[Biopython] help! entrez esearch popset issue

[Bartha Dániel]

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