[Biopython-dev] Bio.WWW; database access

Michiel De Hoon mdehoon at c2b2.columbia.edu
Tue Nov 20 08:39:53 UTC 2007

Hi everybody,

I have now moved the database access code from Bio.WWW.SCOP and
Bio.WWW.InterPro to Bio.SCOP and Bio.InterPro, respectively.
This leaves us with Bio.WWW.NCBI and Bio.WWW.ExPASy.

The latter contains the following functions:
get_prodoc_entry  Interface to the get-prodoc-entry CGI script.
get_prosite_entry Interface to the get-prosite-entry CGI script.
get_sprot_raw     Interface to the get-sprot-raw.pl CGI script.
sprot_search_ful  Interface to the sprot-search-ful CGI script.
sprot_search_de   Interface to the sprot-search-de CGI script.

so it access Prodoc, Prosite, and SwissProt.
The corresponding parsers are in

Bio.Prosite.Prodoc for Prodoc
Bio.Prosite for Prosite
Bio.SwissProt.SProt for SwissProt

(each of these modules also contain some code to access Prodoc, Prosite,
SwissProt over the internet).

My question is: What is the preferred place to put the five functions from

One option is to put get_prodoc_entry in Bio.Prosite.Prodoc,
get_prosite_entry in Bio.Prosite, and get_sprot_raw, sprot_search_ful, and
sprot_search_de in Bio.SwissProt.SProt (actually, I don't understand why we
have a Bio.SwissProt.SProt, since Bio.SwissProt.__init__ is currently empty,
but that's a different issue).

A second option is to have a separate Bio.ExPASy, so to simply rename
Bio.WWW.ExPAsy to Bio.ExPASy.

Any other options I haven't thought of?

I am leaning towards the first option. Any other opinions?


Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1150 St Nicholas Avenue
New York, NY 10032

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