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 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.new_cfg_path = package_paths.data_path('negros_panay_new.cfg')
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 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()
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.file = package_paths.data_path("4pairs_1locus.cfg")
self.bogus_file = package_paths.data_path("bogusdatafilename")