[BioRuby] A class for GEO

[Pjotr Prins]

On Thu, May 06, 2010 at 04:48:32PM +0900, Naohisa GOTO wrote:
> The GEO support was first proposed in September 2008, but it was
> pending because of some matters, and no one wanted to work to merge.

In my repository is a functional GEO XML file format parser, for GEO
experiments, array batches and microarray data. I used it for a meta
analysis.

The main issue was that my implementation caches downloaded XML files.
For 'security' reasons the implementation was rejected. And there were
some other minor syntax things. I never got round to making it Bioruby
compliant. 

I have lost interest in microarrays, but you can simply pull my
branch and have a look at the implementation. It is not my greatest
work, though the code is succinct enough.

It makes sense to make this a plugin.

I may pick it up again when there is enough deep sequencing data on
GEO.

Pj.

PS. Don't use the GEO SOFT format - it is not consistent.