[Biopython] [Entrez/eFetch] "reasonable" package

[Peter Cock]

Yes, GenBank files are nice in that you can just concatenate them.
You can't do that with XML files.

Pete

On Wed, Dec 2, 2015 at 10:11 PM, Damian Menning <dmenning at mail.usf.edu> wrote:
> I did something similar with complete genbank files.  What worked for me was
> just appending to the same file for each run.
>
> Damian
>
> On Wed, Dec 2, 2015 at 12:39 PM, <c.buhtz at posteo.jp> wrote:
>>
>> I asked the Entrez support how should I tread the servers resources
>> with "respect". :)
>>
>> First answer was without discrete numbers but in the second one they
>> told me asking for 500 (retmax for eSearch) is a "reasonable" value
>> because the eBot (a tool they offer on their website) use it, too.
>>
>> No I have nearly 13.000 PIDs I want to fetch their article infos via
>> eFetch. It is a lot. ;)
>>
>> But I am not sure how to do that with biopython. When I separate that
>> in 500-packages I would have 26 different record objects back.
>> I don't like that. I would prefer one big record object I can analyse.
>>
>> Do you see a way to merge this record objects. Or maybe there is
>> another way for that?
>> Or does Biopython.Entrez still handle that problem internal (like the
>> only-3-per-second-querys-rule or the HTTP-POST-decision)?
>>
>> Any suggestions?
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>
>
>
> --
> Damian Menning, Ph.D.
>
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