diff --git a/jass_preprocessing/__main__.py b/jass_preprocessing/__main__.py index 30d6985e955c69f27618fe80b589f39679bd1e4b..9ef13c528af2363abbdc80a24a906fd44b5d1f10 100644 --- a/jass_preprocessing/__main__.py +++ b/jass_preprocessing/__main__.py @@ -62,9 +62,9 @@ def launch_preprocessing(args): print("#SNPs mapped to reference panel: {}".format(mgwas.shape[0])) mgwas = jp.map_reference.compute_snp_alignement(mgwas) mgwas = jp.compute_score.compute_z_score(mgwas) - mgwas = jp.compute_score.compute_sample_size(mgwas, args.diagnostic_folder, tag, args.percent_sample_size) + mgwas = jp.compute_score.compute_sample_size(mgwas, args.diagnostic_folder, tag, float(args.percent_sample_size)) end = time.time() - + print("#SNPs remaining after sample size filter: {}".format(mgwas.shape[0])) print("Preprocessing of {0} in {1}s".format(tag, end-start)) jp.save_output.save_output_by_chromosome(mgwas, args.output_folder, tag)