def main_with_args(args):
print(title_string)
if len(args) < 1:
parser.print_usage()
print(description_string)
return
parameters = parser.parse_args(args)
p_dict = vars(parameters)
if p_dict['debug']:
print('Parsed parameters:')
print(p_dict)
action = p_dict['ldpred_action']
if action == 'coord':
coord_genotypes.main(p_dict)
elif action == 'gibbs':
LDpred_gibbs.main(p_dict)
elif action == 'inf':
LDpred_inf.main(p_dict)
elif action == 'p+t':
LD_pruning_thres.main(p_dict)
elif action == 'score':
validate.main(p_dict)
elif action == 'all':
pass
else:
parser.print_help(sys.stderr)
sys.exit(1)
def main():
if len(sys.argv)==1:
print ('ERROR: No options provided.\n')
parser.print_help(sys.stderr)
sys.exit(1)
parameters = parser.parse_args()
p_dict= vars(parameters)
if p_dict['debug']:
print ('Parsed parameters:')
print(p_dict)
action = p_dict['ldpred_action']
if action=='coord':
coord_genotypes.main(p_dict)
elif action=='gibbs':
LDpred_gibbs.main(p_dict)
elif action=='inf':
LDpred_inf.main(p_dict)
elif action=='p+t':
LD_pruning_thres.main(p_dict)
elif action=='score':
validate.main(p_dict)
elif action=='ldfile':
ld.get_ld_dict(p_dict['cf'], p_dict['ldf'], p_dict['ldr'],wallaceld=True)
elif action=='all':
pass
def main():
parameters = parser.parse_args()
p_dict = vars(parameters)
if p_dict['debug']:
print('Parsed parameters:')
print(p_dict)
action = p_dict['ldpred_action']
if action == 'coord':
coord_genotypes.main(p_dict)
elif action == 'gibbs':
LDpred_gibbs.main(p_dict)
elif action == 'inf':
LDpred_inf.main(p_dict)
elif action == 'p+t':
LD_pruning_thres.main(p_dict)
elif action == 'score':
validate.main(p_dict)
elif action == 'all':
pass
def main():
print(title_string)
if len(sys.argv)==1:
parser.print_help(sys.stderr)
sys.exit(1)
parameters = parser.parse_args()
p_dict= vars(parameters)
if p_dict['debug']:
print ('Parsed parameters:')
print(p_dict)
action = p_dict['ldpred_action']
if action=='coord':
coord_genotypes.main(p_dict)
elif action=='gibbs':
LDpred_gibbs.main(p_dict)
elif action=='inf':
LDpred_inf.main(p_dict)
elif action=='p+t':
LD_pruning_thres.main(p_dict)
elif action=='score':
validate.main(p_dict)
elif action=='all':
pass
def main():
print(title_string)
if len(sys.argv) == 1:
parser.print_help(sys.stderr)
sys.exit(1)
parameters = parser.parse_args()
p_dict = vars(parameters)
if p_dict['debug']:
print('Parsed parameters:')
print(p_dict)
action = p_dict['ldpred_action']
if action == 'coord':
coord_genotypes.main(p_dict)
elif action == 'gibbs':
LDpred_gibbs.main(p_dict)
elif action == 'inf':
LDpred_inf.main(p_dict)
elif action == 'p+t':
LD_pruning_thres.main(p_dict)
elif action == 'score':
validate.main(p_dict)
elif action == 'all':
pass
def test_coord_genotypes(self):
p_dict = make_p_dict(
'--debug',
'coord',
'--gf=%s/test_data/sim1_0_test' % TEST_DIR,
'--vgf=%s/test_data/sim1_0_test' % TEST_DIR,
'--ssf=%s/test_data/sim1_0_ss.txt' % TEST_DIR,
'--ssf-format=LDPRED',
'--out=%s_coord_genotypes.hdf5' % self.tmp_file_prefix,
)
summary_dict = coord_genotypes.main(p_dict)
# summary_dict[11]['value'], if present, is the count of non-matching nts.
# It should be 0.
self.assertEqual(summary_dict.get(11, {}).get('value', 0), 0)
with h5py.File(p_dict['out'], 'r') as h5f:
self.assertEqual(len(h5f['sum_stats']['chrom_1']['betas']), 2000)