Merge branch 'main' of https://gitlab.rrz.uni-hamburg.de/bay2046/cami

cami_src/cami_suite.py

@@ -374,21 +374,16 @@ class cami():
             # for visualization with nvenn
             self.result_gene_sets[cami_method_name] = set(cami_genes)
             
-            
-            # transform all vertex indices to their corresponding gene names in a result set
-            for tool in result_sets:
-                self.result_gene_sets[tool.name] = set([gene_name_map[vertex] for vertex in result_sets[tool]])
+            sys.setrecursionlimit(recursion_limit)
+            # save the results in outputfiles
+            self.generate_output(cami_method_name, seed_genes, cami_vlist, cami_vertices, putative_vertices, cami_genes,
+                                 gene_name_map, codes2tools, cami_scores)
             
          # add seeds to result sets for drugstone and digest
         for toolname in self.result_gene_sets:
             self.result_module_sets[toolname] = self.result_gene_sets[toolname].union(set([gene_name_map[svertex] for svertex in self.seed_lst]))
             print(f'With the {len(seed_genes)} seed genes the module predicted by {toolname} contains {len(self.result_module_sets[toolname])} genes')
 
-            sys.setrecursionlimit(recursion_limit)
-            # save the results in outputfiles
-            self.generate_output(cami_method_name, seed_genes, cami_vlist, cami_vertices, putative_vertices, cami_genes,
-                                 gene_name_map, codes2tools, cami_scores)
-
     def generate_output(self, cami_method, seed_genes, cami_vlist, cami_vertices, putative_vertices, cami_genes,
                         gene_name_map, codes2tools, cami_scores):
         # save all predictions by all tools