Preserve root branch length in Phylo.TreeMixin.prune

Bio/Phylo/BaseTree.py

@@ -660,8 +660,8 @@ class TreeMixin:
     def prune(self, target=None, **kwargs):
         """Prunes a terminal clade from the tree.
 
-        If taxon is from a bifurcation, the connecting node will be collapsed
-        and its branch length added to remaining terminal node. This might be no
+        If the taxon is from a bifurcation, the connecting node will be collapsed
+        and its branch length added to remaining terminal node. This might no
         longer be a meaningful value.
 
         :returns: parent clade of the pruned target
@@ -679,17 +679,14 @@ class TreeMixin:
         parent.clades.remove(path[-1])
         if len(parent) == 1:
             # We deleted a branch from a bifurcation
-            if parent == self.root:
+            child = parent.clades[0]
+            if child.branch_length is not None:
+                child.branch_length += parent.branch_length or 0.0
+            if len(path) == 1:
                 # If we're at the root, move the root upwards
-                # NB: This loses the length of the original branch
-                newroot = parent.clades[0]
-                newroot.branch_length = None
-                parent = self.root = newroot
+                parent = self.root = child
             else:
                 # If we're not at the root, collapse this parent
-                child = parent.clades[0]
-                if child.branch_length is not None:
-                    child.branch_length += parent.branch_length or 0.0
                 if len(path) < 3:
                     grandparent = self.root
                 else:

Doc/Tutorial/chapter_phylo.rst

@@ -352,7 +352,7 @@ function:
    >>> Phylo.write(tree1, "tree1.nwk", "newick")
    1
    >>> Phylo.write(trees, "other_trees.xml", "phyloxml")  # write the remaining trees
-   12
+   13
 
 Convert files between any of the supported formats with the ``convert``
 function:
@@ -364,7 +364,7 @@ function:
    >>> Phylo.convert("tree1.nwk", "newick", "tree1.xml", "nexml")
    1
    >>> Phylo.convert("other_trees.xml", "phyloxml", "other_trees.nex", "nexus")
-   12
+   13
 
 To use strings as input or output instead of actual files, use
 ``StringIO`` as you would with SeqIO and AlignIO:
@@ -681,7 +681,7 @@ tree intact, make a complete copy of the tree first, using Python’s
    sort clades deepest-to-shallowest.
 
 ``prune``
-   Prunes a terminal clade from the tree. If taxon is from a
+   Prunes a terminal clade from the tree. If the taxon is from a
    bifurcation, the connecting node will be collapsed and its branch
    length added to remaining terminal node. This might no longer be a
    meaningful value.

Tests/PhyloXML/phyloxml_examples.xml

@@ -408,6 +408,26 @@
          </clade>
       </clade>
    </phylogeny>
+   <phylogeny rooted="true">
+      <clade>
+         <branch_length>0.04</branch_length>
+         <clade>
+            <branch_length>0.06</branch_length>
+            <clade>
+               <name>A</name>
+               <branch_length>0.102</branch_length>
+            </clade>
+            <clade>
+               <name>B</name>
+               <branch_length>0.23</branch_length>
+            </clade>
+         </clade>
+         <clade>
+            <name>C</name>
+            <branch_length>0.4</branch_length>
+         </clade>
+      </clade>
+   </phylogeny>
    <align:alignment xmlns:align="http://example.org/align">
       <seq name="A">acgtcgcggcccgtggaagtcctctcct</seq>
       <seq name="B">aggtcgcggcctgtggaagtcctctcct</seq>

Tests/test_Phylo.py

@@ -150,7 +150,7 @@ class IOTests(unittest.TestCase):
         trees = Phylo.parse("PhyloXML/phyloxml_examples.xml", "phyloxml")
         with tempfile.NamedTemporaryFile(mode="w") as out_handle:
             count = Phylo.write(trees, out_handle, "phyloxml")
-        self.assertEqual(13, count)
+        self.assertEqual(14, count)
 
     def test_convert_phyloxml_filename(self):
         """Write phyloxml to a given filename."""
@@ -162,7 +162,7 @@ class IOTests(unittest.TestCase):
             count = Phylo.write(trees, tmp_filename, "phyloxml")
         finally:
             os.remove(tmp_filename)
-        self.assertEqual(13, count)
+        self.assertEqual(14, count)
 
     def test_int_labels(self):
         """Read newick formatted tree with numeric labels."""
@@ -471,6 +471,7 @@ class MixinTests(unittest.TestCase):
         tree = self.phylogenies[1]
         parent = tree.prune(name="C")
         self.assertEqual(parent, tree.root)
+        self.assertEqual(tree.root.branch_length, 0.06)
         self.assertEqual(len(parent.clades), 2)
         for clade, name, blen in zip(parent, "AB", (0.102, 0.23)):
             self.assertTrue(clade.is_terminal())
@@ -478,6 +479,10 @@ class MixinTests(unittest.TestCase):
             self.assertAlmostEqual(clade.branch_length, blen)
         self.assertEqual(len(tree.get_terminals()), 2)
         self.assertEqual(len(tree.get_nonterminals()), 1)
+        # Taxon just below root
+        tree = self.phylogenies[13]
+        parent = tree.prune(name="C")
+        self.assertEqual(tree.root.branch_length, 0.1)
 
     def test_split(self):
         """TreeMixin: split() method."""

Tests/test_PhyloXML.py

@@ -96,13 +96,13 @@ class ParseTests(unittest.TestCase):
     test_read_apaf = _test_read_factory(EX_APAF, (1, 0))
     test_read_bcl2 = _test_read_factory(EX_BCL2, (1, 0))
     test_read_made = _test_read_factory(EX_MADE, (6, 0))
-    test_read_phylo = _test_read_factory(EX_PHYLO, (13, 1))
+    test_read_phylo = _test_read_factory(EX_PHYLO, (14, 1))
     test_read_dollo = _test_read_factory(EX_DOLLO, (1, 0))
 
     test_parse_apaf = _test_parse_factory(EX_APAF, 1)
     test_parse_bcl2 = _test_parse_factory(EX_BCL2, 1)
     test_parse_made = _test_parse_factory(EX_MADE, 6)
-    test_parse_phylo = _test_parse_factory(EX_PHYLO, 13)
+    test_parse_phylo = _test_parse_factory(EX_PHYLO, 14)
     test_parse_dollo = _test_parse_factory(EX_DOLLO, 1)
 
     # lvl-2 clades, sub-clade counts, lvl-3 clades