else: print 'There are {} common ids in phenotype files and PD data!'.format( np.sum(phen_ind != -1)) C_test = C[phen_ind] b_cov_test = b_cov[:, phen_ind] b4 = B4(phenotype, genotype) print("B4 shape is {}".format(b4.shape)) t_stat, SE = HASE(b4, a_inv, b_cov_test, C_test, N_con, DF) if mapper.cluster == 'y': Analyser.cluster = True Analyser.chunk = ch Analyser.node = mapper.node[1] Analyser.t_stat = t_stat Analyser.SE = SE Analyser.threshold = args.thr Analyser.out = args.out Analyser.save_result(phen_names[(phen_ind != -1)]) t_stat = None Analyser.t_stat = None gc.collect() else: t_stat, SE = HASE(b4, a_inv, b_cov, C, N_con, DF) Analyser.t_stat = t_stat Analyser.SE = SE Analyser.threshold = args.thr Analyser.out = args.out
phen_ind_inv=np.in1d(names,keys) if np.sum(phen_ind)==0: print 'There is no common ids in phenotype file {} and PD data!'.format((phen.folder._data.filename)) break C_test=C[phen_ind] b_cov_test=b_cov[:,phen_ind] b4 = B4(phenotype,genotype) t_stat,SE =HASE(b4, a_inv, b_cov_test, C_test, N_con, DF) if mapper.cluster=='y': Analyser.cluster=True Analyser.chunk=ch Analyser.node=mapper.node[1] Analyser.t_stat=t_stat Analyser.SE=SE Analyser.threshold=args.thr Analyser.out=args.out Analyser.save_result( names[phen_ind_inv] ) t_stat=None Analyser.t_stat=None gc.collect() else: t_stat,SE=HASE(b4, a_inv, b_cov, C, N_con, DF) Analyser.t_stat=t_stat Analyser.SE=SE Analyser.threshold=args.thr Analyser.out=args.out