print "mret: " + str(mret)
if typ == "Wald":
print "SNPs: " + str(snps)
if typ == "Count":
print "pvals: " + str(pval)
print "\n\n\n"
print "Load Data!"
[y, BED] = getData(bedFil)
print "Calculating MU matrix"
if num < 1:
MU = MU_LMM(BED, (se2, sg2))
else:
MU = MU_LMM(BED, [num, epsilon])
if typ == "Top":
PrivGWAS.Top(MU, y, epsilon, mret, algor, savename)
elif typ == "Count":
PrivGWAS.count(MU, y, epsilon, pval, savename)
elif typ == "Wald":
PrivGWAS.wald(MU, y, epsilon, snps, savename)
elif typ == "Herit":
print "The estimated heritability:"
print "Sigma_e^2 is " + str(MU.se2)
print "Sigma_g^2 is " + str(MU.sg2)
print "Good bye!"
else:
print "Specified task " + typ + " not recognized."
print "Good bye!"
if __name__ == "__main__":
print "SNPs: "+str(snps);
if typ=="Count":
print "pvals: "+str(pval);
print "\n\n\n";
print "Load Data!"
[y,BED]=getData(bedFil);
print "Calculating MU matrix"
if num<1:
MU=MU_LMM(BED,(se2,sg2));
else:
MU=MU_LMM(BED,[num,epsilon]);
if typ=="Top":
PrivGWAS.Top(MU,y,epsilon,mret,algor,savename);
elif typ=="Count":
PrivGWAS.count(MU,y,epsilon,pval,savename);
elif typ=="Wald":
PrivGWAS.wald(MU,y,epsilon,snps,savename);
elif typ=="Herit":
print "The estimated heritability:"
print "Sigma_e^2 is "+str(MU.se2);
print "Sigma_g^2 is "+str(MU.sg2);
print "Good bye!"
else:
print "Specified task "+typ+" not recognized."
print "Good bye!"
if __name__=="__main__":
args=sys.argv;
print "threshold: "+str(pval);
if exact:
print "Use exact method!"
print "\n\n\n";
print "Load Data!"
[y,BED]=getData(bedFil);
print "Calculating MU matrix"
MU=MU_STRAT(BED,k);
if exact:
MU.calcMU(k,exact=True);
n=len(y);
if typ=="Top":
PrivGWAS.Top(MU,y,epsilon,mret,algor,savename,snpList);
elif typ=="Count":
PrivGWAS.count(MU,y,epsilon,pval,savename);
elif typ=="Wald":
PrivGWAS.wald(MU,y,epsilon,snps,savename,coeff=float(n-k-1));
if __name__=="__main__":
args=sys.argv;
if len(args)>1 and args[1][0]!="-":
fil=open(args[1]);
lines=fil.readlines();
fil.close()
args=[];
args.append("UI.py")
print "SNPs: " + str(snps)
if typ == "Count":
print "threshold: " + str(pval)
if exact:
print "Use exact method!"
print "\n\n\n"
print "Load Data!"
[y, BED] = getData(bedFil)
print "Calculating MU matrix"
MU = MU_STRAT(BED, k)
if exact:
MU.calcMU(k, exact=True)
n = len(y)
if typ == "Top":
PrivGWAS.Top(MU, y, epsilon, mret, algor, savename, snpList)
elif typ == "Count":
PrivGWAS.count(MU, y, epsilon, pval, savename)
elif typ == "Wald":
PrivGWAS.wald(MU, y, epsilon, snps, savename, coeff=float(n - k - 1))
if __name__ == "__main__":
args = sys.argv
if len(args) > 1 and args[1][0] != "-":
fil = open(args[1])
lines = fil.readlines()
fil.close()
args = []
args.append("UI.py")
for l in lines:
