time

gseapy/gsea.py

@@ -308,15 +308,15 @@ def load_classes(self, classes: Union[str, List[str], Dict[str, Any]]):
             self.pheno_neg = neg
             self.groups = cls_vector
 
-        if self._outdir is not None:
-            self.to_cls(outdir=self.outdir)
-
     def to_cls(self, outdir: str):
         """Save group information to cls file"""
         with open(os.path.join(outdir, "group.cls"), "w") as f:
             f.write(f"{len(self.groups)} 2 1\n")
             f.write(f"# {self.pheno_pos} {self.pheno_neg}\n")
-            f.write(" ".join(self.groups) + "\n")
+            if isinstance(self.groups, dict):
+                f.write(" ".join(list(self.groups.values())) + "\n")
+            else:
+                f.write(" ".join(self.groups) + "\n")
 
     # @profile
     def run(self):
@@ -411,6 +411,7 @@ def run(self):
         # write output and plotting
         self.to_df(gsum.summaries, gmt, self.ranking)
         if self._outdir is not None:
+            self.to_cls(outdir=self.outdir)
             self.ranking.to_csv(
                 os.path.join(self.outdir, "gsea_data.rnk"), sep="\t", header=False
             )