normalizeTwoPopnStats.py

import sys

unmaskedFracsFileName, winSize = sys.argv[1:]
winSize = int(winSize)

unmaskedFracs = []
if unmaskedFracsFileName != "None":
    with open(unmaskedFracsFileName) as unmaskedFracsFile:
        for line in unmaskedFracsFile:
            unmaskedFracs.append(float(line.strip()))

line = sys.stdin.readline()
first = True
colsToDiv, colsToDivTwice = [], []
repIndex = 0
while line:
    line = line.strip().split()
    if first:
        for i in range(len(line)):
            #if line[i] in "pi1,ss1,thetaH1,H1,HapCount1,pi2,ss2,thetaH2,H2,HapCount2".split(","):
            if line[i] in "pi1,private1,ss1,thetaH1,H1,pi2,private2,ss2,thetaH2,H2,dxy_mean,dxy_min,gmin".split(","):
                colsToDiv.append(i)
            elif line[i] in "hetVar1,hetVar2".split(","):
                colsToDivTwice.append(i)
        first = False
        print("\t".join(line))
    else:
        outLine = []
        if unmaskedFracs:
            numSites = unmaskedFracs[repIndex]*winSize
        else:
            numSites = winSize
        for i in range(len(line)):
            if "inf" in line[i] or "nan" in line[i]:
                outLine.append(line[i])
            elif i in colsToDiv:
                #outLine.append("%s,%f" %(line[i], float(line[i])/numSites))
                outLine.append("%f" %(float(line[i])/numSites))
            elif i in colsToDivTwice:
                outLine.append("%f" %(float(line[i])/numSites**2))
            else:
                outLine.append(line[i])
        print("\t".join(outLine))
        repIndex += 1
    line = sys.stdin.readline()