Beispiel #1
0
def main():
    param_dict = parse_param()
    n_pop = len(param_dict['pop'])

    for chrom in param_dict['chrom']:
        print('##### process chromosome %d #####' % int(chrom))

        ref_dict = parse_genet.parse_ref(param_dict['ref_dir'] + '/snpinfo_mult_hm3', int(chrom))

        vld_dict = parse_genet.parse_bim(param_dict['bim_prefix'], int(chrom))

        sst_dict = {}
        for pp in range(n_pop):
            sst_dict[pp] = parse_genet.parse_sumstats(ref_dict, vld_dict, param_dict['sst_file'][pp], param_dict['pop'][pp], param_dict['n_gwas'][pp])

        ld_blk = {}
        blk_size = {}
        for pp in range(n_pop):
            ld_blk[pp], blk_size[pp] = parse_genet.parse_ldblk(param_dict['ref_dir'], sst_dict[pp], param_dict['pop'][pp], int(chrom))

        snp_dict, beta_dict, frq_dict, idx_dict = parse_genet.align_ldblk(ref_dict, vld_dict, sst_dict, n_pop, int(chrom))

        mcmc_gtb.mcmc(param_dict['a'], param_dict['b'], param_dict['phi'], snp_dict, beta_dict, frq_dict, idx_dict, param_dict['n_gwas'], ld_blk, blk_size,
            param_dict['n_iter'], param_dict['n_burnin'], param_dict['thin'], param_dict['pop'], int(chrom),
            param_dict['out_dir'], param_dict['out_name'], param_dict['meta'], param_dict['seed'])

        print('\n')
Beispiel #2
0
def main():
    param_dict = parse_param()

    for chrom in param_dict['chrom']:
        print('##### process chromosome %d #####' % int(chrom))

        ref_dict = parse_genet.parse_ref(
            param_dict['ref_dir'] + '/snpinfo_1kg_hm3', int(chrom))

        vld_dict = parse_genet.parse_bim(param_dict['bim_prefix'], int(chrom))

        sst_dict = parse_genet.parse_sumstats(ref_dict, vld_dict,
                                              param_dict['sst_file'],
                                              param_dict['n_gwas'])

        ld_blk, blk_size = parse_genet.parse_ldblk(param_dict['ref_dir'],
                                                   sst_dict, int(chrom))

        mcmc_gtb.mcmc(param_dict['a'], param_dict['b'], param_dict['phi'],
                      sst_dict, param_dict['n_gwas'], ld_blk, blk_size,
                      param_dict['n_iter'], param_dict['n_burnin'],
                      param_dict['thin'], int(chrom), param_dict['out_dir'],
                      param_dict['beta_std'])

        print('\n')