[BioPython] Entrez module

[Peter Wilkinson]

I dont seem to be getting any of the EUtils to work.

I have tried the dbIds client sample code:

 >>> result = client.search("dalke", retmax = 100)

Traceback (most recent call last):
   File "<pyshell#24>", line 1, in -toplevel-
     result = client.search("dalke", retmax = 100)
   File "C:\Python23\lib\site-packages\Bio\EUtils\DBIdsClient.py", line 
294, in search
     searchinfo = parse.parse_search(infile, [None])
   File "C:\Python23\lib\site-packages\Bio\EUtils\parse.py", line 219, in 
parse_search
     raise TypeError("Unknown OP code: %r" % (s,))
TypeError: Unknown OP code: u'GROUP'

NCBI changing things around so the EUtils packages breaks?

Peter


At 12:24 PM 8/3/2004, Brad Chapman wrote:
>Hi Peter;
>
> > >I suddenly had an urge to query entrez with python ....
> > >
> > >I have looked through the latest release ... but did not find an entrez
> > >module
>[...]
> > I just found the interface in Bio.WWW
>
>The best way to query Entrez from programs is using the EUtils
>interfaces at NCBI:
>
>http://eutils.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html
>
>Biopython has a interface to EUtils in Bio.EUtils. There is a lot of
>source code documentation within there. For instance, for an example
>of retrieving PubMed information, Bio.EUtils.HistoryClient provides
>some good code examples:
>
>http://www.biopython.org/docs/api/public/Bio.EUtils.HistoryClient-module.html
>
>The only thing you have to do is adjust the imports to be from
>Biopython, like from Bio.EUtils import HistoryClient (sorry, older
>documentation from when EUtils was not within Biopython -- I updated
>this).
>
>If you have specific questions feel free to ask, but the EUtils
>interfaces should definitely be more stable than the older stuff in
>Bio.WWW.
>
>Hope this helps!
>Brad
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