cast command line args

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)
 

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()])