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: break
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 print('Saving data...')