Clustering distance matrix Python

def TMclstr(fp):

import scipy.cluster.hierarchy as sch

import scipy.spatial.distance as ssd

#read represent id list

replist=read_clstr_represent(fp)

lenlist=len(replist)

#read TMscore matrix

vec=[]

f=file(‘TM.txt’)

for i in range(0,lenlist):

for j in range(i+1,lenlist):

a = f.readline().strip().split()

t=1-float(a[2])

vec.append(t)

f.close()

#Clustering

linkage_matrix=sch.linkage(ssd.squareform(vec))

#print linkage_matrix

ind=sch.fcluster(linkage_matrix,0.95)

inx=range(0,lenlist)

data=zip(ind,inx)

data.sort()

for i,j in data:

print replist[j],i