computed data be?  If its some sort of table or 
other simple data you could perhaps use a simple text file; Another idea 
for complicated objects is to use python's pickle module.

How often would the pre-computed data need to be updated?  Every time 
there is a new Gene Ontology release?  It might be better have the 
module download and cache the latest version on request (rather than 
shipping an out of date dataset with Biopython).

I don't think we have anything in Biopython that requires regular 
updates.  Things like genomes and sequence databases are left up to the 
user.

Peter