def initSampleObj(powerDataObj):
'''
initialize a spower.Sample() object using information
contained in a pre-processed 'PowerData' object
'''
sampleObj = Sample()
sampleObj.seed(0, os.getpid())
sampleObj.set(**powerDataObj.data)
return sampleObj
def initSampleAndPowerdata(configFile, srvResFile, srvGeneRep=None):
'''
initialize a spower.Sample() object and a PowerData object
srvGeneRep - gene replicate # to be used in powerdata, randomly sample a gene replicate if None
'''
args, srvData = spowerArgsNData(configFile, srvResFile, srvGeneRep)
powerdata = PowerData(args, [], srvData)
powerdata.update_fixed()
powerdata.update_random()
sampleObj = Sample()
sampleObj.seed(0, os.getpid())
sampleObj.set(**powerdata.data)
return sampleObj, powerdata
from spower.utils import getLogger
from spower.simulator.sampler import Sample
if __name__ == "__main__":
d = Sample(getLogger(1))
d.seed(0, 1)
c = d.clone()
c.seed(0, 1)
#
##### generate disease by PAR
#s = Sample()
#s.seed(0)
#s.set(**powerdata.data)
#L.GenotypeGenerator().apply(s.data)
#L.PARModel(powerdata.data['par'], powerdata.data['PAR_variable']).apply(s.data)#L.ORModel(powerdata.data['odds_ratio']).apply(s.data)
#L.DiseaseEffectGenerator(powerdata.data['baseline_effect']).apply(s.data)
#L.DiseaseStatusGenerator().apply(s.data)
#print powerdata.data['maf']
#print s.get('haplotype1'), s.get('haplotype2')
#print s.get('effect'),
#print s.get('phenotype')
#### generate qt
s = Sample()
s.seed(0)
print dir(s)
s.set(**powerdata.data)
#L.GenotypeGenerator().apply(s.data)
s.set(haplotype1=[0, 0, 1, 0, 0, 0, 1, 0, 1, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0],
haplotype2=[1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1])
L.MeanShiftModel(powerdata.data['mean_shift']).apply(s.data)
L.QtEffectGenerator().apply(s.data)
L.QtValueGenerator().apply(s.data)
print s.get('haplotype1'), s.get('haplotype2')
print s.get('effect')
print s.get('phenotype')
from spower.utils import getLogger
from spower.simulator.sampler import Sample
if __name__ == "__main__":
d = Sample(getLogger(1))
d.seed(0, 1)
c = d.clone()
c.seed(0, 1)
