[glu-genetics] push by bioinformed@gmail.com - Add --signal option to CNV exporters on 2013-06-27 15:35 GMT

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

Revision: e86b1215af41
Branch: default
Author: Kevin Jacobs <kevin....@invitae.com>
Date: Thu Jun 27 08:34:12 2013
Log: Add --signal option to CNV exporters
http://code.google.com/p/glu-genetics/source/detail?r=e86b1215af41

Modified:
/glu/modules/convert/to_bseg.py
/glu/modules/convert/to_gada.py
/glu/modules/convert/to_oncosnp.py
/glu/modules/convert/to_penncnv.py

=======================================
--- /glu/modules/convert/to_bseg.py Wed Aug 17 12:52:21 2011
+++ /glu/modules/convert/to_bseg.py Thu Jun 27 08:34:12 2013
@@ -27,6 +27,8 @@

parser.add_argument('gdatfile', help='GLU GDAT input file')

+ 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('--includesamples', metavar='FILE', action='append',
@@ -50,11 +52,11 @@
transform = GenoTransform.from_object(options)

gdat = GDATFile(options.gdatfile)
- data = gdat.cnv_iter(transform)
+ data = gdat.cnv_iter(transform, raw=options.signal.lower()=='raw')

if gccorrect:
+ manifest = gdat.attrs['ManifestName'].replace('.bpm','')
print 'Loading GC/CpG model for %s...' % manifest
- manifest = gdat.attrs['ManifestName'].replace('.bpm','')
filename = options.gcmodel or '%s/%s.gcm' %
(options.gcmodeldir,manifest)
gcdesign,gcmask = get_gcmodel(filename, gdat.chromosome_index)

=======================================
--- /glu/modules/convert/to_gada.py Wed Aug 17 12:52:21 2011
+++ /glu/modules/convert/to_gada.py Thu Jun 27 08:34:12 2013
@@ -57,6 +57,8 @@

parser.add_argument('gdatfile', help='GLU GDAT input file')

+ 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('--includesamples', metavar='FILE', action='append',
@@ -80,11 +82,11 @@
transform = GenoTransform.from_object(options)

gdat = GDATFile(options.gdatfile)
- data = gdat.cnv_iter(transform)
+ data = gdat.cnv_iter(transform, raw=options.signal.lower()=='raw')
genomap = {'AA':'AA','AB':'AB','BB':'BB',' ':'NC'}

if gccorrect:
- manifest = gdat.attrs['ManifestName'].replace('.bpm','')
+ manifest = gdat.attrs['ManifestName'].replace('.bpm','')
print 'Loading GC/CpG model for %s...' % manifest
filename = options.gcmodel or '%s/%s.gcm' %
(options.gcmodeldir,manifest)
gcdesign,gcmask = get_gcmodel(filename, gdat.chromosome_index)
=======================================
--- /glu/modules/convert/to_oncosnp.py Wed Aug 17 12:52:21 2011
+++ /glu/modules/convert/to_oncosnp.py Thu Jun 27 08:34:12 2013
@@ -57,6 +57,8 @@

parser.add_argument('gdatfile', help='GLU GDAT input file')

+ 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('--includesamples', metavar='FILE', action='append',
@@ -81,11 +83,11 @@

gdat = GDATFile(options.gdatfile)
manifest = gdat.attrs['ManifestName'].replace('.bpm','')
- data = gdat.cnv_iter(transform)
+ data = gdat.cnv_iter(transform, raw=options.signal.lower()=='raw')

if gccorrect:
+ manifest = gdat.attrs['ManifestName'].replace('.bpm','')
print 'Loading GC/CpG model for %s...' % manifest
- manifest = gdat.attrs['ManifestName'].replace('.bpm','')
filename = options.gcmodel or '%s/%s.gcm' %
(options.gcmodeldir,manifest)
gcdesign,gcmask = get_gcmodel(filename, gdat.chromosome_index)

=======================================
--- /glu/modules/convert/to_penncnv.py Wed Aug 17 12:52:21 2011
+++ /glu/modules/convert/to_penncnv.py Thu Jun 27 08:34:12 2013
@@ -27,7 +27,7 @@

transform = GenoTransform.from_object(options)
gdat = GDATFile(options.gdatfile)
- data = gdat.cnv_iter(transform)
+ data = gdat.cnv_iter(transform, raw=options.signal.lower()=='raw')
genomap = {'AA':'AA','AB':'AB','BB':'BB',' ':'NC'}

for sample,snps,geno,lrr,baf in data: