From 54a5ba3b03c036e8d5358e66ccb367ebc0a3caec Mon Sep 17 00:00:00 2001 From: Hanna JULIENNE <hanna.julienne@pasteur.fr> Date: Fri, 21 Feb 2025 10:54:57 +0100 Subject: [PATCH] - Correct naming of custom loadings in create_wk - correct strategy selection order - removed the strategy option --- jass/__main__.py | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/jass/__main__.py b/jass/__main__.py index 4a7cd1e8..39d030fd 100644 --- a/jass/__main__.py +++ b/jass/__main__.py @@ -143,16 +143,17 @@ def compute_worktable(args): pos_Start = args.start_position pos_End = args.end_position - if args.omnibus: - strategy = "jass.models.stats:omnibus_stat" - elif args.sumz: + + if args.sumz: strategy = "jass.models.stats:sumz_stat" elif args.fisher_test: strategy = "jass.models.stats:fisher_test" elif args.meta_analysis: strategy = "jass.models.stats:meta_analysis" else: - strategy = args.strategy + strategy = "jass.models.stats:omnibus_stat" + #elif args.strategy is not None: + # strategy = args.strategy create_worktable_file( phenotype_ids=selected_phenotypes, @@ -169,7 +170,7 @@ def compute_worktable(args): chromosome=chromosome, pos_Start=pos_Start, pos_End=pos_End, - custom_loadings=custom_loadings, + loadings=custom_loadings, ) @@ -400,7 +401,6 @@ def get_parser(): strategies.add_argument("--sumz", action="store_true", default=False) strategies.add_argument("--fisher_test", action="store_true", default=False) strategies.add_argument("--meta_analysis", action="store_true", default=False) - strategies.add_argument("--strategy") parser_create_pd.set_defaults(func=w_create_project_data) @@ -533,7 +533,6 @@ def get_parser(): strategies.add_argument("--sumz", action="store_true", default=False) strategies.add_argument("--fisher_test", action="store_true", default=False) strategies.add_argument("--meta_analysis", action="store_true", default=False) - strategies.add_argument("--strategy") parser_create_wt.set_defaults(func=w_create_worktable) -- GitLab