Commit a889f9c2 authored by Hanna  JULIENNE's avatar Hanna JULIENNE
Browse files

fix commit

parent 62fee36f
...@@ -14,14 +14,14 @@ def launch_chromosome_imputation(args): ...@@ -14,14 +14,14 @@ def launch_chromosome_imputation(args):
z_file = "{0}/z_{1}_{2}.txt".format(args.zscore_folder, args.gwas, args.chrom) z_file = "{0}/z_{1}_{2}.txt".format(args.zscore_folder, args.gwas, args.chrom)
zscore = pd.read_csv(z_file) zscore = pd.read_csv(z_file)
imputer.chromosome_imputation(args.chrom, zscore, ref_panel, ld_folder) imputer.chromosome_imputation(args.chrom, zscore, args.ref_panel, args.ld_folder)
def add_chromosome_imputation_argument(parser): def add_chromosome_imputation_argument(parser):
parser.add_argument('--chrom', required=True, help= "chromosome to impute to the chr\d+ format") parser.add_argument('--chrom', required=True, help= "chromosome to impute to the chr\d+ format")
parser.add_argument('--gwas', required=True, help= "GWAS to impute to the consortia_trait format") parser.add_argument('--gwas', required=True, help= "GWAS to impute to the consortia_trait format")
parser.add_argument('--ref-folder', required=True, help= "reference panel location (used to determine which snp to impute)") parser.add_argument('--ref-folder', required=True, help= "reference panel location (used to determine which snp to impute)")
parser.add_argument('--LD-folder', required=True, help= "Location LD correlation matrices") parser.add_argument('--ld-folder', required=True, help= "Location LD correlation matrices")
parser.add_argument('--zscore-folder', required=True, help= "Location of the zscore files of the gwases to impute") parser.add_argument('--zscore-folder', required=True, help= "Location of the zscore files of the gwases to impute")
parser.add_argument('--output-folder', required=True, help= "Location of the impute zscore files") parser.add_argument('--output-folder', required=True, help= "Location of the impute zscore files")
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