Fix output names

Author: aghozlane

meteor/treebuilder.py

@@ -108,19 +108,15 @@ def execute(self) -> None:
         phylogeny_process.execute()
         # Analyze tree data
         for tree_file in phylogeny_process.tree_files:
-            # Check for a .raxml.bestTree file
-            # raxml_tree_file = self.meteor.tree_dir / f"{msp_file.stem}.raxml.bestTree"
-            # if raxml_tree_file.exists():
-            #     tree_file = raxml_tree_file
-            # else:
-            #     # If no .raxml.bestTree file exists, check for a .tree file
-            #     tree_file = self.meteor.tree_dir / f"{msp_file.stem}.tree"
-            img_file = self.meteor.tree_dir / f"{tree_file.stem}.{self.format}"
+            output = tree_file
+            if tree_file.suffix == ".bestTree":
+                output = tree_file.with_suffix("")
+            img_file = self.meteor.tree_dir / f"{output.stem}.{self.format}"
             # try:
             msp_tree = Tree(str(tree_file.resolve()))
             # Generate a distance msp by msp
             matrix = self.get_msp_distance(msp_tree)
-            matrix.to_csv(self.meteor.tree_dir / f"{tree_file.stem}.tsv", sep="\t")
+            matrix.to_csv(self.meteor.tree_dir / f"{output.stem}.tsv", sep="\t")
             # Draw trees
             if not self.format:
                 pass