[BioPython] How to read SOFT files from GEO?

[Sean Davis]

Maurice Ling wrote:
> 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...
>
I haven't tried it lately, but last I looked, it was not in-sync with 
GEO (which does infrequently change tags/formats).  Also, I think it 
handles GDS only (if I remember correctly).  Only a subset of GEO is 
available as GDS, since they require hand-curation by GEO staff.

http://portal.open-bio.org/pipermail/biopython-dev/2006-May/002352.html

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

Comments and questions are welcome and appreciated.

Sean