def test_genotypes_exact():
"""
Test whether genotype knockoffs with true HMM are accurate
"""
p = 10
K = 3
M = 3
n_train = 1000
n_test = 100000
pInit, Q, pEmit = generate_HMM(p, K, M)
modelX = models.HMM(pInit, Q, pEmit)
X = modelX.sample(n_train)
_, Xfp_file = tempfile.mkstemp()
fp.writeXtoInp(X, Xfp_file)
fastphase = "fastphase" # Name of fastPhase executable
_, out_path = tempfile.mkstemp()
fp.runFastPhase(Xfp_file, out_path, fastphase=fastphase, K=5, numit=25)
r_file = out_path + "_rhat.txt"
alpha_file = out_path + "_alphahat.txt"
theta_file = out_path + "_thetahat.txt"
char_file = out_path + "_origchars"
hmm = fp.loadHMM(r_file, alpha_file, theta_file, char_file)
knockoffs = knockoffGenotypes(hmm["r"],
hmm["alpha"],
hmm["theta"],
seed=123)
hmm_hat = fp.loadHMM(r_file,
alpha_file,
theta_file,
char_file,
compact=False)
modelX_hat = models.HMM(hmm_hat["pInit"], hmm_hat["Q"], hmm_hat["pEmit"])
X_new = modelX_hat.sample(n_test)
Xk_new = knockoffs.sample(X_new)
verify_exchangeability(X_new, Xk_new, tolerance=1e-3)
def test_haplotypes_hmm():
"""
Test whether specialized haplotype knockoff algorithm agrees with special case
"""
p = 10
K = 5
M = 2
n_train = 1000
n_test = 100000
pInit, Q, pEmit = generate_HMM(p, K, M)
modelX = models.HMM(pInit, Q, pEmit)
X = modelX.sample(n_train)
_, Xfp_file = tempfile.mkstemp()
fp.writeXtoInp(X, Xfp_file, phased=True)
fastphase = "fastphase" # Name of fastPhase executable
_, out_path = tempfile.mkstemp()
fp.runFastPhase(Xfp_file,
out_path,
fastphase=fastphase,
phased=True,
K=5,
numit=25)
r_file = out_path + "_rhat.txt"
alpha_file = out_path + "_alphahat.txt"
theta_file = out_path + "_thetahat.txt"
char_file = out_path + "_origchars"
groups = np.repeat(np.arange(p), 3)[:p]
hmm_compact = fp.loadHMM(r_file, alpha_file, theta_file, char_file)
hmm = fp.loadHMM(r_file,
alpha_file,
theta_file,
char_file,
compact=False,
phased=True)
knockoffs = knockoffHMM(hmm["pInit"],
hmm["Q"],
hmm["pEmit"],
groups=groups,
seed=123)
knockoffs_hap = knockoffHaplotypes(hmm_compact["r"], hmm_compact["alpha"], hmm_compact["theta"], \
groups=groups, seed=123)
hmm_hat = fp.loadHMM(r_file,
alpha_file,
theta_file,
char_file,
compact=False,
phased=True)
Xk = knockoffs.sample(X)
Xk_compact = knockoffs_hap.sample(X)
assert np.array_equal(
Xk, Xk_compact), "Knockoffs with trivial groups do not match"
def test_haplotypes_fastphase():
"""
Test whether haplotype knockoffs with HMM fitted by fastPHASE are accurate
"""
p = 10
K = 3
M = 2
n = 1000
pInit, Q, pEmit = generate_HMM(p, K, M)
modelX = models.HMM(pInit, Q, pEmit)
X = modelX.sample(n)
_, Xfp_file = tempfile.mkstemp()
fp.writeXtoInp(X, Xfp_file, phased=True)
fastphase = "fastphase" # Name of fastPhase executable
_, out_path = tempfile.mkstemp()
fp.runFastPhase(Xfp_file,
out_path,
fastphase=fastphase,
phased=True,
K=5,
numit=25)
r_file = out_path + "_rhat.txt"
alpha_file = out_path + "_alphahat.txt"
theta_file = out_path + "_thetahat.txt"
char_file = out_path + "_origchars"
hmm = fp.loadHMM(r_file, alpha_file, theta_file, char_file, phased=True)
knockoffs = knockoffHaplotypes(hmm["r"],
hmm["alpha"],
hmm["theta"],
seed=123)
Xk = knockoffs.sample(X)
verify_exchangeability(X, Xk, tolerance=1e-1)
import numpy as np
from matplotlib import pyplot as plt
from SNPknock.fastphase import loadHMM
from SNPknock import models
from SNPknock import knockoffHMM, knockoffHaplotypes, knockoffGenotypes
import util, pdb
# Load HMM
r_file = "data/haplotypes_rhat.txt"
alpha_file = "data/haplotypes_alphahat.txt"
theta_file = "data/haplotypes_thetahat.txt"
char_file = "data/haplotypes_origchars"
hmm = loadHMM(r_file, alpha_file, theta_file, char_file, compact=True)
hmm_full = loadHMM(r_file, alpha_file, theta_file, char_file, compact=False)
# Sample X
n = 10
modelX = models.HMM(hmm_full['pInit'], hmm_full['Q'], hmm_full['pEmit'])
X = modelX.sample(n)
# Generate the knockoffs
#knockoffs = knockoffHMM(hmm_full['pInit'], hmm_full['Q'], hmm_full['pEmit'])
#Xk = knockoffs.sample(X)
#print("Generated knockoffs")
# Generate the knockoffs (genotypes)
knockoffs_gen = knockoffGenotypes(hmm['r'], hmm['alpha'], hmm['theta'])
Xk = knockoffs_gen.sample(X)
print("Generated knockoffs (genotypes)")
# Generate the knockoffs (haplotypes)