Commit 883db9e9 authored by Hanna  JULIENNE's avatar Hanna JULIENNE
Browse files

added an essential logo when using RAISS with the command line

parent 3901cc4d
......@@ -23,7 +23,7 @@ def launch_chromosome_imputation(args):
def add_chromosome_imputation_argument():
parser = argparse.ArgumentParser()
parser = argparse.ArgumentParser(description="raiss command launch imputation for one trait on one chromosome")
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")
......@@ -41,7 +41,7 @@ def add_chromosome_imputation_argument():
parser.add_argument("--ld-type", help= "Ld can be supplied as plink command --ld-snp-list output files (see raiss.ld_matrix.launch_plink_ld to compute these data using plink) or as a couple of a scipy sparse matrix (.npz )and an .csv containing SNPs index", default="plink")
parser.add_argument('--ref-panel-prefix', help= "prefix for the reference panel files", default = "")
parser.add_argument('--ref-panel-suffix', help= "suffix for the reference panel files", default = ".bim")
parser.add_argument('--minimum-ld', help = "this parameter ensure that their is enough typed SNPs around the imputed to perform a high accuracy imputation", default = 4)
parser.add_argument('--minimum-ld', help = "this parameter ensure that their is enough typed SNPs around the imputed loci to perform a high accuracy imputation", default = 4)
parser.set_defaults(func=launch_chromosome_imputation)
return(parser)
......@@ -53,4 +53,16 @@ def main():
if __name__=="__main__":
print("", file=sys.stderr)
print(" ******* ******* ******* ******* *******", file=sys.stderr)
print(" ** ** ** ** *** ** **", file=sys.stderr)
print(" ** ** ** ** *** ** **", file=sys.stderr)
print(" ** ***** ** ** *** ****** ******", file=sys.stderr)
print(" ** ** *********** *** ** **", file=sys.stderr)
print(" ** ** ** ** *** ** **", file=sys.stderr)
print(" ** ** ** ** ******* ******* *******", file=sys.stderr)
print("", file=sys.stderr)
print("", file=sys.stderr)
main()
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