for freq in args.freqs:
chr, idx, maf = freq
maf = float(maf)
chr, idx = int(chr), int(idx)
# TODO: Sort out frequency semantics
template.chromosomes[chr].frequencies[idx] = 1-maf
# Simulation method
if args.method.lower() == 'constrained':
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:
