arq5x/scurgen — pull request #33 by daler (2012-12-14 20:08:12+00:00)
Title: GUI updates, bigWig support, docs, and more

Big chunk o' commits, but I think the end result is a substantial improvement. The bigWig support speeds things up nicely since data are essentially pre-binned.

Summary of changes:

* sphinx docs with custom template for autodocs and API summary tables
* lots of docstrings to help make sense of things when returning to the code base after a few weeks . . .
* use default chroms from pybedtools
* support for bigWig (see HilbertMatrixBigWig class; use it by simply adding a `bigwig=True` to the `data` section of a config).
* refactored HilbertGUI into HilbertPlot (which exposes all the knobs and dials as an API, useful for batch plotting) and HilbertGUI (which adds the GUI widgets to control said knobs)
* colormap adjustments
* `precompute.py` script which saves a compressed numpy array of precomputed d2rc coords
* save() method now ignores GUI widgets
* chromosome outlines (implemented as a contour)

Example of GUI using bigWig input, with chrom boundaries:
![example screenshot](https://f.cloud.github.com/assets/115406/14045/756cdaec-4627-11e2-8153-dbf40cb511d1.png)