parser.add_option("-i", "--inp", dest="inp", help="*.sync or cmh output file")
parser.add_option("-s", "--snps", dest="snps", help="cmh output with all SNPs")
parser.add_option("-b", "--bins", dest="bins", help="number of bins")
parser.add_option("-m", "--maxdist", dest="maxdist", help="maximum distance to candidate.")
parser.add_option("-o", "--out", dest="out", help="outputfile for boxplot")
parser.add_option("--measure", dest="measure", help="What should be calculated, median (median), geometric mean (gm)")
parser.add_option_group(group)
(options, args) = parser.parse_args()
# 1: Lade die candidaten SNPs
chrh,candl = LDIO.read_candidatehash(options.inp, int(options.maxdist) )
# 2: Iteriere uber alle SNPs
for l in open(str(options.snps),"r"):
snp=PopIO.parse_cmhline(l)
candidates=chrh[snp.chr][snp.pos]
for cand in candidates:
cand.appendSNP(snp)
# 3: itererier ueber alle canidaten
ofh=open(options.out,"w")
for cand in candl:
bins=cand.distributeToBins(int(options.bins))
toprint=[]
toprint.append(cand.chr)
toprint.append(cand.pos)
toprint.append(cand.pvalue)
for t in bins:
value=0
pvalar=[snp.pvalue for snp in t]
parser.add_option("-i", "--inp", dest="inp", help="input = cmh file")
parser.add_option("-p", "--pops", dest="pops", help="define replicates and populations: separate populations with a \",\", e.g.8,9,10 ")
parser.add_option("-t", "--th", dest="th", help="minimum allele count ")
parser.add_option("--test",action="store_true", dest="test",help="run the doctest")
parser.add_option_group(group)
(options, args) = parser.parse_args()
def is_fixed(a,pops,th):
# filter empty lines
"""
"""
for i in pops:
activepop=a[int(i)-1]
alcount=activepop.count_alleles(th)
if alcount>1:
return 0
return 1
pops=options.pops.split(",")
for l in open(str(options.inp),"r"):
if l.rstrip()=="":
continue
p=PopIO.parse_cmhline(l)
isfixed=is_fixed(p.populations,pops,int(options.th))
if isfixed>0:
print l.rstrip()
#2L 4910 A 6:0:0:0:0:0 - 5:0:0:0:0:0 25:0:0:0:0:0 33:0:0:0:0:0
#2L 4911 G 0:0:0:7:0:0 - 0:0:0:5:0:0 0:0:0:27:0:0 0:0:0:33:0:0
#2L 4912 A 7:0:0:0:0:0 - 5:0:0:0:0:0 27:0:0:0:0:0 32:0:0:0:0:0
#2L 4913 G 0:0:0:7:0:0 - 0:0:0:5:0:0 0:0:0:27:0:0 0:0:0:34:0:0
#2L 4914 A 7:0:0:0:0:0 - 5:0:0:0:0:0 26:0:0:0:0:0 33:0:0:0:0:0
#2L 4915 G 0:0:0:8:0:0 - 0:0:0:5:0:0 0:0:0:22:0:0 0:0:0:33:0:0
#2L 4916 A 8:0:0:0:0:0 - 6:0:0:0:0:0 25:0:0:0:0:0 33:0:0:0:0:0
#2L 4917 G 0:0:0:8:0:0 - 0:0:0:6:0:0 0:0:0:23:0:0 0:0:0:32:0:0
#2L 4918 C 0:0:8:0:0:0 - 0:0:6:0:0:0 0:0:22:0:0:0 0:0:30:0:0:0
print "#chr\tpos\trc\tallele_states\t+"""
for l in sync:
if l.rstrip("\n")=="":
continue
p=PopIO.parse_syncline(l)
b=str(p.chr)+"_"+str(p.pos)
bh={"A":0,"C":0,"G":0,"T":0}
for pop in p.populations:
bh["A"]+=pop.A
bh["T"]+=pop.T
bh["C"]+=pop.C
bh["G"]+=pop.G
maxnonrefc=maxkeyfornotrefc(bh,p.refc)
print p.chr+"\t"+str(p.pos)+"\t"+p.refc+"\t"+maxnonrefc+"\t+"
