def test_get_tool_path(self):
p = ToolPathManager.get_tool_path('more')
self.assertEqual(p, 'more')
for name in ['dpp-msbayes.pl', 'msbayes.pl', 'msprior', 'dpp-msprior',
'ABCestimator', 'regress_cli.r']:
p = ToolPathManager.get_tool_path(name)
self.assertEqual(p,
os.path.join(ToolPathManager._bin_dir, name))
def test_get_tool_path(self):
p = ToolPathManager.get_tool_path('more')
self.assertEqual(p, 'more')
for name in [
'dpp-msbayes.pl', 'msbayes.pl', 'msprior', 'dpp-msprior',
'ABCestimator', 'regress_cli.r'
]:
p = ToolPathManager.get_tool_path(name)
self.assertEqual(p, os.path.join(ToolPathManager._bin_dir, name))
def test_abcestimator(self):
summary_path = self.get_test_path(prefix='test-summary-')
post_path = self.get_test_path(prefix='test-posterior-')
with open(post_path, 'w') as out:
stream, close = fileio.process_file_arg(self.posterior_path)
for line in stream:
out.write('{0}'.format(line))
if close:
stream.close()
regress_posterior_path = self.get_test_path(prefix='test-adjusted-')
regress_worker = workers.ABCToolBoxRegressWorker(
temp_fs=self.temp_fs,
observed_path=self.sum_stats_path,
posterior_path=post_path,
parameter_indices=None,
regress_summary_path=summary_path,
regress_posterior_path=regress_posterior_path,
exe_path=None,
stdout_path=None,
stderr_path=None,
keep_temps=False,
bandwidth=None,
num_posterior_quantiles=100)
self.assertFalse(regress_worker.finished)
self.assertEqual(regress_worker.exe_path,
ToolPathManager.get_tool_path('ABCestimator'))
_LOG.info('{0}'.format(regress_worker.exe_path))
regress_worker.start()
self.assertTrue(regress_worker.finished)
self.assertTrue(os.path.isfile(regress_worker.regress_summary_path))
self.assertTrue(os.path.isfile(regress_worker.regress_posterior_path))
self.assertEqual(
self.get_number_of_lines(regress_worker.regress_posterior_path),
101)
def test_abcestimator(self):
summary_path = self.get_test_path(prefix='test-summary-')
post_path = self.get_test_path(prefix='test-posterior-')
with open(post_path, 'w') as out:
stream, close = fileio.process_file_arg(self.posterior_path)
for line in stream:
out.write('{0}'.format(line))
if close:
stream.close()
regress_posterior_path = self.get_test_path(prefix='test-adjusted-')
regress_worker = workers.ABCToolBoxRegressWorker(
temp_fs = self.temp_fs,
observed_path = self.sum_stats_path,
posterior_path = post_path,
parameter_indices = None,
regress_summary_path = summary_path,
regress_posterior_path = regress_posterior_path,
exe_path = None,
stdout_path = None,
stderr_path = None,
keep_temps = False,
bandwidth = None,
num_posterior_quantiles = 100)
self.assertFalse(regress_worker.finished)
self.assertEqual(regress_worker.exe_path,
ToolPathManager.get_tool_path('ABCestimator'))
_LOG.info('{0}'.format(regress_worker.exe_path))
regress_worker.start()
self.assertTrue(regress_worker.finished)
self.assertTrue(os.path.isfile(regress_worker.regress_summary_path))
self.assertTrue(os.path.isfile(regress_worker.regress_posterior_path))
self.assertEqual(self.get_number_of_lines(
regress_worker.regress_posterior_path), 101)
def test_dpp_msbayes(self):
w = workers.MsBayesWorker(temp_fs=self.temp_fs,
sample_size=2,
config_path=self.new_cfg_path,
schema='abctoolbox')
self.assertIsInstance(w, workers.MsBayesWorker)
self.assertFalse(w.finished)
self.assertEqual(w.exe_path,
ToolPathManager.get_tool_path('dpp-msbayes.pl'))
self.assertNotEqual(w.exe_path,
ToolPathManager.get_tool_path('msbayes.pl'))
_LOG.info('{0}'.format(w.exe_path))
w.start()
self._assert_msbayes_success(w, 9, 2)
self.assertEqual(w.exe_path,
ToolPathManager.get_tool_path('dpp-msbayes.pl'))
self.assertNotEqual(w.exe_path,
ToolPathManager.get_tool_path('msbayes.pl'))
def test_dpp_msbayes(self):
w = workers.MsBayesWorker(
temp_fs = self.temp_fs,
sample_size = 2,
config_path = self.new_cfg_path,
schema = 'abctoolbox')
self.assertIsInstance(w, workers.MsBayesWorker)
self.assertFalse(w.finished)
self.assertEqual(w.exe_path,
ToolPathManager.get_tool_path('dpp-msbayes.pl'))
self.assertNotEqual(w.exe_path,
ToolPathManager.get_tool_path('msbayes.pl'))
_LOG.info('{0}'.format(w.exe_path))
w.start()
self._assert_msbayes_success(w, 9, 2)
self.assertEqual(w.exe_path,
ToolPathManager.get_tool_path('dpp-msbayes.pl'))
self.assertNotEqual(w.exe_path,
ToolPathManager.get_tool_path('msbayes.pl'))
def test_obsSumStats(self):
ss_path = self.get_test_path(prefix='sum-stats')
ss_worker = workers.ObsSumStatsWorker(
temp_fs=self.temp_fs,
config_path=self.cfg_path,
output_path=ss_path,
exe_path=None,
schema='abctoolbox',
stat_patterns=parsing.DEFAULT_STAT_PATTERNS,
stderr_path=None,
tag=None)
self.assertFalse(ss_worker.finished)
self.assertEqual(ss_worker.exe_path,
ToolPathManager.get_tool_path('obsSumStats.pl'))
_LOG.info('{0}'.format(ss_worker.exe_path))
ss_worker.start()
self.assertTrue(ss_worker.finished)
self.assertSameFiles([ss_path, self.sum_stats_path])
def test_obsSumStats(self):
ss_path = self.get_test_path(prefix='sum-stats')
ss_worker = workers.ObsSumStatsWorker(
temp_fs = self.temp_fs,
config_path = self.cfg_path,
output_path = ss_path,
exe_path = None,
schema = 'abctoolbox',
stat_patterns = parsing.DEFAULT_STAT_PATTERNS,
stderr_path = None,
tag = None)
self.assertFalse(ss_worker.finished)
self.assertEqual(ss_worker.exe_path,
ToolPathManager.get_tool_path('obsSumStats.pl'))
_LOG.info('{0}'.format(ss_worker.exe_path))
ss_worker.start()
self.assertTrue(ss_worker.finished)
self.assertSameFiles([ss_path, self.sum_stats_path])
def test_eureject(self):
post_path = self.get_test_path(prefix='test-posterior-')
sum_out_path = self.get_test_path(prefix='test-summary-out-')
reject_worker = workers.EuRejectWorker(
temp_fs=self.temp_fs,
observed_path=self.sum_stats_path,
prior_paths=[self.prior_path],
num_posterior_samples=2,
num_standardizing_samples=10,
summary_in_path=None,
summary_out_path=sum_out_path,
posterior_path=post_path,
regression_worker=None,
exe_path=None,
stderr_path=None,
keep_temps=False,
tag='testcase')
self.assertFalse(reject_worker.finished)
self.assertEqual(reject_worker.exe_path,
ToolPathManager.get_tool_path('eureject'))
_LOG.info('{0}'.format(reject_worker.exe_path))
reject_worker.start()
self.assertTrue(reject_worker.finished)
self.assertTrue(os.path.isfile(reject_worker.posterior_path))
self.assertEqual(
self.get_number_of_lines(reject_worker.posterior_path), 3)
self.assertEqual(
self.get_number_of_header_lines(reject_worker.posterior_path), 1)
self.assertTrue(os.path.isfile(reject_worker.summary_out_path))
self.assertEqual(
self.get_number_of_lines(reject_worker.summary_out_path), 4)
self.assertEqual(
self.get_number_of_header_lines(reject_worker.summary_out_path), 1)
self.assertEqual(reject_worker.num_processed, 10)
self.assertEqual(reject_worker.num_summarized, 10)
self.assertEqual(reject_worker.num_retained, 2)
self.assertEqual(reject_worker.prior_paths,
reject_worker.rejection_files)
self.assertEqual(reject_worker.prior_paths,
reject_worker.standardizing_files)
self.assertFalse(os.path.exists(reject_worker.stderr_path))
self.assertFalse(os.path.exists(reject_worker.output_dir))
def test_eureject(self):
post_path = self.get_test_path(prefix='test-posterior-')
sum_out_path = self.get_test_path(prefix='test-summary-out-')
reject_worker = workers.EuRejectWorker(
temp_fs = self.temp_fs,
observed_path = self.sum_stats_path,
prior_paths = [self.prior_path],
num_posterior_samples = 2,
num_standardizing_samples = 10,
summary_in_path = None,
summary_out_path = sum_out_path,
posterior_path = post_path,
regression_worker = None,
exe_path = None,
stderr_path = None,
keep_temps = False,
tag = 'testcase')
self.assertFalse(reject_worker.finished)
self.assertEqual(reject_worker.exe_path,
ToolPathManager.get_tool_path('eureject'))
_LOG.info('{0}'.format(reject_worker.exe_path))
reject_worker.start()
self.assertTrue(reject_worker.finished)
self.assertTrue(os.path.isfile(reject_worker.posterior_path))
self.assertEqual(self.get_number_of_lines(
reject_worker.posterior_path), 3)
self.assertEqual(self.get_number_of_header_lines(
reject_worker.posterior_path), 1)
self.assertTrue(os.path.isfile(reject_worker.summary_out_path))
self.assertEqual(self.get_number_of_lines(
reject_worker.summary_out_path), 4)
self.assertEqual(self.get_number_of_header_lines(
reject_worker.summary_out_path), 1)
self.assertEqual(reject_worker.num_processed, 10)
self.assertEqual(reject_worker.num_summarized, 10)
self.assertEqual(reject_worker.num_retained, 2)
self.assertEqual(reject_worker.prior_paths,
reject_worker.rejection_files)
self.assertEqual(reject_worker.prior_paths,
reject_worker.standardizing_files)
self.assertFalse(os.path.exists(reject_worker.stderr_path))
self.assertFalse(os.path.exists(reject_worker.output_dir))
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")
self.exe = ToolPathManager.get_tool_path('eureject')
