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completing_a_tree.py
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completing_a_tree.py
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import argparse
from Bio import SeqIO
parser = argparse.ArgumentParser()
parser.add_argument('-f', '--File', help='input file', type=str, action = 'store', required = True)
args = parser.parse_args()
file = args.File
def GetTree(edges):
tree_list = []
n_clusters = 0
for n1, n2 in edges:
n1 = int(n1)
n2 = int(n2)
for i in tree_list:
set_i = set(i)
i = list(set_i)
# Is n1 or n2 already listed?
already = []
for i, l in enumerate(tree_list):
if n1 in l or n2 in l:
already.append(i)
# If not
if len(already) == 0:
tree_list.append([n1,n2])
# Else
else:
if len(already) == 1:
# Create a merged list
new_list = []
for i in already:
new_list.extend(tree_list[i])
new_list = new_list + [n1, n2]
new_list = list(set(new_list))
# Remove the old ones
for i in already:
del tree_list[i]
# Append to tree_list
tree_list.append(new_list)
else:
# Create a merged list
new_list = []
for i in already:
new_list.extend(tree_list[i])
new_list = new_list + [n1, n2]
new_list = list(set(new_list))
# Remove the old ones
tree_list = [v for i, v in enumerate(tree_list) if i not in already]
# Append to tree_list
tree_list.append(new_list)
return(tree_list)
with open(file) as f:
data = f.readlines()
data = [i.replace('\n','').split(' ') for i in data]
n_nodes = int(data[0][0])
edges = data[1:]
x = GetTree(edges)
###### Not branched nodes
not_branched = 0
values = []
for i in x:
values.extend(i)
for i in range(1,n_nodes+1):
if i not in values:
not_branched += 1
# Output:
print(len(x) + not_branched - 1)