Enhancement: Use odf files as input

[AMChalkie]

LimmaGP and other genepattern tools output .odf files with differential expression information being able to use these directly would be helpful.

i.e.

vennt.py comparison1.odf,comparison2.odf,comparison3.odf

[drpowell]

I've never seen this before. Is that "odf" as in the "open document format"? Do you have an example?

[AMChalkie]

It is a Broad/GenePattern format:

http://www.broadinstitute.org/cancer/software/genepattern/gp_guides/file-formats/sections/odf

http://www.broadinstitute.org/cancer/software/genepattern/tutorial/linkedFiles/all_aml_train.preprocessed0.odf

[AMChalkie]

Actually in general being able to take the .odf, .gct and .cls/.clm files all together and working with those would be really cool, as these contain:
.odf: de data
.gct: Normalised/raw expression
.cls: sample-grouping (as in used by limmaGP)
.clm: naming betweeen raw sample ID, clean sample ID and sample group.

Just a thought - it seems sensible to be using consistent formats that are shareable. Talking with Mark Cowley about adding .odf output from a standard limma analysis would be useful here, as his limmaGP already deals with a lot of these formats and I'm sure he would be happy to see the results from his program directly input into deugst and vennt.