[glu-genetics] push by bioinformed@gmail.com - Add --signal option on 2013-11-08 13:42 GMT

[glu-ge...@googlecode.com]

Revision: 4d48eee7937d
Branch: default
Author: Kevin Jacobs <kevin....@invitae.com>
Date: Fri Nov 8 13:41:37 2013 UTC
Log: Add --signal option
http://code.google.com/p/glu-genetics/source/detail?r=4d48eee7937d

Modified:
/glu/modules/cnv/plot_events.py

=======================================
--- /glu/modules/cnv/plot_events.py Thu Aug 30 20:42:05 2012 UTC
+++ /glu/modules/cnv/plot_events.py Fri Nov 8 13:41:37 2013 UTC
@@ -504,6 +504,8 @@
parser.add_argument('events', help='Tablular or delimited file of
events')
parser.add_argument('index', help='Index file created by
cnv.index_gdats')

+ parser.add_argument('--signal', metavar='TYPE', default='norm',
choices=['norm','raw'],
+ help='LRR/BAF signal processing: raw
or norm (default)')
parser.add_argument('--gcmodel', metavar='GCM', help='GC model file
to use')
parser.add_argument('--gcmodeldir', metavar='DIR', help='GC models
directory')
parser.add_argument('--outdir', metavar='DIR', help='Plot output
directory', default='.')
@@ -593,7 +595,7 @@

print 'GDAT:ASSAY =',gdatname,assay

- assay_id,genos,lrr,baf = gdat.cnv_data(offset)
+ assay_id,genos,lrr,baf = gdat.cnv_data(offset,
raw=options.signal.lower()=='raw')
normal_mask =
build_normal_mask(len(lrr),chrom_indices,assay_events,options)
valid_mask = (lrr>=-2)&(lrr<=2)
valid_mask &= autosome_mask