def caculateDstatistics(self,
p1,
p2,
p3,
p4,
caculator,
currentchrID,
currentchrLen,
winwidth=None):
win = Util.Window()
"9": 58970518
}
winsize = int(sys.argv[6])
reff = open(sys.argv[1], 'r')
try:
refidx = pickle.load(open(sys.argv[1] + ".myfasteridx", 'rb'))
except IOError:
Util.generateFasterRefIndex(sys.argv[1], sys.argv[1] + ".myfasteridx")
refidx = pickle.load(open(sys.argv[1] + ".myfasteridx", 'rb'))
vcftools = "vcftools"
gapf = open(sys.argv[3], 'r')
scoredsnp = open(sys.argv[4], 'r')
scoredsnp.readline()
sitesingap = open(sys.argv[5], 'w')
if __name__ == '__main__':
win = Util.Window()
i = 0
interferf = open(sys.argv[5] + ".InterferingTEMP", 'w')
for gapregion in gapf:
i += 1
filledsites = []
gaplist = re.split(r"\s+", gapregion.strip())
if not os.path.exists(sys.argv[5] + "temp" + str(i) + ".recode.vcf"):
os.system(
vcftools + " --vcf " + sys.argv[2] +
" --recode --recode-INFO-all --remove-indv DSW33216 --chr " +
gaplist[0] + " --from-bp " + str(gaplist[1]) + " --to-bp " +
str(gaplist[2]) + " --out " + sys.argv[5] + "temp" + str(i))
vcfobj = VCFutil.VCF_Data(sys.argv[5] + "temp" + str(i) +
".recode.vcf")
vcflist = vcfobj.getVcfListByChrom(gaplist[0], MQfilter=0)