def __call__(self, labtekL=None):
if labtekL is None:
labtekL = self.labtekL
print 'BASE_DIR: ', self.baseDir
resD = {}
for labtek in labtekL:
spotConfD = LabtekConfiguration().getSpotConfForLabtek(labtek)
posL = spotConfD.keys()
for pos in posL:
sirna = spotConfD[pos]['sirnaId']
gene = spotConfD[pos]['geneName']
try:
spotRes = spotAnalyzer.spotAnalyzer(labtek, pos,
baseDir=self.baseDir,
spotConfD=spotConfD, prediction_suffix='_prediction_track.dat')
phenoSpotD, countL = spotRes.readPrediction()
id = '%s--%s' % (labtek, pos)
resD[id] = {'initCellCount': countL[0], 'endCellCount': countL[-1],
'proliferation': float(countL[-1]) / float(countL[0]),
'sirna': sirna, 'gene': gene}
except:
resD[id] = {'initCellCount': 0, 'endCellCount': 0,
'proliferation': 0.0,
'sirna':sirna, 'gene': gene}
return resD
def generateControlPlots(self, labtekId, control='scrambled'):
plotDir = os.path.join(self.baseDir, labtekId, 'plots', 'controls')
if not os.path.isdir(plotDir):
os.makedirs(plotDir)
if control == 'scrambled':
ctrlPosL = self.lc.negCtrPosL
elif control== 'empty':
ctrlPosL = self.lc.emptyL
elif control=='incenp':
ctrlPosL = self.lc.incenpL
else:
return
controlDataD = {}
controlDataRawD = {}
controlProliferationD = {}
controlProliferationFitD = {}
spotConfD = LabtekConfiguration().getSpotConfForLabtek(labtekId)
control_len = None
for pos in ctrlPosL:
try:
id = '%s--%s' % (labtekId, pos)
spotRes = spotAnalyzer.spotAnalyzer(labtekId, pos, baseDir=self.baseDir,
spotConfD=spotConfD, prediction_suffix='_prediction_track.dat')
phenoSpotD, countL = spotRes.readPrediction()
if control_len is None:
control_len = len(countL)
if countL[0] > 0:
controlProliferationD[pos] = [float(countL[i])/float(countL[0]) for i in range(len(countL))]
else:
controlProliferationD[pos] = [0.0 for i in range(len(countL))]
controlProliferationFitD[pos] = spotRes.fitCellCount(controlProliferationD[pos])
control_len = min(control_len, len(countL))
# calculate the data for all pheno classes
normD = spotRes.normalizePrediction(phenoSpotD, countL)
fitPredD = spotRes.fitPrediction(normD)
for pheno in phenoSpotD.keys():
if not controlDataRawD.has_key(pheno):
controlDataRawD[pheno] = {}
if not controlDataD.has_key(pheno):
controlDataD[pheno] = {}
controlDataRawD[pheno][pos] = normD[pheno]
controlDataD[pheno][pos] = fitPredD[pheno]
except:
print 'no data for %s' % pos
for pheno in ['Prometaphase', 'MetaphaseAlignment', 'Shape1', 'Shape3', 'Apoptosis']:
try:
full_filename = os.path.join(plotDir, control + '_' + pheno + '.png')
self.plotBundle(controlDataD[pheno], full_filename, colorsD = None, bundlePointsD = controlDataRawD[pheno],
title='%s for control %s' % (pheno, control), y_max=0.4)
# proliferation
full_filename = os.path.join(plotDir, control + '_proliferation.png')
self.plotBundle(controlProliferationFitD, full_filename, bundlePointsD = controlProliferationD, title='proliferation for control %s' % control, y_max=5.0)
except:
print 'no plot for %s' % control
return
