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_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)
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 _estimate(self, Xfp_file='./X.inp'):
fp.writeX(self.X, Xfp_file)
path_to_fp = "/home/roquero/Software/fastPHASE" # Relative path to the fastPhase executable
out_path = "./example" # Prefix to temporary output files produced by fastPhase
fp.runFastPhase(path_to_fp,
Xfp_file,
out_path,
K=self.hidden_states,
numit=self.numit)
r_file = out_path + "_rhat.txt"
alpha_file = out_path + "_alphahat.txt"
theta_file = out_path + "_thetahat.txt"
self.hmm = fp.loadFit(r_file, theta_file, alpha_file, self.X[0, :])
self.knockoffHMM = knockoffHMM(self.hmm["pInit"], self.hmm["Q"],
self.hmm["pEmit"])
def make_knockoff(chromosome=None, grouped_by_chromosome=None, df_SNP=None,
df_geno_experiment=None, df_geno_ensembl=None,
SNP_to_wild_type=None, cache_dir=None, path_to_fp=None,
em_iterations=25, random_seed=123):
# assert chromosome!=None and grouped_by_chromosome!=None and df_SNP!=None
assert chromosome is not None
assert grouped_by_chromosome is not None
assert df_SNP is not None
logger.debug("################")
logger.debug("Chromosome %2d #" % chromosome)
logger.debug("################")
num_experiment_people = len(df_geno_experiment)
num_ensembl_people = len(df_geno_ensembl)
indices = grouped_by_chromosome.groups[chromosome]
df_SNP_chromo = df_SNP.iloc[indices].sort_values('chromosome_position')
SNPs_on_chromosome = df_SNP_chromo['SNP'].values
X_experiment = np.empty((num_experiment_people, len(SNPs_on_chromosome)))
X_ensembl = np.empty((num_ensembl_people, len(SNPs_on_chromosome)))
for X, df in [
(X_experiment, df_geno_experiment),
(X_ensembl, df_geno_ensembl)]:
for j, SNP in enumerate(SNPs_on_chromosome):
X[:, j] = utils.genotype_to_nonwild_type_count(
df[SNP].values, SNP_to_wild_type[SNP])
out_path = '%s/chrom_%d' % (cache_dir, chromosome)
# If all relevant files are found in cache, skip EM recomputation; otherwise,
# redo the whole thing.
target_file_suffix_list = [
'alphahat.txt', 'finallikelihoods', 'origchars', 'rhat.txt', 'thetahat.txt']
already_in_cache = True
for suffix in target_file_suffix_list:
target_path = os.path.join(
cache_dir, 'chrom_%d_%s' % (chromosome, suffix))
if not os.path.exists(target_path):
already_in_cache = False
break
if already_in_cache:
logger.debug("Found chrom %d HMM in cache" % chromosome)
else:
# Write array to file
Xfp_file = '%s/X_%d.inp' % (cache_dir, chromosome)
fp.writeX(X_ensembl, Xfp_file)
# Run fastPhase on data (which runs EM)
fp.runFastPhase(path_to_fp, Xfp_file, out_path,
K=12, numit=em_iterations)
# Read in fastPhase results (i.e., HMM parameters) from file:
r_file = out_path + "_rhat.txt"
alpha_file = out_path + "_alphahat.txt"
theta_file = out_path + "_thetahat.txt"
# Why is X_ensembl[0, :] in the function arguments below?
hmm = fp.loadFit(r_file, theta_file, alpha_file, X_ensembl[0, :])
# Actually produce the knockoffs
knockoffs = knockoffHMM(hmm["pInit"], hmm["Q"], hmm[
"pEmit"], seed=random_seed)
X_knockoffs = knockoffs.sample(X_experiment)
return(X_knockoffs, X_experiment, SNPs_on_chromosome)