[Biopython] Formatting of the xml return from Entrez DB Gene is not parsed correctly

[Michael S. Koeris]

Hi Peter,

I am using

handle = Entrez.efetch(db='gene', id=UID['Activin B'][0][0],  
rettype='xml')
testDic = handle.read()

UID['Activin B'][0][0] is the unique gene number I grabbed earlier  
through an Entrez.esearch and in this case is : 90

Many thanks
Mike





On Sep 11, 2009, at 5:34 AM, Peter wrote:

> On Thu, Sep 10, 2009 at 10:47 PM, Michael S. Koeris
> <michael.koeris at gmail.com> wrote:
>> Hi,
>>
>> I am trying to parse out the nucleic acid accession numbers from an
>> Entrez.efetch query made to the Gene database. For some reason the  
>> parser
>> does not create a dictionary when I call handle.read on it, even  
>> when I
>> force the query to return xml. It just generates a string.
>
> Can you give us a tiny example script? Just fill in the missing bit  
> here ;)
>
> from Bio import Entrez
> handle = Entrez.efetch(...)
> record = Entrez.read(handle)
> print record
>
> Peter