[BioPython] Adding new database types to EUtils

[Luca Beltrame]

Il Tuesday 04 December 2007 12:16:36 Peter ha scritto:

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

It was mostly to check their basic description to see if they were feasible to 
be included in my current work. As I have a large list of accessions, 
fetching them all at once would reduce the time needed to go through them. To 
be more clear, downloading their summary. 

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

I mostly use it when I need to download data set information and expression 
levels. For this simpler task, I turned to Python first as GEOquery has some 
performance issues on my machine.

I'll take a look at NCBI's EUils and see if they support GEO. Thanks for the 
tip.

-- 
Luca Beltrame, MSc. - Molecular Medicine PhD Student
Dipartimento di Scienze e Tecnologie Biomediche - UniMI
CNR - Institute of Biomedical Technologies Research Fellow
E-mail: luca.beltrame at unimi.it - Phone: +39-02-50320924
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