Commit 375a23e4 authored by Hanna  JULIENNE's avatar Hanna JULIENNE
Browse files

fix type

parent 2cc3f8a9
......@@ -16,13 +16,13 @@ def launch_chromosome_imputation(args):
zscore = pd.read_csv(z_file,index_col=0, sep="\t")
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)
imputed_zscore = imputer.chromosome_imputation(args.chrom, zscore, ref_panel, args.ld_folder)
print("Imputation DONE")
z_fo = "{0}/z_{1}_{2}.txt".format(args.output_folder, args.gwas, args.chrom)
imputed_zscore.to_csv(z_fo, sep='\t')
print("Save imputation done ")
print("Save imputation done at {0}".format(z_fo))
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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