[Biopython-dev] [Bug 2393] Bio.GenBank.NCBIDictionary fails with release 1.44

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Mon Nov 12 06:35:27 UTC 2007


------- Comment #6 from mdehoon at ims.u-tokyo.ac.jp  2007-11-12 01:35 EST -------
> Your point about avoiding UEtils is understandable.  How about using the far
> simpler Bio.WWW.NCBI wrapper?  This has basic error checking and means hard
> coding the URL in one place only.  In fact, this could be a good place to put a
> new Dictionary, e.g. Bio.WWW.NCBI.EntrezDictionary rather than
> Bio.Entrez.Dictionary

I'd be happy to use the code from Bio.WWW.NCBI, but I don't think that Bio.WWW
is a good location for an EntrezDictionary class. As a case in point, I didn't
know that Bio.WWW contains code to access NCBI Entrez, and I couldn't guess it
from its name. With a module like Bio.GenBank, it is clear from its name what
it is about. Furthermore, the different submodules Bio.WWW.ExPASy,
Bio.WWW.InterPro, Bio.WWW.NCBI, and Bio.WWW.SCOP don't seem to have much in
common. I think that the existing modules Bio.SwissProt, Bio.Prosite,
Bio.InterPro, Bio.SCOP, containing the respective parsers, are more logical
places to keep the database access code.

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