Closed daler closed 11 years ago
Looks like a fantastic addition! I merged but can't run because I don't have bx.bbi.bigwig_file. Do you know what should be added to setup.py to auto-install this?
I added bx-python to setup.py and am in business. Pushed to repo.
It looks like precomputed.npz is not installed - I get a
IOError: [Errno 2] No such file or directory: '/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/scurgen-0.1.0-py2.7.egg/scurgen/precomputed.npz'
message. Is this a static file that should be installed with the package?
It looks like there is an expectation that the chrom2rc
method is available in all HilbertMatrix* objects. I ran the GUI with a BED file as an input, but it failed when calling chrom2rc, which is present in the BigWig subclass. At first glance it seems that this method should be in the base class?
I haven't figured out the best way to make precomputed.npz
. . . I think ideally it would be when running setup.py upon first install. For now though, run precompute.py
to make the .npz file.
Ah right, I forgot that I used chrom2rc
when making the chrom outlines. You're right, it's no longer bigWig-specific and should be in a base class
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:
bigwig=True
to thedata
section of a config).precompute.py
script which saves a compressed numpy array of precomputed d2rc coordsExample of GUI using bigWig input, with chrom boundaries:![example screenshot](https://f.cloud.github.com/assets/115406/14045/756cdaec-4627-11e2-8153-dbf40cb511d1.png)