default="sync")
parser.add_option_group(group)
(options, args) = parser.parse_args()
########################################################### code ###################################################
################################################## read parameters #################################################
pops = map(int, options.pops.split(","))
out = open(options.out + "_table.txt", "w")
############################################## test for format of input file ###################################
if options.type == "sync":
filehandle = SyncReader(options.input)
else:
filehandle = CMHReader(options.input)
############################### read divergence file #########################################################################
divhash = collections.defaultdict(lambda: "")
for l in open(options.div, "r"):
if "Chr" in l:
continue
a = l.split()
chr, pos, s1a, s2a = a[:4]
ID = chr + "_" + pos
## store simulans specific allele
divhash[ID] = s2a
parser.add_option("--input", dest="input", help="A synchronized input file")
parser.add_option(
"--population",
dest="populations",
help=
"Determine whether the given position is a SNP based on these populations")
parser.add_option("--test",
action="store_true",
dest="test",
help="run the doctest")
parser.add_option_group(group)
(options, args) = parser.parse_args()
popstotest = map(int, options.populations.split(","))
for sync in SyncReader(options.input):
# extract the correct populations
pops = sync.subpopulations(popstotest)
# obtain counts for the two major alleles
(alcount, majora, minora) = modules.RCMH.Utility.getMajorAlleleCount(pops)
toprint = []
toprint.append("data")
toprint.append("{0}_{1}".format(sync.chr, sync.pos))
for a in alcount:
cov = a[0] + a[1]
toprint.append(str(cov))
toprint.append(str(a[1]))
print "\t".join(toprint)
secondchar = "N"
return secondchar
if (options.test):
import doctest
doctest.testmod(verbose=1)
sys.exit()
#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 p in SyncReader(options.sync):
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+"