def from_genomesimla(filename):
"""
Reads positions and frequencies from a genomeSIMLA template file
:param filename: path to the template
:type filename: string
:returns: Template containing the data from the file
:rtype: ChromosomeTemplate
"""
return read_gs_chromosome_template(filename)
def from_genomesimla(filename):
"""
Reads positions and frequencies from a genomeSIMLA template file
:param filename: path to the template
:type filename: string
:returns: Template containing the data from the file
:rtype: ChromosomeTemplate
"""
return read_gs_chromosome_template(filename)
from pydigree.io.genomesimla import read_gs_chromosome_template
from pydigree.population import logistic_growth
parser = argparse.ArgumentParser()
parser.add_argument("--chromosomes", dest="chromosomes", nargs="+", help="genomeSIMLA format chromosome templates")
parser.add_argument("--n0", dest="n0", type=int, help="Initial pool size", default=5000)
parser.add_argument("--rate", dest="rate", type=float, help="Growth rate", default=1.0)
parser.add_argument("--final", type=int, help="Final pool size", default=50000)
parser.add_argument("--gens", type=int, default=20)
parser.add_argument("--initial", help="Prefix for initial data for pool (plink format)")
args = parser.parse_args()
if not (args.chromosomes or args.initial):
print("One of --chromosomes or --initial required")
exit(1)
if args.initial:
pop = pyd.io.read_plink(prefix=args.initial)
pool = ChromosomePool.from_population(pop)
else:
chroms = [read_gs_chromosome_template(x) for x in args.chromosomes]
pool = ChromosomePool(chromosomes=chroms, size=args.n0)
print("Creating pool")
pool.initialize_pool(args.n0)
gensize = lambda x: int(logistic_growth(pool.n0, args.rate, args.final, x))
for x in range(args.gens):
print("Generation {}: {}".format(x, gensize(x)))
pool.iterate_pool(gensize(x))
parser.add_argument('--compress', choices=('bzip2', 'gzip'), action='store')
parser.add_argument('--seed', type=int, help='Random seed', default=None)
args = parser.parse_args()
if args.seed is not None:
pydigree.set_seed(args.seed)
# Read the pedigrees
template = read_ped(args.template)
# Read the chromosomes
if not args.chromosomes:
print('No chromosomes specified!')
exit()
for cfile in args.chromosomes:
c = read_gs_chromosome_template(cfile)
template.add_chromosome(c)
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
parser.add_argument('--seed', type=int, help='Random seed', default=None)
args = parser.parse_args()
if args.seed is not None:
pydigree.set_seed(args.seed)
# Read the pedigrees
template = read_ped(args.template)
# Read the chromosomes
if not args.chromosomes:
print('No chromosomes specified!')
exit()
for cfile in args.chromosomes:
c = read_gs_chromosome_template(cfile)
template.add_chromosome(c)
for freq in args.freqs:
chrom, idx, maf = freq
maf = float(maf)
chrom, idx = int(chrom), int(idx)
# TODO: Sort out frequency semantics
template.chromosomes[chrom].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)
from pydigree.population import logistic_growth
parser = argparse.ArgumentParser()
parser.add_argument('--chromosomes', dest='chromosomes',nargs='+',
help='genomeSIMLA format chromosome templates')
parser.add_argument('--n0', dest='n0', type=int, help='Initial pool size', default=5000)
parser.add_argument('--rate', dest='rate', type=float, help='Growth rate', default=1.0)
parser.add_argument('--final', type=int, help='Final pool size', default=50000)
parser.add_argument('--gens', type=int, default=20)
parser.add_argument('--initial', help='Prefix for initial data for pool (plink format)')
args = parser.parse_args()
if not (args.chromosomes or args.initial):
print('One of --chromosomes or --initial required')
exit(1)
if args.initial:
pop = pyd.io.read_plink(prefix=args.initial)
pool = ChromosomePool.from_population(pop)
else:
chroms = [read_gs_chromosome_template(x) for x in args.chromosomes]
pool = ChromosomePool(chromosomes=chroms, size=args.n0)
print('Creating pool')
pool.initialize_pool(args.n0)
gensize = lambda x: int(logistic_growth(pool.n0, args.rate, args.final, x))
for x in range(args.gens):
print('Generation {}: {}'.format(x, gensize(x)))
pool.iterate_pool(gensize(x))
def from_genomesimla(filename):
return read_gs_chromosome_template(filename)