def verify_matrix(self, ts):
m = ts.get_num_sites()
ldc = tskit.LdCalculator(ts)
A = ldc.get_r2_matrix()
self.assertEqual(A.shape, (m, m))
B = get_r2_matrix(ts)
self.assertTrue(np.allclose(A, B))
# Now look at each row in turn, and verify it's the same
# when we use get_r2 directly.
for j in range(m):
a = ldc.get_r2_array(j, direction=tskit.FORWARD)
b = A[j, j + 1:]
self.assertEqual(a.shape[0], m - j - 1)
self.assertEqual(b.shape[0], m - j - 1)
self.assertTrue(np.allclose(a, b))
a = ldc.get_r2_array(j, direction=tskit.REVERSE)
b = A[j, :j]
self.assertEqual(a.shape[0], j)
self.assertEqual(b.shape[0], j)
self.assertTrue(np.allclose(a[::-1], b))
# Now check every cell in the matrix in turn.
for j in range(m):
for k in range(m):
self.assertAlmostEqual(ldc.get_r2(j, k), A[j, k])
def verify_max_distance(self, ts):
"""
Verifies that the max_distance parameter works as expected.
"""
mutations = list(ts.mutations())
ldc = tskit.LdCalculator(ts)
A = ldc.get_r2_matrix()
j = len(mutations) // 2
for k in range(j):
x = mutations[j + k].position - mutations[j].position
a = ldc.get_r2_array(j, max_distance=x)
self.assertEqual(a.shape[0], k)
self.assertTrue(np.allclose(A[j, j + 1:j + 1 + k], a))
x = mutations[j].position - mutations[j - k].position
a = ldc.get_r2_array(j, max_distance=x, direction=tskit.REVERSE)
self.assertEqual(a.shape[0], k)
self.assertTrue(np.allclose(A[j, j - k:j], a[::-1]))
L = ts.get_sequence_length()
m = len(mutations)
a = ldc.get_r2_array(0, max_distance=L)
self.assertEqual(a.shape[0], m - 1)
self.assertTrue(np.allclose(A[0, 1:], a))
a = ldc.get_r2_array(m - 1, max_distance=L, direction=tskit.REVERSE)
self.assertEqual(a.shape[0], m - 1)
self.assertTrue(np.allclose(A[m - 1, :-1], a[::-1]))
def test_deprecated_aliases(self):
ts = msprime.simulate(20, mutation_rate=10, random_seed=15)
ts = tsutil.subsample_sites(ts, self.num_test_sites)
ldc = tskit.LdCalculator(ts)
A = ldc.get_r2_matrix()
B = ldc.r2_matrix()
self.assertTrue(np.array_equal(A, B))
a = ldc.get_r2_array(0)
b = ldc.r2_array(0)
self.assertTrue(np.array_equal(a, b))
self.assertEqual(ldc.get_r2(0, 1), ldc.r2(0, 1))
def ld_matrix_example(ts):
ld_calc = tskit.LdCalculator(ts)
A = ld_calc.r2_matrix()
# Now plot this matrix.
x = A.shape[0] / pyplot.rcParams["figure.dpi"]
x = max(x, pyplot.rcParams["figure.figsize"][0])
fig, ax = pyplot.subplots(figsize=(x, x))
fig.tight_layout(pad=0)
im = ax.imshow(A, interpolation="none", vmin=0, vmax=1, cmap="Blues")
ax.set_xticks([])
ax.set_yticks([])
for s in "top", "bottom", "left", "right":
ax.spines[s].set_visible(False)
pyplot.gcf().colorbar(im, shrink=0.5, pad=0)
def verify_max_mutations(self, ts):
"""
Verifies that the max mutations parameter works as expected.
"""
mutations = list(ts.mutations())
ldc = tskit.LdCalculator(ts)
A = ldc.get_r2_matrix()
j = len(mutations) // 2
for k in range(j):
a = ldc.get_r2_array(j, max_mutations=k)
self.assertEqual(a.shape[0], k)
self.assertTrue(np.allclose(A[j, j + 1:j + 1 + k], a))
a = ldc.get_r2_array(j, max_mutations=k, direction=tskit.REVERSE)
self.assertEqual(a.shape[0], k)
self.assertTrue(np.allclose(A[j, j - k:j], a[::-1]))
def test_get_r2_array_multiple_instances(self):
# This is the nominal case where we have a separate LdCalculator
# instance in each thread.
ts = self.get_tree_sequence()
ld_calc = tskit.LdCalculator(ts)
A = ld_calc.get_r2_matrix()
m = A.shape[0]
del ld_calc
def worker(thread_index, results):
ld_calc = tskit.LdCalculator(ts)
results[thread_index] = np.array(
ld_calc.get_r2_array(thread_index))
results = run_threads(worker, m)
for j in range(m):
assert np.allclose(results[j], A[j, j + 1:])
def test_get_r2_single_instance(self):
# This is the degenerate case where we have a single LdCalculator
# instance shared by the threads. We should have only one thread
# actually executing get_r2() at one time.
ts = self.get_tree_sequence()
ld_calc = tskit.LdCalculator(ts)
A = ld_calc.get_r2_matrix()
m = A.shape[0]
def worker(thread_index, results):
row = np.zeros(m)
results[thread_index] = row
for j in range(m):
row[j] = ld_calc.get_r2(thread_index, j)
results = run_threads(worker, m)
for j in range(m):
assert np.allclose(results[j], A[j])
def test_get_r2_array_single_instance(self):
# This is the degenerate case where we have a single LdCalculator
# instance shared by the threads. We should have only one thread
# actually executing get_r2_array() at one time. Because the buffer
# is shared by many different instances, we can't make any assertions
# about the returned values --- they are essentially gibberish.
# However, we shouldn't crash and burn, which is what this test
# is here to check for.
ts = self.get_tree_sequence()
ld_calc = tskit.LdCalculator(ts)
m = ts.get_num_mutations()
def worker(thread_index, results):
results[thread_index] = ld_calc.get_r2_array(thread_index).shape
results = run_threads(worker, m)
for j in range(m):
assert results[j][0] == m - j - 1
def test_get_r2_multiple_instances(self):
# This is the nominal case where we have a separate LdCalculator
# instance in each thread.
ts = self.get_tree_sequence()
ld_calc = tskit.LdCalculator(ts)
A = ld_calc.get_r2_matrix()
del ld_calc
m = A.shape[0]
def worker(thread_index, results):
ld_calc = tskit.LdCalculator(ts)
row = np.zeros(m)
results[thread_index] = row
for j in range(m):
row[j] = ld_calc.get_r2(thread_index, j)
results = run_threads(worker, m)
for j in range(m):
self.assertTrue(np.allclose(results[j], A[j]))
def main():
## Define command line args
parser = argparse.ArgumentParser(description="")
parser.add_argument("--trees",
required=True,
dest="trees",
type=str,
help="Coalescent trees for the simulation")
parser.add_argument(
"--output",
required=True,
dest="output",
type=str,
help=
"What name do you want to give to the output file? [DON'T GIVE FILE EXTENSION, THE SCRIPT MAKES TWO OUTPUT FILES"
)
parser.add_argument(
"--island",
dest="island",
action="store_true",
help="Use this flag if the data comes from the Island model")
args = parser.parse_args()
wins = [i for i in range(0, 1000000 + 3000, 1000)]
ts = pyslim.load(args.trees)
# print("recap")
mut_rate = 1e-7 # HARD CODED, SO CHANGE IF NECESSARY
pops = {}
for i in ts.individuals_alive_at(0):
if ts.individual(i).population == 999: continue
try:
pops[ts.individual(i).population].append(i)
except KeyError:
pops[ts.individual(i).population] = [i]
# Let's take a sample of 40 pops and 20 diploids from each and make a new tree from them
sampled_indivs = []
for i in np.random.choice(list(pops.keys()), 1, replace=False):
for j in np.random.choice(np.array(pops[i]), 10, replace=False):
sampled_indivs.extend(ts.individual(j).nodes)
r2_tree2 = ts.simplify(sampled_indivs)
#print(i.population)
# print(ts.sample_size)
## Sprinkle mutations onto the coalescent tree
# print('Sprinkling mutations onto trees')
# print("sprinkle 1")
sprinkled = msprime.mutate(r2_tree2, rate=mut_rate, keep=True)
# MAF_005 = []
# for i in sprinkled.variants():
# print(i.position)
# if sum(i.genotypes)/len(i.genotypes) > 0.01:
# MAF_005.append(1)
# else:
# MAF_005.append(0)
# print( np.array(MAF_005).sum() )
# return
# print("sprinkle 2")
# sprinkled_recap = msprime.mutate(ts, rate= mut_rate, keep=True)
#### print(sprinkled.diversity( windows = [0,1e6,1e6+3000]) )
# sprinkled_recap.diversity( windows = wins+ [1003000]
#))
# plt.step( np.array(wins), sprinkled.diversity( windows = wins+ [1003000top
#]) , "xkcd:crimson" )
# plt.step( np.array(wins), sprinkled_recap.diversity( windows = wins+ [1003000]) , "peachpuff" )
# plt.show()
# return
positions = [i.position for i in sprinkled.variants() if i.position < 1e4]
# print(len(positions))
LD_interval = sprinkled.keep_intervals(np.array([[0, 20000]]))
LD = tskit.LdCalculator(LD_interval)
LD_mat = LD.r2_matrix()
for i in range(len(positions)):
for j in range(len(positions)):
if j >= i:
continue
else:
pw_distances_ij = abs(positions[i] - positions[j])
if pw_distances_ij > 100000: continue
print(pw_distances_ij, LD_mat[i, j])
def worker(thread_index, results):
ld_calc = tskit.LdCalculator(ts)
row = np.zeros(m)
results[thread_index] = row
for j in range(m):
row[j] = ld_calc.get_r2(thread_index, j)
def worker(thread_index, results):
ld_calc = tskit.LdCalculator(ts)
results[thread_index] = np.array(
ld_calc.get_r2_array(thread_index))
def getLD(tree_sequence, output_name):
pops = {}
for i in tree_sequence.individuals_alive_at(0):
if tree_sequence.individual(i).population == 999: continue
try:
pops[tree_sequence.individual(i).population].append(i)
except KeyError:
pops[tree_sequence.individual(i).population] = [i]
# Let's take a sample of 10 individuals from 1 pops and make a new tree from them
sampled_indivs_1 = []
for i in np.random.choice(list(pops.keys()), 1, replace=False):
for j in np.random.choice(np.array(pops[i]), 10, replace=False):
sampled_indivs_1.extend(tree_sequence.individual(j).nodes)
diploids_per_pop = 2
# Let's take a sample of 10 individuals from 20 pops and make a new tree from them
sampled_indivs_2 = []
for i in np.random.choice(list(pops.keys()), 20, replace=False):
for j in np.random.choice(np.array(pops[i]), 2, replace=False):
sampled_indivs_2.extend(tree_sequence.individual(j).nodes)
r2_tree_1 = tree_sequence.simplify(sampled_indivs_1)
mut_tree_1 = msprime.mutate(r2_tree_1, 1e-7)
r2_tree_2 = tree_sequence.simplify(sampled_indivs_2)
mut_tree_2 = msprime.mutate(r2_tree_2, 1e-7)
# print(ts.sample_size)
## Sprinkle mutations onto the coalescent tree
# print('Sprinkling mutations onto trees')
# print("sprinkle 1")
# sprinkled = msprime.mutate(r2_tree2, rate= mut_rate, keep=True)
LD_intervals = [[9000000, 9010000 - 1], [9200000, 9210000 - 1],
[9400000, 9410000 - 1], [9600000, 9610000 - 1],
[9800000, 9810000 - 1]]
LD_intervals = [[7260000, 7270000 - 1]]
LD_output_within = open("within_" + output_name, "w")
for interval in LD_intervals:
positions = [
i.position for i in mut_tree_1.variants()
if i.position >= interval[0] and i.position <= interval[1]
]
LD_interval = mut_tree_1.keep_intervals(np.array([interval]))
LD = tskit.LdCalculator(LD_interval)
LD_mat = LD.r2_matrix()
freq_dict = {}
for variant in LD_interval.variants():
## Calculating the genotype freqs this way assumes that the ref and alt are coded as 1s and 0s, repectively. I'll keep that for now, but will change in a bit
allele_freq = ((variant.genotypes[::2] + variant.genotypes[1::2]) /
2).mean()
freq_dict[variant.position] = allele_freq
print(len(freq_dict.keys()))
print(len(positions))
for i in range(len(positions)):
for j in range(len(positions)):
if j >= i:
continue
else:
if freq_dict[positions[i]] < 0.1 or freq_dict[
positions[j]] < 0.1:
continue
pw_distances_ij = abs(positions[i] - positions[j])
if pw_distances_ij > 10000: continue
LD_output_within.write(",".join(
[str(int(pw_distances_ij)),
str(LD_mat[i, j])]) + "\n")
LD_output_within.close()
print("Now getting 'LD' between pops")
LD_output_between = open("between_" + output_name, "w")
for interval in LD_intervals:
positions = [
i.position for i in mut_tree_2.variants()
if i.position >= interval[0] and i.position <= interval[1]
]
LD_interval = mut_tree_2.keep_intervals(np.array([interval]))
freq_dict = {}
for variant in LD_interval.variants():
## Calculating the genotype freqs this way assumes that the ref and alt are coded as 1s and 0s, repectively. I'll keep that for now, but will change in a bit
genotypes_as_freqs = (variant.genotypes[::2] +
variant.genotypes[1::2]) / 2
freqs_per_pop = ([
i.mean()
for i in chunks(genotypes_as_freqs, int(diploids_per_pop))
])
if sum(freqs_per_pop) / len(freqs_per_pop) < 0.1: continue
freq_dict[variant.position] = freqs_per_pop
for pair in itertools.product(freq_dict.keys(), repeat=2):
pw_distances_ij = abs(pair[0] - pair[1])
if pw_distances_ij == 0: continue
LD_output_between.write(",".join([
str(int(pw_distances_ij)),
str(
scipy.stats.pearsonr(freq_dict[pair[0]], freq_dict[
pair[1]])[0]**2)
]) + "\n")
LD_output_between.close()
return
Ne=Ne,
recombination_map=recombination_map,
model="dtwf",
mutation_rate=mutation_rate)
first_chrom2 = 'not assigned'
n1 = 0
n2 = 0
for variant in tree_sequence.variants():
if variant.position > 1e8:
first_chrom2 = variant.index
n2 += 1
if variant.position < (1e8 - 1):
n1 += 1
r2 = tskit.LdCalculator(tree_sequence).r2_matrix()
allele_frequency_filter = Waples2011.get_allele_filter(
tree_sequence, 0.2, S)
chrom2_filter = np.logical_and(allele_frequency_filter,
np.append(np.zeros(n1), np.ones(n2)))
chrom1_filter = np.logical_and(allele_frequency_filter,
np.append(np.ones(n1), np.zeros(n2)))
filtered_matrix = r2[chrom1_filter][:, chrom2_filter]
obs_r2_drift = np.mean(Waples2011.get_r2_drift(filtered_matrix, S))
obs_r2_uncorrected = np.mean(filtered_matrix)
N_prediction = 1 / (3 * obs_r2_drift)
r2_corrected_list.append(obs_r2_drift)
r2_observed_list.append(obs_r2_uncorrected)
def get_LD_matrix(tree_sequence):
return tskit.LdCalculator(tree_sequence).r2_matrix()
def myLDcalc(tree_sequence, ):
for variant in tree_sequence.variants():
if variant.site.id == 0:
gen1 = variant.genotypes
if variant.site.id == 1:
gen2 = variant.genotypes
break
n = len(gen1)
pA = sum(gen1) / n
pB = sum(gen2) / n
pAB= sum(np.logical_and(gen1, gen2))/n
pab= sum(np.logical_and(1-gen1, 1-gen2))/n
pAb= sum(np.logical_and(gen1, 1-gen2))/n
paB= sum(np.logical_and(1-gen1, gen2))/n
print(sum([pAB, pAb, paB, pab]))
r_unphased = ( pAB - pA * pB ) / np.sqrt(pA * (1-pA) * pB * (1-pB))
r2_phased = (pAB * pab - pAb * paB)**2 / (pA * (1-pA) * pB * (1-pB))
return r_unphased**2, r2_phased
for variant in tree_sequence.variants():
print(
variant.site.id, variant.site.position,
variant.alleles, sep = '\t'
)
print(count_mutations(tree_sequence))
print(tskit.LdCalculator(tree_sequence).r2_matrix())
print(tskit.LdCalculator(tree_sequence).r2(0,1))
print(myLDcalc(tree_sequence))
def get_LD_estimate(Ne, S, n_subpops, m, rate=False, n_loci=100):
# set up population parameters
## migration matrix
M = get_migration_matrix(m, n_subpops)
## sample
population_configurations = [
msprime.PopulationConfiguration(sample_size=S)
] + [
msprime.PopulationConfiguration(sample_size=0)
for i in range(n_subpops - 1)
]
## mutation and recombination : adjust based on Ne to get same number of mutations!
mutation_rate = 0 * 5e-9 / 40
recom_rate = 1e-8
positions = [0, 1e8 - 1, 1e8, 2e8 - 1]
rates = [recom_rate, 0.5, recom_rate, 0]
num_loci = int(positions[-1])
recombination_map = msprime.RecombinationMap(positions=positions,
rates=rates,
num_loci=num_loci)
tree_sequence = msprime.simulate(
Ne=Ne,
recombination_map=recombination_map,
mutation_rate=mutation_rate,
population_configurations=population_configurations,
migration_matrix=M,
model="dtwf")
if not rate:
print("Calculating rate...")
L = 0
for tree in tree_sequence.trees():
L += tree.get_length() * tree.get_total_branch_length()
rate = n_loci / L
tree_sequence = msprime.mutate(tree_sequence,
rate=rate,
random_seed=None,
model=None,
keep=False,
start_time=None,
end_time=None)
first_chrom2 = 'not assigned'
n1 = 0
n2 = 0
for variant in tree_sequence.variants():
if variant.position > 1e8:
first_chrom2 = variant.index
n2 += 1
if variant.position < (1e8 - 1):
n1 += 1
r2 = tskit.LdCalculator(tree_sequence).r2_matrix()
fil = np.zeros((n1 + n2, n1 + n2))
fil[:n1, n1:] = 1
i = 0
for v in tree_sequence.variants():
if sum(v.genotypes / len(v.genotypes)) < 0.05:
fil[:, i] = 0
fil[i, :] = 0
i += 1
fil = fil.astype(int)
r2 = np.where(fil, r2, np.zeros_like(r2))
r2_mean = np.sum(r2) / np.sum(fil)
r2_drift = r2_mean - (1 / (1 * S) / (1 - 1 / (1 * S)))
Ne_est = 1 / (3 * r2_drift)
#print(n1+n2)
#print(Ne_est)
return Ne_est, rate
def getLD(tree_sequence, output_name, selection=False):
if selection == True:
sel_pos_raw = []
for v in tree_sequence.variants():
if v.genotypes.sum() < 4000:
continue ## A rough way of removing low frueqnecy alleles
else:
sel_pos_raw.append(round(v.position / 10000) * 10000)
LD_intervals = [[s, s + 9999] for s in list(set(sel_pos_raw))]
else:
## these genes always evolve neutrally
LD_intervals = [[9000000, 9010000 - 1], [9200000, 9210000 - 1],
[9400000, 9410000 - 1], [9600000, 9610000 - 1],
[9800000, 9810000 - 1]]
print(LD_intervals)
pops = {}
for i in tree_sequence.individuals_alive_at(0):
if tree_sequence.individual(i).population == 999: continue
try:
pops[tree_sequence.individual(i).population].append(i)
except KeyError:
pops[tree_sequence.individual(i).population] = [i]
# Let's take a sample of 10 individuals from 1 pops and make a new tree from them
sampled_indivs = []
for i in np.random.choice(list(pops.keys()), 1, replace=False):
for j in np.random.choice(np.array(pops[i]), 10, replace=False):
sampled_indivs.extend(tree_sequence.individual(j).nodes)
r2_tree2 = tree_sequence.simplify(sampled_indivs)
mut_tree = msprime.mutate(r2_tree2, 1e-7)
# print(pops)
# print(ts.sample_size)
## Sprinkle mutations onto the coalescent tree
# print('Sprinkling mutations onto trees')
# print("sprinkle 1")
# sprinkled = msprime.mutate(r2_tree2, rate= mut_rate, keep=True)
LD_output = open(output_name, "w")
for inter in range(len(LD_intervals)):
interval = LD_intervals[inter]
positions = [
i.position for i in mut_tree.variants()
if i.position >= interval[0] and i.position <= interval[1]
]
LD_interval = mut_tree.keep_intervals(np.array([interval]))
LD = tskit.LdCalculator(LD_interval)
LD_mat = LD.r2_matrix()
for i in range(len(positions)):
for j in range(len(positions)):
if j >= i:
continue
else:
pw_distances_ij = abs(positions[i] - positions[j])
if pw_distances_ij > 10000: continue
LD_output.write(",".join(
[str(inter),
str(pw_distances_ij),
str(LD_mat[i, j])]) + "\n")
LD_output.close()
