[Biopython-dev] Biopython for GDS SOFT?

[Peter (BioPython Dev)]

Ramon Aragues wrote:
> Hi,
> 
> I-ve seen your post on the bipython discussion list (from 2005) about  
> GDS SOFT files.
> 
> Has any work been done on it since then? Can I use biopython for  
> parsing GDS SOFT files?

Yes, I checked in some revisions to the Bio/Geo files in Jan 2006, and 
it seemed to work for me.

http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/Geo/?cvsroot=biopython

I also added the examples the NCBI provided to document their 2005 file 
format changes to the BioPython GEO test suite.

I was only interested in some very basic exploration at the time, and 
then moved on to using Sean Davis' GEOquery for R/BioConductor instead. 
  I found this made statistical analysis and visualisation much easier.

In any event, looking at GDS SOFT files was rather an aside to my main 
research interests...

> I am already using biopython in my framework ( http://sbi.imim.es/piana 
> ) so it would be great if I can use biopython for this as well.

This should be possible once you update the Bio/Geo files to those from 
CVS or the next release of BioPython.  Please let us (me) know how you 
get on...

However, I think you will be on your own in terms of statistical data 
analysis with python.

> Cheers!
> 
> Ramon

Good luck

Peter