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

[Damian Menning]

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.

"There are two types of academics. Those who use the Oxford comma, those
who don't and those who should."

Standard comma - You know Bob, Sue and Greg? They came to my house.
Oxford comma - You know Bob, Sue, and Greg? They came to my house.
Walken Comma - You know, Bob, Sue, and Greg? They came, to my house.
Shatner comma - You, know, Bob, Sue, and Greg? They, came, to my house.
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