[Biopython] help! entrez esearch popset issue

[Iddo Friedberg]

Default number of records returned is 20.

Read about the retmax and retstart arguments to see how to increase that
number:

http://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch




On Tue, Feb 4, 2014 at 5:38 AM, Bartha Dániel <bartha.daniel at agrar.mta.hu>wrote:

> Hi People,
>
> I have an issue with biopythons esearch/efetch, and this drives me crazy.
>
> If I search for something in the PopSet, like this, but the query is
> arbitrary:
>
> query = "Homo sapiens[Organism] NOT mitochondrion[All Fields]";
>
> esearch_handle = Entrez.esearch(db="popset", term=query)
> search_results = Entrez.read(esearch_handle)
> accnos = search_results['IdList']
>
> I get somehow always only 20 results in my IdList, but with the same term,
> many thousands on the website. Is this a bug?
>
> Because by default, on the website, 20 results per page are shown, and
> surprise, my 20 results are equal with the first page. The biopython
> documentation regarding the PopSet DB is not very talkative, so I ask you,
> how do I solve this problem elegant ("python only")?
>
> Since the same constellation doesn't cause any issues by searching in the
> protein or other sequence DB, either has the PopSet DB some tricks I don't
> kow or this is a BUG(?).
>
>
> Regards:
>
> Daniel
>
>
>
> --
> Dániel Bartha, molecular bionics engineer, BSc
> Bioinformatician
> Institute for Veterinary Medical Research
> Centre for Agricultural Research
> Hungarian Academy of Sciences
> Hungária körút 21.
> Budapest
> 1143
> Hungary
>
> e-mail:
> bartha.daniel at agrar.mta.hu
>
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> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>



-- 
Iddo Friedberg
http://iddo-friedberg.net/contact.html
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