elif opt == "-v":
DEBUG = True
elif opt == "-j":
JSON = True
elif opt == "-u":
location = query
elif opt == "-a":
EMAIL = True
ADDRESS= query
else:
print "ERROR: incorrect usage"
usage()
sys.exit
##start of program
if EMAIL:
email = smail.mail(ADDRESS, seq, location)
if(_FILE):
f = open(FILE,"r")
for line in f:
if re.match('A|U|G|C|a|u|c|g', line):
print seq
seq = line.strip()
break
if(re.match('\w+',seq)):
start_sampling(seq)
else:
print "ERROR: Buggy sequence"
sys.exit
##end of main
MUTATION_DEPTH = int(query)
elif opt == "-n":
NSIZE = int(query)
elif opt == "-l":
LOOP_SIZE = int(query)
elif opt =="-d":
DEBUG = True
elif opt == "-t":
if(DEBUG):
print 'Setting threshold to {0}'.format(query)
nAVG = float(query)
elif opt == "-u":
location = query
elif opt == "-a":
EMAIL = True
ADDRESS=query
elif opt == "-c":
CSV = True
else:
print "ERROR: incorrect usage"
usage()
sys.exit
if EMAIL:
email = smail.mail(ADDRESS, SEQUENCE,location)
if(re.match('\w+',SEQUENCE)):
sampling = BootStrap.bootstrap(seq)
initial()
else:
print "ERROR: Buggy or Null Sequence"
sys.exit
