if the same node is provided as first argument to get_common_ancestor…

…, returns itself. Unittest of get_common_ancestor improved.

ete3/coretype/tree.py

@@ -884,10 +884,19 @@ def get_common_ancestor(self, *target_nodes, **kargs):
         # Convert node names into node instances
         target_nodes = _translate_nodes(self, *target_nodes)
 
-        # If only one node is provided, use self as the second target
-        if type(target_nodes) != list:
-            target_nodes = [target_nodes, self]
 
+        if type(target_nodes) != list:
+            # If only one node is provided and is the same as the seed node,
+            # return itself
+            if target_nodes is self:
+                if get_path:
+                    return self, {}
+                else:
+                    return self
+            else:
+                #Otherwise find the common ancestor of current seed node and
+                #the target_node provided
+                target_nodes = [target_nodes, self]
 
         n2path = {}
         reference = []
@@ -2442,7 +2451,7 @@ def cophenetic_matrix(self):
                 else:
                     output[i].append(leaf_distances[n][m])
         return output, allleaves
-                     
+
     def add_face(self, face, column, position="branch-right"):
         """
         .. versionadded: 2.1
@@ -2485,14 +2494,14 @@ def set_style(self, node_style):
 
     @staticmethod
     def from_parent_child_table(parent_child_table):
-        """Converts a parent-child table into an ETE Tree instance. 
-        
+        """Converts a parent-child table into an ETE Tree instance.
+
         :argument parent_child_table: a list of tuples containing parent-child
            relationships. For example: [("A", "B", 0.1), ("A", "C", 0.2), ("C",
            "D", 1), ("C", "E", 1.5)]. Where each tuple represents: [parent, child,
            child-parent-dist]
-        
-        :returns: A new Tree instance 
+
+        :returns: A new Tree instance
 
         :example:
 
@@ -2527,20 +2536,20 @@ def get_node(nodename, dist=None):
 
     @staticmethod
     def from_skbio(skbio_tree, map_attributes=None):
-        """Converts a scikit-bio TreeNode object into ETE Tree object. 
-        
-        :argument skbio_tree: a scikit bio TreeNode instance 
+        """Converts a scikit-bio TreeNode object into ETE Tree object.
+
+        :argument skbio_tree: a scikit bio TreeNode instance
 
         :argument None map_attributes: A list of attribute nanes in the
            scikit-bio tree that should be mapped into the ETE tree
            instance. (name, id and branch length are always mapped)
 
-        :returns: A new Tree instance 
+        :returns: A new Tree instance
 
         :example:
 
         >>> tree = Tree.from_skibio(skbioTree, map_attributes=["value"])
-        
+
         """
         from skbio import TreeNode as skbioTreeNode
 
@@ -2601,8 +2610,3 @@ def _translate_nodes(root, *nodes):
 # Alias
 #: .. currentmodule:: ete3
 Tree = TreeNode
-
-
-
-
-

ete3/test/test_tree.py

@@ -3,6 +3,7 @@
 import unittest
 import random
 import itertools
+import json
 
 import sys
 from six.moves import range
@@ -469,7 +470,7 @@ def test_common_ancestors(self):
         # getting nodes, get_childs, get_sisters, get_tree_root,
         # get_common_ancestor, get_nodes_by_name
         # get_descendants_by_name, is_leaf, is_root
-        t = Tree("(((A,B),C)[&&NHX:tag=common],D)[&&NHX:tag=root:name=root];")
+        t = Tree("(((A,B)N1,C)N2[&&NHX:tag=common],D)[&&NHX:tag=root:name=root];", format=1)
         self.assertEqual(t.get_sisters(), [])
 
         A = t.search_nodes(name="A")[0]
@@ -499,6 +500,24 @@ def test_common_ancestors(self):
         self.assert_(not A.get_tree_root().is_leaf())
         self.assertRaises(TreeError, A.get_common_ancestor, Tree())
 
+        # Test multiple target nodes and get_path argument
+        common, path = t.get_common_ancestor(['A', 'C'], get_path=True)
+        N1 = t & "N1"
+        N2 = t & "N2"
+        expected_path = {A: set([A, root, N1, N2]), C: set([C, N2, root])}
+        self.assertEqual(common, N2)
+        self.assertEqual(path.keys(), expected_path.keys())
+        for k in path.keys():
+            self.assertEqual(list(sorted(path[k])), list(sorted(expected_path[k])))
+
+        # Test common ancestor function using self as single argument (issue #398)
+        common = A.get_common_ancestor(A)
+        self.assert_(common, A)
+        common = C.get_common_ancestor("C")
+        self.assert_(common, C)
+        common, path = C.get_common_ancestor("C", get_path=True)
+        self.assertEqual(common, C)
+        self.assertDictEqual(path, {})
 
     def test_getters_iters(self):
 
@@ -863,12 +882,12 @@ def _astuple(d):
         # RF unrooted in too small trees
         self.assertEqual(_astuple(small.compare(ref1, unrooted=True)),
                          ("NA", "NA", 0.0, "NA", "NA", 2, 1, "NA"))
-        
+
         small = Tree("(A, B);")
         # RF unrooted in too small trees
         self.assertEqual(_astuple(small.compare(ref1, unrooted=False)),
                          ("NA", "NA", 0.0, "NA", "NA", 2, 1, "NA"))
-        
+
         # identical trees, 8 rooted partitions in total (4 an 4), and 6 unrooted
         self.assertEqual(_astuple(s1.compare(ref1)),
                          (0.0, 0.0, 8, 1.0, 1.0, 6, 1, "NA"))