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