def test_ld_block(self):
k = 30
n = 1e4
rho = 1.5e-8
mu = 2.5e-8
length = 200e3
times = arghmm.get_time_points(ntimes=20, maxtime=200e3)
compress = 20
arg = arghmm.sample_arg_dsmc(k,
2 * n,
rho,
start=0,
end=length,
times=times)
muts = arghmm.sample_arg_mutations(arg, mu, times)
seqs = arghmm.make_alignment(arg, muts)
sites = arghmm.seqs2sites(seqs)
#cols = transpose(seqs.values())[::10000]
cols = mget(sites, sites.positions)
cols = cols[:1000]
ld = arghmm.calc_ld_matrix(cols, arghmm.calc_ld_Dp)
heatmap(ld, width=2, height=2)
pause()
def test_emit_internal(self):
"""
Calculate emission probabilities
"""
k = 10
n = 1e4
rho = 1.5e-8 * 20
mu = 2.5e-8 * 20
length = int(10e3) / 20
times = arghmm.get_time_points(ntimes=20, maxtime=200000)
arg = arghmm.sample_arg_dsmc(k,
2 * n,
rho,
start=0,
end=length,
times=times)
muts = arghmm.sample_arg_mutations(arg, mu, times)
seqs = arghmm.make_alignment(arg, muts)
trees, names = arghmm.arg2ctrees(arg, times)
seqs2, nseqs, seqlen = arghmm.seqs2cseqs(seqs, names)
assert arghmm.arghmm_assert_emit_internal(trees, len(times), times, mu,
seqs2, nseqs, seqlen)
def test_emit_parsimony(self):
"""
Calculate emission probabilities with parsimony
"""
k = 10
n = 1e4
rho = 1.5e-8 * 20
mu = 2.5e-8 * 20
length = int(100e3) / 20
times = arghmm.get_time_points(ntimes=20, maxtime=200000)
x = []; y = []
for i in range(20):
print i
arg = arghmm.sample_arg_dsmc(k, 2*n, rho, start=0, end=length,
times=times)
muts = arghmm.sample_arg_mutations(arg, mu, times)
seqs = arghmm.make_alignment(arg, muts)
x.append(arghmm.calc_likelihood(
arg, seqs, mu=mu, times=times, delete_arg=False))
y.append(arghmm.calc_likelihood_parsimony(
arg, seqs, mu=mu, times=times, delete_arg=False))
p = plot(x, y, xlab="true likelihood", ylab="parsimony likelihood")
p.plot([min(x), max(x)], [min(x), max(x)], style="lines")
pause()
def test_compress_align(self):
"""Test the compression of sequence alignments"""
k = 12
n = 1e4
rho = 1.5e-8
mu = 2.5e-8
length = 200e3
times = arghmm.get_time_points(ntimes=20, maxtime=200e3)
compress = 20
arg = arghmm.sample_arg_dsmc(k,
2 * n,
rho,
start=0,
end=length,
times=times)
muts = arghmm.sample_arg_mutations(arg, mu, times)
seqs = arglib.make_alignment(arg, muts)
seqs2, cols = arghmm.compress_align(seqs, compress)
print seqs2.alignlen(), length / compress
delta = [cols[i] - cols[i - 1] for i in range(1, len(cols))]
plot(cols)
plothist(delta, width=1)
variant = [arghmm.is_variant(seqs, i) for i in range(seqs.alignlen())]
print histtab(variant)
print histtab(mget(variant, cols))
pause()
def test_arg_joint(self):
"""
Compute joint probability of an ARG
"""
k = 2
n = 1e4
rho = 1.5e-8 * 20
rho2 = rho
mu = 2.5e-8 * 20
length = 10000
times = arghmm.get_time_points(ntimes=20, maxtime=200000)
refine = 0
arg = arghmm.sample_arg_dsmc(k,
2 * n,
rho,
start=0,
end=length,
times=times)
muts = arghmm.sample_arg_mutations(arg, mu, times=times)
seqs = arglib.make_alignment(arg, muts)
lk = arghmm.calc_joint_prob(arg, seqs, mu=mu, rho=rho, times=times)
print lk
def test_emit(self):
"""
Calculate emission probabilities
"""
k = 10
n = 1e4
rho = 1.5e-8 * 20
mu = 2.5e-8 * 20
length = int(1e3) / 20
times = arghmm.get_time_points(ntimes=20, maxtime=200000)
arg = arghmm.sample_arg_dsmc(k, 2*n, rho, start=0, end=length,
times=times)
muts = arghmm.sample_arg_mutations(arg, mu, times)
seqs = arghmm.make_alignment(arg, muts)
new_name = "n%d" % (k-1)
arg = arghmm.remove_arg_thread(arg, new_name)
trees, names = arghmm.arg2ctrees(arg, times)
seqs2, nseqs, seqlen = arghmm.seqs2cseqs(seqs, names + [new_name])
assert arghmm.arghmm_assert_emit(trees, len(times), times, mu,
seqs2, nseqs, seqlen)
def test_compress_align(self):
"""Test the compression of sequence alignments"""
k = 12
n = 1e4
rho = 1.5e-8
mu = 2.5e-8
length = 200e3
times = arghmm.get_time_points(ntimes=20, maxtime=200e3)
compress = 20
arg = arghmm.sample_arg_dsmc(k, 2*n, rho, start=0, end=length,
times=times)
muts = arghmm.sample_arg_mutations(arg, mu, times)
seqs = arglib.make_alignment(arg, muts)
seqs2, cols = arghmm.compress_align(seqs, compress)
print seqs2.alignlen(), length / compress
delta = [cols[i] - cols[i-1] for i in range(1, len(cols))]
plot(cols)
plothist(delta, width=1)
variant = [arghmm.is_variant(seqs, i) for i in range(seqs.alignlen())]
print histtab(variant)
print histtab(mget(variant, cols))
pause()
def test_state_corr(self):
k = 12
n = 1e4
rho = 1.5e-8 * 20
mu = 2.5e-8 * 20
length = int(1e3) / 20
times = arghmm.get_time_points(ntimes=20, maxtime=200e3)
arg = arghmm.sample_arg_dsmc(k,
2 * n,
rho,
start=0,
end=length,
times=times)
muts = arghmm.sample_arg_mutations(arg, mu, times)
seqs = arglib.make_alignment(arg, muts)
# remove chrom
new_name = "n%d" % (k - 1)
arg = arghmm.remove_arg_thread(arg, new_name)
model = arghmm.ArgHmm(arg,
seqs,
new_name=new_name,
times=times,
rho=rho,
mu=mu)
print "states", len(model.states[0])
nstates = len(model.states[0])
prior = [-util.INF] * nstates
prior[random.randint(0, nstates)] = 0.0
probs1 = list(arghmm.forward_algorithm(model, length, verbose=True))
probs2 = list(
arghmm.forward_algorithm(model, length, prior=prior, verbose=True))
model.rho *= 1e-9
probs3 = list(
arghmm.forward_algorithm(model, length, prior=prior, verbose=True))
p = plot(vsubs(probs1[length - 1], mean(probs1[length - 1])))
p.plot(vsubs(probs2[length - 1], mean(probs2[length - 1])))
p.plot(vsubs(probs3[length - 1], mean(probs3[length - 1])))
pause()
def test_emit_parsimony(self):
"""
Calculate emission probabilities with parsimony
"""
k = 10
n = 1e4
rho = 1.5e-8 * 20
mu = 2.5e-8 * 20
length = int(100e3) / 20
times = arghmm.get_time_points(ntimes=20, maxtime=200000)
x = []
y = []
for i in range(20):
print i
arg = arghmm.sample_arg_dsmc(k,
2 * n,
rho,
start=0,
end=length,
times=times)
muts = arghmm.sample_arg_mutations(arg, mu, times)
seqs = arghmm.make_alignment(arg, muts)
x.append(
arghmm.calc_likelihood(arg,
seqs,
mu=mu,
times=times,
delete_arg=False))
y.append(
arghmm.calc_likelihood_parsimony(arg,
seqs,
mu=mu,
times=times,
delete_arg=False))
p = plot(x, y, xlab="true likelihood", ylab="parsimony likelihood")
p.plot([min(x), max(x)], [min(x), max(x)], style="lines")
pause()
def test_arg_joint(self):
"""
Compute joint probability of an ARG
"""
k = 2
n = 1e4
rho = 1.5e-8 * 20
rho2 = rho
mu = 2.5e-8 * 20
length = 10000
times = arghmm.get_time_points(ntimes=20, maxtime=200000)
refine = 0
arg = arghmm.sample_arg_dsmc(k, 2*n, rho, start=0, end=length,
times=times)
muts = arghmm.sample_arg_mutations(arg, mu, times=times)
seqs = arglib.make_alignment(arg, muts)
lk = arghmm.calc_joint_prob(arg, seqs, mu=mu, rho=rho, times=times)
print lk
def test_sample_arg_popsizes_trees_infer(self):
"""
Fully sample an ARG from stratch using API
"""
k = 6
rho = 1.5e-8 * 20
mu = 2.5e-8 * 20
length = int(10e6) / 20
times = arghmm.get_time_points(ntimes=20, maxtime=160000)
popsizes = [1e4 * (61.-i)/60. for i in range(len(times))]
refine = 5
util.tic("sim ARG")
#arg = arglib.sample_arg_smc(k, 2 * popsizes[0],
# rho, start=0, end=length)
arg = arghmm.sample_arg_dsmc(k, [2*p for p in popsizes],
rho, start=0, end=length, times=times)
util.toc()
muts = arghmm.sample_arg_mutations(arg, mu, times=times)
seqs = arglib.make_alignment(arg, muts)
popsizes2 = [0] * (len(times) - 1)
nsamples = 1
for i in range(nsamples):
arg2 = arghmm.sample_arg(seqs, rho=rho, mu=mu, times=times,
popsizes=popsizes,
refine=refine, verbose=True, carg=True)
popsizes3 = arghmm.est_popsizes_trees(arg2, times, length/1000,
verbose=True)
print(popsizes3)
popsizes2 = vadd(popsizes2, popsizes3)
popsizes2 = vdivs(popsizes2, float(nsamples))
print(popsizes2)
p = plot(times, popsizes, xlog=10, xmin=10)
p.plot(times[1:], popsizes2)
pause()
def test_sample_arg_popsizes_trees_infer(self):
"""
Fully sample an ARG from stratch using API
"""
k = 6
rho = 1.5e-8 * 20
mu = 2.5e-8 * 20
length = int(10e6) / 20
times = arghmm.get_time_points(ntimes=20, maxtime=160000)
popsizes = [1e4 * (61.-i)/60. for i in range(len(times))]
refine = 5
util.tic("sim ARG")
#arg = arglib.sample_arg_smc(k, 2 * popsizes[0],
# rho, start=0, end=length)
arg = arghmm.sample_arg_dsmc(k, [2*p for p in popsizes],
rho, start=0, end=length, times=times)
util.toc()
muts = arghmm.sample_arg_mutations(arg, mu, times=times)
seqs = arglib.make_alignment(arg, muts)
popsizes2 = [0] * (len(times) - 1)
nsamples = 1
for i in range(nsamples):
arg2 = arghmm.sample_arg(seqs, rho=rho, mu=mu, times=times,
popsizes=popsizes,
refine=refine, verbose=True, carg=True)
popsizes3 = arghmm.est_popsizes_trees(arg2, times, length/1000,
verbose=True)
print popsizes3
popsizes2 = vadd(popsizes2, popsizes3)
popsizes2 = vdivs(popsizes2, float(nsamples))
print popsizes2
p = plot(times, popsizes, xlog=10, xmin=10)
p.plot(times[1:], popsizes2)
pause()
def test_state_corr(self):
k = 12
n = 1e4
rho = 1.5e-8 * 20
mu = 2.5e-8 * 20
length = int(1e3) / 20
times = arghmm.get_time_points(ntimes=20, maxtime=200e3)
arg = arghmm.sample_arg_dsmc(k, 2*n, rho, start=0, end=length,
times=times)
muts = arghmm.sample_arg_mutations(arg, mu, times)
seqs = arglib.make_alignment(arg, muts)
# remove chrom
new_name = "n%d" % (k-1)
arg = arghmm.remove_arg_thread(arg, new_name)
model = arghmm.ArgHmm(arg, seqs, new_name=new_name, times=times,
rho=rho, mu=mu)
print "states", len(model.states[0])
nstates = len(model.states[0])
prior = [-util.INF] * nstates
prior[random.randint(0, nstates)] = 0.0
probs1 = list(arghmm.forward_algorithm(model, length, verbose=True))
probs2 = list(arghmm.forward_algorithm(model, length, prior=prior,
verbose=True))
model.rho *= 1e-9
probs3 = list(arghmm.forward_algorithm(model, length, prior=prior,
verbose=True))
p = plot(vsubs(probs1[length-1], mean(probs1[length-1])))
p.plot(vsubs(probs2[length-1], mean(probs2[length-1])))
p.plot(vsubs(probs3[length-1], mean(probs3[length-1])))
pause()
def test_ld_block(self):
k = 30
n = 1e4
rho = 1.5e-8
mu = 2.5e-8
length = 200e3
times = arghmm.get_time_points(ntimes=20, maxtime=200e3)
compress = 20
arg = arghmm.sample_arg_dsmc(k, 2*n, rho, start=0, end=length,
times=times)
muts = arghmm.sample_arg_mutations(arg, mu, times)
seqs = arghmm.make_alignment(arg, muts)
sites = arghmm.seqs2sites(seqs)
#cols = transpose(seqs.values())[::10000]
cols = mget(sites, sites.positions)
cols = cols[:1000]
ld = arghmm.calc_ld_matrix(cols, arghmm.calc_ld_Dp)
heatmap(ld, width=2, height=2)
pause()
def test_est_arg_popsize(self):
"""
Fully sample an ARG from stratch using API
"""
k = 20
rho = 1.5e-8 * 20
mu = 2.5e-8 * 20
length = int(2e6) / 20
times = arghmm.get_time_points(ntimes=20, maxtime=200000)
popsize = 1e4
popsize2 = 1e4 * .5
a = int(.3 * length)
b = int(.7 * length)
refine = 0
util.tic("sim ARG")
arg = arglib.sample_arg_smc(k, 2 * popsize,
rho, start=0, end=a)
arg = arglib.sample_arg_smc(k, 2 * popsize2,
rho, start=a, end=b,
init_tree=arg)
arg = arglib.sample_arg_smc(k, 2 * popsize,
rho, start=b, end=length,
init_tree=arg)
# sim seq
mut = arghmm.sample_arg_mutations(arg, mu, times)
seqs = arghmm.make_alignment(arg, mut)
util.toc()
# sample arg
util.tic("sample arg")
arg2 = arghmm.sample_arg(seqs, rho=rho, mu=mu, times=times,
popsizes=1e4, carg=True)
arg2 = arghmm.resample_climb_arg(arg2, seqs, popsizes=1e4,
rho=rho, mu=mu, times=times,
refine=200)
arg2 = arghmm.resample_all_arg(arg2, seqs, popsizes=1e4,
rho=rho, mu=mu, times=times,
refine=200)
util.toc()
x = []; y = []
for (start, end), tree in arglib.iter_tree_tracks(arg2):
arglib.remove_single_lineages(tree)
x.append(start)
y.append(mle_popsize_tree(tree, mintime=0))
# thin popsizes
x2 = list(range(0, length, length//5000)); y2 = []
j = 0
for i in range(len(x2)):
while j < len(x) and x[j] < x2[i]:
j += 1
y2.append(y[min(j, len(y)-1)])
x3, y3 = stats.smooth2(x2, y2, 100e3)
p = plot(x, y, ymin=0)
p.plot(x3, y3, style='lines')
p.plot([0, a, a, b, b, length],
[popsize, popsize, popsize2, popsize2, popsize, popsize],
style='lines')
pause()
def test_est_arg_popsize(self):
"""
Fully sample an ARG from stratch using API
"""
k = 20
rho = 1.5e-8 * 20
mu = 2.5e-8 * 20
length = int(2e6) / 20
times = arghmm.get_time_points(ntimes=20, maxtime=200000)
popsize = 1e4
popsize2 = 1e4 * .5
a = int(.3 * length)
b = int(.7 * length)
refine = 0
util.tic("sim ARG")
arg = arglib.sample_arg_smc(k, 2 * popsize,
rho, start=0, end=a)
arg = arglib.sample_arg_smc(k, 2 * popsize2,
rho, start=a, end=b,
init_tree=arg)
arg = arglib.sample_arg_smc(k, 2 * popsize,
rho, start=b, end=length,
init_tree=arg)
# sim seq
mut = arghmm.sample_arg_mutations(arg, mu, times)
seqs = arghmm.make_alignment(arg, mut)
util.toc()
# sample arg
util.tic("sample arg")
arg2 = arghmm.sample_arg(seqs, rho=rho, mu=mu, times=times,
popsizes=1e4, carg=True)
arg2 = arghmm.resample_climb_arg(arg2, seqs, popsizes=1e4,
rho=rho, mu=mu, times=times,
refine=200)
arg2 = arghmm.resample_all_arg(arg2, seqs, popsizes=1e4,
rho=rho, mu=mu, times=times,
refine=200)
util.toc()
x = []; y = []
for (start, end), tree in arglib.iter_tree_tracks(arg2):
arglib.remove_single_lineages(tree)
x.append(start)
y.append(mle_popsize_tree(tree, mintime=0))
# thin popsizes
x2 = range(0, length, length//5000); y2 = []
j = 0
for i in range(len(x2)):
while j < len(x) and x[j] < x2[i]:
j += 1
y2.append(y[min(j, len(y)-1)])
x3, y3 = stats.smooth2(x2, y2, 100e3)
p = plot(x, y, ymin=0)
p.plot(x3, y3, style='lines')
p.plot([0, a, a, b, b, length],
[popsize, popsize, popsize2, popsize2, popsize, popsize],
style='lines')
pause()
