[Biopython] Blank Returns from Entrez.efetch()

[Michiel de Hoon]

Have you looked at the EUtils examples on the NCBI website? It shows one example for efetch from the protein database.

--Michiel.

--- On Sat, 1/9/10, Brett Bowman <bnbowman at gmail.com> wrote:

> From: Brett Bowman <bnbowman at gmail.com>
> Subject: [Biopython] Blank Returns from Entrez.efetch()
> To: biopython at biopython.org
> Date: Saturday, January 9, 2010, 5:53 PM
> I'm trying to query Entrez for a
> series of protein IDs with Biopython,
> but not having much success.  The sample code given in
> the tutorial
> works perfectly:
> 
> >>> handle = Entrez.efetch(db="nucleotide",
> id="186972394", rettype="gb")
> >>> print handle.read()
> 
> But when I change that to proteins and my IDs, I get an
> empty handle
> as a result:
> 
> >>> handle = Entrez.efetch(db="protein",
> id="Q81T62.1", rettype="gb")
> 
> I've tried this on Biopython 1.51 and 1.53, installed on
> Ubuntu 9.10,
> and I've tried it with every rettype imaginable, with no
> success.  Any
> ideas as to where I am going wrong?
> 
> -Brett Bowman
> Woelk Lab
> UCSD School of Medicine
> UCSD/SDSU Joint Program in Bioinformatics
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