[BioPython] Problem with Entrez?

Sebastian Bassi sbassi at gmail.com
Sun Aug 24 23:00:08 UTC 2008


On Sun, Aug 24, 2008 at 7:46 PM, Sebastian Bassi <sbassi at gmail.com> wrote:
>> As a workaround I specify the format with  rettype='gb'
> Sorry, the workaround is to set retmode to xml:
> handle = Entrez.efetch(db="nucleotide", id="326625", retmode='xml')
> But I thought that this should be default behivor.

My proposed solution is:

Change line

variables = {'db' : db}

To:

variables = {'db' : db , 'retmode' : 'xml'}

In Bio/Entrez/__init__.py

Doing this, it work as expected, but I don't know if this breaks something else.


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