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