#ARG_CHECKER.check(args,mode='meta-stage')
##### Init data readers #####
if args.derivatives is None:
raise ValueError('For meta-stage analysis partial derivatives data are required!')
mapper=Mapper()
mapper.chunk_size=MAPPER_CHUNK_SIZE
mapper.genotype_names=args.study_name
mapper.reference_name=args.ref_name
mapper.load(args.mapper)
mapper.load_flip(args.mapper)
mapper.cluster=args.cluster
mapper.node=args.node
Analyser=HaseAnalyser()
pard=[]
for i,j in enumerate(args.derivatives):
pard.append(Reader('partial') )
pard[i].start(j, study_name=args.study_name[i])
pard[i].folder.load()
PD=[False if isinstance(i.folder._data.b4, type(None) ) else True for i in pard]
if np.sum(PD)!=len(pard) and np.sum(PD)!=0:
raise ValueError('All study should have b4 data for partial derivatives!')
from hdgwas.tools import Timer,HaseAnalyser, Reference
import argparse
import pandas as pd
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:
