fix error during tree pruning

lib/scripts/filter_input_tree.py

@@ -185,14 +185,24 @@ else:
 trim_t = t.copy(method="deepcopy")
 
 if sp_present:
-    trim_t.prune(sp_present)
+    trim_t.prune(sp_present,preserve_branch_length=True)
+    # Check father node transition if Condition == 1
+    for n in trim_t.traverse("postorder"):
+        if (hasattr(n, "Condition") and n.Condition == "1"):
+            if not (hasattr(n, "Transition") and n.Transition == "1"):
+                parent_n = n.up
+                if not parent_n.Condition == "1":
+                    if not (hasattr(parent_n, "Transition") and parent_n.Transition == "1"):
+                        n.Transition = "1"
+
     sister_T = True
     while sister_T:
         sister_T=False
         for n in trim_t.traverse("postorder"):
+            # Check for 2 sister Transitions
             children = n.get_children()
             if len(children) == 2:
-                if hasattr(children[0], "Transition" ) and  hasattr(children[1], "Transition" ):
+                if hasattr(children[0], "Transition") and  hasattr(children[1], "Transition"):
                     if children[0].Transition == "1" and children[1].Transition == "1":
                         n.Transition = "1"
                         n.Condition = "1"