def parse_comparestring(comp):
a = comp.split(",")
baselist = []
derivedlist = []
for e in a:
b, d = map(int, e.split("-"))
baselist.append(b)
derivedlist.append(d)
return (baselist, derivedlist)
parser = OptionParser()
parser.add_option("--sync",
dest="sync",
help="A file containing the cmh results")
parser.add_option("--compare",
dest="comp",
help="A comparision string as with the cmh-test")
(options, args) = parser.parse_args()
baselist, derivedlist = parse_comparestring(options.comp)
for chr, pos, mami, s in SyncReaderMajMin(options.sync):
# [2L,15,(C,A),(108,45),(90,47))
basec, derc = parse_line(s, baselist, derivedlist)
hshc = get_hshc(basec, derc)
topr = [chr, str(pos), str(hshc)]
print "\t".join(topr)
baselist = []
derivedlist = []
for e in a:
b, d = map(int, e.split("-"))
baselist.append(b)
derivedlist.append(d)
return (baselist, derivedlist)
parser = OptionParser()
parser.add_option("--sync",
dest="sync",
help="A file containing the cmh results")
parser.add_option("--compare",
dest="comp",
help="A comparision string as with the cmh-test")
(options, args) = parser.parse_args()
baselist, derivedlist = parse_comparestring(options.comp)
for chr, start, end, syncs in SyncWindowReader(SyncReaderMajMin(options.sync),
1000):
if len(syncs) == 0:
continue
basec, derc = parse_line(syncs, baselist, derivedlist)
hsc = get_hshcwindow(basec, derc)
topr = [chr, str(start), str(hsc)]
print "\t".join(topr)