[Biopython-dev] Re: [BioPython] documentation issues

[Michiel Jan Laurens de Hoon]

I asked NCBI about this and it turned out that this was due to an error at NCBI. 
The error was fixed and the code below works again with Biopython's CVS version. 
With release 1.30, a different error appears, which was fixed in CVS about six 
months ago. Maybe it is time for a new release?

--Michiel.

Michiel Jan Laurens de Hoon wrote:
> andrea rossi wrote:
> 
>>     from Bio import GenBank
>>
>>     gi_list = GenBank.search_for("Opuntia AND rpl16")
>>     print " gi_list[0] ", gi_list[0]
>>
>> I get the message:
>>
>>     gi_list[0]  Error: Sequence Viewer does not have any Presentations
>> for code='uilist_text'
>>
>> instead of:
>>
>>    ['6273291', '6273290', '6273289', '6273287', '6273286', '6273285',
>> '6273284']
> 
> 
> It seems that NCBI no longer accepts the "uilist" identifier. E.g. try 
> the url
> 
> http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?retmode=text&tool=EUtils_P 
> 
> ython_client&db=nucleotide&email=biopython-dev%40biopython.org&rettype=uilist&id 
> 
> =6273291
> 
> Does anybody know what this should be?
> 
> 

-- 
Michiel de Hoon, Assistant Professor
University of Tokyo, Institute of Medical Science
Human Genome Center
4-6-1 Shirokane-dai, Minato-ku
Tokyo 108-8639
Japan
http://bonsai.ims.u-tokyo.ac.jp/~mdehoon