Commit 48a615de authored by Hanna  JULIENNE's avatar Hanna JULIENNE
Browse files

cast command line args

parent 2533e552
Pipeline #7903 passed with stages
in 1 minute and 27 seconds
......@@ -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)
......
......@@ -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()])
......
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