use regex on Bio.Nexus.Trees.Tree parser (#4624)

Bio/Nexus/Trees.py

@@ -14,6 +14,7 @@
 """
 
 import random
+import re
 import sys
 from . import Nodes
 
@@ -23,6 +24,10 @@
 NODECOMMENT_START = "[&"
 NODECOMMENT_END = "]"
 
+_re_block_delimiters = re.compile(
+    rf"({re.escape(NODECOMMENT_START)}|{re.escape(NODECOMMENT_END)}|[(),])"
+)
+
 
 class TreeError(Exception):
     """Provision for the management of Tree exceptions."""
@@ -85,48 +90,62 @@ def _parse(self, tree):
         # Remove any leading/trailing white space - want any string starting
         # with " (..." should be recognised as a leaf, "(..."
         tree = tree.strip()
+
         if tree.count("(") != tree.count(")"):
             raise TreeError("Parentheses do not match in (sub)tree: " + tree)
         if tree.count("(") == 0:  # a leaf
             # check if there's a colon, or a special comment, or both  after the taxon name
             nodecomment = tree.find(NODECOMMENT_START)
             colon = tree.find(":")
             if colon == -1 and nodecomment == -1:  # none
-                return [tree, [None]]
+                branch, comment = tree, [None]
             elif colon == -1 and nodecomment > -1:  # only special comment
-                return [tree[:nodecomment], self._get_values(tree[nodecomment:])]
+                branch, comment = tree[:nodecomment], self._get_values(
+                    tree[nodecomment:]
+                )
             elif colon > -1 and nodecomment == -1:  # only numerical values
-                return [tree[:colon], self._get_values(tree[colon + 1 :])]
+                branch, comment = tree[:colon], self._get_values(tree[colon + 1 :])
             elif (
                 colon < nodecomment
             ):  # taxon name ends at first colon or with special comment
-                return [tree[:colon], self._get_values(tree[colon + 1 :])]
+                branch, comment = tree[:colon], self._get_values(tree[colon + 1 :])
             else:
-                return [tree[:nodecomment], self._get_values(tree[nodecomment:])]
+                branch, comment = tree[:nodecomment], self._get_values(
+                    tree[nodecomment:]
+                )
+
+            return [branch, comment]
         else:
             closing = tree.rfind(")")
             val = self._get_values(tree[closing + 1 :])
             if not val:
                 val = [None]
+
             subtrees = []
             plevel = 0
             prev = 1
             incomment = False
-            for p in range(1, closing):
-                if not incomment and tree[p] == "(":
-                    plevel += 1
-                elif not incomment and tree[p] == ")":
-                    plevel -= 1
-                elif tree[p:].startswith(NODECOMMENT_START):
-                    incomment = True
-                elif incomment and tree[p] == NODECOMMENT_END:
-                    incomment = False
-                elif not incomment and tree[p] == "," and plevel == 0:
-                    subtrees.append(tree[prev:p])
-                    prev = p + 1
 
+            blocks = _re_block_delimiters.split(tree[1:closing])
+
+            for idx, blk in enumerate(blocks):
+                if not incomment:
+                    if blk == "(":
+                        plevel += 1
+                    elif blk == ")":
+                        plevel -= 1
+                    elif blk == NODECOMMENT_START:
+                        incomment = True
+                    elif blk == "," and plevel == 0:
+                        p = sum(len(blk) for blk in blocks[: idx + 1])
+                        subtrees.append(tree[prev:p])
+                        prev = p + 1
+                elif blk == NODECOMMENT_END:
+                    incomment = False
             subtrees.append(tree[prev:closing])
+
             subclades = [self._parse(subtree) for subtree in subtrees]
+
             return [subclades, val]
 
     def _add_subtree(self, parent_id=None, tree=None):