print("python3 %s COMMAND study [file] [source] [refPop] [chro]" % (sys.argv[0]))
print("""COMMAND is
prepareData
iHS
statIHS
XPEHH
statXPEHH
if command is prepareData, source has the phasedset and
refPop the reference population
""")
sys.exit(-1)
command = sys.argv[1]
myKaryo = sys.argv[2]
karyo.loadBuiltIn(myKaryo)
lexec = MEGA.executor
maxChro = 23 # Needs refactor... No hard max
def removeFixed(tmp, final):
fhap = open("%s.hap" % tmp)
haplo = fhap.readline().rstrip().split(' ')
alleles = [set([a]) for a in haplo]
for l in fhap:
haplo = l.rstrip().split(' ')
for i in range(len(haplo)):
alleles[i].add(haplo[i])
fhap.close()
f = open("%d.uiHS" % (knum,))
for l in f:
val = [x for x in l.rstrip().split(" ") if x != ''][5]
if val.find("inf") == -1 and val.find("nan") == -1:
uvals.append(float(val))
f.close()
f = open("%d.iHS" % (knum,))
for l in f:
val = l.rstrip().split("\t")[2]
if val.find("inf") == -1 and val.find("nan") == -1:
vals.append(float(val))
f.close()
pylab.clf()
pylab.hist(vals, 100)
pylab.hist(uvals, 100)
pylab.savefig("uiHS.png")
#pylab.savefig("uiHS.eps")
def doSet(setDir):
cwd = os.getcwd()
os.chdir(setDir)
if args.operation in ["ALL", "iHS"]:
doiHS(args.minSNPs, args.windowSize)
if args.operation in ["ALL", "xpEHH"]:
doxpEHH(args.windowSize)
os.chdir(cwd)
karyo.loadBuiltIn(args.karyo)
doSet(MEGA.cacheDB + "/sets/" + args.karyo + "/" + args.hash)