[Biopython-dev] Bio.WWW; database access

Peter biopython-dev at maubp.freeserve.co.uk
Wed Nov 14 08:58:14 UTC 2007

Michiel De Hoon wrote:
>> However, what about the fact that some online resources (e.g. GenBank) 
>> will return several sorts of data (e.g. journal references and 
>> sequences) and/or in a range of file formats (e.g. GenBank, Fasta, XML, 
>> ...).  In this situation, having the online interface separate from the 
>> format parsers makes some sense.
> I agree. My suggestion would be
> 1) Split Bio.WWW.ExPASy (access to Swissprot, Prodoc, Prosite) between
> Bio.SwissProt, Bio.Prosite, and Bio.Prodoc as appropriate 
> 2) Put Bio.WWW.InterPro in Bio.InterPro
> 3) Put Bio.WWW.SCOP in Bio.SCOP
> 4) NCBI Entrez is a special case since it contains many different sorts of
> data. Bio.GenBank doesn't seem to be the best place for it, as NCBI Entrez is
> much more than GenBank. I would therefore suggest to move Bio.WWW.NCBI to
> Bio.Entrez (currently an empty module in Biopython), and merge this code with
> the database access code in Bio.GenBank and Bio.EUtils.
> --Michiel.

That organisation sounds fine.

When you say move, do you mean just move - which will break existing 
scripts, or perhaps copy the stuff and mark the old version depreciated?

P.S. Is this sort of large scale rearrangement the sort of changes SVN 
is meant to track better than CVS?


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