scripts: don't check if tree is rooted when not necessary

lib/scripts/parse_input_tree_bpp_sim_part.py

@@ -3,6 +3,7 @@
 #===================================================================================================
 
 ######### output trees for simulation
+t, nodeId = read_input_tree()
 
 ### tree.only_node_ids.nhx: a tree with numbered nodes
 t.write(format=1, features=["ND"], outfile = "%s/tree.only_node_ids.nhx" %(OutDirName),format_root_node=True)

lib/scripts/parse_input_tree_common_part.py

@@ -92,52 +92,54 @@ elif OutDirName: # if OutDirName is not a empty string we create the directory
 #===================================================================================================
 # Read input tree
 #===================================================================================================
-try:
-    t=Tree(TreeFile.name)
-except Exception as exc:
-    logger.error(str(exc))
-    sys.exit(1)
-
-if t:
-    features = []
-    for n in t.traverse("postorder"): # get all features:
-        features.extend(list(set(dir(n)) - set(dir(Tree()))))
-        features = list(set(features)) # list(set(*)) = remove duplicates
-    logger.info("No detected tag" if not features else "Detected tags: "+", ".join([f for f in features]))
-    
-    #check rooted tree
-    nb_root_children = len(t.get_children())
-    if nb_root_children > 2:
-        logger.error("Unrooted tree")
+def read_input_tree(ensure_tree_is_rooted = True):
+    try:
+        t=Tree(TreeFile.name)
+    except Exception as exc:
+        logger.error(str(exc))
         sys.exit(1)
 
-    if "ND" in features:
-        logger.warning("\"ND\" is in the detected tags but it will be removed by the programm")
-        features.remove("ND")
-    
-    if not "Condition" in features:
-        logger.error("\"Condition\" must be in the detected tags. \"Condition:1\" must identify nodes under the convergent model under Ha")
+    if t:
+        features = []
+        for n in t.traverse("postorder"): # get all features:
+            features.extend(list(set(dir(n)) - set(dir(Tree()))))
+            features = list(set(features)) # list(set(*)) = remove duplicates
+        logger.info("No detected tag" if not features else "Detected tags: "+", ".join([f for f in features]))
+
+        #check rooted tree
+        nb_root_children = len(t.get_children())
+        if ensure_tree_is_rooted and nb_root_children > 2:
+            logger.error("Unrooted tree")
+            sys.exit(1)
+
+        if "ND" in features:
+            logger.warning("\"ND\" is in the detected tags but it will be removed by the programm")
+            features.remove("ND")
+
+        if not "Condition" in features:
+            logger.error("\"Condition\" must be in the detected tags. \"Condition:1\" must identify nodes under the convergent model under Ha")
+            sys.exit(1)
+        if not "Transition" in features:
+            logger.error("\"Transition\" must be in the detected tags. \"Transition:1\" must identify nodes where there are transitions")
+            sys.exit(1)
+
+        if "Transition" in features:
+            logger.info("\"Transition\" is in the detected tags. \"Transition:1\" will be use to indicate OneChange model on this node")
+
+        # Check existing bl
+        branch_lengths = []
+        nodeId = 0
+        for node in t.traverse("postorder"):
+            node.add_features(ND=nodeId)
+            branch_lengths.append(node.dist)
+            nodeId = nodeId + 1
+        logger.debug("Branch length %s", branch_lengths)
+
+        if set(branch_lengths) == set([1.0]):
+            logger.warning("No branch length in %s, all branch length will be put to 1",tree_filename)
+
+    if not (t and branch_lengths):
         sys.exit(1)
-    if not "Transition" in features:
-        logger.error("\"Transition\" must be in the detected tags. \"Transition:1\" must identify nodes where there are transitions")
-        sys.exit(1)
-
-    if "Transition" in features:
-        logger.info("\"Transition\" is in the detected tags. \"Transition:1\" will be use to indicate OneChange model on this node")
-
-    # Check existing bl
-    branch_lengths = []
-    nodeId = 0
-    for node in t.traverse("postorder"):
-        node.add_features(ND=nodeId)
-        branch_lengths.append(node.dist)
-        nodeId = nodeId + 1
-    logger.debug("Branch length %s", branch_lengths)
-
-    if set(branch_lengths) == set([1.0]):
-        logger.warning("No branch length in %s, all branch length will be put to 1",tree_filename)
-
-if not (t and branch_lengths):
-    sys.exit(1)
 
-logger.info("Tree (%s) ok after checking", TreeFile.name)
+    logger.info("Tree (%s) ok after checking", TreeFile.name)
+    return(t, nodeId)

lib/scripts/parse_input_tree_diffsel_part.py

@@ -2,6 +2,8 @@
 # Create output files
 #===================================================================================================
 
+t, nodeId = read_input_tree(ensure_tree_is_rooted = False)
+
 #########  output trees for detection
 all_node_ids = range(nodeId-1)
 conv_node_ids = [n.ND for n in t.search_nodes(Condition = "1")]

lib/scripts/parse_input_tree_pcoc_part.py

 #########  output trees for detection
 
+t, _ = read_input_tree()
+
 ### tree.only_convergent_tags.nhx: a tree with only Condition and Transition tags
 t.write(format=1, features=["Condition","Transition"], outfile = "%s/tree.only_convergent_tags.nhx" %(OutDirName))

lib/scripts/parse_input_tree_topological_part.py

@@ -67,5 +67,6 @@ def build_conv_topo(t):
 
       return tconv
 
+t, _ = read_input_tree()
 tconv = build_conv_topo(t)
 tconv.write(format=1, outfile = "%s/tree.topological" %(OutDirName))