From d9c78ca590fc79e53aad664aa2fc202117a906f9 Mon Sep 17 00:00:00 2001
From: Eric Talevich <eric.talevich@gmail.com>
Date: Mon, 26 Aug 2013 13:15:25 -0700
Subject: [PATCH] NewickIO: parse branch lengths in scientific notation (Issue
 #220)

Included a unit test for it, too.

Thanks to mathli for reporting this bug and offering a fix.
---
 Bio/Phylo/NewickIO.py | 17 +++++++++--------
 Tests/test_Phylo.py   |  7 +++++++
 2 files changed, 16 insertions(+), 8 deletions(-)

diff --git a/Bio/Phylo/NewickIO.py b/Bio/Phylo/NewickIO.py
index 38cf2a1b424..698b37a6e38 100644
--- a/Bio/Phylo/NewickIO.py
+++ b/Bio/Phylo/NewickIO.py
@@ -20,13 +20,13 @@
 class NewickError(Exception):
     """Exception raised when Newick object construction cannot continue."""
     pass
-    
-    
+
+
 tokens = [
     (r"\(",                         'open parens'),
     (r"\)",                         'close parens'),
     (r"[^\s\(\)\[\]\'\:\;\,]+",     'unquoted node label'),
-    (r"\:[0-9]*\.?[0-9]+",          'edge length'),
+    (r"\:[0-9]*\.?[0-9]+([eE][+-]?[0-9]+)?", 'edge length'),
     (r"\,",                         'comma'),
     (r"\[(\\.|[^\]])*\]",           'comment'),
     (r"\'(\\.|[^\'])*\'",           'quoted node label'),
@@ -70,11 +70,11 @@ def _parse_confidence(text):
         # assert 0 <= current_clade.confidence <= 1
     except ValueError:
         return None
-        
-        
+
+
 def _format_comment(text):
     return '[%s]' % (text.replace('[', '\\[').replace(']', '\\]'))
-    
+
 def _get_comment(clade):
     if hasattr(clade, 'comment') and clade.comment:
         return _format_comment(str(clade.comment))
@@ -207,12 +207,13 @@ def new_clade(self, parent=None):
     def process_clade(self, clade):
         """Final processing of a parsed clade. Removes the node's parent and
         returns it."""
-        if (clade.name and not (self.values_are_confidence or self.comments_are_confidence)
+        if (clade.name and not (self.values_are_confidence or
+                                self.comments_are_confidence)
             and clade.confidence is None):
             clade.confidence = _parse_confidence(clade.name)
             if not clade.confidence is None:
                 clade.name = None
-            
+
         if hasattr(clade, 'parent'):
             parent = clade.parent
             parent.clades.append(clade)
diff --git a/Tests/test_Phylo.py b/Tests/test_Phylo.py
index d1512e77955..a766f86f748 100644
--- a/Tests/test_Phylo.py
+++ b/Tests/test_Phylo.py
@@ -67,6 +67,13 @@ def test_newick_write(self):
                 if c is not None)
         self.assertEqual(internal_names, set(('E', 'F')))
 
+    def test_newick_read_scinot(self):
+        """Parse Newick branch lengths in scientific notation."""
+        tree = Phylo.read(StringIO("(foo:1e-1,bar:0.1)"), 'newick')
+        clade_a = tree.clade[0]
+        self.assertEqual(clade_a.name, 'foo')
+        self.assertAlmostEqual(clade_a.branch_length, 0.1)
+
     def test_format_branch_length(self):
         """Custom format string for Newick branch length serialization."""
         tree = Phylo.read(StringIO('A:0.1;'), 'newick')