[BioPython] How to read SOFT files from GEO?

[Maurice Ling]

Sean Davis wrote:

> Maurice Ling wrote:
>
>> Hi,
>>
>> Are there any examples to read SOFT file from GEO? I've looked in the 
>> cookbook and there isn't any mention about GEO.
>>   
>
> I don't know of biopython code to do this, but there is a package for 
> the R statistical language that will do this.  The nice thing about 
> doing this from R is that there are hundreds of tools that can then be 
> applied to whatever data you like.  The package is part of 
> Bioconductor (http://www.bioconductor.org) and is called GEOquery.  
> And of course, you can use R from python using Rpy.
>
> Sean
>
> P.S.  Legal disclaimer--I am the author of said package, so take my 
> words with the appropriate grain of salt.
>
In biopython's CVS, there is a subdirectory called Geo. So I thought 
that might be for SOFT files...

ML

P.S. So I know who to ask when I have questions about GEOquery.