if not opts:
usage()
sys.exit(2)
except getopt.GetoptError:
print "Incorrect options passed"
usage()
sys.exit(2)
params = parseopts(opts)
# check if command-line options are valid
try:
checkopts(params)
except (ValueError, KeyError):
sys.exit(2)
# load data
if params['format'] == 'bed':
G = parse_bed.load(params['inputfile'])
elif params['format'] == 'str':
G = parse_str.load(params['inputfile'])
G = np.require(G, dtype=np.uint8, requirements='C')
# run the variational algorithm
Q, P, other = fastStructure.infer_variational_parameters(G, params['K'], \
params['outputfile'], params['mintol'], \
params['prior'], params['cv'])
# write out inferred parameters
write_output(Q, P, other, params)
if not opts:
usage()
sys.exit(2)
except getopt.GetoptError:
print "Incorrect options passed"
usage()
sys.exit(2)
params = parseopts(opts)
# check if command-line options are valid
try:
checkopts(params)
except (ValueError,KeyError):
sys.exit(2)
# load data
if params['format']=='bed':
G = parse_bed.load(params['inputfile'])
elif params['format']=='str':
G = parse_str.load(params['inputfile'])
G = np.require(G, dtype=np.uint8, requirements='C')
# run the variational algorithm
Q, P, other = fastStructure.infer_variational_parameters(G, params['K'], \
params['outputfile'], params['mintol'], \
params['prior'], params['cv'])
# write out inferred parameters
write_output(Q, P, other, params)