[Biopython-dev] Accessing ExPASy through Bio.SwissProt /Bio.SeqIO

[Michiel De Hoon]

Hi everybody,

To summarize, I rewrote the chapter on SwissProt/Prosite/Prodoc/ExPASy and
put it here:

http://biopython.org/DIST/docs/tutorial/Tutorial-proposal.html#htoc51

(chapter 6 in the tutorial)

This is merely a proposal on how this should work; none of this is in CVS
yet.
Please let us know if you have any objections.
If there are no objections, I can upload the new code to CVS. That would
conclude my work on Bio.WWW.ExPASy; the final (and biggest) part of my work
on Bio.WWW will be to look at the various Biopython modules to interact with
NCBI (Genbank, EUtils).

Two comments:
1) In this proposal, I am using SwissProt.parse instead of SeqIO.parse since
the latter does not (yet) store all information contained in a SwissProt
file. I'd be happy though to move to SeqIO.parse for SwissProt also once it
does.
2) It may be nice to have a SwissProt.read and SeqIO.read to read and return
exactly one record from the handle, in addition to parse() to create an
iterator to read multiple records.

--Michiel.


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


-------------- next part --------------
A non-text attachment was scrubbed...
Name: winmail.dat
Type: application/ms-tnef
Size: 3662 bytes
Desc: not available
URL: <http://lists.open-bio.org/pipermail/biopython-dev/attachments/20071207/0442ab19/attachment-0002.bin>