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

[Karolis Ramanauskas]

I see, you can never make everyone happy. Thanks.

On Wed, Feb 29, 2012 at 04:28, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> On Wed, Feb 29, 2012 at 4:01 AM, Karolis Ramanauskas <karolisr at gmail.com> wrote:
>> 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.
>>
>> Karolis
>
> Hi Karolis,
>
> That has downsides too - take the NCBI QBLAST API for calling an
> online BLAST search at the NCBI. Biopython has default values
> which (I presume) once matched the NCBI, but the NCBI has changed
> things. As a result, the defaults have diverged and we often see user
> queries about why their BLAST results via Biopython are different.
>
> You could write to the NCBI Entrez team and urge them to consider
> backwards compatibility more strongly.
>
> Peter
>
> P.S. I've added an FAQ entry about EFetch defaults to the tutorial:
> https://github.com/biopython/biopython/commit/2a2ef7ab7b5a9c3ed3891922df7e2d47e2701faf