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# Copyright 2005-2008 by Frank Kauff & Cymon J. Cox. All rights reserved. 

# This code is part of the Biopython distribution and governed by its 

# license. Please see the LICENSE file that should have been included 

# as part of this package. 

# 

# Bug reports welcome: fkauff@biologie.uni-kl.de or on Biopython's bugzilla. 

"""Tree class to handle phylogenetic trees. 

 

Provides a set of methods to read and write newick-format tree descriptions, 

get information about trees (monphyly of taxon sets, congruence between trees, 

common ancestors,...) and to manipulate trees (reroot trees, split terminal 

nodes). 

""" 

 

from __future__ import print_function 

 

import random 

import sys 

from . import Nodes 

 

PRECISION_BRANCHLENGTH=6 

PRECISION_SUPPORT=6 

NODECOMMENT_START='[&' 

NODECOMMENT_END=']' 

 

 

class TreeError(Exception): 

    pass 

 

 

class NodeData(object): 

    """Stores tree-relevant data associated with nodes (e.g. branches or otus).""" 

    def __init__(self,taxon=None,branchlength=0.0,support=None,comment=None): 

        self.taxon=taxon 

        self.branchlength=branchlength 

        self.support=support 

        self.comment=comment 

 

 

class Tree(Nodes.Chain): 

    """Represents a tree using a chain of nodes with on predecessor (=ancestor) 

    and multiple successors (=subclades). 

    """ 

    # A newick tree is parsed into nested list and then converted to a node list in two stages 

    # mostly due to historical reasons. This could be done in one swoop). Note: parentheses ( ) and 

    # colon : are not allowed in taxon names. This is against NEXUS standard, but makes life much 

    # easier when parsing trees. 

 

    ## NOTE: Tree should store its data class in something like self.dataclass=data, 

    ## so that nodes that are generated have easy access to the data class 

    ## Some routines use automatically NodeData, this needs to be more concise 

 

    def __init__(self,tree=None,weight=1.0,rooted=False,name='',data=NodeData,values_are_support=False,max_support=1.0): 

        """Ntree(self,tree).""" 

        Nodes.Chain.__init__(self) 

        self.dataclass=data 

        self.__values_are_support=values_are_support 

        self.max_support=max_support 

        self.weight=weight 

        self.rooted=rooted 

        self.name=name 

        root=Nodes.Node(data()) 

        self.root = self.add(root) 

        if tree:    # use the tree we have 

            # if Tree is called from outside Nexus parser, we need to get rid of linebreaks, etc 

            tree=tree.strip().replace('\n', '').replace('\r', '') 

            # there's discrepancy whether newick allows semicolons et the end 

            tree=tree.rstrip(';') 

            subtree_info, base_info = self._parse(tree) 

            root.data = self._add_nodedata(root.data, [[], base_info]) 

            self._add_subtree(parent_id=root.id, tree=subtree_info) 

 

    def _parse(self, tree): 

        """Parses (a,b,c...)[[[xx]:]yy] into subcomponents and travels down recursively.""" 

        #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]] 

            elif colon==-1 and nodecomment>-1: # only special comment 

                return [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:])] 

            elif colon < nodecomment: # taxon name ends at first colon or with special comment 

                return [tree[:colon], self._get_values(tree[colon+1:])] 

            else: 

                return [tree[:nodecomment], self._get_values(tree[nodecomment:])] 

        else: 

            closing=tree.rfind(')') 

            val=self._get_values(tree[closing+1:]) 

            if not val: 

                val=[None] 

            subtrees=[] 

            plevel=0 

            prev=1 

            for p in range(1, closing): 

                if tree[p]=='(': 

                    plevel+=1 

                elif tree[p]==')': 

                    plevel-=1 

                elif tree[p]==',' and plevel==0: 

                    subtrees.append(tree[prev:p]) 

                    prev=p+1 

            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): 

        """Adds leaf or tree (in newick format) to a parent_id.""" 

        if parent_id is None: 

            raise TreeError('Need node_id to connect to.') 

        for st in tree: 

            nd=self.dataclass() 

            nd = self._add_nodedata(nd, st) 

            if isinstance(st[0], list): # it's a subtree 

                sn=Nodes.Node(nd) 

                self.add(sn, parent_id) 

                self._add_subtree(sn.id, st[0]) 

            else: # it's a leaf 

                nd.taxon=st[0] 

                leaf=Nodes.Node(nd) 

                self.add(leaf, parent_id) 

 

    def _add_nodedata(self, nd, st): 

        """Add data to the node parsed from the comments, taxon and support. 

        """ 

        if isinstance(st[1][-1], str) and st[1][-1].startswith(NODECOMMENT_START): 

            nd.comment=st[1].pop(-1) 

        # if the first element is a string, it's the subtree node taxon 

        elif isinstance(st[1][0], str): 

            nd.taxon = st[1][0] 

            st[1] = st[1][1:] 

        if len(st)>1: 

            if len(st[1])>=2: # if there's two values, support comes first. Is that always so? 

                nd.support=st[1][0] 

                if st[1][1] is not None: 

                    nd.branchlength=st[1][1] 

            elif len(st[1])==1: # otherwise it could be real branchlengths or support as branchlengths 

                if not self.__values_are_support: # default 

                    if st[1][0] is not None: 

                        nd.branchlength=st[1][0] 

                else: 

                    nd.support=st[1][0] 

        return nd 

 

    def _get_values(self, text): 

        """Extracts values (support/branchlength) from xx[:yyy], xx.""" 

 

        if text=='': 

            return None 

        nodecomment = None 

        if NODECOMMENT_START in text: # if there's a [&....] comment, cut it out 

            nc_start=text.find(NODECOMMENT_START) 

            nc_end=text.find(NODECOMMENT_END) 

            if nc_end==-1: 

                raise TreeError('Error in tree description: Found %s without matching %s' 

                                % (NODECOMMENT_START, NODECOMMENT_END)) 

            nodecomment=text[nc_start:nc_end+1] 

            text=text[:nc_start]+text[nc_end+1:] 

 

        # pase out supports and branchlengths, with internal node taxa info 

        values = [] 

        taxonomy = None 

        for part in [t.strip() for t in text.split(":")]: 

            if part: 

                try: 

                    values.append(float(part)) 

                except ValueError: 

                    assert taxonomy is None, "Two string taxonomies?" 

                    taxonomy = part 

        if taxonomy: 

            values.insert(0, taxonomy) 

        if nodecomment: 

            values.append(nodecomment) 

        return values 

 

    def _walk(self,node=None): 

        """Return all node_ids downwards from a node.""" 

 

        if node is None: 

            node=self.root 

        for n in self.node(node).succ: 

            yield n 

            for sn in self._walk(n): 

                yield sn 

 

    def node(self, node_id): 

        """Return the instance of node_id. 

 

        node = node(self,node_id) 

        """ 

        if node_id not in self.chain: 

            raise TreeError('Unknown node_id: %d' % node_id) 

        return self.chain[node_id] 

 

    def split(self,parent_id=None,n=2,branchlength=1.0): 

        """Speciation: generates n (default two) descendants of a node. 

 

        [new ids] = split(self,parent_id=None,n=2,branchlength=1.0): 

        """ 

        if parent_id is None: 

            raise TreeError('Missing node_id.') 

        ids=[] 

        parent_data=self.chain[parent_id].data 

        for i in range(n): 

            node=Nodes.Node() 

            if parent_data: 

                node.data=self.dataclass() 

                # each node has taxon and branchlength attribute 

                if parent_data.taxon: 

                    node.data.taxon=parent_data.taxon+str(i) 

                node.data.branchlength=branchlength 

            ids.append(self.add(node, parent_id)) 

        return ids 

 

    def search_taxon(self, taxon): 

        """Returns the first matching taxon in self.data.taxon. Not restricted to terminal nodes. 

 

        node_id = search_taxon(self,taxon) 

        """ 

        for id, node in self.chain.items(): 

            if node.data.taxon==taxon: 

                return id 

        return None 

 

    def prune(self, taxon): 

        """Prunes a terminal taxon from the tree. 

 

        id_of_previous_node = prune(self,taxon) 

        If taxon is from a bifurcation, the connectiong node will be collapsed 

        and its branchlength added to remaining terminal node. This might be no 

        longer a meaningful value' 

        """ 

 

        id=self.search_taxon(taxon) 

        if id is None: 

            raise TreeError('Taxon not found: %s' % taxon) 

        elif id not in self.get_terminals(): 

            raise TreeError('Not a terminal taxon: %s' % taxon) 

        else: 

            prev=self.unlink(id) 

            self.kill(id) 

            if len(self.node(prev).succ)==1: 

                if prev==self.root: # we deleted one branch of a bifurcating root, then we have to move the root upwards 

                    self.root=self.node(self.root).succ[0] 

                    self.node(self.root).branchlength=0.0 

                    self.kill(prev) 

                else: 

                    succ=self.node(prev).succ[0] 

                    new_bl=self.node(prev).data.branchlength+self.node(succ).data.branchlength 

                    self.collapse(prev) 

                    self.node(succ).data.branchlength=new_bl 

            return prev 

 

    def get_taxa(self,node_id=None): 

        """Return a list of all otus downwards from a node. 

 

        nodes = get_taxa(self,node_id=None) 

        """ 

 

        if node_id is None: 

            node_id=self.root 

        if node_id not in self.chain: 

            raise TreeError('Unknown node_id: %d.' % node_id) 

        if self.chain[node_id].succ==[]: 

            if self.chain[node_id].data: 

                return [self.chain[node_id].data.taxon] 

            else: 

                return None 

        else: 

            list=[] 

            for succ in self.chain[node_id].succ: 

                list.extend(self.get_taxa(succ)) 

            return list 

 

    def get_terminals(self): 

        """Return a list of all terminal nodes.""" 

        return [i for i in self.all_ids() if self.node(i).succ==[]] 

 

    def is_terminal(self, node): 

        """Returns True if node is a terminal node.""" 

        return self.node(node).succ==[] 

 

    def is_internal(self, node): 

        """Returns True if node is an internal node.""" 

        return len(self.node(node).succ)>0 

 

    def is_preterminal(self, node): 

        """Returns True if all successors of a node are terminal ones.""" 

        if self.is_terminal(node): 

            return False not in [self.is_terminal(n) for n in self.node(node).succ] 

        else: 

            return False 

 

    def count_terminals(self,node=None): 

        """Counts the number of terminal nodes that are attached to a node.""" 

        if node is None: 

            node=self.root 

        return len([n for n in self._walk(node) if self.is_terminal(n)]) 

 

    def collapse_genera(self,space_equals_underscore=True): 

        """Collapses all subtrees which belong to the same genus (i.e share the same first word in their taxon name.)""" 

 

        while True: 

            for n in self._walk(): 

                if self.is_terminal(n): 

                    continue 

                taxa=self.get_taxa(n) 

                genera=[] 

                for t in taxa: 

                    if space_equals_underscore: 

                        t=t.replace(' ', '_') 

                    try: 

                        genus=t.split('_', 1)[0] 

                    except: 

                        genus='None' 

                    if genus not in genera: 

                        genera.append(genus) 

                if len(genera)==1: 

                    self.node(n).data.taxon=genera[0]+' <collapsed>' 

                    #now we kill all nodes downstream 

                    nodes2kill=[kn for kn in self._walk(node=n)] 

                    for kn in nodes2kill: 

                        self.kill(kn) 

                    self.node(n).succ=[] 

                    break # break out of for loop because node list from _walk will be inconsistent 

            else: # for loop exhausted: no genera to collapse left 

                break # while 

 

    def sum_branchlength(self,root=None,node=None): 

        """Adds up the branchlengths from root (default self.root) to node. 

 

        sum = sum_branchlength(self,root=None,node=None) 

        """ 

 

        if root is None: 

            root=self.root 

        if node is None: 

            raise TreeError('Missing node id.') 

        blen=0.0 

        while node is not None and node is not root: 

            blen+=self.node(node).data.branchlength 

            node=self.node(node).prev 

        return blen 

 

    def set_subtree(self, node): 

        """Return subtree as a set of nested sets. 

 

        sets = set_subtree(self,node) 

        """ 

 

        if self.node(node).succ==[]: 

            return self.node(node).data.taxon 

        else: 

            try: 

                return frozenset(self.set_subtree(n) for n in self.node(node).succ) 

            except: 

                print(node) 

                print(self.node(node).succ) 

                for n in self.node(node).succ: 

                    print("%s %s" % (n, self.set_subtree(n))) 

                print([self.set_subtree(n) for n in self.node(node).succ]) 

                raise 

 

    def is_identical(self, tree2): 

        """Compare tree and tree2 for identity. 

 

        result = is_identical(self,tree2) 

        """ 

        return self.set_subtree(self.root)==tree2.set_subtree(tree2.root) 

 

    def is_compatible(self,tree2,threshold,strict=True): 

        """Compares branches with support>threshold for compatibility. 

 

        result = is_compatible(self,tree2,threshold) 

        """ 

 

        # check if both trees have the same set of taxa. strict=True enforces this. 

        missing2=set(self.get_taxa())-set(tree2.get_taxa()) 

        missing1=set(tree2.get_taxa())-set(self.get_taxa()) 

        if strict and (missing1 or missing2): 

            if missing1: 

                print('Taxon/taxa %s is/are missing in tree %s' % (','.join(missing1), self.name)) 

            if missing2: 

                print('Taxon/taxa %s is/are missing in tree %s' % (','.join(missing2), tree2.name)) 

            raise TreeError('Can\'t compare trees with different taxon compositions.') 

        t1=[(set(self.get_taxa(n)), self.node(n).data.support) for n in self.all_ids() if 

            self.node(n).succ and 

            (self.node(n).data and self.node(n).data.support and self.node(n).data.support>=threshold)] 

        t2=[(set(tree2.get_taxa(n)), tree2.node(n).data.support) for n in tree2.all_ids() if 

            tree2.node(n).succ and 

            (tree2.node(n).data and tree2.node(n).data.support and tree2.node(n).data.support>=threshold)] 

        conflict=[] 

        for (st1, sup1) in t1: 

            for (st2, sup2) in t2: 

                if not st1.issubset(st2) and not st2.issubset(st1):                     # don't hiccup on upstream nodes 

                    intersect, notin1, notin2=st1 & st2, st2-st1, st1-st2                 # all three are non-empty sets 

                    # if notin1==missing1 or notin2==missing2  <==> st1.issubset(st2) or st2.issubset(st1) ??? 

                    if intersect and not (notin1.issubset(missing1) or notin2.issubset(missing2)):         # omit conflicts due to missing taxa 

                        conflict.append((st1, sup1, st2, sup2, intersect, notin1, notin2)) 

        return conflict 

 

    def common_ancestor(self, node1, node2): 

        """Return the common ancestor that connects two nodes. 

 

        node_id = common_ancestor(self,node1,node2) 

        """ 

 

        l1=[self.root]+self.trace(self.root, node1) 

        l2=[self.root]+self.trace(self.root, node2) 

        return [n for n in l1 if n in l2][-1] 

 

    def distance(self, node1, node2): 

        """Add and return the sum of the branchlengths between two nodes. 

        dist = distance(self,node1,node2) 

        """ 

 

        ca=self.common_ancestor(node1, node2) 

        return self.sum_branchlength(ca, node1)+self.sum_branchlength(ca, node2) 

 

    def is_monophyletic(self, taxon_list): 

        """Return node_id of common ancestor if taxon_list is monophyletic, -1 otherwise. 

 

        result = is_monophyletic(self,taxon_list) 

        """ 

        if isinstance(taxon_list, str): 

            taxon_set=set([taxon_list]) 

        else: 

            taxon_set=set(taxon_list) 

        node_id=self.root 

        while True: 

            subclade_taxa=set(self.get_taxa(node_id)) 

            if subclade_taxa==taxon_set:                                        # are we there? 

                return node_id 

            else:                                                               # check subnodes 

                for subnode in self.chain[node_id].succ: 

                    if set(self.get_taxa(subnode)).issuperset(taxon_set):  # taxon_set is downstream 

                        node_id=subnode 

                        break   # out of for loop 

                else: 

                    return -1   # taxon set was not with successors, for loop exhausted 

 

    def is_bifurcating(self,node=None): 

        """Return True if tree downstream of node is strictly bifurcating.""" 

        if node is None: 

            node=self.root 

        if node==self.root and len(self.node(node).succ)==3:  # root can be trifurcating, because it has no ancestor 

            return self.is_bifurcating(self.node(node).succ[0]) and \ 

                    self.is_bifurcating(self.node(node).succ[1]) and \ 

                    self.is_bifurcating(self.node(node).succ[2]) 

        if len(self.node(node).succ)==2: 

            return self.is_bifurcating(self.node(node).succ[0]) and self.is_bifurcating(self.node(node).succ[1]) 

        elif len(self.node(node).succ)==0: 

            return True 

        else: 

            return False 

 

    def branchlength2support(self): 

        """Move values stored in data.branchlength to data.support, and set branchlength to 0.0 

 

        This is necessary when support has been stored as branchlength (e.g. paup), and has thus 

        been read in as branchlength. 

        """ 

 

        for n in self.chain: 

            self.node(n).data.support=self.node(n).data.branchlength 

            self.node(n).data.branchlength=0.0 

 

    def convert_absolute_support(self, nrep): 

        """Convert absolute support (clade-count) to rel. frequencies. 

 

        Some software (e.g. PHYLIP consense) just calculate how often clades appear, instead of 

        calculating relative frequencies.""" 

 

        for n in self._walk(): 

            if self.node(n).data.support: 

                self.node(n).data.support/=float(nrep) 

 

    def has_support(self,node=None): 

        """Returns True if any of the nodes has data.support != None.""" 

        for n in self._walk(node): 

            if self.node(n).data.support: 

                return True 

        else: 

            return False 

 

    def randomize(self,ntax=None,taxon_list=None,branchlength=1.0,branchlength_sd=None,bifurcate=True): 

        """Generates a random tree with ntax taxa and/or taxa from taxlabels. 

 

        new_tree = randomize(self,ntax=None,taxon_list=None,branchlength=1.0,branchlength_sd=None,bifurcate=True) 

        Trees are bifurcating by default. (Polytomies not yet supported). 

        """ 

 

        if not ntax and taxon_list: 

            ntax=len(taxon_list) 

        elif not taxon_list and ntax: 

            taxon_list=['taxon'+str(i+1) for i in range(ntax)] 

        elif not ntax and not taxon_list: 

            raise TreeError('Either numer of taxa or list of taxa must be specified.') 

        elif ntax != len(taxon_list): 

            raise TreeError('Length of taxon list must correspond to ntax.') 

        # initiate self with empty root 

        self.__init__() 

        terminals=self.get_terminals() 

        # bifurcate randomly at terminal nodes until ntax is reached 

        while len(terminals)<ntax: 

            newsplit=random.choice(terminals) 

            new_terminals=self.split(parent_id=newsplit, branchlength=branchlength) 

            # if desired, give some variation to the branch length 

            if branchlength_sd: 

                for nt in new_terminals: 

                    bl=random.gauss(branchlength, branchlength_sd) 

                    if bl<0: 

                        bl=0 

                    self.node(nt).data.branchlength=bl 

            terminals.extend(new_terminals) 

            terminals.remove(newsplit) 

        # distribute taxon labels randomly 

        random.shuffle(taxon_list) 

        for (node, name) in zip(terminals, taxon_list): 

            self.node(node).data.taxon=name 

 

    def display(self): 

        """Quick and dirty lists of all nodes.""" 

        table=[('#', 'taxon', 'prev', 'succ', 'brlen', 'blen (sum)', 'support', 'comment')] 

        #Sort this to be consistent across CPython, Jython, etc 

        for i in sorted(self.all_ids()): 

            n=self.node(i) 

            if not n.data: 

                table.append((str(i), '-', str(n.prev), str(n.succ), '-', '-', '-', '-')) 

            else: 

                tx=n.data.taxon 

                if not tx: 

                    tx='-' 

                blength="%0.2f" % n.data.branchlength 

                if blength is None: 

                    blength='-' 

                    sum_blength='-' 

                else: 

                    sum_blength="%0.2f" % self.sum_branchlength(node=i) 

                support=n.data.support 

                if support is None: 

                    support='-' 

                else: 

                    support="%0.2f" % support 

                comment=n.data.comment 

                if comment is None: 

                    comment='-' 

                table.append((str(i), tx, str(n.prev), str(n.succ), 

                             blength, sum_blength, support, comment)) 

        print('\n'.join('%3s %32s %15s %15s %8s %10s %8s %20s' % l for l in table)) 

        print('\nRoot:  %s' % self.root) 

 

    def to_string(self,support_as_branchlengths=False,branchlengths_only=False,plain=True,plain_newick=False,ladderize=None,ignore_comments=True): 

        """Return a paup compatible tree line.""" 

        # if there's a conflict in the arguments, we override plain=True 

        if support_as_branchlengths or branchlengths_only: 

            plain=False 

        self.support_as_branchlengths=support_as_branchlengths 

        self.branchlengths_only=branchlengths_only 

        self.ignore_comments=ignore_comments 

        self.plain=plain 

 

        def make_info_string(data,terminal=False): 

            """Creates nicely formatted support/branchlengths.""" 

            # CHECK FORMATTING 

            if self.plain: # plain tree only. That's easy. 

                info_string= '' 

            elif self.support_as_branchlengths: # support as branchlengths (eg. PAUP), ignore actual branchlengths 

                if terminal:    # terminal branches have 100% support 

                    info_string= ':%1.2f' % self.max_support 

                elif data.support: 

                    info_string= ':%1.2f' % (data.support) 

                else: 

                    info_string=':0.00' 

            elif self.branchlengths_only: # write only branchlengths, ignore support 

                info_string= ':%1.5f' % (data.branchlength) 

            else:   # write suport and branchlengths (e.g. .con tree of mrbayes) 

                if terminal: 

                    info_string= ':%1.5f' % (data.branchlength) 

                else: 

                    if data.branchlength is not None and data.support is not None:  # we have blen and suppport 

                        info_string= '%1.2f:%1.5f' % (data.support, data.branchlength) 

                    elif data.branchlength is not None:                             # we have only blen 

                        info_string= '0.00000:%1.5f' % (data.branchlength) 

                    elif data.support is not None:                                  # we have only support 

                        info_string= '%1.2f:0.00000' % (data.support) 

                    else: 

                        info_string= '0.00:0.00000' 

            if not ignore_comments and hasattr(data, 'nodecomment'): 

                info_string=str(data.nodecomment)+info_string 

            return info_string 

 

        def ladderize_nodes(nodes,ladderize=None): 

            """Sorts node numbers according to the number of terminal nodes.""" 

            if ladderize in ['left', 'LEFT', 'right', 'RIGHT']: 

                succnode_terminals = sorted((self.count_terminals(node=n), n) for n in nodes) 

                if (ladderize=='right' or ladderize=='RIGHT'): 

                    succnode_terminals.reverse() 

                if succnode_terminals: 

                    succnodes=zip(*succnode_terminals)[1] 

                else: 

                    succnodes=[] 

            else: 

                succnodes=nodes 

            return succnodes 

 

        def newickize(node,ladderize=None): 

            """Convert a node tree to a newick tree recursively.""" 

 

            if not self.node(node).succ:    # terminal 

                return self.node(node).data.taxon+make_info_string(self.node(node).data, terminal=True) 

            else: 

                succnodes=ladderize_nodes(self.node(node).succ, ladderize=ladderize) 

                subtrees=[newickize(sn, ladderize=ladderize) for sn in succnodes] 

                return '(%s)%s' % (','.join(subtrees), make_info_string(self.node(node).data)) 

 

        treeline=['tree'] 

        if self.name: 

            treeline.append(self.name) 

        else: 

            treeline.append('a_tree') 

        treeline.append('=') 

        if self.weight != 1: 

            treeline.append('[&W%s]' % str(round(float(self.weight), 3))) 

        if self.rooted: 

            treeline.append('[&R]') 

        succnodes=ladderize_nodes(self.node(self.root).succ) 

        subtrees=[newickize(sn, ladderize=ladderize) for sn in succnodes] 

        treeline.append('(%s)' % ','.join(subtrees)) 

        if plain_newick: 

            return treeline[-1] 

        else: 

            return ' '.join(treeline)+';' 

 

    def __str__(self): 

        """Short version of to_string(), gives plain tree""" 

        return self.to_string(plain=True) 

 

    def unroot(self): 

        """Defines a unrooted Tree structure, using data of a rooted Tree.""" 

 

        # travel down the rooted tree structure and save all branches and the nodes they connect 

 

        def _get_branches(node): 

            branches=[] 

            for b in self.node(node).succ: 

                branches.append([node, b, self.node(b).data.branchlength, self.node(b).data.support]) 

                branches.extend(_get_branches(b)) 

            return branches 

 

        self.unrooted=_get_branches(self.root) 

        # if root is bifurcating, then it is eliminated 

        if len(self.node(self.root).succ)==2: 

            # find the two branches that connect to root 

            rootbranches=[b for b in self.unrooted if self.root in b[:2]] 

            b1=self.unrooted.pop(self.unrooted.index(rootbranches[0])) 

            b2=self.unrooted.pop(self.unrooted.index(rootbranches[1])) 

            # Connect them two each other. If both have support, it should be identical (or one set to None?). 

            # If both have branchlengths, they will be added 

            newbranch=[b1[1], b2[1], b1[2]+b2[2]] 

            if b1[3] is None: 

                newbranch.append(b2[3]) # either None (both rootbranches are unsupported) or some support 

            elif b2[3] is None: 

                newbranch.append(b1[3]) # dito 

            elif b1[3]==b2[3]: 

                newbranch.append(b1[3]) # identical support 

            elif b1[3]==0 or b2[3]==0: 

                newbranch.append(b1[3]+b2[3]) # one is 0, take the other 

            else: 

                raise TreeError('Support mismatch in bifurcating root: %f, %f' 

                                % (float(b1[3]), float(b2[3]))) 

            self.unrooted.append(newbranch) 

 

    def root_with_outgroup(self,outgroup=None): 

 

        def _connect_subtree(parent, child): 

            """Hook subtree starting with node child to parent.""" 

            for i, branch in enumerate(self.unrooted): 

                if parent in branch[:2] and child in branch[:2]: 

                    branch=self.unrooted.pop(i) 

                    break 

            else: 

                raise TreeError('Unable to connect nodes for rooting: nodes %d and %d are not connected' 

                                % (parent, child)) 

            self.link(parent, child) 

            self.node(child).data.branchlength=branch[2] 

            self.node(child).data.support=branch[3] 

            #now check if there are more branches connected to the child, and if so, connect them 

            child_branches=[b for b in self.unrooted if child in b[:2]] 

            for b in child_branches: 

                if child==b[0]: 

                    succ=b[1] 

                else: 

                    succ=b[0] 

                _connect_subtree(child, succ) 

 

        # check the outgroup we're supposed to root with 

        if outgroup is None: 

            return self.root 

        outgroup_node=self.is_monophyletic(outgroup) 

        if outgroup_node==-1: 

            return -1 

        # if tree is already rooted with outgroup on a bifurcating root, 

        # or the outgroup includes all taxa on the tree, then we're fine 

        if (len(self.node(self.root).succ)==2 and outgroup_node in self.node(self.root).succ) or outgroup_node==self.root: 

            return self.root 

 

        self.unroot() 

        # now we find the branch that connects outgroup and ingroup 

        #print(self.node(outgroup_node).prev) 

        for i, b in enumerate(self.unrooted): 

            if outgroup_node in b[:2] and self.node(outgroup_node).prev in b[:2]: 

                root_branch=self.unrooted.pop(i) 

                break 

        else: 

            raise TreeError('Unrooted and rooted Tree do not match') 

        if outgroup_node==root_branch[1]: 

            ingroup_node=root_branch[0] 

        else: 

            ingroup_node=root_branch[1] 

        # now we destroy the old tree structure, but keep node data. Nodes will be reconnected according to new outgroup 

        for n in self.all_ids(): 

            self.node(n).prev=None 

            self.node(n).succ=[] 

        # now we just add both subtrees (outgroup and ingroup) branch for branch 

        root=Nodes.Node(data=NodeData())            # new root 

        self.add(root)                              # add to tree description 

        self.root=root.id                           # set as root 

        self.unrooted.append([root.id, ingroup_node, root_branch[2], root_branch[3]])  # add branch to ingroup to unrooted tree 

        self.unrooted.append([root.id, outgroup_node, 0.0, 0.0])   # add branch to outgroup to unrooted tree 

        _connect_subtree(root.id, ingroup_node)      # add ingroup 

        _connect_subtree(root.id, outgroup_node)     # add outgroup 

        # if theres still a lonely node in self.chain, then it's the old root, and we delete it 

        oldroot=[i for i in self.all_ids() if self.node(i).prev is None and i!=self.root] 

        if len(oldroot)>1: 

            raise TreeError('Isolated nodes in tree description: %s' 

                            % ','.join(oldroot)) 

        elif len(oldroot)==1: 

            self.kill(oldroot[0]) 

        return self.root 

 

    def merge_with_support(self,bstrees=None,constree=None,threshold=0.5,outgroup=None): 

        """Merges clade support (from consensus or list of bootstrap-trees) with phylogeny. 

 

        tree=merge_bootstrap(phylo,bs_tree=<list_of_trees>) 

        or 

        tree=merge_bootstrap(phylo,consree=consensus_tree with clade support) 

        """ 

 

        if bstrees and constree: 

            raise TreeError('Specify either list of bootstrap trees or consensus tree, not both') 

        if not (bstrees or constree): 

            raise TreeError('Specify either list of bootstrap trees or consensus tree.') 

        # no outgroup specified: use the smallest clade of the root 

        if outgroup is None: 

            try: 

                succnodes = self.node(self.root).succ 

                smallest = min((len(self.get_taxa(n)), n) for n in succnodes) 

                outgroup = self.get_taxa(smallest[1]) 

            except: 

                raise TreeError("Error determining outgroup.") 

        else: # root with user specified outgroup 

            self.root_with_outgroup(outgroup) 

 

        if bstrees: # calculate consensus 

            constree=consensus(bstrees, threshold=threshold, outgroup=outgroup) 

        else: 

            if not constree.has_support(): 

                constree.branchlength2support() 

            constree.root_with_outgroup(outgroup) 

        # now we travel all nodes, and add support from consensus, if the clade is present in both 

        for pnode in self._walk(): 

            cnode=constree.is_monophyletic(self.get_taxa(pnode)) 

            if cnode>-1: 

                self.node(pnode).data.support=constree.node(cnode).data.support 

 

 

def consensus(trees, threshold=0.5,outgroup=None): 

    """Compute a majority rule consensus tree of all clades with relative frequency>=threshold from a list of trees.""" 

 

    total=len(trees) 

    if total==0: 

        return None 

    # shouldn't we make sure that it's NodeData or subclass?? 

    dataclass=trees[0].dataclass 

    max_support=trees[0].max_support 

    clades={} 

    #countclades={} 

    alltaxa=set(trees[0].get_taxa()) 

    # calculate calde frequencies 

    c=0 

    for t in trees: 

        c+=1 

        #if c%100==0: 

        #    print(c) 

        if alltaxa!=set(t.get_taxa()): 

            raise TreeError('Trees for consensus must contain the same taxa') 

        t.root_with_outgroup(outgroup=outgroup) 

        for st_node in t._walk(t.root): 

            subclade_taxa=sorted(t.get_taxa(st_node)) 

            subclade_taxa=str(subclade_taxa) # lists are not hashable 

            if subclade_taxa in clades: 

                clades[subclade_taxa]+=float(t.weight)/total 

            else: 

                clades[subclade_taxa]=float(t.weight)/total 

            #if subclade_taxa in countclades: 

            #    countclades[subclade_taxa]+=t.weight 

            #else: 

            #    countclades[subclade_taxa]=t.weight 

    # weed out clades below threshold 

    delclades=[c for c, p in clades.items() if round(p, 3)<threshold] # round can be necessary 

    for c in delclades: 

        del clades[c] 

    # create a tree with a root node 

    consensus=Tree(name='consensus_%2.1f' % float(threshold), data=dataclass) 

    # each clade needs a node in the new tree, add them as isolated nodes 

    for c, s in clades.items(): 

        node=Nodes.Node(data=dataclass()) 

        node.data.support=s 

        node.data.taxon=set(eval(c)) 

        consensus.add(node) 

    # set root node data 

    consensus.node(consensus.root).data.support=None 

    consensus.node(consensus.root).data.taxon=alltaxa 

    # we sort the nodes by no. of taxa in the clade, so root will be the last 

    consensus_ids=consensus.all_ids() 

    consensus_ids.sort(lambda x, y:len(consensus.node(x).data.taxon)-len(consensus.node(y).data.taxon)) 

    # now we just have to hook each node to the next smallest node that includes all taxa of the current 

    for i, current in enumerate(consensus_ids[:-1]): # skip the last one which is the root 

        #print('----') 

        #print('current: %s' % consensus.node(current).data.taxon) 

        # search remaining nodes 

        for parent in consensus_ids[i+1:]: 

            #print('parent: %s' % consensus.node(parent).data.taxon) 

            if consensus.node(parent).data.taxon.issuperset(consensus.node(current).data.taxon): 

                break 

        else: 

            sys.exit('corrupt tree structure?') 

        # internal nodes don't have taxa 

        if len(consensus.node(current).data.taxon)==1: 

            consensus.node(current).data.taxon=consensus.node(current).data.taxon.pop() 

            # reset the support for terminal nodes to maximum 

            #consensus.node(current).data.support=max_support 

        else: 

            consensus.node(current).data.taxon=None 

        consensus.link(parent, current) 

    # eliminate root taxon name 

    consensus.node(consensus_ids[-1]).data.taxon=None 

    if alltaxa != set(consensus.get_taxa()): 

        raise TreeError('FATAL ERROR: consensus tree is corrupt') 

    return consensus