Commit 12959804 authored by Hanna  JULIENNE's avatar Hanna JULIENNE
Browse files

fix launch_chromosome_imputation

parent e3237089
......@@ -14,7 +14,11 @@ def launch_chromosome_imputation(args):
z_file = "{0}/z_{1}_{2}.txt".format(args.zscore_folder, args.gwas, args.chrom)
zscore = pd.read_csv(z_file)
imputer.chromosome_imputation(args.chrom, zscore, args.ref_folder, args.ld_folder)
ref_panel_file = args.ref_folder + "/"+ args.chrom +".eur.1pct.bim"
ref_panel = pd.read_csv(ref_panel_file, sep="\t", names=['chr', "nothing", 'pos', 'Ref_all', 'alt_all'], index_col = 1)
imputer.chromosome_imputation(args.chrom, zscore, ref_panel, args.ld_folder)
def add_chromosome_imputation_argument(parser):
parser.add_argument('--chrom', required=True, help= "chromosome to impute to the chr\d+ format")
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