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")