[glu-genetics] push by bioinformed@gmail.com - Add ability to specify extra variables for use in file naming and plot... on 2013-02-08 16:52 GMT

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

Revision: e80f17030992
Branch: default
Author: Kevin B. Jacobs <jac...@bioinformed.com>
Date: Fri Feb 8 08:51:44 2013
Log: Add ability to specify extra variables for use in file naming and
plot
titles.
http://code.google.com/p/glu-genetics/source/detail?r=e80f17030992

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

=======================================
--- /glu/modules/cnv/plot_gdat.py Fri Jul 20 09:54:30 2012
+++ /glu/modules/cnv/plot_gdat.py Fri Feb 8 08:51:44 2013
@@ -1,4 +1,4 @@
- # -*- coding: utf-8 -*-
+# -*- coding: utf-8 -*-

__gluindex__ = True
__abstract__ = 'Plot intensity and allelic ratio data from a single GDAT
file'
@@ -11,15 +11,8 @@
import sys

import numpy as np
-import scipy
-import scipy.stats

-from itertools import groupby
-from operator import itemgetter,attrgetter
-
-from collections import namedtuple
-
-from glu.lib.fileutils import table_reader, table_writer
+from glu.lib.fileutils import table_reader

from glu.modules.cnv.gdat import GDATFile, get_gcmodel, gc_correct
from glu.modules.cnv.plot import plot_chromosome
@@ -27,6 +20,41 @@
from glu.lib.genolib.transform import GenoTransform


+def load_extravars(filename):
+ extravars = {}
+
+ if not filename:
+ return extravars,extravars
+
+ data = table_reader(filename)
+ header = next(data)
+
+ if 'GDAT' not in header:
+ raise ValueError('extravars must have a "GDAT" column')
+
+ if 'ASSAY' not in header:
+ raise ValueError('extravars must have an "ASSAY" column')
+
+ for row in data:
+ vars = dict(zip(header,row))
+ gdat = vars.get('GDAT')
+ assay = vars.get('ASSAY')
+
+ if not gdat or not assay:
+ continue
+
+ key = gdat,assay
+
+ if key in extravars:
+ raise KeyError('duplicate extra variable information for %s' % key)
+
+ extravars[key] = vars
+
+ extradummy = dict( (k,'') for k in header )
+
+ return extravars,extradummy
+
+
def option_parser():
from glu.lib.glu_argparse import GLUArgumentParser

@@ -45,6 +73,9 @@
help='Plot name template
(default={GDAT}_{ASSAY}_chr{CHROMOSOME}.png)')
parser.add_argument('--title', metavar='VAL', default='Intensity
plot of {GDAT}:{ASSAY} chr{CHROMOSOME}',
help="Plot name template
(default='Intensity plot of {GDAT}:{ASSAY} chr{CHROMOSOME}')")
+ parser.add_argument('--extravars', metavar='FILE',
+ help='Table of extra variables on
each sample to add information to the '
+ 'title and filename template. Table
must have GDAT and ASSAY columns.')
parser.add_argument('--includesamples', metavar='FILE', action='append',
help='List of samples to include,
all others will be skipped')
parser.add_argument('--excludesamples', metavar='FILE', action='append',
@@ -60,7 +91,8 @@
gccorrect = bool(options.gcmodel or options.gcmodeldir)
gdat = GDATFile(options.gdat)

- gdatname
= '_'.join(os.path.basename(gdat.filename).replace('.gdat','').split('_')[:2])
+ gdatraw = os.path.basename(gdat.filename).replace('.gdat','')
+ gdatname = '_'.join(gdatraw.split('_')[:2])
manifest = gdat.attrs['ManifestName'].replace('.bpm','')

print 'Loading manifest for %s...' % manifest
@@ -84,6 +116,8 @@
else:
include = exclude = None

+ extravars,extradummy = load_extravars(options.extravars)
+
for offset,assay in enumerate(gdat.samples):
if include is not None and assay not in include:
continue
@@ -130,7 +164,14 @@
chrom_baf[mask].mean(),1.96*chrom_baf[mask].std(),
het_baf.mean(),1.96*het_baf.std())

- variables = dict(GDAT=gdatname,ASSAY=assay,CHROMOSOME=chrom)
+ extra = extravars.get( (gdatraw,assay), {} )
+ if not extra:
+ extra = extravars.get( (gdatname,assay), {} )
+ defvars = dict(GDAT=gdatname,ASSAY=assay,CHROMOSOME=chrom)
+
+ variables = extradummy.copy()
+ variables.update(extra)
+ variables.update(defvars)

plotname = options.template.format(**variables)
plotname = '%s/%s' % (options.outdir,plotname)