add tests

lib/scripts/rename_input_tree_ali_tdg09.py

@@ -93,6 +93,33 @@ except Exception as exc:
 
 logger.info("Ali (%s) ok after checking", AliFile.name)
 
+
+leaves_names = [ l.name for l in t.get_leaves()]
+seq_names = [ s.name for s in alignment]
+logger.info("leaves names: %s",leaves_names )
+logger.info("sequences names: %s",seq_names )
+
+seq_not_in_tree = set(seq_names) - set(leaves_names)
+leaves_not_in_ali = set(leaves_names) - set(seq_names)
+
+if len(set(seq_names)) != len(seq_names):
+    logger.error("There are duplicated sequence names")
+    sys.exit(1)
+if len(set(leaves_names)) != len(leaves_names):
+    logger.error("There are duplicated leaf names")
+    sys.exit(1)
+
+if seq_not_in_tree:
+    logger.error("Some sequences do not match with a leaf: %s",",".join(list(seq_not_in_tree)))
+    logger.error("All sequence names must match with a leaf")
+    sys.exit(1)
+elif leaves_not_in_ali:
+    logger.error("Some leaves do not match with a sequence: %s",",".join(list(leaves_not_in_ali)))
+    sys.exit(1)
+else:
+    logger.info("Sequence and leaf names match.")
+
+
 #===================================================================================================
 # Create output files
 #===================================================================================================