Nevermind....RE: [BioPython] EUtils and SNPs

Bonis Sanz, Julio JBonis at
Wed Nov 10 09:20:27 EST 2004


I found myself the answer to my last question:  :)

>>> eutils = ThinClient.ThinClient()
>>> dbids = DBIds("snp",["6313"])
>>> infile = eutils.efetch_using_dbids(dbids,rettype='flt',retmode='html')

-----Mensaje original-----
De: biopython-bounces at
[mailto:biopython-bounces at]En nombre de Bonis Sanz,
Enviado el: miércoles, 10 de noviembre de 2004 15:03
Para: biopython at
Asunto: RE: [BioPython] EUtils and SNPs

By the way:

I want to send this to EUtils:

but snp is not defined as a valid db in DBIds ... any fast solution?

where are the DBIds databases defined?


Julio Bonis Sanz

-----Mensaje original-----
De: Andrew Dalke [mailto:dalke at]
Enviado el: miércoles, 10 de noviembre de 2004 8:46
Para: Bonis Sanz, Julio
CC: biopython at
Asunto: Re: [BioPython] EUtils and SNPs

Hi Julio,

> But now it doesnt work. The reason is that in EUtils (PubMed) now it 
> is needed to add a parameter... "extrafeat=1" to get the SNPs 
> (variations).....

Interesting.  That isn't documented that I know about.  How did you
find out about it?

> I have "fix" the problem touching the code in the script 
> /EUtils/

Okay, I'll add that to the EUtils v.2 package I announced here a
couple months ago.  Haven't gotten any feedback on it.  Anyone tried it?

> Maybe te biopython developers team want to include this in someway for 
> future releases.

Mmm, so the question is how to pass extra parameters from the NCBIDict
to the EUtils package.

I've been working on other projects since that preview release.  I'll
bump up the priority on it.

					dalke at

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