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# Copyright 2005-2008 by Frank Kauff & Cymon J. Cox. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""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 (re-root trees, split terminal
nodes).
"""
import random
import sys
from . import Nodes
PRECISION_BRANCHLENGTH = 6
PRECISION_SUPPORT = 6
NODECOMMENT_START = "[&"
NODECOMMENT_END = "]"
class TreeError(Exception):
"""Provision for the management of Tree exceptions."""
pass
class NodeData:
"""Store tree-relevant data associated with nodes (e.g. branches or otus)."""
def __init__(self, taxon=None, branchlength=0.0, support=None, comment=None):
"""Initialize the class."""
self.taxon = taxon
self.branchlength = branchlength
self.support = support
self.comment = comment
class Tree(Nodes.Chain):
"""Represent 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):
"""Parse (a,b,c...)[[[xx]:]yy] into subcomponents and travels down recursively (PRIVATE)."""
# 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
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
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):
"""Add leaf or tree (in newick format) to a parent_id (PRIVATE)."""
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 (PRIVATE)."""
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):
"""Extract values (support/branchlength) from xx[:yyy], xx (PRIVATE)."""
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 :]
# parse 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 (PRIVATE)."""
if node is None:
node = self.root
for n in self.node(node).succ:
yield n
yield from self._walk(n)
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):
"""Return 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):
"""Prune 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(f"Taxon not found: {taxon}")
elif id not in self.get_terminals():
raise TreeError(f"Not a terminal taxon: {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):
"""Return True if node is a terminal node."""
return self.node(node).succ == []
def is_internal(self, node):
"""Return True if node is an internal node."""
return len(self.node(node).succ) > 0
def is_preterminal(self, node):
"""Return 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):
"""Count 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):
"""Collapse 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 IndexError:
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 = list(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):
"""Add 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 Exception:
print(node)
print(self.node(node).succ)
for n in self.node(node).succ:
print(f"{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):
"""Compare 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)
"""
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 /= nrep
def has_support(self, node=None):
"""Return 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,
):
"""Generate 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 number 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")
]
for i in 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 = f"{n.data.branchlength:0.2f}"
if blength is None:
blength = "-"
sum_blength = "-"
else:
sum_blength = f"{self.sum_branchlength(node=i):0.2f}"
support = n.data.support
if support is None:
support = "-"
else:
support = f"{support:0.2f}"
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" % line for line in table)
)
print(f"\nRoot: {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):
"""Create 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 = f":{self.max_support:1.2f}"
elif data.support:
info_string = f":{data.support:1.2f}"
else:
info_string = ":0.00"
elif self.branchlengths_only: # write only branchlengths, ignore support
info_string = f":{data.branchlength:1.5f}"
else: # write support and branchlengths (e.g. .con tree of mrbayes)
if terminal:
info_string = f":{data.branchlength:1.5f}"
else:
if (
data.branchlength is not None and data.support is not None
): # we have blen and support
info_string = f"{data.support:1.2f}:{data.branchlength:1.5f}"
elif data.branchlength is not None: # we have only blen
info_string = f"0.00000:{data.branchlength:1.5f}"
elif data.support is not None: # we have only support
info_string = f"{data.support:1.2f}:0.00000"
else:
info_string = "0.00:0.00000"
if not ignore_comments:
try:
info_string = str(data.nodecomment) + info_string
except AttributeError:
pass
return info_string
def ladderize_nodes(nodes, ladderize=None):
"""Sort 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 = list(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 f"({','.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(f"[&W{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(f"({','.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):
"""Define 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):
"""Define a tree's root with a reference group outgroup."""
def _connect_subtree(parent, child):
"""Attach subtree starting with node child to parent (PRIVATE)."""
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 there's 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(f"Isolated nodes in tree description: {','.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
):
"""Merge 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 Exception:
raise TreeError("Error determining outgroup.") from None
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
for t in trees:
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] += t.weight / total
else:
clades[subclade_taxa] = 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=f"consensus_{float(threshold):2.1f}", 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(key=lambda x: len(consensus.node(x).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
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