qiime/qiime — pull request #875 by wdwvt1 (2013-04-18 06:19:43+00:00)
Title: new: make_bipartitenetwork.py

This pull request adds a new script called make_bipartite_network.py to QIIME. Creation of bipartite networks has been cumbersome with make_otu_network.py since we upgraded to biom format. In addition the code was hard to maintain and most users I queried hadn't ever heard of it or used its features. This code aims to replace the functionality of that code with a significantly easier interface that provides more flexibility and more control over the parameters that have proved important in making Cytoscape visualizations. Included are a script, library code, tests, and test data. As @lkursell and I are the only ones who seem to use this script on a frequent basis I think it would be good if he and one of the core development team reviewed this script before inclusion.

On a related note, I think we should eliminate the make_otu_network.py before QIIME 1.7 as it really does not work with the biom format and it doesn't produce output sufficient to get a plot -- you have to roll a lot of your own code to make it work. I have not eliminated it in this pull request because 1) that seems like a different issue, and 2) I haven't yet been able to make sense of some parts of the G_test portions of the code well enough to know if we need to port that functionality (though I know Luke and I don't use it and I don't know of someone who does).