Minor bug fix.

Traverse tree optionally doesn't reset params.
Fix tip parsing bug.

Author: evogytis

baltic/baltic.py

@@ -167,7 +167,7 @@ def subtree(self,k=None,traverse_condition=None,stem=True):
             Returns a new baltic tree instance.
             Note - custom traversal functions can result in multitype trees.
             If this is undesired call singleType() on the resulting subtree afterwards. """
-        subtree=copy.deepcopy(self.traverse_tree(k,include_condition=lambda k:True,traverse_condition=traverse_condition))
+        subtree=copy.deepcopy(self.traverse_tree(k,include_condition=lambda k:True,traverse_condition=traverse_condition,reset_branches=False))
 
         if subtree is None or len([k for k in subtree if k.branchType=='leaf'])==0:
             return None
@@ -256,14 +256,15 @@ def treeStats(self):
 
         print('\nNumbers of objects in tree: %d (%d nodes and %d leaves)\n'%(len(obs),len(nodes),len(self.getExternal()))) ## report numbers of different objects in the tree
 
-    def traverse_tree(self,cur_node=None,include_condition=lambda k:k.branchType=='leaf',traverse_condition=lambda k:True,collect=None,verbose=False):
-        if cur_node==None: ## if no starting point defined - start from root
+    def traverse_tree(self,cur_node=None,include_condition=lambda k:k.branchType=='leaf',traverse_condition=lambda k:True,collect=None,reset_branches=True,verbose=False):
+        if reset_branches:
             for k in self.Objects: ## reset various parameters
                 if k.branchType=='node':
                     k.leaves=set()
                     k.childHeight=None
                 k.height=None
 
+        if cur_node==None: ## if no starting point defined - start from root
             if verbose==True: print('Initiated traversal from root')
             cur_node=self.root
 
@@ -286,7 +287,7 @@ def traverse_tree(self,cur_node=None,include_condition=lambda k:k.branchType=='l
         elif cur_node.branchType=='node': ## cur_node is node
             for child in filter(traverse_condition,cur_node.children): ## only traverse through children we're interested
                 if verbose==True: print('visiting child %s'%(child.index))
-                self.traverse_tree(cur_node=child,include_condition=include_condition,traverse_condition=traverse_condition,verbose=verbose,collect=collect) ## recurse through children
+                self.traverse_tree(cur_node=child,include_condition=include_condition,traverse_condition=traverse_condition,verbose=verbose,collect=collect,reset_branches=False) ## recurse through children
                 if verbose==True: print('child %s done'%(child.index))
             assert len(cur_node.children)>0, 'Tried traversing through hanging node without children. Index: %s'%(cur_node.index)
             cur_node.childHeight=max([child.childHeight if child.branchType=='node' else child.height for child in cur_node.children])
@@ -982,7 +983,7 @@ def make_tree(data,ll=None,verbose=False):
     """
     patterns = {
         'beast_tip': r'(\(|,)([0-9]+)(\[|\:)',
-        'non_beast_tip': r'(\(|,)(\'|\")*([^\(\):\[]+)(\'|\"|)(\[)*'
+        'non_beast_tip': r'(\(|,)(\'|\")*([^\(\):\[\'\"]+)(\'|\"|)*(\[)*'
     }
     if isinstance(data,str)==False: ## tree string is not an instance of string (could be unicode) - convert
         data=str(data)