# Copyright (C) 2013 by Yanbo Ye (yeyanbo289@gmail.com)
#
# This file is originally 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.
#
# The file is adapted by She Zhang (shezhang620@gmail.com) on 04/13/2020 to fix a
# bug in the construction of the UPGMA tree and made suitable for being used by
# ProDy.
"""Classes and methods for tree construction."""
import itertools
import copy
import numbers
from Bio.Phylo import BaseTree
from Bio.Phylo.TreeConstruction import _DistanceMatrix as DistanceMatrix
__all__ = ['_Matrix', 'DistanceMatrix', 'TreeConstructor', 'DistanceTreeConstructor']
class _Matrix:
"""Base class for distance matrix or scoring matrix.
Accepts a list of names and a lower triangular matrix.::
matrix = [[0],
[1, 0],
[2, 3, 0],
[4, 5, 6, 0]]
represents the symmetric matrix of
[0,1,2,4]
[1,0,3,5]
[2,3,0,6]
[4,5,6,0]
:Parameters:
names : list
names of elements, used for indexing
matrix : list
nested list of numerical lists in lower triangular format
Examples
--------
>>> from Bio.Phylo.TreeConstruction import _Matrix
>>> names = ['Alpha', 'Beta', 'Gamma', 'Delta']
>>> matrix = [[0], [1, 0], [2, 3, 0], [4, 5, 6, 0]]
>>> m = _Matrix(names, matrix)
>>> m
_Matrix(names=['Alpha', 'Beta', 'Gamma', 'Delta'], matrix=[[0], [1, 0], [2, 3, 0], [4, 5, 6, 0]])
You can use two indices to get or assign an element in the matrix.
>>> m[1,2]
3
>>> m['Beta','Gamma']
3
>>> m['Beta','Gamma'] = 4
>>> m['Beta','Gamma']
4
Further more, you can use one index to get or assign a list of elements related to that index.
>>> m[0]
[0, 1, 2, 4]
>>> m['Alpha']
[0, 1, 2, 4]
>>> m['Alpha'] = [0, 7, 8, 9]
>>> m[0]
[0, 7, 8, 9]
>>> m[0,1]
7
Also you can delete or insert a column&row of elemets by index.
>>> m
_Matrix(names=['Alpha', 'Beta', 'Gamma', 'Delta'], matrix=[[0], [7, 0], [8, 4, 0], [9, 5, 6, 0]])
>>> del m['Alpha']
>>> m
_Matrix(names=['Beta', 'Gamma', 'Delta'], matrix=[[0], [4, 0], [5, 6, 0]])
>>> m.insert('Alpha', [0, 7, 8, 9] , 0)
>>> m
_Matrix(names=['Alpha', 'Beta', 'Gamma', 'Delta'], matrix=[[0], [7, 0], [8, 4, 0], [9, 5, 6, 0]])
"""
def __init__(self, names, matrix=None):
"""Initialize matrix.
Arguments are a list of names, and optionally a list of lower
triangular matrix data (zero matrix used by default).
"""
# check names
if isinstance(names, list) and all(isinstance(s, str) for s in names):
if len(set(names)) == len(names):
self.names = names
else:
raise ValueError("Duplicate names found")
else:
raise TypeError("'names' should be a list of strings")
# check matrix
if matrix is None:
# create a new one with 0 if matrix is not assigned
matrix = [[0] * i for i in range(1, len(self) + 1)]
self.matrix = matrix
else:
# check if all elements are numbers
if (
isinstance(matrix, list)
and all(isinstance(l, list) for l in matrix)
and all(
isinstance(n, numbers.Number)
for n in [item for sublist in matrix for item in sublist]
)
):
# check if the same length with names
if len(matrix) == len(names):
# check if is lower triangle format
if [len(m) for m in matrix] == list(range(1, len(self) + 1)):
self.matrix = matrix
else:
raise ValueError("'matrix' should be in lower triangle format")
else:
raise ValueError("'names' and 'matrix' should be the same size")
else:
raise TypeError("'matrix' should be a list of numerical lists")
def __getitem__(self, item):
"""Access value(s) by the index(s) or name(s).
For a _Matrix object 'dm'::
dm[i] get a value list from the given 'i' to others;
dm[i, j] get the value between 'i' and 'j';
dm['name'] map name to index first
dm['name1', 'name2'] map name to index first
"""
# Handle single indexing
if isinstance(item, (int, str)):
index = None
if isinstance(item, int):
index = item
elif isinstance(item, str):
if item in self.names:
index = self.names.index(item)
else:
raise ValueError("Item not found.")
else:
raise TypeError("Invalid index type.")
# check index
if index > len(self) - 1:
raise IndexError("Index out of range.")
return [self.matrix[index][i] for i in range(0, index)] + [
self.matrix[i][index] for i in range(index, len(self))
]
# Handle double indexing
elif len(item) == 2:
row_index = None
col_index = None
if all(isinstance(i, int) for i in item):
row_index, col_index = item
elif all(isinstance(i, str) for i in item):
row_name, col_name = item
if row_name in self.names and col_name in self.names:
row_index = self.names.index(row_name)
col_index = self.names.index(col_name)
else:
raise ValueError("Item not found.")
else:
raise TypeError("Invalid index type.")
# check index
if row_index > len(self) - 1 or col_index > len(self) - 1:
raise IndexError("Index out of range.")
if row_index > col_index:
return self.matrix[row_index][col_index]
else:
return self.matrix[col_index][row_index]
else:
raise TypeError("Invalid index type.")
def __setitem__(self, item, value):
"""Set value by the index(s) or name(s).
Similar to __getitem__::
dm[1] = [1, 0, 3, 4] set values from '1' to others;
dm[i, j] = 2 set the value from 'i' to 'j'
"""
# Handle single indexing
if isinstance(item, (int, str)):
index = None
if isinstance(item, int):
index = item
elif isinstance(item, str):
if item in self.names:
index = self.names.index(item)
else:
raise ValueError("Item not found.")
else:
raise TypeError("Invalid index type.")
# check index
if index > len(self) - 1:
raise IndexError("Index out of range.")
# check and assign value
if isinstance(value, list) and all(
isinstance(n, numbers.Number) for n in value
):
if len(value) == len(self):
for i in range(0, index):
self.matrix[index][i] = value[i]
for i in range(index, len(self)):
self.matrix[i][index] = value[i]
else:
raise ValueError("Value not the same size.")
else:
raise TypeError("Invalid value type.")
# Handle double indexing
elif len(item) == 2:
row_index = None
col_index = None
if all(isinstance(i, int) for i in item):
row_index, col_index = item
elif all(isinstance(i, str) for i in item):
row_name, col_name = item
if row_name in self.names and col_name in self.names:
row_index = self.names.index(row_name)
col_index = self.names.index(col_name)
else:
raise ValueError("Item not found.")
else:
raise TypeError("Invalid index type.")
# check index
if row_index > len(self) - 1 or col_index > len(self) - 1:
raise IndexError("Index out of range.")
# check and assign value
if isinstance(value, numbers.Number):
if row_index > col_index:
self.matrix[row_index][col_index] = value
else:
self.matrix[col_index][row_index] = value
else:
raise TypeError("Invalid value type.")
else:
raise TypeError("Invalid index type.")
def __delitem__(self, item):
"""Delete related distances by the index or name."""
index = None
if isinstance(item, int):
index = item
elif isinstance(item, str):
index = self.names.index(item)
else:
raise TypeError("Invalid index type.")
# remove distances related to index
for i in range(index + 1, len(self)):
del self.matrix[i][index]
del self.matrix[index]
# remove name
del self.names[index]
def insert(self, name, value, index=None):
"""Insert distances given the name and value.
:Parameters:
name : str
name of a row/col to be inserted
value : list
a row/col of values to be inserted
"""
if isinstance(name, str):
# insert at the given index or at the end
if index is None:
index = len(self)
if not isinstance(index, int):
raise TypeError("Invalid index type.")
# insert name
self.names.insert(index, name)
# insert elements of 0, to be assigned
self.matrix.insert(index, [0] * index)
for i in range(index, len(self)):
self.matrix[i].insert(index, 0)
# assign value
self[index] = value
else:
raise TypeError("Invalid name type.")
def __len__(self):
"""Matrix length."""
return len(self.names)
def __repr__(self):
"""Return Matrix as a string."""
return self.__class__.__name__ + "(names=%s, matrix=%s)" % tuple(
map(repr, (self.names, self.matrix))
)
def __str__(self):
"""Get a lower triangular matrix string."""
matrix_string = "\n".join(
[
self.names[i] + "\t" + "\t".join([str(n) for n in self.matrix[i]])
for i in range(0, len(self))
]
)
matrix_string = matrix_string + "\n\t" + "\t".join(self.names)
return matrix_string
[docs]class TreeConstructor:
"""Base class for all tree constructor."""
[docs] def build_tree(self, msa):
"""Caller to built the tree from a MultipleSeqAlignment object.
This should be implemented in subclass.
"""
raise NotImplementedError("Method not implemented!")
[docs]class DistanceTreeConstructor(TreeConstructor):
"""Distance based tree constructor.
:Parameters:
method : str
Distance tree construction method, 'nj'(default) or 'upgma'.
Examples
--------
Loading a small PHYLIP alignment from which to compute distances, and then
build a upgma Tree::
from Bio.Phylo.TreeConstruction import DistanceTreeConstructor
from Bio.Phylo.TreeConstruction import DistanceCalculator
from Bio import AlignIO
aln = AlignIO.read(open('TreeConstruction/msa.phy'), 'phylip')
constructor = DistanceTreeConstructor()
calculator = DistanceCalculator('identity')
dm = calculator.get_distance(aln)
upgmatree = constructor.upgma(dm)
print(upgmatree)
Output::
Tree(rooted=True)
Clade(branch_length=0, name='Inner4')
Clade(branch_length=0.18749999999999994, name='Inner1')
Clade(branch_length=0.07692307692307693, name='Epsilon')
Clade(branch_length=0.07692307692307693, name='Delta')
Clade(branch_length=0.11057692307692304, name='Inner3')
Clade(branch_length=0.038461538461538464, name='Inner2')
Clade(branch_length=0.11538461538461536, name='Gamma')
Clade(branch_length=0.11538461538461536, name='Beta')
Clade(branch_length=0.15384615384615383, name='Alpha')
Build a NJ Tree::
njtree = constructor.nj(dm)
print(njtree)
Output::
Tree(rooted=False)
Clade(branch_length=0, name='Inner3')
Clade(branch_length=0.18269230769230765, name='Alpha')
Clade(branch_length=0.04807692307692307, name='Beta')
Clade(branch_length=0.04807692307692307, name='Inner2')
Clade(branch_length=0.27884615384615385, name='Inner1')
Clade(branch_length=0.051282051282051266, name='Epsilon')
Clade(branch_length=0.10256410256410259, name='Delta')
Clade(branch_length=0.14423076923076922, name='Gamma')
"""
methods = ["nj", "upgma"]
def __init__(self, method="nj"):
"""Initialize the class."""
if isinstance(method, str) and method in self.methods:
self.method = method
else:
raise TypeError(
"Bad method: "
+ method
+ ". Available methods: "
+ ", ".join(self.methods)
)
[docs] def upgma(self, distance_matrix):
"""Construct and return an UPGMA tree.
Constructs and returns an Unweighted Pair Group Method
with Arithmetic mean (UPGMA) tree.
:Parameters:
distance_matrix : DistanceMatrix
The distance matrix for tree construction.
"""
if not isinstance(distance_matrix, DistanceMatrix):
raise TypeError("Must provide a DistanceMatrix object.")
# make a copy of the distance matrix to be used
dm = copy.deepcopy(distance_matrix)
# init terminal clades
clades = [BaseTree.Clade(None, name) for name in dm.names]
# init minimum index
min_i = 0
min_j = 0
inner_count = 0
while len(dm) > 1:
min_dist = dm[1, 0]
# find minimum index
for i in range(1, len(dm)):
for j in range(0, i):
if min_dist >= dm[i, j]:
min_dist = dm[i, j]
min_i = i
min_j = j
# create clade
clade1 = clades[min_i]
clade2 = clades[min_j]
inner_count += 1
inner_clade = BaseTree.Clade(None, "Inner" + str(inner_count))
inner_clade.clades.append(clade1)
inner_clade.clades.append(clade2)
# assign branch length
clade1.branch_length = min_dist * 1.0 / 2 - self._height_of(clade1)
clade2.branch_length = min_dist * 1.0 / 2 - self._height_of(clade2)
# update node list
clades[min_j] = inner_clade
del clades[min_i]
# rebuild distance matrix,
# set the distances of new node at the index of min_j
for k in range(0, len(dm)):
if k != min_i and k != min_j:
dm[min_j, k] = (dm[min_i, k] + dm[min_j, k]) * 1.0 / 2
dm.names[min_j] = "Inner" + str(inner_count)
del dm[min_i]
inner_clade.branch_length = 0
return BaseTree.Tree(inner_clade)
[docs] def nj(self, distance_matrix):
"""Construct and return a Neighbor Joining tree.
:Parameters:
distance_matrix : DistanceMatrix
The distance matrix for tree construction.
"""
if not isinstance(distance_matrix, DistanceMatrix):
raise TypeError("Must provide a DistanceMatrix object.")
# make a copy of the distance matrix to be used
dm = copy.deepcopy(distance_matrix)
# init terminal clades
clades = [BaseTree.Clade(None, name) for name in dm.names]
# init node distance
node_dist = [0] * len(dm)
# init minimum index
min_i = 0
min_j = 0
inner_count = 0
# special cases for Minimum Alignment Matrices
if len(dm) == 1:
root = clades[0]
return BaseTree.Tree(root, rooted=False)
elif len(dm) == 2:
# minimum distance will always be [1,0]
min_i = 1
min_j = 0
clade1 = clades[min_i]
clade2 = clades[min_j]
clade1.branch_length = dm[min_i, min_j] / 2.0
clade2.branch_length = dm[min_i, min_j] - clade1.branch_length
inner_clade = BaseTree.Clade(None, "Inner")
inner_clade.clades.append(clade1)
inner_clade.clades.append(clade2)
clades[0] = inner_clade
root = clades[0]
return BaseTree.Tree(root, rooted=False)
while len(dm) > 2:
# calculate nodeDist
for i in range(0, len(dm)):
node_dist[i] = 0
for j in range(0, len(dm)):
node_dist[i] += dm[i, j]
node_dist[i] = node_dist[i] / (len(dm) - 2)
# find minimum distance pair
min_dist = dm[1, 0] - node_dist[1] - node_dist[0]
min_i = 0
min_j = 1
for i in range(1, len(dm)):
for j in range(0, i):
temp = dm[i, j] - node_dist[i] - node_dist[j]
if min_dist > temp:
min_dist = temp
min_i = i
min_j = j
# create clade
clade1 = clades[min_i]
clade2 = clades[min_j]
inner_count += 1
inner_clade = BaseTree.Clade(None, "Inner" + str(inner_count))
inner_clade.clades.append(clade1)
inner_clade.clades.append(clade2)
# assign branch length
clade1.branch_length = (
dm[min_i, min_j] + node_dist[min_i] - node_dist[min_j]
) / 2.0
clade2.branch_length = dm[min_i, min_j] - clade1.branch_length
# update node list
clades[min_j] = inner_clade
del clades[min_i]
# rebuild distance matrix,
# set the distances of new node at the index of min_j
for k in range(0, len(dm)):
if k != min_i and k != min_j:
dm[min_j, k] = (
dm[min_i, k] + dm[min_j, k] - dm[min_i, min_j]
) / 2.0
dm.names[min_j] = "Inner" + str(inner_count)
del dm[min_i]
# set the last clade as one of the child of the inner_clade
root = None
if clades[0] == inner_clade:
clades[0].branch_length = 0
clades[1].branch_length = dm[1, 0]
clades[0].clades.append(clades[1])
root = clades[0]
else:
clades[0].branch_length = dm[1, 0]
clades[1].branch_length = 0
clades[1].clades.append(clades[0])
root = clades[1]
return BaseTree.Tree(root, rooted=False)
def _height_of(self, clade):
"""Calculate clade height -- the longest path to any terminal (PRIVATE)."""
if clade.is_terminal():
height = 0
else:
height = max(self._height_of(c) + c.branch_length for c in clade.clades)
return height
