[BioPython] BioEutils

[Peter Wilkinson]

This is my first attempt with this package ... on win32 with what I think 
is the latest Biopython.


I would like to look up records for image clones like:

clone = client.search("IMAGE:624360",db="nucleotide")

This would be the way I look for a clone in the nucleotide set using the 
search field on the root of the ncbi homepage.  I know that this clone is 
in nucleotide, but this query does not work here, I get a result of length = 0.

or by accession number if the clone has one:

clone = client.search("AA759046",db="nucleotide")

however I get the following error

Traceback (most recent call last):
   File "<pyshell#8>", line 1, in -toplevel-
     clone = client.search("AA759046",db="nucleotide")
   File "C:\Python23\lib\site-packages\Bio\EUtils\HistoryClient.py", line 
354, in search
     searchinfo = parse.parse_search(infile, self.webenv_ref)
   File "C:\Python23\lib\site-packages\Bio\EUtils\parse.py", line 201, in 
parse_search
     for ele in pom["TranslationStack"]:
   File "C:\Python23\lib\site-packages\Bio\EUtils\POM.py", line 355, in 
__getitem__
     raise IndexError, "no item matches"
IndexError: no item matches.


I might be doing something wrong here, but I am just following the help 
manual.

Peter W.


At 12:44 PM 8/3/2004, Peter Wilkinson wrote:
>That is good to know. I will have a loot at the EUtils first.
>
>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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>
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