fixed main

jass/__main__.py

@@ -25,7 +25,7 @@ def compute_worktable(args):
     selected_phenotypes = args.phenotypes
     worktable_path = args.worktable_path
     remove_nan = not (args.keep_nans)
-    significance_treshold = args.significance_treshold
+    significance_treshold = float(args.significance_treshold)
     post_filtering = args.post_filtering
     custom_loadings=args.custom_loadings
 
@@ -48,8 +48,11 @@ def w_create_worktable(args):
 
 def w_create_project_data(args):
     compute_worktable(args)
+    worktable_path = args.worktable_path
+    manhattan_plot_path = args.manhattan_plot_path
+    quadrant_plot_path = args.quadrant_plot_path
     create_global_plot(worktable_path, manhattan_plot_path)
-    create_quadrant_plot(worktable_path, quadrant_plot_path, significance_treshold = significance_treshold)
+    create_quadrant_plot(worktable_path, quadrant_plot_path, significance_treshold = float(args.significance_treshold))
 
 
 def w_create_inittable(args):
@@ -66,11 +69,6 @@ def w_create_inittable(args):
         init_table_path,
     )
 
-
-
-
-
-
 def w_plot_manhattan(args):
     worktable_path = args.worktable_path
     plot_path = args.plot_path
@@ -208,6 +206,12 @@ def get_parser():
         default=True,
         help="If a filtering to remove outlier will be applied (in this case the result of SNPs considered aberant will not appear in the worktable)"
     )
+
+    parser_create_wt.add_argument(
+        "--custom-loadings",
+        required=False,
+        help="path toward a csv file containing custom loading for sumZ tests",
+    )
     parser_create_wt.add_argument("--keep-nans", action="store_true", default=False)
     strategies = parser_create_wt.add_mutually_exclusive_group()
     strategies.add_argument("--omnibus", action="store_true", default=True)