random.shuffle(haplotypes)
haplotypes = haplotypes[0:numSample]
newHap = []
for i in range(0,numSample):
newHap.append([])
# print "numMut\t" + str(len(mutations))
for i in range(0,len(mutations)):
bla = map(lambda x : x[i], haplotypes)
occ = reduce(lambda x,y: int(x) + int(y) , bla )
if not (occ == 0 or occ == numSample):
for j in range(0,len(haplotypes)) :
newHap[j].append(bla[j])
haplotypes = []
for h in newHap:
haplotypes.append( "".join(h) )
print "#snp\t%d" % len(haplotypes[0])
print "#h\t%d" % len(set(map(lambda x : "".join(x), haplotypes)))
pi = sumStatLib.nucDiv(haplotypes, seqLen ) # :TRICKY:
print "pi\t%f" % pi
print "sfs"
sfsDict = sumStatLib.sfs(haplotypes)
for key in sfsDict.keys():
print "%d\t%d" % (key, sfsDict[key])
' ', ETA()]
pbar = ProgressBar(widgets=widgets, maxval=numRep-1)
pbar.start()
numSnp = []
numHap = []
pies = []
sfsDict = {}
for i in range(0,numRep-1):
pbar.update(i)
haplotypes = oneSample(numSamp)
numSnp.append(len(haplotypes[0]) )
numHap.append(len(set(haplotypes)))
pies.append(sumStatLib.nucDiv(haplotypes, seqLen)) # :TRICKY:
tmpDict = sumStatLib.sfs(haplotypes)
ctr += 1
for key in tmpDict:
if sfsDict.has_key(key):
sfsDict[key] += float(tmpDict[key])
else :
sfsDict[key] = float(tmpDict[key])
pbar.finish()
for key in sfsDict.keys():
sfsDict[key] /= float(numRep)
