[Biopython-dev] Genbank dbSNP support

[Peter]

On Mon, Mar 31, 2008 at 11:13 PM, Tiago Antão <tiagoantao at gmail.com> wrote:
> Hi,
>
>  Any plans for dbSNP support?
>  http://www.ncbi.nlm.nih.gov/SNP/index.html
>
>  I think I would volunteer to implement this. A simple solution would
>  be to add both databases and return types. Michiel (I suppose this is
>  code that you are actively maintaining, or it is Peter?), can I send
>  you a diff? I have done this once already for genome -
>  http://portal.open-bio.org/pipermail/biopython/2007-January/003347.html

I think Michiel has been dealing with this sort of stuff
(NCBIDictionary and Bio.Entrez).  I would file an enhancement bug, and
attach your patch to it.

>  dbSNP can return different types (
>  http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetchseq_help.html#rettypeparam
>  ) so a few parsers would be needed for complete support. But that can
>  be done later...

We should already be able to parse their Fasta, GenBank or GenPept
output.  The lists of IDs should also be trivial.  I haven't looked at
the other formats.

Peter