"1": 42145699,
'2': 49200776,
'3': 50652576,
"4": 40408058,
"5": 47253416,
"6": 36015257,
"7": 35964515,
"8": 40690061,
"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"):
action="store_false",
dest="verbose",
default=True,
help="don't print status messages to stdout")
(options, args) = parser.parse_args()
refFastaName1 = options.reffa[0]
refFastaName2 = options.reffa[1]
reffastaidxName1 = refFastaName1 + ".myfasteridx"
reffastaidxName2 = refFastaName2 + ".myfasteridx"
try:
refidxByChr2 = pickle.load(open(reffastaidxName2, 'rb'))
refidxByChr1 = pickle.load(open(reffastaidxName1, 'rb'))
except IOError:
Util.generateFasterRefIndex(refFastaName1, reffastaidxName1)
Util.generateFasterRefIndex(refFastaName2, reffastaidxName2)
refidxByChr1 = pickle.load(open(reffastaidxName1, 'rb'))
refidxByChr2 = pickle.load(open(reffastaidxName2, 'rb'))
commsample_idxlistinM = []
commsample_idxlistinV = []
degenerateM = {
"R": "AG",
"Y": "CT",
"M": "AC",
"K": "GT",
"S": "GC",
"W": "AT",
"A": "AA",
"T": "TT",
"C": "CC",
# if options.depthfile!=None:
# print(options.depthfile,"no need")
# originalspeciesref=options.ancenstralref
# colname=re.search(r'[^/]*$',originalspeciesref).group(0)
# colname=re.sub(r"[^\w^\d]","_",colname);colname=colname[:10]
# print(colname)
# ancestralalleletabletools.dbvariant.operateDB("callproc", "mysql_sp_add_column", data=(ancestralalleletabletools.dbvariant, toplevelsnptablename, colname, "char(128)", "default null"))
OUTFILENAME = "ducksnpflankseq.fa"
outfile = open(options.chromlistfilename + "snpflankseq.fa", 'w')
duckrefhandler = open(options.ref, 'r')
try:
duckrefindex = pickle.load(open(options.ref + ".myfasteridx",
'rb'))
# originalspeciesindex = pickle.load(open(originalspeciesref + ".myindex", 'rb'))
except IOError:
Util.generateFasterRefIndex(options.ref,
options.ref + ".myfasteridx")
duckrefindex = pickle.load(open(options.ref + ".myfasteridx",
'rb'))
# try:
# originalspeciesindex = pickle.load(open(originalspeciesref + ".myindex", 'rb'))
# except IOError:
# Util.generateIndexByChrom(originalspeciesref, originalspeciesref + ".myindex")
# originalspeciesindex = pickle.load(open(originalspeciesref + ".myindex", 'rb'))
chrom_lenlist = []
chromlistfile = open(options.chromlistfilename, "r")
for chrrow in chromlistfile:
chrrowlist = re.split(r'\s+', chrrow.strip())
chrom_lenlist.append(
(chrrowlist[0].strip(), int(chrrowlist[1].strip())))
for currentchrID, currentchrLen in chrom_lenlist:
for chrlist, vcflikeFileName, corresponding_ref, flanklen in options.variantfilewithref:
chromlistfile = open(chrlist, "r")
chrmap = {}
for rec in chromlistfile:
reclist = re.split(r'\s+', rec.strip())
chrmap[reclist[0]] = reclist[1]
flanklen = int(flanklen)
duckrefhandler = open(corresponding_ref, 'r')
try:
duckrefindex = pickle.load(
open(corresponding_ref + ".myfasteridx", 'rb'))
# originalspeciesindex = pickle.load(open(originalspeciesref + ".myindex", 'rb'))
except IOError:
Util.generateFasterRefIndex(corresponding_ref,
corresponding_ref + ".myfasteridx",
chrsignal=options.chrsignal)
duckrefindex = pickle.load(
open(corresponding_ref + ".myfasteridx", 'rb'))
vcflikefile = open(vcflikeFileName, 'r')
vcflinesalchr = vcflikefile.readlines()
#1，read variations
chrom = None
snpsOfOneChrom = []
startpostocollecteSNP = 1
while vcflinesalchr:
snpline = vcflinesalchr.pop(0).strip()
if snpline[0] == "#" or snpline.lower().find("chrom") == 0: #title
continue
else: