From 48a615de40bab0dacb0d8755ffb0ee4f538a3708 Mon Sep 17 00:00:00 2001 From: hanna julienne <hanna.julienne@pasteur.fr> Date: Thu, 29 Nov 2018 17:49:12 +0100 Subject: [PATCH] cast command line args --- jass_preprocessing/__main__.py | 1 - jass_preprocessing/compute_score.py | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/jass_preprocessing/__main__.py b/jass_preprocessing/__main__.py index 9c62d8c..ce5fb5e 100644 --- a/jass_preprocessing/__main__.py +++ b/jass_preprocessing/__main__.py @@ -36,7 +36,6 @@ def launch_preprocessing(args): start = time.time() GWAS_link = jp.map_gwas.walkfs(args.gwas_folder, args.gwas_filename)[2] mapgw = jp.map_gwas.map_columns_position(GWAS_link, args.gwas_info) - print(mapgw) gw_df = jp.map_gwas.read_gwas(GWAS_link, mapgw) diff --git a/jass_preprocessing/compute_score.py b/jass_preprocessing/compute_score.py index db0e324..c275ceb 100644 --- a/jass_preprocessing/compute_score.py +++ b/jass_preprocessing/compute_score.py @@ -51,7 +51,7 @@ def compute_sample_size(mgwas, diagnostic_folder, trait, perSS = 0.7): warnings.warn("Some snp had an infinite sample size") myW_thres = np.percentile(myN.dropna(), 90) - ss_thres = perSS * myW_thres + ss_thres = int(perSS) * myW_thres mgwas["computed_N"] = myN plt.clf() p1 = sns.distplot(mgwas.computed_N[~mgwas.computed_N.isna()]) -- GitLab