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'
