if args.action == 'liftover': imp.perform_liftover(args.study, args.output, assembly=args.chain_file, backend=args.backend, submit=not args.nosubmit) elif args.action == 'phase': imp.perform_phase(args.study, args.output, additional_shapeit_parameters=args.additional_shapeit_parameters, backend=args.backend, submit=not args.nosubmit) elif args.action == 'impute' or args.action == 'phase_impute' or args.action == 'liftover_phase_impute': if not args.reference: raise Exception('You need to define a reference panel. Use the --reference parameter. For a list for all available reference panels, use --list') imp.perform_impute(args.study, args.output, args.reference, additional_impute2_parameters=args.additional_impute2_parameters, additional_shapeit_parameters=args.additional_impute2_parameters, perform_liftover_argument=args.action == 'liftover_phase_impute', assembly=args.chain_file, perform_phase_argument=args.action == 'phase_impute', custom_chromosomes=args.chromosomes, sample_batch_size=args.sample_batch_size, position_batch_size=args.position_batch_size, java_executable=args.java_executable, backend=args.backend, submit=not args.nosubmit) else: print description print 'For a full set of options run:' print 'python molgenis-impute.py --help' print 'For documentation check: https://github.com/molgenis/molgenis-imputation'
raise Exception('You need to define a directory where the study panel is, in order to perform this action (parameter --study)') if not args.output: raise Exception('You need to define a directory where the output results will be stored (parameter --output') if args.action == 'liftover': imp.perform_liftover(args.study, args.output, backend=args.backend, submit=not args.nosubmit) elif args.action == 'phase': imp.perform_phase(args.study, args.output, additional_shapeit_parameters=args.additional_shapeit_parameters, backend=args.backend, submit=not args.nosubmit) elif args.action == 'impute': if not args.reference: raise Exception('You need to define a reference panel. Use the --reference parameter. For a list for all available reference panels, use --list') imp.perform_impute(args.study, args.output, args.reference, additional_impute2_parameters=args.additional_impute2_parameters, custom_chromosomes=args.chromosomes, sample_batch_size=args.sample_batch_size, position_batch_size=args.position_batch_size, backend=args.backend, submit=not args.nosubmit) else: print description print 'For a full set of options run:' print 'python molgenis-impute.py --help' print 'For documentation check: https://github.com/molgenis/molgenis-imputation'