def test_some_std(self):
k0 = self.snpdata.read_kernel(standardizer=Unit()).val
from pysnptools.kernelreader import SnpKernel
k1 = self.snpdata.read_kernel(standardizer=Unit())
np.testing.assert_array_almost_equal(k0, k1.val, decimal=10)
from pysnptools.snpreader import SnpData
snpdata2 = SnpData(iid=self.snpdata.iid,
sid=self.snpdata.sid,
pos=self.snpdata.pos,
val=np.array(self.snpdata.val))
s = str(snpdata2)
snpdata2.standardize()
s = str(snpdata2)
snpreader = Bed(self.currentFolder + "/examples/toydata",
count_A1=False)
k2 = snpreader.read_kernel(standardizer=Unit(), block_size=500).val
np.testing.assert_array_almost_equal(k0, k2, decimal=10)
from pysnptools.standardizer.identity import Identity
from pysnptools.standardizer.diag_K_to_N import DiagKtoN
for dtype in [sp.float64, sp.float32]:
for std in [Unit(), Beta(1, 25), Identity(), DiagKtoN()]:
s = str(std)
np.random.seed(0)
x = np.array(np.random.randint(3, size=[60, 100]), dtype=dtype)
x2 = x[:, ::2]
x2b = np.array(x2)
#LATER what's this about? It doesn't do non-contiguous?
#assert not x2.flags['C_CONTIGUOUS'] and not x2.flags['F_CONTIGUOUS'] #set up to test non contiguous
#assert x2b.flags['C_CONTIGUOUS'] or x2b.flags['F_CONTIGUOUS'] #set up to test non contiguous
#a,b = std.standardize(x2b),std.standardize(x2)
#np.testing.assert_array_almost_equal(a,b)
logging.info("done")
def test_some_std(self):
k0 = self.snpdata.read_kernel(standardizer=Unit()).val
from pysnptools.kernelreader import SnpKernel
k1 = self.snpdata.read_kernel(standardizer=Unit())
np.testing.assert_array_almost_equal(k0, k1.val, decimal=10)
from pysnptools.snpreader import SnpData
snpdata2 = SnpData(iid=self.snpdata.iid,sid=self.snpdata.sid,pos=self.snpdata.pos,val=np.array(self.snpdata.val))
s = str(snpdata2)
snpdata2.standardize()
s = str(snpdata2)
snpreader = Bed(self.currentFolder + "/examples/toydata",count_A1=False)
k2 = snpreader.read_kernel(standardizer=Unit(),block_size=500).val
np.testing.assert_array_almost_equal(k0, k2, decimal=10)
from pysnptools.standardizer.identity import Identity
from pysnptools.standardizer.diag_K_to_N import DiagKtoN
for dtype in [sp.float64,sp.float32]:
for std in [Unit(),Beta(1,25),Identity(),DiagKtoN()]:
s = str(std)
np.random.seed(0)
x = np.array(np.random.randint(3,size=[60,100]),dtype=dtype)
x2 = x[:,::2]
x2b = np.array(x2)
#LATER what's this about? It doesn't do non-contiguous?
#assert not x2.flags['C_CONTIGUOUS'] and not x2.flags['F_CONTIGUOUS'] #set up to test non contiguous
#assert x2b.flags['C_CONTIGUOUS'] or x2b.flags['F_CONTIGUOUS'] #set up to test non contiguous
#a,b = std.standardize(x2b),std.standardize(x2)
#np.testing.assert_array_almost_equal(a,b)
logging.info("done")
def test_npz(self):
logging.info("in test_npz")
snpreader = Bed(self.currentFolder + "/../examples/toydata",count_A1=False)
kerneldata1 = snpreader.read_kernel(standardizer=stdizer.Unit())
s = str(kerneldata1)
output = "tempdir/kernelreader/toydata.kernel.npz"
create_directory_if_necessary(output)
KernelNpz.write(output,kerneldata1)
kernelreader2 = KernelNpz(output)
kerneldata2 = kernelreader2.read()
np.testing.assert_array_almost_equal(kerneldata1.val, kerneldata2.val, decimal=10)
logging.info("done with test")
def test_subset(self):
logging.info("in test_subset")
snpreader = Bed(self.currentFolder + "/../examples/toydata",count_A1=False)
snpkernel = SnpKernel(snpreader,stdizer.Unit())
krsub = snpkernel[::2,::2]
kerneldata1 = krsub.read()
expected = snpreader.read_kernel(stdizer.Unit())[::2].read()
np.testing.assert_array_almost_equal(kerneldata1.val, expected.val, decimal=10)
krsub2 = snpkernel[::2]
kerneldata2 = krsub2.read()
np.testing.assert_array_almost_equal(kerneldata2.val, expected.val, decimal=10)
logging.info("done with test")
def test_npz(self):
logging.info("in test_npz")
snpreader = Bed(self.currentFolder + "/../examples/toydata.5chrom.bed",
count_A1=False)
kerneldata1 = snpreader.read_kernel(standardizer=stdizer.Unit())
s = str(kerneldata1)
output = "tempdir/kernelreader/toydata.kernel.npz"
create_directory_if_necessary(output)
KernelNpz.write(output, kerneldata1)
kernelreader2 = KernelNpz(output)
kerneldata2 = kernelreader2.read()
np.testing.assert_array_almost_equal(kerneldata1.val,
kerneldata2.val,
decimal=10)
logging.info("done with test")
def test_subset(self):
logging.info("in test_subset")
snpreader = Bed(self.currentFolder + "/../examples/toydata.5chrom.bed",
count_A1=False)
snpkernel = SnpKernel(snpreader, stdizer.Unit())
krsub = snpkernel[::2, ::2]
kerneldata1 = krsub.read()
expected = snpreader.read_kernel(stdizer.Unit())[::2].read()
np.testing.assert_array_almost_equal(kerneldata1.val,
expected.val,
decimal=10)
krsub2 = snpkernel[::2]
kerneldata2 = krsub2.read()
np.testing.assert_array_almost_equal(kerneldata2.val,
expected.val,
decimal=10)
logging.info("done with test")
class TestFastLMM(unittest.TestCase):
@classmethod
def setUpClass(self):
from fastlmm.util.util import create_directory_if_necessary
create_directory_if_necessary(self.tempout_dir, isfile=False)
self.pythonpath = os.path.abspath(os.path.join(os.path.dirname(os.path.realpath(__file__)),"..","..",".."))
self.snpreader_whole = Bed(self.pythonpath + "/tests/datasets/synth/all",count_A1=False)
self.covariate_whole = Pheno(self.pythonpath + "/tests/datasets/synth/cov.txt")
self.pheno_whole = Pheno(self.pythonpath + "/tests/datasets/synth/pheno_10_causals.txt")
tempout_dir = "tempout/fastlmm"
def file_name(self,testcase_name):
temp_fn = os.path.join(self.tempout_dir,testcase_name+".dat")
if os.path.exists(temp_fn):
os.remove(temp_fn)
return temp_fn
def test_api(self):
train_idx = np.r_[10:self.snpreader_whole.iid_count] # iids 10 and on
test_idx = np.r_[0:10] # the first 10 iids
#####################################################
# Train and standardize cov and then apply to test
#####################################################
cov_train, unit_trained = self.covariate_whole[train_idx,:].read().standardize(Unit(),return_trained=True)
cov_test = self.covariate_whole[test_idx,:].read().standardize(unit_trained)
#####################################################
# standardize whole kernel from snps (both ways) and then pull out the 3 parts
#####################################################
whole_kernel = SnpKernel(self.covariate_whole,Unit()).read().standardize(DiagKtoN())
train_kernel = whole_kernel[train_idx].read(order='A',view_ok=True)
test_kernel = whole_kernel[train_idx,test_idx].read(order='A',view_ok=True)
test_test_kernel = whole_kernel[test_idx,test_idx].read(order='A',view_ok=True)
#####################################################
# create train_train, train_test, and test_test based on just the training snps (both standardizations)
#####################################################
K_train = SnpKernel(self.snpreader_whole[train_idx,:],Unit(),block_size=100)
train_train_kernel, snp_trained, kernel_trained = K_train._read_with_standardizing(to_kerneldata=True, kernel_standardizer=DiagKtoN(), return_trained=True)
K_whole_test = _SnpWholeTest(train=self.snpreader_whole[train_idx,:],test=self.snpreader_whole[test_idx,:],standardizer=snp_trained,block_size=100)
train_idx2 = K_whole_test.iid0_to_index(self.snpreader_whole.iid[train_idx]) #The new reader may have the iids in a different order than the original reader
train_test_kernel = K_whole_test[train_idx2,:].read().standardize(kernel_trained)
test_idx2 = K_whole_test.iid0_to_index(self.snpreader_whole.iid[test_idx])
test_test_kernel = K_whole_test[test_idx2,:].read().standardize(kernel_trained)
#####################################################
# How does predict look with whole_test as input?
#####################################################
# a. - standardize whole up front
whole_kernel = SnpKernel(self.snpreader_whole,Unit(),block_size=100).read().standardize()
train_kernel = whole_kernel[train_idx].read(order='A',view_ok=True)
whole_test_kernel = whole_kernel[:,test_idx].read(order='A',view_ok=True)
fastlmm1 = FastLMM(snp_standardizer=SS_Identity(), kernel_standardizer=KS_Identity())
fastlmm1.fit(K0_train=train_kernel, X=self.covariate_whole, y=self.pheno_whole) #iid intersection means we won't really be using whole covar or pheno
predicted_pheno, covar = fastlmm1.predict(K0_whole_test=whole_test_kernel, X=self.covariate_whole,count_A1=False)
output_file = self.file_name("whole")
Dat.write(output_file,predicted_pheno)
self.compare_files(predicted_pheno,"whole")
# b -- just files
fastlmm2 = FastLMM()
fastlmm2.fit(K0_train=self.snpreader_whole[train_idx,:], X=self.covariate_whole, y=self.pheno_whole[train_idx,:]) #iid intersection means we won't really be using whole covar
predicted_pheno, covar = fastlmm2.predict(K0_whole_test=self.snpreader_whole[test_idx,:], X=self.covariate_whole,count_A1=False)
self.compare_files(predicted_pheno,"one")
def test_notebook1(self):
do_plot=False
import matplotlib.pyplot as plt
from pysnptools.snpreader import Pheno,Bed
bed = Bed(self.pythonpath + "/tests/datasets/synth/all",count_A1=False)
cov = Pheno(self.pythonpath + "/tests/datasets/synth/cov.txt")
pheno = Pheno(self.pythonpath + "/tests/datasets/synth/pheno_10_causals.txt").read()
# Now we learn from the first 400 students.
training = bed[:400,:] #!!!later: the learning code doesn't like it if there are two instances of bed[:400] that are not "is -equal"
fastlmm2 = FastLMM(GB_goal=2).fit(K0_train=training,
X=cov[:400,:],
y=pheno[:400,:])
# Predict on training data:
predicted_score,covariance = fastlmm2.predict(K0_whole_test=training,
X=cov[:400,:],count_A1=False)
assert np.array_equal(pheno.iid[:400],predicted_score.iid), "for plots to make sense, the iids must be in the order"
if do_plot:
plt.plot(pheno.val[:400,:],predicted_score.val,"b.",[-5,5],[-5,5],"-r")
plt.errorbar(pheno.val[:400,:],predicted_score.val, yerr=np.sqrt(np.diag(covariance.val)),fmt='.')
plt.xlabel('score (actual train)')
plt.ylabel('predicted (test on train with stdev)')
plt.show()
# How well does this model predict the (unseen) TEST data?
predicted_score,covariance = fastlmm2.predict(K0_whole_test=bed[400:500,:],
X=cov[400:500,:],count_A1=False)
assert np.array_equal(pheno.iid[400:500],predicted_score.iid), "for plots to make sense, the iids must be in the order"
if do_plot:
plt.plot(pheno.val[400:500,:],predicted_score.val,"b.",[-5,5],[-5,5],"-r")
plt.errorbar(pheno.val[400:500,:],predicted_score.val, yerr=np.sqrt(np.diag(covariance.val)),fmt='.')
plt.xlabel('score (actual test)')
plt.ylabel('predicted')
plt.show()
def test_one(self):
logging.info("TestLmmTrain test_one")
train_idx = np.r_[10:self.snpreader_whole.iid_count] # iids 10 and on
test_idx = np.r_[0:10] # the first 10 iids
G0_train = self.snpreader_whole[train_idx,:]
covariate_train = self.covariate_whole[train_idx,:]
pheno_train = self.pheno_whole[train_idx,:]
fastlmm1 = FastLMM(GB_goal=2).fit(K0_train=G0_train, X=covariate_train, y=pheno_train)
filename = self.tempout_dir + "/model_one.flm.p"
pstutil.create_directory_if_necessary(filename)
joblib.dump(fastlmm1, filename)
fastlmm2 = joblib.load(filename)
# predict on test set
G0_test = self.snpreader_whole[test_idx,:]
covariate_test = self.covariate_whole[test_idx,:]
predicted_pheno, covar = fastlmm2.predict(K0_whole_test=G0_test, X=covariate_test,count_A1=False)
output_file = self.file_name("one")
Dat.write(output_file,predicted_pheno)
pheno_actual = self.pheno_whole[test_idx,:].read().val[:,0]
#pylab.plot(pheno_actual, predicted_pheno.val,".")
#pylab.show()
self.compare_files(predicted_pheno,"one")
def test_str(self):
logging.info("TestLmmTrain test_str")
G0_train = self.pythonpath + "/tests/datasets/synth/all"
covariate_train = None
pheno_train = self.pythonpath + "/tests/datasets/synth/pheno_10_causals.txt"
fastlmm1 = FastLMM(GB_goal=2).fit(K0_train=G0_train, X=covariate_train, y=pheno_train,count_A1=False)
filename = self.tempout_dir + "/model_str.flm.p"
pstutil.create_directory_if_necessary(filename)
joblib.dump(fastlmm1, filename)
fastlmm2 = joblib.load(filename)
# predict on same
G0_test = G0_train
covariate_test = covariate_train
predicted_pheno, covar = fastlmm2.predict(K0_whole_test=G0_test, X=covariate_test,count_A1=False)
output_file = self.file_name("str")
Dat.write(output_file,predicted_pheno)
#pheno_actual = self.pheno_whole[test_idx,:].read().val[:,0]
#pylab.plot(pheno_actual, predicted_pheno.val,".")
#pylab.show()
self.compare_files(predicted_pheno,"str")
def test_lr_no_K0(self):
logging.info("TestLinRegTrain test_lr_no_k0")
train_idx = np.r_[10:self.snpreader_whole.iid_count] # iids 10 and on
test_idx = np.r_[0:10] # the first 10 iids
covariate_train3 = self.covariate_whole[train_idx,:].read()
covariate_train3.val = np.array([[float(num)] for num in xrange(covariate_train3.iid_count)])
pheno_train3 = self.pheno_whole[train_idx,:].read()
np.random.seed(0)
pheno_train3.val = covariate_train3.val * 2.0 + 100 + np.random.normal(size=covariate_train3.val.shape) # y = 2*x+100+normal(0,1)
#Learn model, save, load
fastlmm3x = FastLMM(GB_goal=2).fit(X=covariate_train3, y=pheno_train3)
filename = self.tempout_dir + "/model3.flm.p"
joblib.dump(fastlmm3x, filename)
fastlmm3 = joblib.load(filename)
#Predict with model (test on train)
predicted_pheno, covariance = fastlmm3.predict(K0_whole_test=KernelIdentity(pheno_train3.iid), X=covariate_train3,count_A1=False) #test on train
output_file = self.file_name("lr_no_k0")
Dat.write(output_file,predicted_pheno)
self.compare_files(predicted_pheno,"lr_no_k0")
def test_lr_as_lmm(self):
do_plot = False
#later why does this test case generate two intersect info messages instead of just one?
import pylab
logging.info("TestLmmTrain test_lr_as_lmm")
###############################################################
# Create a linear data set with just a little noise
###############################################################
train_idx = np.r_[10:self.snpreader_whole.iid_count] # iids 10 and on
test_idx = np.r_[0:10] # the first 10 iids
#make covar just numbers 0,1,...
covar = self.covariate_whole.read()
covar.val = np.array([[float(num)] for num in xrange(covar.iid_count)])
covar._name = 'np.array([[float(num)] for num in xrange(covar.iid_count)])'
covariate_train = covar[train_idx,:].read()
covariate_test = covar[test_idx,:].read()
#make pheno # pheno = 2*covar+100+normal(0,1)*10
pheno = self.pheno_whole.read()
np.random.seed(0)
pheno.val = covar.val * 2.0 + 100 + np.random.normal(size=covar.val.shape)*10
pheno_train = pheno[train_idx,:].read()
pheno_test = pheno[test_idx,:].read()
if do_plot:
#Plot training x and y, testing x and y
pylab.plot(covariate_train.val, pheno_train.val,".",covariate_test.val, pheno_test.val,".")
pylab.suptitle("Plot training x and y, testing x and y")
pylab.show()
###############################################################
# Show that linear regression does a good job predicting
###############################################################
Xtrain = np.c_[covariate_train.val,np.ones((covariate_train.iid_count,1))]
Xtest = np.c_[covariate_test.val,np.ones((covariate_test.iid_count,1))]
lsqSol = np.linalg.lstsq(Xtrain, pheno_train.val[:,0],rcond=-1)
bs=lsqSol[0] #weights
r2=lsqSol[1] #squared residuals
D=lsqSol[2] #rank of design matrix
N=pheno_train.iid_count
REML = False
if not REML:
sigma2 = float(r2/N)
nLL = N*0.5*np.log(2*np.pi*sigma2) + N*0.5
else:
sigma2 = float(r2 / (N-D))
nLL = N*0.5*np.log(2*np.pi*sigma2) + 0.5/sigma2*r2;
nLL -= 0.5*D*np.log(2*np.pi*sigma2);#REML term
predicted = Xtest.dot(bs)
yerr = [np.sqrt(sigma2)] * len(predicted)
if do_plot:
pylab.plot(covariate_test.val, pheno_test.val,"g.",covariate_test.val, predicted,"r.")
pylab.xlim([-1, 10])
pylab.errorbar(covariate_test.val, predicted,yerr,linestyle='None')
pylab.suptitle("real linear regression: actual to prediction")
pylab.show()
###############################################################
# Use LMM as LR and apply test on train
###############################################################
for force_full_rank in [True, False]:
#Learn model, save, load
fastlmmx = FastLMM(GB_goal=2,force_full_rank=force_full_rank).fit(K0_train=covariate_train, X=None, y=pheno_train)
filename = self.tempout_dir + "/model_lr_as_lmm.flm.p"
pstutil.create_directory_if_necessary(filename)
joblib.dump(fastlmmx, filename)
fastlmm = joblib.load(filename)
do_test_on_train = True
if do_test_on_train:
#Predict with model (test on train)
predicted_pheno, covar = fastlmm.predict(K0_whole_test=covariate_train, X=None,count_A1=False) #test on train
output_file = self.file_name("lr_as_lmma_")
Dat.write(output_file,predicted_pheno)
covar2 = SnpData(iid=covar.row,sid=covar.col[:,1],val=covar.val) #kludge to write kernel to text format
output_file = self.file_name("lr_as_lmma.cov_")
Dat.write(output_file,covar2)
yerr = np.sqrt(np.diag(covar.val))
predicted = predicted_pheno.val
if do_plot:
pylab.plot(covariate_train.val, pheno_train.val,"g.",covariate_train.val, predicted,"r.")
pylab.xlim([0, 50])
pylab.ylim([100, 200])
pylab.errorbar(covariate_train.val, predicted,yerr,linestyle='None')
pylab.suptitle("test on train: train X to true target (green) and prediction (red)")
pylab.show()
self.compare_files(predicted_pheno,"lr_as_lmma_")
self.compare_files(covar2,"lr_as_lmma.cov_")
###############################################################
# Use LMM as LR and apply test on test
###############################################################
#Predict with model (test on test)
predicted_pheno, covar = fastlmm.predict(K0_whole_test=covariate_test, X=None,count_A1=False) #test on train
output_file = self.file_name("lr_as_lmmb_")
Dat.write(output_file,predicted_pheno)
covar2 = SnpData(iid=covar.row,sid=covar.col[:,1],val=covar.val) #kludge to write kernel to text format
output_file = self.file_name("lr_as_lmmb.cov_")
Dat.write(output_file,covar2)
yerr = np.sqrt(np.diag(covar.val))
predicted = predicted_pheno.val
if do_plot:
pylab.plot(covariate_test.val, pheno_test.val,"g.",covariate_test.val, predicted,"r.")
pylab.xlim([-1, 10])
pylab.errorbar(covariate_test.val, predicted,yerr,linestyle='None')
pylab.suptitle("test on test: test X to true target (green) and prediction (red)")
pylab.show()
## Plot y and predicted y (test on train)
#pylab.plot(pheno_test.val,predicted_pheno.val,".")
#pylab.suptitle(name+": test on test: true target to prediction")
#pylab.show()
self.compare_files(predicted_pheno,"lr_as_lmmb_")
self.compare_files(covar2,"lr_as_lmmb.cov_")
def test_lr2(self):
do_plot = False
import pylab
logging.info("TestLmmTrain test_lr2")
train_idx = np.r_[10:self.snpreader_whole.iid_count] # iids 10 and on
test_idx = np.r_[0:10] # the first 10 iids
#make covar just numbers 0,1,...
covar = self.covariate_whole.read()
covar.val = np.array([[float(num)] for num in xrange(covar.iid_count)])
covariate_train = covar[train_idx,:].read()
covariate_test = covar[test_idx,:].read()
K0_whole_test = KernelIdentity(covar.iid,covariate_test.iid)
#make pheno # pheno = 2*covar+100+normal(0,1)*10
pheno = self.pheno_whole.read()
np.random.seed(0)
pheno.val = covar.val * 2.0 + 100 + np.random.normal(size=covar.val.shape)*10
pheno_train = pheno[train_idx,:].read()
pheno_test = pheno[test_idx,:].read()
if do_plot:
#Plot training x and y, testing x and y
pylab.plot(covariate_train.val, pheno_train.val,".",covariate_test.val, pheno_test.val,".")
pylab.suptitle("Plot training x and y, testing x and y")
pylab.show()
Xtrain = np.c_[covariate_train.val,np.ones((covariate_train.iid_count,1))]
Xtest = np.c_[covariate_test.val,np.ones((covariate_test.iid_count,1))]
lsqSol = np.linalg.lstsq(Xtrain, pheno_train.val[:,0],rcond=-1)
bs=lsqSol[0] #weights
r2=lsqSol[1] #squared residuals
D=lsqSol[2] #rank of design matrix
N=pheno_train.iid_count
REML = False
if not REML:
sigma2 = float(r2/N)
nLL = N*0.5*np.log(2*np.pi*sigma2) + N*0.5
else:
sigma2 = float(r2 / (N-D))
nLL = N*0.5*np.log(2*np.pi*sigma2) + 0.5/sigma2*r2;
nLL -= 0.5*D*np.log(2*np.pi*sigma2);#REML term
predicted = Xtest.dot(bs)
yerr = [np.sqrt(sigma2)] * len(predicted)
if do_plot:
pylab.plot(covariate_test.val, pheno_test.val,"g.",covariate_test.val, predicted,"r.")
pylab.xlim([-1, 10])
pylab.errorbar(covariate_test.val, predicted,yerr,linestyle='None')
pylab.suptitle("real linear regression: actual to prediction")
pylab.show()
#These should all give the same result
first_name = None
for name,K0_train,K0_whole_test in [("Identity Kernel",
KernelIdentity(self.snpreader_whole.iid[train_idx]),
KernelIdentity(self.snpreader_whole.iid,test=self.snpreader_whole.iid[test_idx])),
#!!!later("sid_count=0", self.snpreader_whole[train_idx,[]],self.snpreader_whole[test_idx,[]])
]:
logging.info(name)
first_name = first_name or name
#Learn model, save, load
fastlmmx = FastLMM(GB_goal=2).fit(K0_train=K0_train, X=covariate_train, y=pheno_train)
filename = self.tempout_dir + "/model_lr2.flm.p"
joblib.dump(fastlmmx, filename)
fastlmm = joblib.load(filename)
do_test_on_train = True
if do_test_on_train:
#Predict with model (test on train)
predicted_pheno, covar = fastlmm.predict(K0_whole_test=K0_train, X=covariate_train,count_A1=False) #test on train
output_file = self.file_name("lr2a_"+name)
Dat.write(output_file,predicted_pheno)
covar2 = SnpData(iid=covar.row,sid=covar.col[:,1],val=covar.val) #kludge to write kernel to text format
output_file = self.file_name("lr2a.cov_"+name)
Dat.write(output_file,covar2)
yerr = np.sqrt(np.diag(covar.val))
predicted = predicted_pheno.val
if do_plot:
pylab.plot(covariate_train.val, pheno_train.val,"g.",covariate_train.val, predicted,"r.")
pylab.xlim([0, 50])
pylab.ylim([100, 200])
pylab.errorbar(covariate_train.val, predicted,yerr,linestyle='None')
pylab.suptitle(name+": test on train: train X to true target (green) and prediction (red)")
pylab.show()
self.compare_files(predicted_pheno,"lr2a_"+first_name)
self.compare_files(covar2,"lr2a.cov_"+first_name)
#Predict with model (test on test)
predicted_pheno, covar = fastlmm.predict(K0_whole_test=K0_whole_test, X=covariate_test,count_A1=False) #test on train
output_file = self.file_name("lr2b_"+name)
Dat.write(output_file,predicted_pheno)
covar2 = SnpData(iid=covar.row,sid=covar.col[:,1],val=covar.val) #kludge to write kernel to text format
output_file = self.file_name("lr2b.cov_"+name)
Dat.write(output_file,covar2)
yerr = np.sqrt(np.diag(covar.val))
predicted = predicted_pheno.val
if do_plot:
pylab.plot(covariate_test.val, pheno_test.val,"g.",covariate_test.val, predicted,"r.")
pylab.xlim([-1, 10])
pylab.errorbar(covariate_test.val, predicted,yerr,linestyle='None')
pylab.suptitle(name+": test on test: test X to true target (green) and prediction (red)")
pylab.show()
## Plot y and predicted y (test on train)
#pylab.plot(pheno_test.val,predicted_pheno.val,".")
#pylab.suptitle(name+": test on test: true target to prediction")
#pylab.show()
self.compare_files(predicted_pheno,"lr2b_"+first_name)
self.compare_files(covar2,"lr2b.cov_"+first_name)
def test_str2(self):
logging.info("TestLmmTrain test_str2")
#Standardize train and test together
whole_kernel = self.snpreader_whole.read_kernel(Unit())
train_idx = np.r_[10:self.snpreader_whole.iid_count] # iids 10 and on
test_idx = np.r_[0:10] # the first 10 iids
covariate_train = self.covariate_whole[train_idx,:]
pheno_train = self.pheno_whole[train_idx,:]
K0_train_filename = self.tempout_dir + "/model_str2.kernel.npz"
pstutil.create_directory_if_necessary(K0_train_filename)
from pysnptools.kernelreader import KernelNpz
KernelNpz.write(K0_train_filename,whole_kernel[train_idx].read(order='A',view_ok=True))
fastlmm1 = FastLMM(GB_goal=2).fit(K0_train=K0_train_filename, X=covariate_train, y=pheno_train)
filename = self.tempout_dir + "/model_str2.flm.p"
pstutil.create_directory_if_necessary(filename)
joblib.dump(fastlmm1, filename)
fastlmm2 = joblib.load(filename)
# predict on test set
G0_test = self.snpreader_whole[test_idx,:]
covariate_test = self.covariate_whole[test_idx,:]
predicted_pheno, covar = fastlmm2.predict(K0_whole_test=whole_kernel[:,test_idx].read(order='A',view_ok=True), X=covariate_test,count_A1=False)
output_file = self.file_name("str2")
Dat.write(output_file,predicted_pheno)
#pheno_actual = self.pheno_whole[test_idx,:].read().val[:,0]
#pylab.plot(pheno_actual, predicted_pheno.val,".")
#pylab.show()
self.compare_files(predicted_pheno,"str2")
#Creating multiple tests so that will run faster when on cluster.
def test_fasttwoK(self):
logging.info("TestLmmTrain test_fasttwoK")
self._fasttwoK(None,None)
def test_fasttwoK_force_low_rank(self):
logging.info("TestLmmTrain test_fasttwoK_force_low_rank")
self._fasttwoK(True,None)
def test_fasttwoK_GB2(self):
logging.info("TestLmmTrain test_fasttwoK_GB2")
self._fasttwoK(None,2)
def test_fasttwoK_force_low_rank_GB2(self):
logging.info("TestLmmTrain test_fasttwoK_force_low_rank_GB2")
self._fasttwoK(True,2)
def _fasttwoK(self,force_low_rank,GB_goal):
train_idx = np.r_[10:self.snpreader_whole.iid_count] # iids 10 and on
test_idx = np.r_[0:10] # the first 10 iids
G0_train = self.snpreader_whole[train_idx,:]
G1_train = SnpData(iid=G0_train.iid,sid=[item+"_1" for item in G0_train.sid],val=G0_train.read().val,pos=G0_train.pos,name="Different SNP names for {0}".format(G0_train))
covariate_train = self.covariate_whole[train_idx,:]
pheno_train = self.pheno_whole[train_idx,:]
logging.info("force_low_rank = {0}".format(force_low_rank))
fastlmm1 = FastLMM(force_low_rank=force_low_rank,GB_goal=GB_goal).fit(K0_train=G0_train, K1_train=G1_train, X=covariate_train, y=pheno_train, mixing=.1)
filename = self.tempout_dir + "/model_fasttwoK.flm.p"
pstutil.create_directory_if_necessary(filename)
joblib.dump(fastlmm1, filename)
fastlmm2 = joblib.load(filename)
# predict on test set
G0_test = self.snpreader_whole[test_idx,:]
G1_test = SnpData(iid=G0_test.iid,sid=[item+"_1" for item in G0_test.sid],val=G0_test.read().val,pos=G0_test.pos,name="Different SNP names for {0}".format(G0_test))
covariate_test = self.covariate_whole[test_idx,:]
predicted_pheno, covar = fastlmm2.predict(K0_whole_test=G0_test, K1_whole_test=G1_test, X=covariate_test,count_A1=False)
output_file = self.file_name("fasttwoK"+("_force_low" if force_low_rank else "")+("GB{0}".format(GB_goal) if GB_goal is not None else ""))
Dat.write(output_file,predicted_pheno)
pheno_actual = self.pheno_whole[test_idx,:].read().val[:,0]
#pylab.plot(pheno_actual, predicted_pheno.val,".")
#pylab.show()
self.compare_files(predicted_pheno,"one")
def test_lowrank(self):
logging.info("TestLmmTrain test_lowrank")
snpreader = self.snpreader_whole[:,:100]
train_idx = np.r_[10:snpreader.iid_count] # iids 10 and on
test_idx = np.r_[0:10] # the first 10 iids
G0_train = snpreader[train_idx,:]
G0_test = snpreader[test_idx,:]
pheno_whole = self.pheno_whole.read()
pheno_whole.val *= 100
pheno_whole.val += 1000
mean_low, covar_low = FastLMM(force_low_rank=True,GB_goal=2).fit(K0_train=G0_train, y=pheno_whole[train_idx,:], X=self.covariate_whole[train_idx,:]). predict(K0_whole_test=G0_test,X=self.covariate_whole[test_idx,:],count_A1=False)
mean_full, covar_full = FastLMM(force_full_rank=True,GB_goal=2).fit(K0_train=G0_train, y=pheno_whole[train_idx,:], X=self.covariate_whole[train_idx,:]).predict(K0_whole_test=G0_test,X=self.covariate_whole[test_idx,:],count_A1=False)
np.testing.assert_allclose(mean_low.val, mean_full.val)
np.testing.assert_allclose(covar_low.val,covar_full.val)
logging.info("finished with TestLmmTrain test_lowrank")
def test_twoK(self):
logging.info("TestLmmTrain test_twoK")
train_idx = np.r_[10:self.snpreader_whole.iid_count] # iids 10 and on
test_idx = np.r_[0:10] # the first 10 iids
G0_train = self.snpreader_whole[train_idx,:]
covariate_train = self.covariate_whole[train_idx,:]
pheno_train = self.pheno_whole[train_idx,:]
fastlmm1 = FastLMM(GB_goal=2).fit(K0_train=G0_train, K1_train=G0_train, X=covariate_train, y=pheno_train)
filename = self.tempout_dir + "/model_one.flm.p"
pstutil.create_directory_if_necessary(filename)
joblib.dump(fastlmm1, filename)
fastlmm2 = joblib.load(filename)
# predict on test set
G0_test = self.snpreader_whole[test_idx,:]
covariate_test = self.covariate_whole[test_idx,:]
predicted_pheno, covar = fastlmm2.predict(K0_whole_test=G0_test, K1_whole_test=G0_test, X=covariate_test,count_A1=False)
output_file = self.file_name("one")
Dat.write(output_file,predicted_pheno)
pheno_actual = self.pheno_whole[test_idx,:].read().val[:,0]
#pylab.plot(pheno_actual, predicted_pheno.val,".")
#pylab.show()
self.compare_files(predicted_pheno,"one")
def test_lr(self):
import matplotlib.pyplot as plt
import pylab
logging.info("TestLmmTrain test_lr")
train_idx = np.r_[10:self.snpreader_whole.iid_count] # iids 10 and on
test_idx = np.r_[0:10] # the first 10 iids
G0_train = self.snpreader_whole[train_idx,:]
covariate_train3 = self.covariate_whole[train_idx,:].read()
covariate_train3.val = np.array([[float(num)] for num in xrange(covariate_train3.iid_count)])
pheno_train3 = self.pheno_whole[train_idx,:].read()
np.random.seed(0)
pheno_train3.val = covariate_train3.val * 2.0 + 100 + np.random.normal(size=covariate_train3.val.shape) # y = 2*x+100+normal(0,1)
##Plot training x and y
#pylab.plot(covariate_train3.val, pheno_train3.val,".")
#pylab.show()
for force_full_rank,force_low_rank in [(True,False),(False,True)]:
#Learn model, save, load
fastlmm3x = FastLMM(force_full_rank=force_full_rank,force_low_rank=force_low_rank,GB_goal=2).fit(K0_train=G0_train, X=covariate_train3, y=pheno_train3)
filename = self.tempout_dir + "/model_lr.flm.p"
pstutil.create_directory_if_necessary(filename)
joblib.dump(fastlmm3x, filename)
fastlmm3 = joblib.load(filename)
#Predict with model (test on train)
predicted_pheno, covar = fastlmm3.predict(K0_whole_test=G0_train, X=covariate_train3,count_A1=False) #test on train
output_file = self.file_name("lr")
Dat.write(output_file,predicted_pheno)
## Plot training x and y, and training x with predicted y
#do_plot = True
#if do_plot:
# pylab.plot(covariate_train3.val, pheno_train3.val,covariate_train3.val,predicted_pheno.val,".")
# pylab.show()
# # Plot y and predicted y (test on train)
# pheno_actual = pheno_train3.val[:,0]
# pylab.plot(pheno_actual,predicted_pheno.val,".")
# pylab.show()
self.compare_files(predicted_pheno,"lr")
def test_lmm(self):
do_plot = False
iid_count = 500
seed = 0
import pylab
logging.info("TestLmmTrain test_lmm")
iid = [["cid{0}P{1}".format(iid_index,iid_index//250)]*2 for iid_index in xrange(iid_count)]
train_idx = np.r_[10:iid_count] # iids 10 and on
test_idx = np.r_[0:10] # the first 10 iids
#Every person is 100% related to everyone in one of 5 families
K0a = KernelData(iid=iid,val=np.empty([iid_count,iid_count]),name="related by distance")
for iid_index0 in xrange(iid_count):
for iid_index1 in xrange(iid_count):
K0a.val[iid_index0,iid_index1] = 1 if iid_index0 % 5 == iid_index1 % 5 else 0
if iid_index1 < iid_index0:
assert K0a.val[iid_index0,iid_index1] == K0a.val[iid_index1,iid_index0]
#every person lives on a line from 0 to 1
# They are related to every other person as a function of distance on the line
np.random.seed(seed)
home = np.random.random([iid_count])
K0b = KernelData(iid=iid,val=np.empty([iid_count,iid_count]),name="related by distance")
for iid_index in xrange(iid_count):
K0b.val[iid_index,:] = 1 - np.abs(home-home[iid_index])**.1
#make covar just numbers 0,1,...
covar = SnpData(iid=iid,sid=["x"],val=np.array([[float(num)] for num in xrange(iid_count)]))
covariate_train = covar[train_idx,:].read()
covariate_test = covar[test_idx,:].read()
for name, h2, K0 in [("clones", 1, K0a),("line_world",.75,K0b)]:
sigma2x = 100
varg = sigma2x * h2
vare = sigma2x * (1-h2)
#######################################################################
#make pheno # pheno = 2*covar+100+normal(0,1)*2.5+normal(0,K)*7.5
#######################################################################
#random.multivariate_normal is sensitive to mkl_num_thread, so we control it.
if 'MKL_NUM_THREADS' in os.environ:
mkl_num_thread = os.environ['MKL_NUM_THREADS']
else:
mkl_num_thread = None
os.environ['MKL_NUM_THREADS'] = '1'
np.random.seed(seed)
p1 = covar.val * 2.0 + 100
p2 = np.random.normal(size=covar.val.shape)*np.sqrt(vare)
p3 = (np.random.multivariate_normal(np.zeros(iid_count),K0.val)*np.sqrt(varg)).reshape(-1,1)
if mkl_num_thread is not None:
os.environ['MKL_NUM_THREADS'] = mkl_num_thread
else:
del os.environ['MKL_NUM_THREADS']
pheno = SnpData(iid=iid,sid=["pheno0"],val= p1 + p2 + p3)
pheno_train = pheno[train_idx,:].read()
pheno_test = pheno[test_idx,:].read()
if do_plot:
#Plot training x and y, testing x and y
pylab.plot(covariate_train.val, pheno_train.val,".",covariate_test.val, pheno_test.val,".")
pylab.suptitle(name + ": Plot training x and y, testing x and y")
pylab.show()
Xtrain = np.c_[covariate_train.val,np.ones((covariate_train.iid_count,1))]
Xtest = np.c_[covariate_test.val,np.ones((covariate_test.iid_count,1))]
lsqSol = np.linalg.lstsq(Xtrain, pheno_train.val[:,0],rcond=-1)
bs=lsqSol[0] #weights
r2=lsqSol[1] #squared residuals
D=lsqSol[2] #rank of design matrix
N=pheno_train.iid_count
REML = False
if not REML:
sigma2 = float(r2/N)
nLL = N*0.5*np.log(2*np.pi*sigma2) + N*0.5
else:
sigma2 = float(r2 / (N-D))
nLL = N*0.5*np.log(2*np.pi*sigma2) + 0.5/sigma2*r2;
nLL -= 0.5*D*np.log(2*np.pi*sigma2);#REML term
predicted = Xtest.dot(bs)
yerr = [np.sqrt(sigma2)] * len(predicted)
if do_plot:
pylab.plot(covariate_test.val, pheno_test.val,"g.",covariate_test.val, predicted,"r.")
pylab.xlim([-1, 10])
pylab.errorbar(covariate_test.val, predicted,yerr,linestyle='None')
pylab.suptitle(name + ": real linear regression: actual to prediction")
pylab.show()
for factor in [1,100,.02]:
K0 = K0.read()
K0.val *= factor
K0_train = K0[train_idx]
K0_whole_test = K0[:,test_idx]
#Learn model, save, load
fastlmmx = FastLMM(GB_goal=2).fit(K0_train=K0_train, X=covariate_train, y=pheno_train)
v2 = np.var(p2)
v3 = np.var(p3)
logging.debug("Original h2 of {0}. Generated h2 of {1}. Learned h2 of {2}".format(h2, v3/(v2+v3), fastlmmx.h2raw))
filename = self.tempout_dir + "/model_lmm.flm.p"
pstutil.create_directory_if_necessary(filename)
joblib.dump(fastlmmx, filename)
fastlmm = joblib.load(filename)
do_test_on_train = True
if do_test_on_train:
#Predict with model (test on train)
predicted_pheno, covar_pheno = fastlmm.predict(K0_whole_test=K0_train, X=covariate_train,count_A1=False) #test on train
output_file = self.file_name("lmma_"+name)
Dat.write(output_file,predicted_pheno)
covar2 = SnpData(iid=covar_pheno.row,sid=covar_pheno.col[:,1],val=covar_pheno.val) #kludge to write kernel to text format
output_file = self.file_name("lmma.cov_"+name)
Dat.write(output_file,covar2)
yerr = np.sqrt(np.diag(covar_pheno.val))
predicted = predicted_pheno.val
if do_plot:
pylab.plot(covariate_train.val, pheno_train.val,"g.",covariate_train.val, predicted,"r.")
pylab.xlim([0, 50])
pylab.ylim([100, 200])
pylab.errorbar(covariate_train.val, predicted,yerr,linestyle='None')
pylab.suptitle(name+": test on train: train X to true target (green) and prediction (red)")
pylab.show()
self.compare_files(predicted_pheno,"lmma_"+name)
self.compare_files(covar2,"lmma.cov_"+name)
predicted_pheno0, covar_pheno0 = fastlmm.predict(K0_whole_test=K0_train[:,0], X=covariate_train[0,:],count_A1=False) #test on train #0
assert np.abs(predicted_pheno0.val[0,0] - predicted_pheno.val[0,0]) < 1e-6, "Expect a single case to get the same prediction as a set of cases"
assert np.abs(covar_pheno0.val[0,0] - covar_pheno.val[0,0]) < 1e-6, "Expect a single case to get the same prediction as a set of cases"
#Predict with model (test on test)
predicted_phenoB, covar_phenoB = fastlmm.predict(K0_whole_test=K0_whole_test, X=covariate_test,count_A1=False) #test on test
output_file = self.file_name("lmmb_"+name)
Dat.write(output_file,predicted_phenoB)
covar2 = SnpData(iid=covar_phenoB.row,sid=covar_phenoB.col[:,1],val=covar_phenoB.val) #kludge to write kernel to text format
output_file = self.file_name("lmmb.cov_"+name)
Dat.write(output_file,covar2)
yerr = np.sqrt(np.diag(covar_phenoB.val))
predicted = predicted_phenoB.val
if do_plot:
pylab.plot(covariate_test.val, pheno_test.val,"g.",covariate_test.val, predicted,"r.")
pylab.xlim([-1, 10])
pylab.errorbar(covariate_test.val, predicted,yerr,linestyle='None')
pylab.suptitle(name+": test on test: test X to true target (green) and prediction (red)")
pylab.show()
self.compare_files(predicted_phenoB,"lmmb_"+name)
self.compare_files(covar2,"lmmb.cov_"+name)
predicted_phenoB0, covar_phenoB0 = fastlmm.predict(K0_whole_test=K0_whole_test[:,0], X=covariate_test[0,:],count_A1=False) #test on a single test case
assert np.abs(predicted_phenoB0.val[0,0] - predicted_phenoB.val[0,0]) < 1e-6, "Expect a single case to get the same prediction as a set of cases"
assert np.abs(covar_phenoB0.val[0,0] - covar_phenoB.val[0,0]) < 1e-6, "Expect a single case to get the same prediction as a set of cases"
#Predict with model test on some train and some test
some_idx = range(covar.iid_count)
some_idx.remove(train_idx[0])
some_idx.remove(test_idx[0])
covariate_some = covar[some_idx,:]
K0_whole_some = K0[:,some_idx]
predicted_phenoC, covar_phenoC = fastlmm.predict(K0_whole_test=K0_whole_some, X=covariate_some,count_A1=False)
for idxC, iidC in enumerate(predicted_phenoC.iid):
meanC = predicted_phenoC.val[idxC]
varC = covar_phenoC.val[idxC,idxC]
if iidC in predicted_pheno.iid:
predicted_pheno_ref = predicted_pheno
covar_pheno_ref = covar_pheno
else:
assert iidC in predicted_phenoB.iid
predicted_pheno_ref = predicted_phenoB
covar_pheno_ref = covar_phenoB
idx_ref = predicted_pheno_ref.iid_to_index([iidC])[0]
mean_ref = predicted_pheno_ref.val[idx_ref]
var_ref = covar_pheno_ref.val[idx_ref,idx_ref]
assert np.abs(meanC - mean_ref) < 1e-6
assert np.abs(varC - var_ref) < 1e-6
def test_snps(self):
logging.info("TestLmmTrain test_snps")
train_idx = np.r_[10:self.snpreader_whole.iid_count] # iids 10 and on
test_idx = np.r_[0:10] # the first 10 iids
# Show it using the snps
G0_train = self.snpreader_whole[train_idx,:]
covariate_train3 = self.covariate_whole[train_idx,:].read()
pheno_train3 = self.pheno_whole[train_idx,:].read()
pheno_train3.val = G0_train[:,0:1].read().val*2
#pylab.plot(G0_train[:,0:1].read().val[:,0], pheno_train3.val[:,0],".")
#pylab.show()
#Learn model, save, load
fastlmm3x = FastLMM(GB_goal=2).fit(K0_train=G0_train, X=covariate_train3, y=pheno_train3)
filename = self.tempout_dir + "/model_snps.flm.p"
pstutil.create_directory_if_necessary(filename)
joblib.dump(fastlmm3x, filename)
fastlmm3 = joblib.load(filename)
#Predict with model (test on train)
predicted_pheno, covar = fastlmm3.predict(K0_whole_test=G0_train, X=covariate_train3,count_A1=False) #test on train
output_file = self.file_name("snps")
Dat.write(output_file,predicted_pheno)
### Plot training x and y, and training x with predicted y
#pylab.plot(G0_train[:,0:1].read().val[:,0], pheno_train3.val,".",G0_train[:,0:1].read().val[:,0],predicted_pheno.val,".")
#pylab.show()
### Plot y and predicted y (test on train)
#pheno_actual = pheno_train3.val[:,0]
#pylab.plot(pheno_actual,predicted_pheno.val,".")
#pylab.show()
self.compare_files(predicted_pheno,"snps")
def test_kernel(self):
logging.info("TestLmmTrain test_kernel")
train_idx = np.r_[10:self.snpreader_whole.iid_count] # iids 10 and on
test_idx = np.r_[0:10] # the first 10 iids
# Show it using the snps
K0_train = self.snpreader_whole[train_idx,:].read_kernel(Unit())
covariate_train3 = self.covariate_whole[train_idx,:].read()
pheno_train3 = self.pheno_whole[train_idx,:].read()
pheno_train3.val = self.snpreader_whole[train_idx,0:1].read().val*2
assert np.array_equal(K0_train.iid,covariate_train3.iid), "Expect iids to be the same (so that early and late Unit standardization will give the same result)"
assert np.array_equal(K0_train.iid,pheno_train3.iid), "Expect iids to be the same (so that early and late Unit standardization will give the same result)"
#pylab.plot(G0_train[:,0:1].read().val[:,0], pheno_train3.val[:,0],".")
#pylab.show()
#Learn model, save, load
fastlmm3x = FastLMM(GB_goal=2).fit(K0_train=K0_train, X=covariate_train3, y=pheno_train3)
filename = self.tempout_dir + "/model_snps.flm.p"
pstutil.create_directory_if_necessary(filename)
joblib.dump(fastlmm3x, filename)
fastlmm3 = joblib.load(filename)
#Predict with model (test on train)
predicted_pheno, covar = fastlmm3.predict(K0_whole_test=K0_train, X=covariate_train3,count_A1=False) #test on train
output_file = self.file_name("kernel")
Dat.write(output_file,predicted_pheno)
#### Plot training x and y, and training x with predicted y
#pylab.plot(self.snpreader_whole[train_idx,0:1].read().val[:,0], pheno_train3.val,".",self.snpreader_whole[train_idx,0:1].read().val[:,0],predicted_pheno.val,".")
#pylab.show()
#### Plot y and predicted y (test on train)
#pheno_actual = pheno_train3.val[:,0]
#pylab.plot(pheno_actual,predicted_pheno.val,".")
#pylab.show()
self.compare_files(predicted_pheno,"snps") #"kernel" and "snps" test cases should give the same results
def test_kernel_one(self):
logging.info("TestLmmTrain test_kernel_one")
train_idx = np.r_[10:self.snpreader_whole.iid_count] # iids 10 and on
test_idx = np.r_[0:10] # the first 10 iids
K0_train = SnpKernel(self.snpreader_whole[train_idx,:],standardizer=Unit())
covariate_train = self.covariate_whole[train_idx,:]
pheno_train = self.pheno_whole[train_idx,:]
assert np.array_equal(K0_train.iid,covariate_train.iid), "Expect iids to be the same (so that early and late Unit standardization will give the same result)"
assert np.array_equal(K0_train.iid,pheno_train.iid), "Expect iids to be the same (so that early and late Unit standardization will give the same result)"
fastlmm1 = FastLMM(GB_goal=2).fit(K0_train=K0_train, X=covariate_train, y=pheno_train)
filename = self.tempout_dir + "/model_kernel_one.flm.p"
pstutil.create_directory_if_necessary(filename)
joblib.dump(fastlmm1, filename)
fastlmm2 = joblib.load(filename)
# predict on test set
G0_test = self.snpreader_whole[test_idx,:]
covariate_test = self.covariate_whole[test_idx,:]
predicted_pheno, covar = fastlmm2.predict(K0_whole_test=G0_test, X=covariate_test,count_A1=False)
output_file = self.file_name("kernel_one")
Dat.write(output_file,predicted_pheno)
pheno_actual = self.pheno_whole[test_idx,:].read().val[:,0]
#pylab.plot(pheno_actual, predicted_pheno.val,".")
#pylab.show()
self.compare_files(predicted_pheno,"one") #Expect same results as SNPs "one"
def compare_files(self,answer,ref_base):
reffile = TestFeatureSelection.reference_file("fastlmm/"+ref_base+".dat")
reference=Dat(reffile).read()
assert np.array_equal(answer.col,reference.col), "sid differs. File '{0}'".format(reffile)
assert np.array_equal(answer.row,reference.row), "iid differs. File '{0}'".format(reffile)
for iid_index in xrange(reference.row_count):
for sid_index in xrange(reference.col_count):
a_v = answer.val[iid_index,sid_index]
r_v = reference.val[iid_index,sid_index]
assert abs(a_v - r_v) < 1e-4 or abs(a_v - r_v)/abs(r_v) < 1e5, "Value at {0},{1} differs too much from file '{2}'".format(iid_index,sid_index,reffile)
def test_doctest(self):
old_dir = os.getcwd()
os.chdir(os.path.dirname(os.path.realpath(__file__))+"/..")
result = doctest.testfile("../fastlmm_predictor.py")
os.chdir(old_dir)
assert result.failed == 0, "failed doc test: " + __file__
