[BioPython] biopython and dbSNP (2)

[Peter (BioPython List)]

Teemu Kuulasmaa wrote:
> Hi,
> 
> I made some experimentations and got GenBank.search_for() and 
> GenBank.download_many() to work with dbSNP. However, I didn't succeed to 
> get GenBank.NCBIDictionary() to work. I do not know if this is right way 
> to do it. It would by nice if someone (biopython-dev) could speak out on 
> the matter.
> 
> Here are two very small diffs (against biopython version 1.41) that were 
> required to get dbSNP sequence retrieval to work:

I'm not familiar with this aspect of the GenBank support, but your code 
looks OK to me.

I tried your two changes on the CVS version of EUtils and GenBank and it 
works for me (the GenBank file has had significant changes to the file 
parser).

One question is are the GenBank.search_for() and GenBank.download_many() 
functions intended just for "GenBank" (officially just the nucleotides?) 
or other sequence based EUtils databases like proteins, snp, ..., or 
even genomes.

Unless anyone else cares to comment, I'll commit Teemu's two small 
changes in the next few days.

As to getting GenBank.NCBIDictionary() to work with the snp database, 
its not as easy as it looks.

Peter