sim = ConstrainedMendelianSimulation(template, replications=args.replications)
elif args.method.lower() == 'genedrop':
sim = NaiveGeneDroppingSimulation(template, replications=args.replications)
# Read effects file
if args.effectfile:
trait = Architecture.from_file(args.effectsfile)
trait.name = 'affected'
else:
trait = Architecture('affected','dichotomous')
# More effects. Specified effects override file effects.
if args.effects:
for effect in args.effects:
chr, pos, a, k = effect
locus = int(chr), int(pos)
a, k = int(a), int(k)
trait.add_effect(locus, a, k)
if args.lthresh:
trait.set_liability_threshold(args.lthresh)
if args.effects or args.effectfile:
sim.set_trait(trait)
if args.constraintfile:
sim.read_constraints(args.constraintfile)
sim.prefix = args.prefix
sim.run(verbose=args.verbosity, output_predicate=args.predicate, compression=args.compress, writeibd=args.ibd)
