def main():
param_dict = parse_param()
for chrom in param_dict['chrom']:
print('##### process chromosome %d #####' % int(chrom))
if '1kg' in os.path.basename(param_dict['ref_dir']):
ref_dict = parse_genet.parse_ref(
param_dict['ref_dir'] + '/snpinfo_1kg_hm3', int(chrom))
elif 'ukbb' in os.path.basename(param_dict['ref_dir']):
ref_dict = parse_genet.parse_ref(
param_dict['ref_dir'] + '/snpinfo_ukbb_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'], param_dict['seed'])
print('\n')
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')