[BioPython] Adding new database types to EUtils

Peter biopython at maubp.freeserve.co.uk
Tue Dec 4 11:16:36 UTC 2007


> Hello.
> I've been trying to use EUtils to do run some queries through NCBI, but
> apparently GEO isn't present in the database list defined by [Biopython's] EUtils:

I guess the first thing to do is double check that the NCBI EUtils API
will support
GEO files, and then see if you can manage to fetch anything "by hand".

It is very simple to construct a URL by hand to fetch a GEO file
directly (bypassing EUtils).

Once you have downloaded the GEO files, what do you plan to do with them?
Biopython's GEO parser is very basic...

Peter

P.S. If you use R/BioConductor, I would recommend Sean Davis' GEOquery
for this sort of thing.



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