def parsimony_up2(subtree, nodelist, parent, siblings):
"""parsimony part: up direction -> from root to leafs"""
# Arguments:
# subtree
# 0 1 2 3 4
# nodelist - [id, depth, originaltag, finaltag, calc[taglist]]
# parent - nodelist element
# siblings - [nodelist element]
element = find_element_in_nodelist(subtree.name, nodelist)
parent_tag = parent[4][
0] # parent[4] could look like [['0', '1'], ['1']] or [['1']]
both_tags = []
both_tags.append(parent_tag)
for sibling in siblings:
both_tags.append(sibling[4][0])
# get intersection or union
tag_list = get_intersect_or_union(both_tags)
# add new tag
element[4].append(tag_list)
# go on with children
if not subtree.is_terminal():
children = []
for clade in subtree.clades:
child = find_element_in_nodelist(clade.name, nodelist)
children.append(child)
for i in range(0, len(subtree.clades)):
clade = subtree.clades[i]
child = find_element_in_nodelist(clade.name, nodelist)
sublist = deepcopy(children)
del sublist[i]
parsimony_up2(clade, nodelist, element, sublist)
return
def parsimony_up(subtree, nodelist, parent, siblings):
"""parsimony part: up direction -> from root to leafs"""
# Arguments:
# subtree
# 0 1 2 3 4
# nodelist - [id, depth, originaltag, finaltag, calc[taglist]]
# parent - nodelist element
# siblings - [nodelist element]
parent_tag = parent[4] # parent[4] could look like [0, 1] or [1]
siblings_tags = []
siblings_tags += parent_tag
for sibling in siblings:
siblings_tags += sibling[4]
element = find_element_in_nodelist(subtree.name, nodelist)
# calculate and add mean
mean = sum(siblings_tags) / len(siblings_tags)
element[4].append(mean)
# go on with children
if not subtree.is_terminal():
children = []
for clade in subtree.clades:
child = find_element_in_nodelist(clade.name, nodelist)
children.append(child)
for i in range(0, len(subtree.clades) - 1):
clade = subtree.clades[i]
child = find_element_in_nodelist(clade.name, nodelist)
sublist = deepcopy(children)
del sublist[i]
parsimony_up(clade, nodelist, element, sublist)
return
def sankoff_parsimony(tree, nodelist):
"""Using rpy2 for forwarding to R code"""
# ---- cache tree for R script ---
random_name = str(randint(0, 1000))
path_simulated_tree = 'code/bufferfiles/simulated_tree' + random_name + '.tre'
path_tagged_tree = 'code/bufferfiles/tagged_tree' + random_name + '.tre'
Phylo.write(tree, path_simulated_tree, 'newick')
prepare_tree(tree.clade, nodelist)
Phylo.write(tree, path_tagged_tree, 'newick')
# -------- R code --------
path = "code/utilities/castor_parsimony_simulation.R"
f = open(path, "r")
code = ''.join(f.readlines())
print("---------------- prepare R script ----------------")
code_Array = code.split("data/subtree/Eukaryota.tre")
code = path_simulated_tree.join(code_Array)
code_Array = code.split("code/bufferfiles/tagged_tree.tre")
code = path_tagged_tree.join(code_Array)
result = rpy2.robjects.r(code)
# assume that...
likelihoods = rpy2.robjects.globalenv['likelihoods'][0]
# The rows in this matrix will be in the order in which tips and
# nodes are indexed in the tree, i.e. the rows 1,..,Ntips store the probabilities for
# tips, while rows (Ntips+1),..,(Ntips+Nnodes) store the probabilities for nodes.
leaf_nodes = rpy2.robjects.globalenv['state_ids']
number_of_tips = rpy2.robjects.globalenv['number_of_tips']
internal_nodes = rpy2.robjects.globalenv['internal_nodes']
l = int(len(likelihoods) / 3)
j = 0
k = 0
for i in range(2 * l, 3 * l):
if j < number_of_tips[0]:
element = find_element_in_nodelist(leaf_nodes[j], nodelist)
if element[3] == '': # if unknown
# set finaltag:
element[3] = likelihoods[i]
j += 1
else:
element = find_element_in_nodelist(internal_nodes[k], nodelist)
# set finaltag:
element[3] = likelihoods[i]
k += 1
return
def my_parsimony(tree_clade, nodelist):
"""mean based parsimony"""
# down:
parsimony_down(tree_clade, nodelist)
# up:
parent = find_element_in_nodelist(tree_clade.name, nodelist)
children = []
for clade in tree_clade.clades:
child = find_element_in_nodelist(clade.name, nodelist)
children.append(child)
for i in range(0, len(tree_clade.clades)):
clade = tree_clade.clades[i]
child = find_element_in_nodelist(clade.name, nodelist)
sublist = deepcopy(children)
del sublist[i]
parsimony_up(clade, nodelist, parent, sublist)
# final:
parsimony_final(tree_clade, nodelist)
return
def parsimony_down(subtree, nodelist):
"""parsimony part: down direction -> from leafs to root"""
# Arguments:
# subtree
# 0 1 2 3 4
# nodelist - [id, depth, originaltag, finaltag, calc[taglist]]
child_tags = []
for clade in subtree.clades:
child = find_element_in_nodelist(clade.name, nodelist)
# if child is not tagged, first tag it:
if child[4] == []:
parsimony_down(clade, nodelist)
child_tags.append(child[4][0])
element = find_element_in_nodelist(subtree.name, nodelist)
# get intersection or union
tag_list = get_intersect_or_union(child_tags)
# add new tag
element[4].append(tag_list)
return
def fitch_parsimony(tree_clade, nodelist, version):
"""parsimony implemented from [COO98] - changed for multifurcating trees"""
# down:
parsimony_down(tree_clade, nodelist)
# up:
parent = find_element_in_nodelist(tree_clade.name, nodelist)
children = []
for clade in tree_clade.clades:
child = find_element_in_nodelist(clade.name, nodelist)
children.append(child)
for i in range(0, len(tree_clade.clades)):
clade = tree_clade.clades[i]
child = find_element_in_nodelist(clade.name, nodelist)
sublist = deepcopy(children)
del sublist[i]
# ToDo: decide which one, next ToDo: a second parsimony down?
Fitch_Versions.parsimony_up(clade, nodelist, parent, sublist, version)
# final:
parsimony_final(tree_clade, nodelist)
return
def parsimony_down(subtree, nodelist):
"""parsimony part: down direction -> from leafs to root"""
# Arguments:
# subtree
# 0 1 2 3 4
# nodelist - [id, depth, originaltag, finaltag, calc[taglist]]
mean = 0
for clade in subtree.clades:
child = find_element_in_nodelist(clade.name, nodelist)
# if child is not tagged, first tag it:
if child[4] == []:
parsimony_down(clade, nodelist)
# if child is leaf node:
if clade.is_terminal():
if child[4][0] == [0, 1]: # if unknown
child[4][0] = 0.5
else:
child[4][0] = child[4][0][0]
mean = mean + child[4][0] # else: +0 for 'P'
element = find_element_in_nodelist(subtree.name, nodelist)
# calculate and add mean
mean = mean / len(subtree.clades)
element[4].append(mean)
return
def prepare_tree(subtree, nodelist):
"""tag all leafs"""
# Arguments:
# subtree
# 0 1 2 3 4
# nodelist - [id, depth, originaltag, finaltag, calc[taglist]]
if subtree.is_terminal():
element = find_element_in_nodelist(subtree.name, nodelist)
if len(element[4][0]) > 1:
subtree.name = ''
else:
subtree.name = str(element[4][0][0])
for clade in subtree.clades:
prepare_tree(clade, nodelist)
return
def prepare_tree(subtree):
"""tag all leafs"""
# Arguments:
# subtree
# 0 1 2
# nodelist - [ott_id, originaltag, finaltag]
element = find_element_in_nodelist(subtree.name, nodelist)
if subtree.is_terminal():
if element[1] == '' or element[1] == 'NA':
subtree.name = subtree.name + '$(' + element[2] + ')'
else:
subtree.name = subtree.name + '$' + element[1]
else:
subtree.name = subtree.name + '$(' + element[2] + ')'
for clade in subtree.clades:
prepare_tree(clade)
return
def prepare_tree(subtree):
"""tag all leafs"""
# Arguments:
# subtree
# 0 1 2 3 4 5
# nodelist - [id, originaltag, finaltag, depth, heights, nr_children]
global nodelist
if subtree.is_terminal():
element = find_element_in_nodelist(subtree.name, nodelist)
if element[1] == 'NA':
subtree.name = ''
else:
subtree.name = str(element[1])
for clade in subtree.clades:
prepare_tree(clade)
return
def parsimony_final(subtree, nodelist):
"""parsimony final part: combine multiple tags of node to one final tag"""
# Arguments:
# subtree
# 0 1 2 3 4
# nodelist - [id, depth, originaltag, finaltag, calc[taglist]]
element = find_element_in_nodelist(subtree.name, nodelist)
if subtree.is_terminal() and element[4][0] != 0.5:
element[3] = element[4][0]
else:
# calculate mean
mean = sum(element[4]) / len(element[4])
element[3] = str(round(mean, 2))
# go on with children
if not subtree.is_terminal():
for clade in subtree.clades:
parsimony_final(clade, nodelist)
return
def parsimony_final(subtree, nodelist):
"""parsimony final part: combine multiple tags of node to one final tag"""
# Arguments:
# subtree
# 0 1 2 3 4
# nodelist - [id, depth, originaltag, finaltag, calc[taglist]]
element = find_element_in_nodelist(subtree.name, nodelist)
if subtree.is_terminal() and len(element[4][0]) == 1:
element[3] = element[4][0][0]
else:
# get intersection or union
tag_list = get_intersect_or_union(element[4])
# add final tag
tag_string = ""
for tag in tag_list:
tag_string += str(tag) + "&"
tag_string = tag_string[:len(tag_string)-1]
element[3] = tag_string
# go on with children
if not subtree.is_terminal():
for clade in subtree.clades:
parsimony_final(clade, nodelist)
return
def sankoff_parsimony(run_id):
"""Using rpy2 for forwarding to R code"""
# Arguments:
# tree
# 0 1 2 3 4 5
# nodelist - [id, originaltag, finaltag, depth, heights, nr_children]
# run_id
global nodelist
read_nodelist()
tagged_tree_path = 'code/bufferfiles/tagged_tree.tre'
if run_id >= 0:
randomly_change_nodelist()
tagged_tree_path = './code/bufferfiles/tagged_tree' + str(
run_id) + '.tre'
# ---- cache tree for R script ---
cache_tree(tagged_tree_path)
# -------- R code --------
f = open(r_path, "r")
code = ''.join(f.readlines())
if run_id >= 0:
print(
colored("---------------- prepare R script ----------------",
"green"))
code_Array = code.split("code/bufferfiles/tagged_tree.tre")
code = tagged_tree_path.join(code_Array)
print(colored("---------------- run castor ----------------", "green"))
rpy2.robjects.r(code)
# assume that...
likelihoods = rpy2.robjects.globalenv['likelihoods'][0]
# The rows in this matrix will be in the order in which tips and
# nodes are indexed in the tree, i.e. the rows 1,..,Ntips store the probabilities for
# tips, while rows (Ntips+1),..,(Ntips+Nnodes) store the probabilities for nodes.
leaf_nodes = rpy2.robjects.globalenv['state_ids']
number_of_tips = rpy2.robjects.globalenv['number_of_tips']
internal_nodes = rpy2.robjects.globalenv['internal_nodes']
print(
colored("---------------- save likelihoods ----------------", "green"))
l = int(len(likelihoods) / 3)
j = 0
k = 0
for i in range(2 * l, 3 * l):
if j < number_of_tips[0]:
element = find_element_in_nodelist(leaf_nodes[j], nodelist)
if element[2] == '': # if unknown
# set finaltag:
element[2] = likelihoods[i]
j += 1
else:
element = find_element_in_nodelist(internal_nodes[k], nodelist)
# set finaltag:
element[2] = likelihoods[i]
k += 1
return nodelist