def main(arg1, arg2):
with open(arg1) as f:
content = f.readlines()
# you may also want to remove whitespace characters like `\n` at the end of each line
content = [x.strip() for x in content]
t2 = Tree(content[0])
###print(t2)
triplets = []
taxa = []
for i in range(0, len(content)):
t1 = Tree(content[i])
leaves, triplets = tp.triplet_decompose(t1, triplets)
t2 = Tree(content[i])
###print(t2)
taxa += leaves
###print(triplets)
triplets_dict = defaultdict(list)
for t in triplets:
trip_key = [t[1][0], t[1][1], t[0]]
trip_key.sort()
trip_key = str(trip_key).strip('[]')
trip_key = trip_key.replace("'", '')
trip_key = trip_key.replace(" ", "")
if (t in triplets_dict[trip_key]) is False:
triplets_dict[trip_key].append(t)
###print(triplets_dict)
Cpc = physic_pc(list(set(taxa)), triplets, triplets_dict)
def main(arg1, arg2):
with open(arg1) as f:
content = f.readlines()
# you may also want to remove whitespace characters like `\n` at the end of each line
content = [x.strip() for x in content]
t2=Tree(content[0])
####print(t2)
triplets=[]
taxa=[]
good=[]
bad=[]
for i in range(1,len(content)):
t1=Tree(content[i])
####print(t1)
leaves,triplets=tp.triplet_decompose(t1,triplets)
#t2=Tree(content[i])
####print(t2)
taxa+=leaves
Super_triplet=[]
t2=content[0]
Super_leaves,Supers_triplets=tp.main(t2,Super_triplet)
R_pi=intersection(triplets,Super_triplet)
final_tree=check_pi(R_pi,Tree(t2))
###print("final ishhhhhh: --",final_tree)
#main("test1.txt",2)
def main(arg1, arg2):
with open(arg1) as f:
content = f.readlines()
# you may also want to remove whitespace characters like `\n` at the end of each line
content = [x.strip() for x in content]
t2=Tree(content[0])
###print(t2)
triplets=[]
taxa=[]
for i in range(0,len(content)):
t1=Tree(content[i])
leaves,triplets=tp.triplet_decompose(t1,triplets)
t2=Tree(content[i])
###print(t2)
taxa+=leaves
###print(triplets)
triplets_dict=defaultdict(list)
for t in triplets:
trip_key=[t[1][0],t[1][1],t[0]]
trip_key.sort()
trip_key=str(trip_key).strip('[]')
trip_key=trip_key.replace("'", '')
trip_key=trip_key.replace(" ", "")
if (t in triplets_dict[trip_key]) is False :
triplets_dict[trip_key].append(t)
###print(triplets_dict)
Cpc=pc.physic_pc(list(set(taxa)),triplets,triplets_dict)
#print(Cpc)
'''Super_triplet=[]
#t2=content[0]
Super_leaves,Supers_triplets=tp.triplet_decompose(Cpc,Super_triplet)
R_pi=intersection(triplets,Super_triplet)
print(R_pi)
final_tree=pi.check_pi(Cpc,R_pi)
#print("final is: --",final_tree)'''
return Cpc
def main(arg1, arg2):
with open(arg1) as f:
content = f.readlines()
content = [x.strip() for x in content]
t2 = Tree(content[0])
#print(t2)
triplets = []
taxa = []
for i in range(0, len(content)):
t1 = Tree(content[i])
t1.resolve_polytomy()
leaves, triplets = tp.triplet_decompose(t1, triplets)
#t2=Tree(content[i])
#print(t2)
taxa += leaves
#print(set(taxa))
Cpc = build(list(set(taxa)), triplets)
#print(Cpc)
Cpc.show()
return Cpc
def main(arg1, arg2):
with open(arg1) as f:
content = f.readlines()
triplets = []
taxa = []
good = []
bad = []
for i in range(0, len(content)):
#####print(i)
t1 = Tree(content[i])
t1.resolve_polytomy()
#####print(t1.write(format=9))
leaves, triplets = tp.triplet_decompose(t1, triplets)
#t2=Tree(content[i])
#####print(t2)
#####print(triplets)
taxa += leaves
taxa_com = set(taxa)
#####print(triplets)
d = {ni: indi for indi, ni in enumerate(taxa)}
rows, cols = (len(taxa), len(taxa))
triplets_dict = defaultdict(list)
for t in triplets:
trip_key = [t[1][0], t[1][1], t[0]]
trip_key.sort()
trip_key = str(trip_key).strip('[]')
trip_key = trip_key.replace("'", '')
trip_key = trip_key.replace(" ", "")
if (t in triplets_dict[trip_key]) is False:
triplets_dict[trip_key].append(t)
#t2=MaxCut.main(arg1, arg2)
t2, overlap_per1, inconsist_per1, triplets_dict1 = MaxCut.main(arg1, 2)
print(
"-------------------------------------bulid-------------------------------------------------"
)
trees = []
t2.show()
for node in t2.traverse("postorder"):
children_node = node.get_children()
if len(children_node) > 2:
trees += children_node
trees.append(t2)
#print(trees)
taxa = []
dict_leaves = {}
for i in range(len(trees)):
c = trees[i]
c.detach()
for leaves in c:
if leaves.name != '':
dict_leaves[leaves.name] = i
taxa.append(leaves.name)
newick_supertrees = []
###print("last tree",trees[len(trees)-1])
with open(arg1) as f:
content = f.readlines()
# you may also want to remove whitespace characters like `\n` at the end of each line
content = [x.strip() for x in content]
t2 = Tree(content[0])
for i in range(0, len(content) - 2):
t1 = Tree(content[i + 1])
t1.resolve_polytomy()
for leaves in t1:
leaves.name = "leaf" + str(dict_leaves[leaves.name])
for i in range(len(trees)):
current_leaf_set = t1.search_nodes(name="leaf" + str(i))
#####print(current_leaf_set)
if len(current_leaf_set) > 1:
for j in range(1, len(current_leaf_set)):
current_leaf_set[j].delete()
newick_supertrees.append(t1.write(format=9))
#####print(newick_supertrees)
trees_structure, overlap_per1, inconsist_per1, triplets_dict1 = MaxCut.main(
newick_supertrees, 1)
#####print("------------structure-------------")
#####print(overlap_per,inconsist_per)
#####print(trees_structure)
for i in range(len(trees)):
node_add = trees_structure.search_nodes(name="leaf" + str(i))
if len(node_add) > 0:
node_add = node_add[0]
node_add_parent = node_add.up
###print(trees[i])
node_add_parent.add_child(trees[i])
node_add.detach()
taxa = set(taxa)
final_taxa = []
for nodes in trees_structure:
if nodes.is_leaf():
if nodes.name != '':
final_taxa.append(nodes.name)
trees_structure.prune(final_taxa)
trees_structure.show()
supertree_triplets = []
ST_triplets_dict = defaultdict(list)
st_leaves, supertree_triplets, ST_triplets_dict = tp_d.triplet_decompose(
trees_structure, supertree_triplets, ST_triplets_dict)
total = 1
#triplets_dict=defaultdict(list)
overlap = 0
inconsist = 0
for keys in triplets_dict:
overlap += len(
intersection(triplets_dict[keys], ST_triplets_dict[keys]))
total += len(triplets_dict[keys])
if len(triplets_dict[keys]) > 1:
inconsist += len(triplets_dict[keys])
overlap_per = overlap / total
inconsist_per = inconsist / total
#####print(taxa_com)
##print(trees_structure)
return trees_structure, overlap_per, inconsist_per
def main(arg1, arg2):
if arg2 == 2:
with open(arg1) as f:
content = f.readlines()
else:
content = arg1
####print(content)
# you may also want to remove whitespace characters like `\n` at the end of each line
#content = [x.strip() for x in content]
t2 = Tree(content[0])
#print(t2)
triplets = []
taxa = []
good = []
bad = []
for i in range(0, len(content)):
####print(i)
t1 = Tree(content[i])
#t1.show()
###print(t1.write(format=9))
t1.resolve_polytomy()
for leaf in t1:
if leaf.is_leaf() is True:
taxa.append(leaf.name)
leaves, triplets = tp.triplet_decompose(t1, triplets)
#print("leaves",leaves)
#t2=Tree(content[i])
####print(triplets)
#taxa+=leaves
taxa = set(taxa)
#print(triplets)
#print("taxa",taxa)
d = {ni: indi for indi, ni in enumerate(taxa)}
rows, cols = (len(taxa), len(taxa))
triplets_dict = defaultdict(list)
for t in triplets:
trip_key = [t[1][0], t[1][1], t[0]]
trip_key.sort()
trip_key = str(trip_key).strip('[]')
trip_key = trip_key.replace("'", '')
trip_key = trip_key.replace(" ", "")
if (t in triplets_dict[trip_key]) is False:
triplets_dict[trip_key].append(t)
#print(triplets_dict)
####print(good)
####print(bad)
####print(clades)
####print("__________________________________________________________")
####print(outgroup)
#g = Graph(connections, outgroup, good, bad, directed=True)
####print(g._graph_good)
####print(g._weights)
#triplets_dict=defaultdict(list)
supertree = Max_cut(taxa, triplets_dict)
#print("supertree",supertree)
#supertree.show()
'''supertree_triplets=[]
ST_triplets_dict=defaultdict(list)
st_leaves,supertree_triplets,ST_triplets_dict=tp_d.triplet_decompose(supertree,supertree_triplets,ST_triplets_dict)
total=1
overlap=0
inconsist=0
for keys in triplets_dict:
overlap += len(intersection(triplets_dict[keys],ST_triplets_dict[keys]))
total+=len(triplets_dict[keys])
if len(triplets_dict[keys])>1:
inconsist+=len(triplets_dict[keys])
overlap_per=overlap/total
inconsist_per=inconsist/total
#t2=Tree("((ah, ((ae, ab), ai)), ((ag, aa), (ac, (ad, (aj, af)))));")
####print(t2)
#triplet_test.main(arg1,supertree,True,25)
##print(supertree)'''
return supertree, 0, 0, triplets_dict