prog2_ksTest.py

import numpy.random as rd

timePoint = 12


inFIleName = "E:/evolutinoarypattern/RMB2_B10.freebayes_snps/RMB2_B10.merge.2.csv"
inFile = open(inFIleName, 'r')

outFileName = "E:/evolutinoarypattern/RMB2_B10.freebayes_snps/RMB2_B10.ks.csv"
outFile = open(outFileName, 'w')

while(True):
	ref, alt = [], []
	
	line = inFile.readline()
	if( line == ''):	break
	line = line.strip().split('\t')
	
	ref.append(int(line[5]))
	alt.append(int(line[6]))
	
	i = 0
	while (i < timePoint-1):
		line = inFile.readline()
		if(line==''):	break
		line = line.strip().split('\t')
		
		ref.append(int(line[5]))
		alt.append(int(line[6]))
		i = i +1
	
	
	p_0 = sum(alt) / ( sum(ref) + sum(alt) )
	p_mt = []
		
	for a_mt, r_mt in zip(alt,ref):
		mt = a_mt + r_mt
		if( mt == 0):
			p_mt.append(0)
		else:
			p_mt.append( (a_mt / (a_mt + r_mt)) )
				
	ks = [abs(p_0 - p) for p in p_mt ]

	maxKS = max(ks)
	val = '%.4f'%maxKS
	outFile.write(str(val) + '\n')

outFile.close()
inFile.close()