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

[Peter Cock]

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