raise ValueError(
'{} table does not have ID or CHR,bp columns'.format(
args.snp_id_exc))
mapper.load(args.mapper)
mapper.load_flip(args.mapper)
mapper.cluster = args.cluster
mapper.node = args.node
else:
if len(args.genotype) == 1:
mapper = Mapper()
mapper.chunk_size = MAPPER_CHUNK_SIZE
mapper.genotype_names = args.study_name
mapper.reference_name = args.ref_name
mapper.cluster = args.cluster
mapper.node = args.node
mapper.n_study = 1
mapper.n_keys = gen[0].folder._data.names.shape[0]
mapper.keys = np.array(gen[0].folder._data.names.tolist())
mapper.values = np.array(range(mapper.n_keys)).reshape(-1, 1)
mapper.flip[args.study_name[0]] = np.array([1] * mapper.n_keys)
if args.snp_id_exc is not None or args.snp_id_inc is not None:
raise ValueError(
'You can not exclude or include variants to analysis without mapper!'
)
else:
raise ValueError(
'You can not run regression analysis with several genotype data without mapper!'
)
#mapper=None
Analyser = HaseAnalyser()
print mapper.exclude.head()
if 'ID' not in mapper.exclude.columns and ('CHR' not in mapper.exclude.columns or 'bp' not in mapper.exclude.columns):
raise ValueError('{} table does not have ID or CHR,bp columns'.format(args.snp_id_exc))
mapper.load(args.mapper)
mapper.load_flip(args.mapper)
mapper.cluster=args.cluster
mapper.node=args.node
else:
if len(args.genotype)==1:
mapper=Mapper()
mapper.chunk_size=MAPPER_CHUNK_SIZE
mapper.genotype_names=args.study_name
mapper.reference_name=args.ref_name
mapper.cluster=args.cluster
mapper.node=args.node
mapper.n_study=1
mapper.n_keys=gen[0].folder._data.names.shape[0]
mapper.keys=np.array(gen[0].folder._data.names.tolist())
mapper.values=np.array(range(mapper.n_keys)).reshape(-1,1)
mapper.flip=np.array([1]*mapper.n_keys).reshape(-1,1)
if args.snp_id_exc is not None or args.snp_id_inc is not None:
raise ValueError('You can not exclude or include variants to analysis without mapper!')
else:
raise ValueError('You can not run regression analysis with several genotype data without mapper!')
#mapper=None
Analyser=HaseAnalyser()
Analyser.threshold=args.thr
Analyser.out=args.out
haseregression(phen,gen,cov, mapper, Analyser,args.maf,intercept=args.intercept)
