def test_two(self): #!!! rather a big test case
from pysnptools.util.mapreduce1.runner import Local, LocalMultiProc
logging.info("TestSingleSnpAllPlusSelect test_two")
do_plot = False
bed_fn = self.pythonpath + "/tests/datasets/synth/all.bed"
pheno_fn = self.pythonpath + "/tests/datasets/synth/pheno_10_causals.txt"
cov_fn = self.pythonpath + "/tests/datasets/synth/cov.txt"
# partition snps on chr5 vs rest
test_chr = 5
snp_reader = Bed(bed_fn, count_A1=False)
test_snps = snp_reader[:, snp_reader.pos[:, 0] == test_chr]
mf_name = "lmpl" #"lmpl" "local", "coreP", "nodeP", "socketP", "nodeE", "lmp"
runner = mf_to_runner_function(mf_name)(20)
output_file_name = self.file_name("two")
for GB_goal in [None, 2]:
results = single_snp_all_plus_select(
test_snps=test_snps,
G=bed_fn,
pheno=pheno_fn,
covar=cov_fn,
k_list=[int(k) for k in np.logspace(0, 7, base=2, num=7)],
n_folds=7,
seed=42,
do_plot=do_plot,
GB_goal=GB_goal,
output_file_name=output_file_name,
runner=runner,
count_A1=False)
logging.info(results.head())
self.compare_files(results, "two")
def test_notebook(self):
do_plot = False
mf_name = "lmp" #"local", "coreP", "nodeP", "socketP", "nodeE", "lmp"
runner = mf_to_runner_function(mf_name)(4)
output_file_name = self.file_name("notebook")
logging.info("TestSingleSnpAllPlusSelect test_one")
# define file names
snp_reader = Bed(self.pythonpath + "/tests/datasets/synth/all",
count_A1=False)
pheno_fn = self.pythonpath + "/tests/datasets/synth/pheno_10_causals.txt"
cov_fn = self.pythonpath + "/tests/datasets/synth/cov.txt"
# find the chr5 SNPs
test_snps = snp_reader[:, snp_reader.pos[:, 0] == 5]
#select the 2nd kernel and run GWAS
results = single_snp_all_plus_select(test_snps=test_snps,
G=snp_reader,
pheno=pheno_fn,
GB_goal=2,
do_plot=do_plot,
output_file_name=output_file_name,
runner=runner,
count_A1=False)
self.compare_files(results, "notebook")
def test_three(self): #!!! rather a big test case
from pysnptools.util.mapreduce1.runner import Local, LocalMultiProc
logging.info("TestSingleSnpAllPlusSelect test_three")
bed_fn = self.pythonpath + "/tests/datasets/synth/all.bed"
bed_fn = Bed(bed_fn, count_A1=False)
pheno_fn = self.pythonpath + "/tests/datasets/synth/pheno_10_causals.txt"
cov_fn = self.pythonpath + "/tests/datasets/synth/cov.txt"
mf_name = "lmp" #"local", "coreP", "nodeP", "socketP", "nodeE", "lmp"
runner = mf_to_runner_function(mf_name)(4)
output_file_name = self.file_name("three")
results = single_snp_all_plus_select(
test_snps=bed_fn,
pheno=pheno_fn,
covar=cov_fn,
k_list=[int(k) for k in np.logspace(0, 7, base=2, num=7)],
n_folds=7,
seed=42,
do_plot=False,
GB_goal=2,
output_file_name=output_file_name,
runner=runner,
count_A1=False)
logging.info(results)
self.compare_files(results, "three")
def test_three(self): #!!! rather a big test case
from fastlmm.util.runner import Local, HPC, LocalMultiProc
logging.info("TestSingleSnpAllPlusSelect test_three")
bed_fn = self.pythonpath + "/tests/datasets/synth/all.bed"
bed_fn = Bed(bed_fn)
pheno_fn = self.pythonpath + "/tests/datasets/synth/pheno_10_causals.txt"
cov_fn = self.pythonpath + "/tests/datasets/synth/cov.txt"
mf_name = "lmp" #"local", "coreP", "nodeP", "socketP", "nodeE", "lmp"
runner = mf_to_runner_function(mf_name)(4)
output_file_name = self.file_name("three")
results = single_snp_all_plus_select(test_snps=bed_fn, pheno=pheno_fn,
covar=cov_fn,
k_list = [int(k) for k in np.logspace(0, 7, base=2, num=7)],
n_folds=7,
seed = 42,
do_plot=False,
GB_goal=2,
output_file_name=output_file_name,
runner = runner
)
logging.info(results)
self.compare_files(results,"three")
def test_two(self): #!!! rather a big test case
from fastlmm.util.runner import Local, HPC, LocalMultiProc
logging.info("TestSingleSnpAllPlusSelect test_two")
do_plot = False
bed_fn = self.pythonpath + "/tests/datasets/synth/all.bed"
pheno_fn = self.pythonpath + "/tests/datasets/synth/pheno_10_causals.txt"
cov_fn = self.pythonpath + "/tests/datasets/synth/cov.txt"
# partition snps on chr5 vs rest
test_chr = 5
snp_reader = Bed(bed_fn)
test_snps = snp_reader[:,snp_reader.pos[:,0] == test_chr]
mf_name = "lmpl" #"lmpl" "local", "coreP", "nodeP", "socketP", "nodeE", "lmp"
runner = mf_to_runner_function(mf_name)(20)
output_file_name = self.file_name("two")
for GB_goal in [None,2]:
results = single_snp_all_plus_select(test_snps=test_snps, G=bed_fn, pheno=pheno_fn,
covar=cov_fn,
k_list = [int(k) for k in np.logspace(0, 7, base=2, num=7)],
n_folds=7,
seed = 42,
do_plot=do_plot,
GB_goal=GB_goal,
output_file_name=output_file_name,
runner = runner
)
logging.info(results.head())
self.compare_files(results,"two")
def too_slow_test_notebook(self):
do_plot = False
runner = LocalMultiProc(multiprocessing.cpu_count(), mkl_num_threads=2)
output_file_name = self.file_name("notebook")
logging.info("TestSingleSnpAllPlusSelect test_notebook")
# define file names
snp_reader = Bed(self.pythonpath + "/tests/datasets/synth/all.bed",
count_A1=False)
pheno_fn = self.pythonpath + "/tests/datasets/synth/pheno_10_causals.txt"
cov_fn = self.pythonpath + "/tests/datasets/synth/cov.txt"
# find the chr5 SNPs
test_snps = snp_reader[:, snp_reader.pos[:, 0] == 5]
#select the 2nd kernel and run GWAS
results = single_snp_all_plus_select(test_snps=test_snps,
G=snp_reader,
pheno=pheno_fn,
GB_goal=2,
do_plot=do_plot,
output_file_name=output_file_name,
runner=runner,
count_A1=False)
self.compare_files(results, "notebook")
def test_one(self):
from fastlmm.util.runner import Local, HPC, LocalMultiProc
logging.info("TestSingleSnpAllPlusSelect test_one")
snps = self.bedbase
pheno = self.phen_fn
covar = self.cov_fn
output_file_name = self.file_name("one")
results = single_snp_all_plus_select(test_snps=snps, pheno=pheno,
covar=covar,
k_list = np.logspace(start=0, stop=1, num=2, base=2),
n_folds=2,
do_plot=False,
output_file_name = output_file_name,
GB_goal=2,
#runner = LocalMultiProc(taskcount=20,mkl_num_threads=5,just_one_process=True)
)
self.compare_files(results,"one")
def test_one(self):
logging.info("TestSingleSnpAllPlusSelect test_one")
snps = self.bedbase
pheno = self.phen_fn
covar = self.cov_fn
output_file_name = self.file_name("one")
results = single_snp_all_plus_select(
test_snps=snps,
pheno=pheno,
covar=covar,
k_list=np.logspace(start=0, stop=1, num=2, base=2),
n_folds=2,
do_plot=False,
output_file_name=output_file_name,
GB_goal=2,
#runner = LocalMultiProc(taskcount=20,mkl_num_threads=5,just_one_process=True)
count_A1=False)
self.compare_files(results, "one")
def test_notebook(self):
do_plot = False
mf_name = "lmp" #"local", "coreP", "nodeP", "socketP", "nodeE", "lmp"
runner = mf_to_runner_function(mf_name)(4)
output_file_name = self.file_name("notebook")
logging.info("TestSingleSnpAllPlusSelect test_one")
# define file names
snp_reader = Bed(self.pythonpath + "/tests/datasets/synth/all")
pheno_fn = self.pythonpath + "/tests/datasets/synth/pheno_10_causals.txt"
cov_fn = self.pythonpath + "/tests/datasets/synth/cov.txt"
# find the chr5 SNPs
test_snps = snp_reader[:,snp_reader.pos[:,0] == 5]
#select the 2nd kernel and run GWAS
results = single_snp_all_plus_select(test_snps=test_snps,G=snp_reader,pheno=pheno_fn,GB_goal=2,do_plot=do_plot,output_file_name=output_file_name,runner=runner)
self.compare_files(results,"notebook")
def too_slow_test_three(self):
logging.info("TestSingleSnpAllPlusSelect test_three")
bed_fn = self.pythonpath + "/tests/datasets/synth/all.bed"
bed_fn = Bed(bed_fn, count_A1=False)
pheno_fn = self.pythonpath + "/tests/datasets/synth/pheno_10_causals.txt"
cov_fn = self.pythonpath + "/tests/datasets/synth/cov.txt"
runner = LocalMultiProc(multiprocessing.cpu_count(), mkl_num_threads=2)
output_file_name = self.file_name("three")
results = single_snp_all_plus_select(
test_snps=bed_fn,
pheno=pheno_fn,
covar=cov_fn,
k_list=[int(k) for k in np.logspace(0, 7, base=2, num=7)],
n_folds=7,
seed=42,
do_plot=False,
GB_goal=2,
output_file_name=output_file_name,
runner=runner,
count_A1=False)
logging.info(results)
self.compare_files(results, "three")
