diff --git a/jass/__main__.py b/jass/__main__.py index dba983274adcc66881a32efe6e0e54e4770d643c..551bd53947b71df5a7bd3c0df0988100cc50ac25 100644 --- a/jass/__main__.py +++ b/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)