def setUp(self): self.set_up() self.unordered_path = package_paths.data_path( 'div-model-results-unordered.txt') self.ordered_path = package_paths.data_path( 'div-model-results-ordered.txt') self.post_ordered_path = package_paths.data_path( os.path.join('posterior-sample.txt.gz'))
def test_modified_sample_table_error(self): observed_config = package_paths.data_path('ambig_config1.cfg') prior_config = package_paths.data_path('ambig_config2.cfg') args = ['-o', observed_config, '-p', prior_config, ] self.assertRaises(errors.SampleTableError, self.exe_main_dmc, args) shutil.move(observed_config + '.orig', observed_config)
def setUp(self): self.set_up() self.test_path = self.get_test_path() self.cfg_path = package_paths.data_path('4pairs_1locus.cfg') self.gz_path = package_paths.data_path( 'abctoolbox_posterior_density_file.txt.gz') self.ungz_path = package_paths.data_path( 'abctoolbox_posterior_density_file.txt')
def setUp(self): self.set_up() self.cfg_path = package_paths.data_path('negros_panay.cfg') self.new_cfg_path = package_paths.data_path('negros_panay_new.cfg') self.sum_stats_path = package_paths.data_path( 'negros_panay_sum_stats_sort0.txt') self.prior_path = package_paths.data_path( 'negros_panay_new_prior_sample_10.txt') self.posterior_path = package_paths.data_path( 'posterior-sample.txt.gz')
def test_modified_sample_table_error(self): observed_config = package_paths.data_path('ambig_config1.cfg') prior_config = package_paths.data_path('ambig_config2.cfg') args = [ '-o', observed_config, '-p', prior_config, ] self.assertRaises(errors.SampleTableError, self.exe_main_dmc, args) shutil.move(observed_config + '.orig', observed_config)
def setUp(self): self.set_up() self.ordered_path = package_paths.data_path( os.path.join('posterior-sample.txt.gz')) post = parsing.parse_parameters(self.ordered_path) self.partition_collection = pymsbayes.utils.stats.PartitionCollection( post['taus'])
def setUp(self): self.info_path = os.path.join(package_paths.TEST_DATA_DIR, 'pymsbayes-results', 'pymsbayes-info.txt') self.prior_configs = { 1: package_paths.data_path('negros_panay_3pairs_new_dpp.cfg'), 2: package_paths.data_path('negros_panay_3pairs_new_uniform.cfg'), 3: package_paths.data_path('negros_panay_3pairs_new_ushaped.cfg'), } self.observed_configs = self.prior_configs self.observed_paths = { 1: os.path.join(package_paths.TEST_DATA_DIR, 'pymsbayes-results', 'observed-summary-stats', 'observed-1.txt'), 2: os.path.join(package_paths.TEST_DATA_DIR, 'pymsbayes-results', 'observed-summary-stats', 'observed-2.txt'), 3: os.path.join(package_paths.TEST_DATA_DIR, 'pymsbayes-results', 'observed-summary-stats', 'observed-3.txt'), }
def test_diff_sample_table_error(self): observed_config = package_paths.data_path('negros_panay_new.cfg') prior_config = package_paths.data_path('negros_panay_3pairs.cfg') args = ['-o', observed_config, '-p', prior_config, '-r', '1', ] self.assertRaises(errors.SampleTableError, self.exe_main_dmc, args) args = ['-o', observed_config, '-p', prior_config, ] self.assertRaises(errors.SampleTableError, self.exe_main_dmc, args) prior_config = package_paths.data_path('negros_panay_new_diff.cfg') args = ['-o', observed_config, '-p', prior_config, '-r', '1', ] self.assertRaises(errors.SampleTableError, self.exe_main_dmc, args) args = ['-o', observed_config, '-p', prior_config, ] self.assertRaises(errors.SampleTableError, self.exe_main_dmc, args)
def test_diff_sample_table_error(self): observed_config = package_paths.data_path('negros_panay_new.cfg') prior_config = package_paths.data_path('negros_panay_3pairs.cfg') args = [ '-o', observed_config, '-p', prior_config, '-r', '1', ] self.assertRaises(errors.SampleTableError, self.exe_main_dmc, args) args = [ '-o', observed_config, '-p', prior_config, ] self.assertRaises(errors.SampleTableError, self.exe_main_dmc, args) prior_config = package_paths.data_path('negros_panay_new_diff.cfg') args = [ '-o', observed_config, '-p', prior_config, '-r', '1', ] self.assertRaises(errors.SampleTableError, self.exe_main_dmc, args) args = [ '-o', observed_config, '-p', prior_config, ] self.assertRaises(errors.SampleTableError, self.exe_main_dmc, args)
def setUp(self): self.set_up() self.cfg_path = package_paths.data_path('4pairs_1locus.cfg') self.cfg_path2 = package_paths.data_path('4pairs_1locus_maxt5.cfg') self.np_new_cfg = package_paths.data_path('negros_panay_new.cfg') self.np_new_sps_cfg = package_paths.data_path('negros_panay_new_subs_per_site.cfg') self.np_cfg = package_paths.data_path('negros_panay_timescale.cfg') self.np_sps_cfg = package_paths.data_path('negros_panay_timescale_subs_per_site.cfg') self.seed = GLOBAL_RNG.randint(1, 999999999) self.rng = random.Random() self.rng.seed(self.seed) self.output_dir = self.get_test_subdir(prefix='dmc-test-') self.output_prefix = self.temp_fs.token_id
def setUp(self): self.set_up() self.cfg_path = package_paths.data_path('4pairs_1locus.cfg') self.cfg_path2 = package_paths.data_path('4pairs_1locus_maxt5.cfg') self.np_new_cfg = package_paths.data_path('negros_panay_new.cfg') self.np_new_sps_cfg = package_paths.data_path( 'negros_panay_new_subs_per_site.cfg') self.np_cfg = package_paths.data_path('negros_panay_timescale.cfg') self.np_sps_cfg = package_paths.data_path( 'negros_panay_timescale_subs_per_site.cfg') self.seed = GLOBAL_RNG.randint(1, 999999999) self.rng = random.Random() self.rng.seed(self.seed) self.output_dir = self.get_test_subdir(prefix='dmc-test-') self.output_prefix = self.temp_fs.token_id
def setUp(self): self.set_up() self.test_path = self.get_test_path() self.cfg_path = package_paths.data_path('4pairs_1locus.cfg')
def setUp(self): self.file = package_paths.data_path("4pairs_1locus.cfg") self.bogus_file = package_paths.data_path("bogusdatafilename") self.exe = ToolPathManager.get_tool_path('eureject')
def setUp(self): self.new_cfg_path = package_paths.data_path('negros_panay_new.cfg')
def setUp(self): self.set_up() self.pdf_path = package_paths.data_path( 'abctoolbox_posterior_density_file.txt')
def setUp(self): self.set_up() self.psf_path = package_paths.data_path( 'abctoolbox_posterior_summary_file.txt')
def test_time_scale_old_multi_locus(self): cu_cfg_path = package_paths.data_path('4pairs_5loci_old_cu_time.cfg') args = ['-o', cu_cfg_path, '-p', cu_cfg_path, '-r', 1, '-n', 400, '--num-posterior-samples', 200, '--num-standardizing-samples', 300, '-q', 100, '--np', 4, '--seed', self.seed, '--debug'] self._exe_dmc(args, return_code=0) results1 = self.get_result_paths(1, 'm1', 1, 400) self.assertTrue(os.path.exists(results1['prior-dir'])) self.assertTrue(os.path.exists(results1['sample'])) out_dir1 = self.get_test_subdir(prefix='sps-') sps_cfg_path = package_paths.data_path('4pairs_5loci_old_sps_time.cfg') args = ['-o', sps_cfg_path, '-p', sps_cfg_path, '-r', 1, '-n', 400, '--num-posterior-samples', 200, '--num-standardizing-samples', 300, '-q', 100, '--np', 4, '--seed', self.seed, '--debug'] self._exe_dmc(args, return_code=0, output_dir = out_dir1) results2 = self.get_result_paths(1, 'm1', 1, 400, output_dir = out_dir1) self.assertTrue(os.path.exists(results2['prior-dir'])) self.assertTrue(os.path.exists(results2['sample'])) results_old = configobj.ConfigObj(results1['summary']) results_sps = configobj.ConfigObj(results2['summary']) old_times = self.get_value_list(results1['sample']) sps_times = self.get_value_list(results2['sample']) old_pis = self.get_value_list(results1['sample'], 'pi.') sps_pis = self.get_value_list(results2['sample'], 'pi.') old_pi_bs = self.get_value_list(results1['sample'], 'pi.net.') sps_pi_bs = self.get_value_list(results2['sample'], 'pi.net.') mean_theta = 0.01 self.assertEqual(len(old_times), len(sps_times)) for i in range(len(old_times)): self.assertAlmostEqual( self.convert_time(t = old_times[i], mean_theta = mean_theta, mu = 1.0), self.convert_sps_time(t = sps_times[i], mu = 1.0), places = 7) self.assertAlmostEqual(old_pis[i], sps_pis[i]) self.assertAlmostEqual(old_pi_bs[i], sps_pi_bs[i]) self.assertAlmostEqual( self.convert_time(t = float(results_old['PRI.E.t']['mean']), mean_theta = mean_theta, mu = 1.0), self.convert_sps_time(t = float(results_sps['PRI.E.t']['mean']), mu = 1.0), places = 7) self.assertAlmostEqual( self.convert_time(t = float(results_old['PRI.E.t']['mean']), mean_theta = mean_theta, mu = 1e-8), self.convert_sps_time(t = float(results_sps['PRI.E.t']['mean']), mu = 1e-8), places = 3) self.assertAlmostEqual( self.convert_time(t = float(results_old['PRI.E.t']['median']), mean_theta = mean_theta, mu = 1.0), self.convert_sps_time(t = float(results_sps['PRI.E.t']['median']), mu = 1.0), places = 7) self.assertAlmostEqual( self.convert_time(t = float(results_old['PRI.omega']['median']), mean_theta = mean_theta, mu = 1.0), self.convert_sps_time(t = float(results_sps['PRI.omega']['median']), mu = 1.0), places = 7) self.assertAlmostEqual( self.convert_time(t = float(results_old['PRI.E.t']['range'][0]), mean_theta = mean_theta, mu = 1.0), self.convert_sps_time(t = float(results_sps['PRI.E.t']['range'][0]), mu = 1.0), places = 7) self.assertAlmostEqual( self.convert_time(t = float(results_old['PRI.E.t']['range'][1]), mean_theta = mean_theta, mu = 1.0), self.convert_sps_time(t = float(results_sps['PRI.E.t']['range'][1]), mu = 1.0), places = 7) self.assertAlmostEqual( self.convert_time(t = float(results_old['PRI.omega']['range'][0]), mean_theta = mean_theta, mu = 1.0), self.convert_sps_time(t = float(results_sps['PRI.omega']['range'][0]), mu = 1.0), places = 7) self.assertAlmostEqual( self.convert_time(t = float(results_old['PRI.omega']['range'][1]), mean_theta = mean_theta, mu = 1.0), self.convert_sps_time(t = float(results_sps['PRI.omega']['range'][1]), mu = 1.0), places = 7)
def setUp(self): self.dir = package_paths.data_path() self.file = package_paths.data_path("4pairs_1locus.cfg")
def test_time_scale_old_multi_locus(self): cu_cfg_path = package_paths.data_path('4pairs_5loci_old_cu_time.cfg') args = [ '-o', cu_cfg_path, '-p', cu_cfg_path, '-r', 1, '-n', 400, '--num-posterior-samples', 200, '--num-standardizing-samples', 300, '-q', 100, '--np', 4, '--seed', self.seed, '--debug' ] self._exe_dmc(args, return_code=0) results1 = self.get_result_paths(1, 'm1', 1, 400) self.assertTrue(os.path.exists(results1['prior-dir'])) self.assertTrue(os.path.exists(results1['sample'])) out_dir1 = self.get_test_subdir(prefix='sps-') sps_cfg_path = package_paths.data_path('4pairs_5loci_old_sps_time.cfg') args = [ '-o', sps_cfg_path, '-p', sps_cfg_path, '-r', 1, '-n', 400, '--num-posterior-samples', 200, '--num-standardizing-samples', 300, '-q', 100, '--np', 4, '--seed', self.seed, '--debug' ] self._exe_dmc(args, return_code=0, output_dir=out_dir1) results2 = self.get_result_paths(1, 'm1', 1, 400, output_dir=out_dir1) self.assertTrue(os.path.exists(results2['prior-dir'])) self.assertTrue(os.path.exists(results2['sample'])) results_old = configobj.ConfigObj(results1['summary']) results_sps = configobj.ConfigObj(results2['summary']) old_times = self.get_value_list(results1['sample']) sps_times = self.get_value_list(results2['sample']) old_pis = self.get_value_list(results1['sample'], 'pi.') sps_pis = self.get_value_list(results2['sample'], 'pi.') old_pi_bs = self.get_value_list(results1['sample'], 'pi.net.') sps_pi_bs = self.get_value_list(results2['sample'], 'pi.net.') mean_theta = 0.01 self.assertEqual(len(old_times), len(sps_times)) for i in range(len(old_times)): self.assertAlmostEqual(self.convert_time(t=old_times[i], mean_theta=mean_theta, mu=1.0), self.convert_sps_time(t=sps_times[i], mu=1.0), places=7) self.assertAlmostEqual(old_pis[i], sps_pis[i]) self.assertAlmostEqual(old_pi_bs[i], sps_pi_bs[i]) self.assertAlmostEqual( self.convert_time(t=float(results_old['PRI.E.t']['mean']), mean_theta=mean_theta, mu=1.0), self.convert_sps_time(t=float(results_sps['PRI.E.t']['mean']), mu=1.0), places=7) self.assertAlmostEqual( self.convert_time(t=float(results_old['PRI.E.t']['mean']), mean_theta=mean_theta, mu=1e-8), self.convert_sps_time(t=float(results_sps['PRI.E.t']['mean']), mu=1e-8), places=3) self.assertAlmostEqual( self.convert_time(t=float(results_old['PRI.E.t']['median']), mean_theta=mean_theta, mu=1.0), self.convert_sps_time(t=float(results_sps['PRI.E.t']['median']), mu=1.0), places=7) self.assertAlmostEqual( self.convert_time(t=float(results_old['PRI.omega']['median']), mean_theta=mean_theta, mu=1.0), self.convert_sps_time(t=float(results_sps['PRI.omega']['median']), mu=1.0), places=7) self.assertAlmostEqual( self.convert_time(t=float(results_old['PRI.E.t']['range'][0]), mean_theta=mean_theta, mu=1.0), self.convert_sps_time(t=float(results_sps['PRI.E.t']['range'][0]), mu=1.0), places=7) self.assertAlmostEqual( self.convert_time(t=float(results_old['PRI.E.t']['range'][1]), mean_theta=mean_theta, mu=1.0), self.convert_sps_time(t=float(results_sps['PRI.E.t']['range'][1]), mu=1.0), places=7) self.assertAlmostEqual(self.convert_time(t=float( results_old['PRI.omega']['range'][0]), mean_theta=mean_theta, mu=1.0), self.convert_sps_time(t=float( results_sps['PRI.omega']['range'][0]), mu=1.0), places=7) self.assertAlmostEqual(self.convert_time(t=float( results_old['PRI.omega']['range'][1]), mean_theta=mean_theta, mu=1.0), self.convert_sps_time(t=float( results_sps['PRI.omega']['range'][1]), mu=1.0), places=7)
def setUp(self): self.file = package_paths.data_path("4pairs_1locus.cfg") self.bogus_file = package_paths.data_path("bogusdatafilename")
def setUp(self): self.set_up() self.cfg_path = package_paths.data_path('4pairs_1locus.cfg') self.workq = multiprocessing.Queue() self.resultq = multiprocessing.Queue()