[Biopython] Entrez.efetch issue with the returning data type

[Anna Kostikova]

Dear Peter,

Thanks a lot for the prompt response. Yes, exactly, it was retmode="text" thing.
Thanks a lot again!

Anna

2012/2/28 Peter Cock <p.j.a.cock at googlemail.com>:
> On Tue, Feb 28, 2012 at 1:28 PM, Anna Kostikova
> <anna.kostikova at gmail.com> wrote:
>> Dear list,
>>
>> Since today I've started to have an issue with Entrez.efetch utility,
>> and in particular with the rettype parameter. Essentially, the format
>> of the data returned when I specify
>> Entrez.efetch(db='nucleotide',id='JQ042818.1',rettype='gb') does not
>> correspond anymore to a genbank datatype. Few days ago all was fine.
>> What is going on?
>
> The NCBI changed the defaults in mid Feb 2012 with the release of
> EFetch v2.0 - you must now add retmode="text" to the Entrez fetch
> call otherwise you'll probably get XML back. We mentioned this on
> the release notes for Biopython 1.59, but I should probably add this
> link as well:
>
> http://www.ncbi.nlm.nih.gov/mailman/pipermail/utilities-announce/2012-February/000085.html
>
> Peter