Commit e59f1f07 authored by Hanna  JULIENNE's avatar Hanna JULIENNE

change default R2-thershold to 0.6 and correct type bug in main

parent f3be1a6a
Pipeline #8819 passed with stages
in 1 minute and 33 seconds
......@@ -31,7 +31,7 @@ def launch_chromosome_imputation(args):
#Formatting and filtering
# and Saving results
z_fo = "{0}/z_{1}_{2}.txt".format(args.output_folder, args.gwas, args.chrom)
filter_output(imputed_zscore, z_fo, args.R2_threshold)
filter_output(imputed_zscore, z_fo, float(args.R2_threshold))
print("Save imputation done at {0}".format(z_fo))
def add_chromosome_imputation_argument():
......@@ -50,7 +50,7 @@ def add_chromosome_imputation_argument():
parser.add_argument('--l2-regularization', help= "Size of the buffer around the imputation window", default = 0.1)
parser.add_argument('--eigen-threshold', help= "threshold under which eigen vectors are removed for the computation of the pseudo inverse", default = 0.1)
parser.add_argument('--R2-threshold', help= "R square (imputation quality) threshold bellow which SNPs are filtered from the output", default = 0.8)
parser.add_argument('--R2-threshold', help= "R square (imputation quality) threshold bellow which SNPs are filtered from the output", default = 0.6)
parser.set_defaults(func=launch_chromosome_imputation)
return(parser)
......
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