def main():
try:
opts, args = getopt.getopt(sys.argv[1:], "m:e:H:S:O:N:t:s:r:F:n:")
except getopt.GetoptError as err:
# print help information and exit:
print(err) # will print something like "option -a not recognized"
usage()
sys.exit(2)
N = 1000 # pop size
e = 0.25 # s.d. of effect sizes
S = 1 # V(S)
H = None # desired b-sense H^2
mu_del_ttl = None # Mutation rate (per gamete, per generation) to alleles affecting trait value
r = 0.5 # rec. rate b/w loci (per diploid, per gen)
Opt = 0.0 # Value of optimum after 10N gens
ofile = None
seed = 0
t = None
nsam = 100
for o, a in opts:
if o == '-m':
mu_del_ttl = float(a)
elif o == '-e':
e = float(a)
elif o == '-H':
H = float(a)
elif o == '-S':
S = float(a)
elif o == '-O':
Opt = float(a)
elif o == '-N':
N = int(a)
elif o == '-s':
seed = int(a)
elif o == '-r':
r = float(a)
elif o == '-F':
ofile = a
elif o == '-t':
t = int(a)
elif o == '-n':
nsam = int(a)
if H is None:
usage()
sys.exit(2)
if mu_del_ttl is None:
usage()
sys.exit(2)
if ofile is None:
usage()
sys.exit(2)
if t is None:
t = 0.1 * float(N)
#Constants:
NLOCI = 10
NREPS = 64
##The next 2 are the 'sizes' of each locus in scaled params. Roughly 100kb in 'humans' in terms of pi.
theta = 100.0
rho = 100.0
#Can start working now:
REP = 0
out = pd.HDFStore(ofile, "w", complevel=6, complib='zlib')
little_r_per_locus = rho / (4.0 * float(N))
mu_n_region = theta / (4.0 * float(N))
rnge = fp.GSLrng(seed)
rngs = fp.GSLrng(seed)
nlist = np.array([N] * (10 * N), dtype=np.uint32)
fitness = qtm.MlocusAdditiveTrait()
sregions = [fp.GaussianS(0, 1, 1, e, 1.0)] * NLOCI
for BATCH in range(16): #16*64=1024
x = fp.MlocusPopVec(NREPS, N, NLOCI)
sampler = fp.PopSampler(len(x), nsam, rngs)
qtm.evolve_qtraits_mloc_sample_fitness(
rnge,
x,
sampler,
fitness,
nlist,
[mu_n_region] * NLOCI,
[mu_del_ttl / float(NLOCI)] * NLOCI,
sregions,
[little_r_per_locus] * NLOCI,
[0.5] * (NLOCI - 1), #loci unlinked
sample=t,
VS=S)
samples = sampler.get()
get_summstats_parallel(samples, REP, out)
sampler = fp.PopSampler(nsam, rngs)
qtm.evolve_qtraits_mloc_sample_fitnes(
rnge,
x,
sampler,
fitness,
nlist,
[mu_n_region] * NLOCI,
[mu_del_ttl / float(NLOCI)] * NLOCI,
sregions,
[little_r_per_locus] * NLOCI,
[0.5] * (NLOCI - 1), #loci unlinked
sample=t,
VS=S,
optimum=Opt)
samples = sampler.get()
get_summstats_parallel(samples, REP, out)
REP += NREPS
out.close()
def main():
try:
opts, args = getopt.getopt(sys.argv[1:],"m:e:H:S:O:N:s:r:",["traj="])
except getopt.GetoptError as err:
# print help information and exit:
print(err) # will print something like "option -a not recognized"
usage()
sys.exit(2)
N=1000 # pop size
e = 0.25 # s.d. of effect sizes
S = 1 # V(S)
H = None # desired b-sense H^2
mu_del_ttl = None # Mutation rate (per gamete, per generation) to alleles affecting trait value
r = 0.5 # rec. rate b/w loci (per diploid, per gen)
Opt = 0.0 # Value of optimum after 10N gens
trajFile=None
seed = 0
for o,a in opts:
if o == '-m':
mu_del_ttl = float(a)
elif o == '-e':
e = float(a)
elif o == '-H':
H = float(a)
elif o == '-S':
S = float(a)
elif o == '-O':
Opt = float(a)
elif o == '-N':
N=int(a)
elif o == '-s':
seed = int(a)
elif o == '-r':
r = float(a)
elif o == '--traj':
trajFile=a
if H is None:
usage()
sys.exit(2)
if mu_del_ttl is None:
usage()
sys.exit(2)
if trajFile is None:
usage()
sys.exit(2)
#Constants:
NLOCI=10
NREPS=64
##The next 2 are the 'sizes' of each locus in scaled params. Roughly 100kb in 'humans' in terms of pi.
theta=100.0
rho=100.0
#Can start working now:
REP=0
out=pd.HDFStore(trajFile,"w",complevel=6,complib='zlib')
little_r_per_locus = rho/(4.0*float(N))
mu_n_region=theta/(4.0*float(N))
rnge=fp.GSLrng(seed)
nlist=np.array([N]*(10*N),dtype=np.uint32)
fitness = qtm.MlocusAdditiveTrait()
sregions=[fp.GaussianS(0,1,1,e,1.0)]*NLOCI
for BATCH in range(16): #16*64=1024
x = fp.MlocusPopVec(NREPS,N,NLOCI)
sampler=fp.FreqSampler(len(x))
qtm.evolve_qtraits_mloc_sample_fitness(rnge,x,sampler,fitness,nlist,
[mu_n_region]*NLOCI,
[mu_del_ttl/float(NLOCI)]*NLOCI,
sregions,
[little_r_per_locus]*NLOCI,
[0.5]*(NLOCI-1),#loci unlinked
sample=1,VS=S)
traj1=sampler.get()
sampler=fp.FreqSampler(len(x))
qtm.evolve_qtraits_mloc_sample_fitness(rnge,x,sampler,fitness,nlist,
[mu_n_region]*NLOCI,
[mu_del_ttl/float(NLOCI)]*NLOCI,
sregions,
[little_r_per_locus]*NLOCI,
[0.5]*(NLOCI-1),#loci unlinked
sample=1,VS=S,optimum=Opt)
traj2=sampler.get()
m=fp.tidy_trajectories(fp.merge_trajectories(traj1,traj2))
for i in m:
temp=pd.DataFrame(i)
temp['rep']=[REP]*len(temp.index)
out.append('traj',temp)
REP+=1
out.close()
little_r_per_locus=rho_per_locus/(4.0*float(N))
mu_n_region=theta_neutral_per_locus/(4.0*float(N))
mu_del_ttl=1e-3
#sigmas=[0.1]*NLOCI
hdf=pd.HDFStore("cumVA.h5",'w')
fmodel = fpw.MlocusAdditive()
sregions = []
for i in range(NLOCI):
sregions.append(fp.GaussianS(i,i+1,1,0.1))
REPLICATE=0
for batch in range(1): #4,000 reps...
pops = fp.MlocusPopVec(NREPS,N,NLOCI)
sampler = fp.NothingSampler(len(pops))
x = qtm.evolve_qtraits_mloc_sample_fitness(rnge,pops,sampler,fmodel,
nlist[:(10*N)],
[mu_n_region]*NLOCI,
[mu_del_ttl/float(NLOCI)]*NLOCI,
sregions,
[little_r_per_locus]*NLOCI,
[0.5]*(NLOCI-1),#loci unlinked
sample=1)
sampler = fp.VASampler(len(pops))
qtm.evolve_qtraits_mloc_sample_fitness(rnge,pops,sampler,fmodel,
nlist, #Evolve 15N gens past optimum shift
[mu_n_region]*NLOCI,
[mu_del_ttl/float(NLOCI)]*NLOCI,
sregions,
def main():
try:
opts, args = getopt.getopt(sys.argv[1:], "m:e:H:S:O:N:t:s:F:r:n:d:", [
"theta=", "rho=", "trait=", "sampler=", "nsam=", "cores=",
"batches=", "nstub=", "sstub=", "nloci=", "fixations=", "t2=",
"g2="
]) #,"neutral="])
except getopt.GetoptError as err:
# print help information and exit:
print(err) # will print something like "option -a not recognized"
usage()
sys.exit(2)
#set up default params
N = 1000 # pop size
t = None # 0.1N
t2 = None
e = 0.25 # s.d. of effect sizes
S = 1 # V(S)
H = 1.0 # desired b-sense H^2
m = None # Mutation rate (per gamete, per generation) to alleles affecting trait value
r = 0.5 #Recombination rate between locis
Opt = 0.0 # Value of optimum after 10N gens
ofile = None
seed = 0
NLOCI = 10 #The total number of loci to simulate
#NeutralLocus = 5 #The index of the locus where no causal mutations will occur
theta = 100 # mutational size of region where neutral mutations occur
rho = 100 # recombination size of region where neutral mutations occur
traitString = "additive"
samplerString = None
ncores = 64
nbatches = 16
dominance = 1.0
ssize = None
fixationsFileName = None
G2 = None
nstub = None
sstub = None
for o, a in opts:
if o == '-m':
m = float(a)
elif o == '-e':
e = float(a)
elif o == '-H':
H = float(a)
elif o == '-S':
S = float(a)
elif o == '-O':
Opt = float(a)
elif o == '-N':
N = int(a)
elif o == '-t':
t = int(a)
t2 = t
elif o == '-s':
seed = int(a)
elif o == '-F':
ofile = a
elif o == '-r':
r = float(a)
elif o == '--nsam':
ssize = int(a)
elif o == '--theta':
theta = float(a)
elif o == '--rho':
rho = float(a)
elif o == '--trait':
traitString = a
if a not in valid_trait_models:
print("Error: invalid trait model")
usage()
sys.exit(0)
elif o == '--sampler':
samplerString = a
if a not in valid_sampler_names:
print("Error: invalid sampler name")
usage()
sys.exit(0)
elif o == '--cores':
ncores = int(a)
if ncores < 1:
print("--ncores must be > 0")
usage()
sys.exit(0)
elif o == '--batches':
nbatches = int(a)
if nbatches < 1:
print("--nbatches myst be > 0")
usage()
sys.exit(0)
elif o == '--nloci':
NLOCI = int(a)
if NLOCI < 2:
rpint("--nloci must be > 1")
usage()
sys.exit(0)
elif o == "--fixations":
fixationsFileName = a
elif o == "--t2":
t2 = int(a)
elif o == "--g2":
G2 = int(a)
elif o == "--nstub":
nstub = a
elif o == '--sstub':
sstub = a
#elif o == "--neutral":
# if a != "None":
# NeutralLocus=int(a)
# else:
# NeutralLocus=a
if samplerString is None:
print("Error: sampler must be defined")
usage()
sys.exit(0)
if t is None:
print("Error: sampling interval must be defined")
usage()
sys.exit(0)
if t2 is None:
t2 = t
if m is None:
usage()
sys.exit(2)
if ofile is None:
usage()
sys.exit(2)
if G2 is None:
G2 = 10 * N
#Can start working now:
REP = 0
out = pd.HDFStore(ofile, "w", complevel=6, complib='zlib')
if fixationsFileName is not None:
if os.path.exists(fixationsFileName):
os.remove(fixationsFileName)
little_r_per_locus = rho / (4.0 * float(N))
mu_n_region = theta / (4.0 * float(N))
rnge = fp.GSLrng(seed)
rngs = fp.GSLrng(seed)
nlist = np.array([N] * (10 * N), dtype=np.uint32)
fitness = get_trait_model(traitString)
sregions = [fp.GaussianS(0, 1, 1, e, dominance)] * NLOCI
neutral_mut_rates = [mu_n_region] * NLOCI
causal_mut_rates = [m / float(NLOCI)] * NLOCI
#if NeutralLocus is not None:
# causal_mut_rates[NeutralLocus]=0.0
for BATCH in range(nbatches):
x = fp.MlocusPopVec(ncores, N, NLOCI)
nstub_t = None
sstub_t = None
if nstub is not None:
nstub_t = nstub + b'.pre_shift.batch' + str(BATCH)
if sstub is not None:
sstub_t = sstub + b'.pre_shift.batch' + str(BATCH)
sampler = get_sampler(samplerString, len(x), Opt, ssize, rngs, nstub_t,
sstub_t)
qtm.evolve_qtraits_mloc_sample_fitness(
rnge,
x,
sampler,
fitness,
nlist,
neutral_mut_rates,
causal_mut_rates,
sregions,
[little_r_per_locus] * NLOCI,
[r] * (NLOCI - 1), #loci unlinked
sample=t,
VS=S)
write_output(sampler, out, NLOCI, REP)
if nstub is not None:
nstub_t = nstub + b'.post_shift.batch' + str(BATCH)
if sstub is not None:
sstub_t = sstub + b'.post_shift.batch' + str(BATCH)
sampler = get_sampler(samplerString, len(x), Opt, ssize, rngs, nstub_t,
sstub_t)
qtm.evolve_qtraits_mloc_sample_fitness(
rnge,
x,
sampler,
fitness,
nlist[:G2],
neutral_mut_rates,
causal_mut_rates,
sregions,
[little_r_per_locus] * NLOCI,
[r] * (NLOCI - 1), #loci unlinked
sample=t2,
VS=S,
optimum=Opt)
write_output(sampler, out, NLOCI, REP)
if fixationsFileName is not None:
write_fixations(x, fixationsFileName, REP)
REP += len(x)
if fixationsFileName is not None:
con = sqlite3.connect(fixationsFileName)
con.execute("create index gen on fixations (generation)")
con.execute("create index gen_rep on fixations (generation,rep)")
con.close()
out.close()
def run_batch(argtuple):
args, repid, batch = argtuple
print("seed for batch = ", args.seed)
nstub = "neutral.mu" + str(args.mu) + ".opt" + str(args.opt)
sstub = "selected.mu" + str(args.mu) + ".opt" + str(args.opt)
rnge = fp.GSLrng(args.seed)
NANC = 7310
locus_boundaries = [(float(i + i * 11), float(i + i * 11 + 11))
for i in range(args.nloci)]
nregions = [
fp.Region(j[0], j[1], args.theta / (4. * float(NANC)), coupled=True)
for i, j in zip(range(args.nloci), locus_boundaries)
]
recregions = [
fp.Region(j[0], j[1], args.rho / (4. * float(NANC)), coupled=True)
for i, j in zip(range(args.nloci), locus_boundaries)
]
sregions = [
fp.GaussianS(j[0] + 5., j[0] + 6., args.mu, args.sigmu, coupled=False)
for i, j in zip(range(args.nloci), locus_boundaries)
]
f = qtm.MlocusAdditiveTrait()
nlist = np.array(get_nlist1(), dtype=np.uint32)
pops = fp.MlocusPopVec(args.ncores, nlist[0], args.nloci)
sampler = fp.NothingSampler(len(pops))
d = datetime.datetime.now()
print("starting batch, ", batch, "at ", d.now())
qtm.evolve_qtraits_mloc_regions_sample_fitness(rnge, pops, sampler, f,
nlist[0:], nregions,
sregions, recregions,
[0.5] * (args.nloci - 1), 0,
0, 0.)
d = datetime.datetime.now()
print(d.now())
nlist = np.array(get_nlist2(), dtype=np.uint32)
qtm.evolve_qtraits_mloc_regions_sample_fitness(rnge, pops, sampler, f,
nlist[0:], nregions,
sregions, recregions,
[0.5] * (args.nloci - 1), 0,
args.opt)
d = datetime.datetime.now()
print(d.now())
if args.statfile is not None:
sched = lsp.scheduler_init(args.TBB)
for pi in pops:
#Apply the sampler 1 population at a time.
#This saves a fair bit of RAM.
neutralFile = nstub + '.rep' + str(repid) + '.gz'
selectedFile = sstub + '.rep' + str(repid) + '.gz'
BIGsampler = fp.PopSampler(1,
6000,
rnge,
False,
neutralFile,
selectedFile,
recordSamples=True,
boundaries=locus_boundaries)
fp.apply_sampler_single(pi, BIGsampler)
if args.statfile is not None:
for di in BIGsampler:
process_samples((di, args.statfile, locus_boundaries, repid))
repid += 1
pops.clear()
pops = None