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): ...@@ -36,7 +36,6 @@ def launch_preprocessing(args):
start = time.time() start = time.time()
GWAS_link = jp.map_gwas.walkfs(args.gwas_folder, args.gwas_filename)[2] 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) mapgw = jp.map_gwas.map_columns_position(GWAS_link, args.gwas_info)
print(mapgw)
gw_df = jp.map_gwas.read_gwas(GWAS_link, 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): ...@@ -51,7 +51,7 @@ def compute_sample_size(mgwas, diagnostic_folder, trait, perSS = 0.7):
warnings.warn("Some snp had an infinite sample size") warnings.warn("Some snp had an infinite sample size")
myW_thres = np.percentile(myN.dropna(), 90) myW_thres = np.percentile(myN.dropna(), 90)
ss_thres = perSS * myW_thres ss_thres = int(perSS) * myW_thres
mgwas["computed_N"] = myN mgwas["computed_N"] = myN
plt.clf() plt.clf()
p1 = sns.distplot(mgwas.computed_N[~mgwas.computed_N.isna()]) p1 = sns.distplot(mgwas.computed_N[~mgwas.computed_N.isna()])
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment