Problem in Python script of NJ

Question

[anasjamshed]

I am trying to implement the NJ algorithm in python :

import sys
import numpy as np
import scipy as scipy
import itertools
from sys import maxsize

def calculateQ(d):
    r = d.shape[0]
    q = np.zeros((r,r))
    for i in range(r):
        for j in range(r):
            if i == j:
                q[i][j] = 0
            else:
                sumI = 0
                sumJ = 0
                for k in range(r):
                    sumI += d[i][k]
                    sumJ += d[j][k]
                q[i][j] = (r-2) * d[i][j] - sumI - sumJ

    return q

def findLowestPair(q):
    r = q.shape[0]
    minVal = maxsize
    for i in range(0,r):
        for j in range(i,r):
            if (q[i][j] < minVal):
                minVal = q[i][j]
                minIndex = (i,j)
    return minIndex


def doDistOfPairMembersToNewNode(i,j,d):
    r = d.shape[0]
    sumI = 0
    sumJ = 0
    for k in range(r):
        sumI += d[i][k]
        sumJ += d[j][k]

    dfu = (1. / (2. * (r - 2.))) * ((r - 2.) * d[i][j] + sumI - sumJ)
    dgu = (1. / (2. * (r - 2.))) * ((r - 2.) * d[i][j] - sumI + sumJ)

    return (dfu,dgu)

def calculateNewDistanceMatrix(f,g,d):
    print (d)
    r = d.shape[0]
    nd = np.zeros((r-1,r-1))

    # Copy over the old data to this matrix
    ii = jj = 1
    for i in range(0,r):
        if i == f or i == g:
            continue
        for j in range(0,r):
            if j == f or j == g:
                continue
            nd[ii][jj] = d[i][j]
            jj += 1
        ii += 1
        jj = 1

    # Calculate the first row and column
    ii = 1
    for i in range (0,r):
        if i == f or i == g:
            continue
        nd[0][ii] = (d[f][i] + d[g][i] - d[f][g]) / 2.
        nd[ii][0] = (d[f][i] + d[g][i] - d[f][g]) / 2.
        ii += 1

    return nd

def doNeighbourJoining(d):
    labels = ["Human","Chimp","Gorilla","Orangutan","Gibbon"]

    while d.shape[0] > 1:
        q = calculateQ(d)
        lowestPair = findLowestPair(q)
        print ("Joining")
        print (lowestPair[0])
        print (lowestPair[1])
        # newlabel = "%s%s" % (labels[lowestPair[0]], labels[lowestPair[1]])
        # print "lowestPair[0]=%i\tlowestPair[1]=%i" % (lowestPair[0], lowestPair[1])
        # print labels
        # print newlabel
        # del labels[lowestPair[0]]
        # del labels[lowestPair[1]]
        # labels.insert(0,newlabel)

        i = lowestPair[0]
        j = lowestPair[1]

        pairDist = doDistOfPairMembersToNewNode(i,j,d)
        d = calculateNewDistanceMatrix(i,j,d)
        # print d


def run(distMatrix):
    doNeighbourJoining(distMatrix)

if __name__ == "__main__":
    if len(sys.argv) > 1:
        print ("Usage: neighbour-joining.py")

    distMatrix = np.array(
        [
            [  0,  79,  92,  144, 162],
            [ 79,   0,  95,  154, 169],
            [ 92,  102,   0,  150,  169],
            [ 144,  154,  150,   0,  169],
            [163, 173,  169,  169,   0],

         ]
        )

run(distMatrix)

But I am getting the following error:

---> 47     dfu = (1. / (2. * (r - 2.))) * ((r - 2.) * d[i][j] + sumI - sumJ)
     48     dgu = (1. / (2. * (r - 2.))) * ((r - 2.) * d[i][j] - sumI + sumJ)
     49 

ZeroDivisionError: float division by zero

The code gives a 5X5 matrix, then a 4x4 and 3x3 matrix as an output. But, it should output a 2x2 and 1X1 as well

Can anyone help me?