help="path to save result folder")
parser.add_argument(
"-df",
type=float,
default=None,
help="degree of freedom = ( #subjects in study - #covariates - 1 )")
parser.add_argument("-N",
type=int,
default=None,
help="file number to read")
#TODO (low) add reference panel
args = parser.parse_args()
Analyser = HaseAnalyser()
print args
Analyser.DF = args.df
Analyser.result_path = args.r
Analyser.file_number = args.N
results = OrderedDict()
results['RSID'] = np.array([])
results['p_value'] = np.array([])
results['t-stat'] = np.array([])
results['phenotype'] = np.array([])
results['SE'] = np.array([])
results['MAF'] = np.array([])
results['BETA'] = np.array([])
while True:
Analyser.summary()
if Analyser.results is None:
import numpy as np
if __name__=="__main__":
os.environ['HASEDIR']=os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
parser = argparse.ArgumentParser(description='Script analyse results of HASE')
parser.add_argument("-r", required=True,help="path to hase results")
parser.add_argument("-o", "--out", type=str, required=True,help="path to save result folder")
parser.add_argument("-df", type=float,default=None, help="degree of freedom = ( #subjects in study - #covariates - 1 )")
#TODO (low) add reference panel
args = parser.parse_args()
Analyser=HaseAnalyser()
print args
Analyser.DF=args.df
Analyser.result_path=args.r
results={}
results['RSID']=np.array([])
results['p_value']=np.array([])
results['t-stat']=np.array([])
results['phenotype']=np.array([])
results['SE']=np.array([])
results['MAF']=np.array([])
results['BETA'] = np.array([])
while True:
Analyser.summary()
if Analyser.results is None:
break
