[Biopython] Blank Returns from Entrez.efetch()

Brett Bowman bnbowman at gmail.com
Sat Jan 9 22:53:31 UTC 2010


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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