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

Karolis Ramanauskas karolisr at gmail.com
Wed Feb 29 04:01:30 UTC 2012

Good day,

I think it would be a good idea to not rely on the NCBI defaults in
Biopython and hardcode retmode and other defaults directly into the
Biopython methods. Basically having defaults that Biopython
guarantees. That way the defaults will not change haphazardly when
NCBI decides to change things. Of course users will still be able to
set their own parameters if they do not use default behavior, but this
would reduce unexpected changes and the need to go over long stretches
of code and change things.


On Tue, Feb 28, 2012 at 09:15, Anna Kostikova <anna.kostikova at gmail.com> wrote:
> 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
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