def test_Config_file(self):
methods_needing_args = {
'inter_gene_max_space': [('set_1/Flagellum', 4),
('set_1/T2SS', 2)],
'max_nb_genes': [('set_1/Flagellum', 6), ('set_1/T3SS', 3)],
'min_genes_required': [('set_1/Flagellum', 8), ('set_1/T4SS', 4)],
'min_mandatory_genes_required': [('set_1/Flagellum', 12),
('set_1/T6SS', 6)],
'multi_loci': {'set_1/Flagellum', 'T4SS'}
}
self.parsed_args.cfg_file = self.find_data(
os.path.join('conf_files', 'macsy_models.conf'))
cfg = Config(self.defaults, self.parsed_args)
expected_values = {k: v for k, v in self.defaults.items()}
expected_values['cfg_file'] = self.parsed_args.cfg_file
expected_values.update(methods_needing_args)
for opt, val in expected_values.items():
if opt == 'out_dir':
self.assertEqual(
cfg.out_dir(),
os.path.join(cfg.res_search_dir(),
f'macsyfinder-{strftime("%Y%m%d_%H-%M-%S")}'))
elif opt == 'multi_loci':
self.assertTrue(cfg.multi_loci('set_1/Flagellum'))
self.assertTrue(cfg.multi_loci('set_1/T4SS'))
self.assertFalse(cfg.multi_loci('set_1/T6SS'))
elif opt in methods_needing_args:
for model, genes in expected_values[opt]:
self.assertEqual(getattr(cfg, opt)(model), genes)
else:
self.assertEqual(getattr(cfg, opt)(), val)
def test_Config_args(self):
methods_needing_args = {
'inter_gene_max_space': [('set_1/Flagellum', '14'),
('set_1/T2SS', '12')],
'max_nb_genes': [('set_1/Flagellum', '16'), ('set_1/T3SS', '13')],
'min_genes_required': [('set_1/Flagellum', '18'),
('set_1/T4SS', '14')],
'min_mandatory_genes_required': [('set_1/Flagellum', '22'),
('set_1/T6SS', '16')],
'multi_loci':
'set_1/Flagellum, set_1/T4SS',
}
for opt, value in methods_needing_args.items():
setattr(self.parsed_args, opt, value)
simple_opt = {
'hmmer': 'foo',
'i_evalue_sel': 20,
'replicon_topology': 'linear',
'db_type': 'gembase',
'sequence_db': self.find_data(os.path.join('base',
'test_1.fasta')),
'topology_file': __file__ # test only the existence of a file
}
for opt, val in simple_opt.items():
setattr(self.parsed_args, opt, val)
cfg = Config(self.defaults, self.parsed_args)
expected_values = {k: v for k, v in self.defaults.items()}
expected_values.update(methods_needing_args)
expected_values.update(simple_opt)
for opt, val in expected_values.items():
if opt == 'out_dir':
self.assertEqual(
cfg.out_dir(),
os.path.join(cfg.res_search_dir(),
f'macsyfinder-{strftime("%Y%m%d_%H-%M-%S")}'))
elif opt == 'multi_loci':
self.assertTrue(cfg.multi_loci('set_1/Flagellum'))
self.assertTrue(cfg.multi_loci('set_1/T4SS'))
self.assertFalse(cfg.multi_loci('set_1/T6SS'))
elif opt in methods_needing_args:
for model, genes in expected_values[opt]:
self.assertEqual(getattr(cfg, opt)(model), int(genes))
elif opt == 'models_dir':
self.assertEqual(
getattr(cfg, opt)(), self.defaults['system_models_dir'])
else:
self.assertEqual(
getattr(cfg, opt)(),
val,
msg=
f"{opt} failed: expected: val '{val}' != got '{getattr(cfg, opt)()}'"
)
def test_Config_file_n_args(self):
cfg_needing_args = {
'inter_gene_max_space': [('set_1/Flagellum', '4'),
('set_1/T2SS', '2')],
'max_nb_genes': [('set_1/Flagellum', '6'), ('set_1/T3SS', '3')],
'min_genes_required': [('set_1/Flagellum', '8'),
('set_1/T4SS', '4')],
'min_mandatory_genes_required': [('set_1/Flagellum', '12'),
('set_1/T6SS', '6')],
'multi_loci':
'set_1/Flagellum, set_1/T4SS',
}
self.parsed_args.cfg_file = self.find_data(
os.path.join('conf_files', 'macsy_models.conf'))
expected_values = {k: v for k, v in self.defaults.items()}
expected_values['cfg_file'] = self.parsed_args.cfg_file
expected_values.update(cfg_needing_args)
cmd_needing_args = {
'min_genes_required': [('set_1/Flagellum', 18), ('T4SS', 14)],
'min_mandatory_genes_required': [('set_1/Flagellum', 22),
('set_1/T6SS', 16)],
}
for opt, value in cmd_needing_args.items():
setattr(self.parsed_args, opt,
' '.join([f"{m} {v}" for m, v in value]))
simple_opt = {'hmmer': 'foo', 'i_evalue_sel': 20, 'db_type': 'gembase'}
for opt, val in simple_opt.items():
setattr(self.parsed_args, opt, val)
cfg = Config(self.defaults, self.parsed_args)
expected_values.update(cmd_needing_args)
expected_values.update(simple_opt)
for opt, exp_val in expected_values.items():
if opt == 'out_dir':
self.assertEqual(
cfg.out_dir(),
os.path.join(cfg.res_search_dir(),
f"macsyfinder-{strftime('%Y%m%d_%H-%M-%S')}"))
elif opt == 'multi_loci':
self.assertTrue(cfg.multi_loci('set_1/Flagellum'))
self.assertTrue(cfg.multi_loci('set_1/T4SS'))
self.assertFalse(cfg.multi_loci('set_1/T6SS'))
elif opt in cfg_needing_args:
for model, val in expected_values[opt]:
self.assertEqual(getattr(cfg, opt)(model), int(val))
elif opt == 'models_dir':
self.assertEqual(
getattr(cfg, opt)(), self.defaults['system_models_dir'])
else:
self.assertEqual(getattr(cfg, opt)(), exp_val)
def test_Config(self):
cfg = Config(self.defaults, self.parsed_args)
methods_needing_args = {
'inter_gene_max_space': None,
'max_nb_genes': None,
'min_genes_required': None,
'min_mandatory_genes_required': None,
'multi_loci': None
}
for opt, val in self.defaults.items():
if opt == 'out_dir':
self.assertEqual(
cfg.out_dir(),
os.path.join(cfg.res_search_dir(),
f'macsyfinder-{strftime("%Y%m%d_%H-%M-%S")}'))
elif opt == 'multi_loci':
self.assertFalse(cfg.multi_loci('whatever'))
elif opt in methods_needing_args:
self.assertEqual(
getattr(cfg, opt)('whatever'),
val,
msg=
f"test of '{opt}' failed : expected{getattr(cfg, opt)('whatever')} != got {val}"
)
else:
self.assertEqual(
getattr(cfg, opt)(),
val,
msg=
f"test of '{opt}' failed : expected{getattr(cfg, opt)()} != got {val}"
)
def test_Config_default_conf_file(self):
methods_needing_args = {
'inter_gene_max_space': [('set_1/Flagellum', 4),
('set_1/T2SS', 2)],
'max_nb_genes': [('set_1/Flagellum', 6), ('set_1/T3SS', 3)],
'min_genes_required': [('set_1/Flagellum', 8), ('set_1/T4SS', 4)],
'min_mandatory_genes_required': [('set_1/Flagellum', 12),
('set_1/T6SS', 6)],
'multi_loci': {'set_1/Flagellum', 'set_1/T4SS'}
}
with tempfile.TemporaryDirectory() as tmpdirname:
ori_conf_file = self.find_data(
os.path.join('conf_files', 'macsy_models.conf'))
dest_conf_file = os.path.join(tmpdirname, 'macsyfinder.conf')
shutil.copy(ori_conf_file, dest_conf_file)
os.environ['MACSY_CONF'] = dest_conf_file
virtual_env = os.environ.get("VIRTUAL_ENV")
del os.environ["VIRTUAL_ENV"]
try:
cfg = Config(self.defaults, self.parsed_args)
expected_values = {k: v for k, v in self.defaults.items()}
expected_values.update(methods_needing_args)
for opt, val in expected_values.items():
if opt == 'out_dir':
self.assertEqual(
cfg.out_dir(),
os.path.join(
cfg.res_search_dir(),
f'macsyfinder-{strftime("%Y%m%d_%H-%M-%S")}'))
elif opt == 'multi_loci':
self.assertTrue(cfg.multi_loci('set_1/Flagellum'))
self.assertTrue(cfg.multi_loci('set_1/T4SS'))
self.assertFalse(cfg.multi_loci('set_1/T6SS'))
elif opt in methods_needing_args:
for model, genes in expected_values[opt]:
self.assertEqual(getattr(cfg, opt)(model), genes)
elif opt == 'models_dir':
self.assertEqual(
getattr(cfg, opt)(),
self.defaults['system_models_dir'])
else:
self.assertEqual(getattr(cfg, opt)(), val)
finally:
os.environ["VIRTUAL_ENV"] = virtual_env
def test_project_config_file(self):
os.chdir(self.tmp_dir)
methods_needing_args = {
'inter_gene_max_space': [('set_1/Flagellum', 4),
('set_1/T2SS', 2)],
'max_nb_genes': [('set_1/Flagellum', 6), ('set_1/T3SS', 3)],
'min_genes_required': [('set_1/Flagellum', 8), ('set_1/T4SS', 4)],
'min_mandatory_genes_required': [('set_1/Flagellum', 12),
('set_1/T6SS', 6)],
'multi_loci': {'set_1/Flagellum', 'T4SS'}
}
hmmer_opts_in_file = {'coverage_profile': 0.8, 'e_value_search': 0.12}
try:
shutil.copyfile(
self.find_data(os.path.join('conf_files', 'project.conf')),
os.path.join(self.tmp_dir, 'macsyfinder.conf'))
cfg = Config(self.defaults, self.parsed_args)
expected_values = {k: v for k, v in self.defaults.items()}
expected_values.update(methods_needing_args)
expected_values.update(hmmer_opts_in_file)
for opt, val in expected_values.items():
if opt == 'out_dir':
self.assertEqual(
cfg.out_dir(),
os.path.join(
cfg.res_search_dir(),
f'macsyfinder-{strftime("%Y%m%d_%H-%M-%S")}'))
elif opt == 'multi_loci':
self.assertTrue(cfg.multi_loci('set_1/Flagellum'))
self.assertTrue(cfg.multi_loci('set_1/T4SS'))
self.assertFalse(cfg.multi_loci('set_1/T6SS'))
elif opt in methods_needing_args:
for model, genes in expected_values[opt]:
self.assertEqual(getattr(cfg, opt)(model), genes)
elif opt == 'models_dir':
self.assertEqual(
getattr(cfg, opt)(),
self.defaults['system_models_dir'])
else:
self.assertEqual(getattr(cfg, opt)(), val)
except:
os.chdir(self._current_dir)
class Test(unittest.TestCase):
_data_dir = os.path.join(os.path.dirname(__file__), "datatest")
def setUp(self):
l = logging.getLogger()
l.manager.loggerDict.clear()
if hasattr(self, 'cfg'):
try:
shutil.rmtree(self.cfg.working_dir)
except Exception as err:
pass
self.tmp_dir = tempfile.gettempdir()
def tearDown(self):
logging.shutdown()
l = logging.getLogger()
l.manager.loggerDict.clear()
if hasattr(self, 'cfg'):
try:
shutil.rmtree(self.cfg.working_dir)
except Exception as err:
pass
def test_build_indexes(self):
self.cfg = Config(cfg_file="nimportnaoik",
sequence_db=os.path.join(self._data_dir, "base",
"test_base.fa"),
db_type='gembase',
def_dir=os.path.join(self._data_dir, 'DEF'),
profile_dir=os.path.join(self._data_dir, 'profiles'),
res_search_dir=self.tmp_dir)
self.assertFalse(self.cfg.build_indexes)
self.tearDown()
kwargs = {
'cfg_file': "nimportnaoik",
'sequence_db': os.path.join(self._data_dir, "base",
"test_base.fa"),
'db_type': 'gembase',
'def_dir': os.path.join(self._data_dir, 'DEF'),
'profile_dir': os.path.join(self._data_dir, 'profiles'),
'build_indexes': True
}
config = Config(cfg_file="nimportnaoik",
sequence_db=os.path.join(self._data_dir, "base",
"test_base.fa"),
db_type='gembase',
def_dir=os.path.join(self._data_dir, 'DEF'),
profile_dir=os.path.join(self._data_dir, 'profiles'),
res_search_dir=self.tmp_dir,
build_indexes=True)
self.assertTrue(config.build_indexes)
def test_default(self):
self.cfg = Config(cfg_file="nimportnaoik",
sequence_db=os.path.join(self._data_dir, "base",
"test_base.fa"),
db_type='gembase',
def_dir=os.path.join(self._data_dir, 'DEF'),
profile_dir=os.path.join(self._data_dir, 'profiles'),
res_search_dir=self.tmp_dir)
self.assertEqual(self.cfg.hmmer_exe, 'hmmsearch')
def test_coverage_profile(self):
self.cfg = Config(
cfg_file="nimportnaoik",
sequence_db=os.path.join(self._data_dir, "base", "test_base.fa"),
db_type='gembase',
def_dir=os.path.join(self._data_dir, 'DEF'),
profile_dir=os.path.join(self._data_dir, 'profiles'),
res_search_dir=self.tmp_dir,
)
self.assertEqual(self.cfg.coverage_profile, 0.5)
self.tearDown()
self.cfg = Config(
cfg_file="nimportnaoik",
sequence_db=os.path.join(self._data_dir, "base", "test_base.fa"),
db_type='gembase',
def_dir=os.path.join(self._data_dir, 'DEF'),
profile_dir=os.path.join(self._data_dir, 'profiles'),
coverage_profile=0.6,
res_search_dir=self.tmp_dir,
)
self.assertEqual(self.cfg.coverage_profile, 0.6)
self.tearDown()
#coverage_profile must be a float
kwargs = {
'cfg_file': "nimportnaoik",
'sequence_db': os.path.join(self._data_dir, "base",
"test_base.fa"),
'db_type': 'gembase',
'def_dir': os.path.join(self._data_dir, 'DEF'),
'profile_dir': os.path.join(self._data_dir, 'profiles'),
'coverage_profile': "foo",
'res_search_dir': self.tmp_dir
}
self.assertRaises(ValueError, Config, **kwargs)
def test_def_dir(self):
kwargs = {
'cfg_file': "nimportnaoik",
'sequence_db': os.path.join(self._data_dir, "base",
"test_base.fa"),
'db_type': 'gembase',
'profile_dir': os.path.join(self._data_dir, 'profiles'),
'def_dir': '/kjhdsjkg938268235764kjdsg',
'res_search_dir': self.tmp_dir
}
real_def_dir = os.path.join(os.path.dirname(__file__), '..', 'data',
'DEF'),
self.assertRaises(ValueError, Config, **kwargs)
def_dir = os.path.join(tempfile.gettempdir(), 'macsyfinder_DEF')
if not os.path.exists(def_dir):
os.mkdir(def_dir)
self.cfg = Config(cfg_file="nimportnaoik",
sequence_db=os.path.join(self._data_dir, "base",
"test_base.fa"),
db_type='gembase',
def_dir=def_dir,
profile_dir=os.path.join(self._data_dir, 'profiles'),
res_search_dir=self.tmp_dir)
self.assertEqual(def_dir, self.cfg.def_dir)
shutil.rmtree(def_dir)
self.tearDown()
def_dir = os.path.join(os.path.dirname(__file__), '..', 'data', 'DEF')
self.cfg = Config(cfg_file="nimportnaoik",
sequence_db=os.path.join(self._data_dir, "base",
"test_base.fa"),
db_type='gembase',
def_dir=def_dir,
profile_dir=os.path.join(self._data_dir, 'profiles'),
res_search_dir=self.tmp_dir)
self.assertEqual(def_dir, self.cfg.def_dir)
def test_e_value_res(self):
kwargs = {
'cfg_file': "nimportnaoik",
'sequence_db': os.path.join(self._data_dir, "base",
"test_base.fa"),
'db_type': 'gembase',
'def_dir': os.path.join(self._data_dir, 'DEF'),
'profile_dir': os.path.join(self._data_dir, 'profiles'),
'e_value_res': 'foo',
'res_search_dir': self.tmp_dir
}
self.assertRaises(ValueError, Config, **kwargs)
self.cfg = Config(cfg_file="nimportnaoik",
sequence_db=os.path.join(self._data_dir, "base",
"test_base.fa"),
db_type='gembase',
def_dir=os.path.join(self._data_dir, 'DEF'),
profile_dir=os.path.join(self._data_dir, 'profiles'),
res_search_dir=self.tmp_dir)
self.assertEqual(self.cfg.e_value_res, 1)
self.tearDown()
self.cfg = Config(cfg_file="nimportnaoik",
sequence_db=os.path.join(self._data_dir, "base",
"test_base.fa"),
db_type='gembase',
def_dir=os.path.join(self._data_dir, 'DEF'),
profile_dir=os.path.join(self._data_dir, 'profiles'),
e_value_res=0.7,
res_search_dir=self.tmp_dir)
self.assertEqual(self.cfg.e_value_res, 0.7)
self.tearDown()
kwargs = {
'cfg_file': "nimportnaoik",
'sequence_db': os.path.join(self._data_dir, "base",
"test_base.fa"),
'db_type': 'gembase',
'def_dir': os.path.join(self._data_dir, 'DEF'),
'profile_dir': os.path.join(self._data_dir, 'profiles'),
'e_value_res': 0.7,
'i_evalue_sel': 1,
'res_search_dir': self.tmp_dir
}
self.assertRaises(ValueError, Config, **kwargs)
def test_hmmer_exe(self):
self.cfg = Config(cfg_file="nimportnaoik",
sequence_db=os.path.join(self._data_dir, "base",
"test_base.fa"),
db_type='gembase',
def_dir=os.path.join(self._data_dir, 'DEF'),
profile_dir=os.path.join(self._data_dir, 'profiles'),
res_search_dir=self.tmp_dir)
self.assertEqual(self.cfg.hmmer_exe, 'hmmsearch')
self.tearDown()
self.cfg = Config(cfg_file="nimportnaoik",
sequence_db=os.path.join(self._data_dir, "base",
"test_base.fa"),
db_type='gembase',
def_dir=os.path.join(self._data_dir, 'DEF'),
profile_dir=os.path.join(self._data_dir, 'profiles'),
hmmer_exe='truc',
res_search_dir=self.tmp_dir)
self.assertEqual(self.cfg.hmmer_exe, 'truc')
def test_index_db_exe(self):
self.cfg = Config(cfg_file="nimportnaoik",
sequence_db=os.path.join(self._data_dir, "base",
"test_base.fa"),
db_type='gembase',
def_dir=os.path.join(self._data_dir, 'DEF'),
profile_dir=os.path.join(self._data_dir, 'profiles'),
res_search_dir=self.tmp_dir)
self.assertEqual(self.cfg.index_db_exe, 'makeblastdb')
self.tearDown()
self.cfg = Config(cfg_file="nimportnaoik",
sequence_db=os.path.join(self._data_dir, "base",
"test_base.fa"),
db_type='gembase',
def_dir=os.path.join(self._data_dir, 'DEF'),
profile_dir=os.path.join(self._data_dir, 'profiles'),
index_db_exe='truc',
res_search_dir=self.tmp_dir)
self.assertEqual(self.cfg.index_db_exe, 'truc')
def test_i_value_sel(self):
kwargs = {
'cfg_file': "nimportnaoik",
'sequence_db': os.path.join(self._data_dir, "base",
"test_base.fa"),
'db_type': 'gembase',
'def_dir': os.path.join(self._data_dir, 'DEF'),
'profile_dir': os.path.join(self._data_dir, 'profiles'),
'i_evalue_sel': 'foo',
'res_search_dir': self.tmp_dir
}
self.assertRaises(ValueError, Config, **kwargs)
self.cfg = Config(cfg_file="nimportnaoik",
sequence_db=os.path.join(self._data_dir, "base",
"test_base.fa"),
db_type='gembase',
def_dir=os.path.join(self._data_dir, 'DEF'),
profile_dir=os.path.join(self._data_dir, 'profiles'),
res_search_dir=self.tmp_dir)
self.assertEqual(self.cfg.i_evalue_sel, 0.001)
self.tearDown()
self.cfg = Config(cfg_file="nimportnaoik",
sequence_db=os.path.join(self._data_dir, "base",
"test_base.fa"),
db_type='gembase',
def_dir=os.path.join(self._data_dir, 'DEF'),
profile_dir=os.path.join(self._data_dir, 'profiles'),
i_evalue_sel=0.7,
res_search_dir=self.tmp_dir)
self.assertEqual(self.cfg.i_evalue_sel, 0.7)
self.tearDown()
kwargs = {
'cfg_file': "nimportnaoik",
'sequence_db': os.path.join(self._data_dir, "base",
"test_base.fa"),
'db_type': 'gembase',
'def_dir': os.path.join(self._data_dir, 'DEF'),
'profile_dir': os.path.join(self._data_dir, 'profiles'),
'e_value_res': 0.7,
'i_evalue_sel': 1,
'res_search_dir': self.tmp_dir
}
self.assertRaises(ValueError, Config, **kwargs)
def test_db_type(self):
self.cfg = Config(cfg_file="nimportnaoik",
sequence_db=os.path.join(self._data_dir, "base",
"test_base.fa"),
db_type='gembase',
def_dir=os.path.join(self._data_dir, 'DEF'),
profile_dir=os.path.join(self._data_dir, 'profiles'),
res_search_dir=self.tmp_dir)
self.assertEqual(self.cfg.db_type, 'gembase')
self.tearDown()
kwargs = {
'cfg_file': "nimportnaoik",
'sequence_db': os.path.join(self._data_dir, "base",
"test_base.fa"),
'db_type': 'foo',
'def_dir': os.path.join(self._data_dir, 'DEF'),
'profile_dir': os.path.join(self._data_dir, 'profiles'),
'res_search_dir': self.tmp_dir
}
self.assertRaises(ValueError, Config, **kwargs)
def test_previous_run(self):
out_dir = os.path.join(self.tmp_dir, 'macsy_test_config')
kwargs = {
'cfg_file': "nimportnaoik",
'sequence_db': os.path.join(self._data_dir, "base",
"test_base.fa"),
'db_type': 'gembase',
'def_dir': os.path.join(self._data_dir, 'DEF'),
'profile_dir': os.path.join(self._data_dir, 'profiles'),
'previous_run': 'foo',
'res_search_dir': out_dir
}
self.assertRaises(ValueError, Config, **kwargs)
try:
shutil.rmtree(out_dir)
except:
pass
self.tearDown()
try:
cfg_base = Config(cfg_file="nimportnaoik",
sequence_db=os.path.join(self._data_dir, "base",
"test_base.fa"),
db_type='gembase',
def_dir=os.path.join(self._data_dir, 'DEF'),
profile_dir=os.path.join(self._data_dir,
'profiles'),
res_search_dir=self.tmp_dir)
self.assertIsNone(cfg_base.previous_run)
cfg_base.save(cfg_base.working_dir)
#wait
time.sleep(1)
new_cfg = Config(previous_run=cfg_base.working_dir)
self.assertEqual(new_cfg.previous_run, cfg_base.working_dir)
finally:
# close loggers filehandles, so they don't block file deletion
# in shutil.rmtree calls in Windows
logging.shutdown()
try:
shutil.rmtree(new_cfg.working_dir)
except:
pass
try:
shutil.rmtree(cfg_base.working_dir)
except:
pass
def test_profile_dir(self):
kwargs = {
'cfg_file': "nimportnaoik",
'sequence_db': os.path.join(self._data_dir, "base",
"test_base.fa"),
'db_type': 'gembase',
'def_dir': os.path.join(self._data_dir, 'DEF'),
'profile_dir': 'foo',
'res_search_dir': self.tmp_dir
}
self.assertRaises(ValueError, Config, **kwargs)
profile_dir = os.path.join(os.path.dirname(__file__), '..', 'data',
'profiles')
self.cfg = Config(cfg_file="nimportnaoik",
sequence_db=os.path.join(self._data_dir, "base",
"test_base.fa"),
db_type='gembase',
def_dir=os.path.join(self._data_dir, 'DEF'),
profile_dir=profile_dir,
res_search_dir=self.tmp_dir)
self.assertEqual(self.cfg.profile_dir, profile_dir)
def test_profile_suffix(self):
self.cfg = Config(cfg_file="nimportnaoik",
sequence_db=os.path.join(self._data_dir, "base",
"test_base.fa"),
db_type='gembase',
def_dir=os.path.join(self._data_dir, 'DEF'),
profile_dir=os.path.join(self._data_dir, 'profiles'),
res_search_dir=self.tmp_dir)
self.assertEqual(self.cfg.profile_suffix, '.hmm')
self.tearDown()
profile_suffix = 'foo'
self.cfg = Config(cfg_file="nimportnaoik",
sequence_db=os.path.join(self._data_dir, "base",
"test_base.fa"),
db_type='gembase',
def_dir=os.path.join(self._data_dir, 'DEF'),
profile_dir=os.path.join(self._data_dir, 'profiles'),
profile_suffix=profile_suffix,
res_search_dir=self.tmp_dir)
self.assertEqual(self.cfg.profile_suffix, profile_suffix)
def test_replicon_topology(self):
self.cfg = Config(cfg_file="nimportnaoik",
sequence_db=os.path.join(self._data_dir, "base",
"test_base.fa"),
db_type='gembase',
def_dir=os.path.join(self._data_dir, 'DEF'),
profile_dir=os.path.join(self._data_dir, 'profiles'),
res_search_dir=self.tmp_dir)
self.assertEqual(self.cfg.replicon_topology, 'circular')
self.tearDown()
self.cfg = Config(cfg_file="nimportnaoik",
sequence_db=os.path.join(self._data_dir, "base",
"test_base.fa"),
db_type='gembase',
def_dir=os.path.join(self._data_dir, 'DEF'),
profile_dir=os.path.join(self._data_dir, 'profiles'),
replicon_topology='linear',
res_search_dir=self.tmp_dir)
self.assertEqual(self.cfg.replicon_topology, 'linear')
self.tearDown()
kwargs = {
'cfg_file': "nimportnaoik",
'sequence_db': os.path.join(self._data_dir, "base",
"test_base.fa"),
'db_type': 'gembase',
'def_dir': os.path.join(self._data_dir, 'DEF'),
'profile_dir': os.path.join(self._data_dir, 'profiles'),
'replicon_topology': 'foo',
'res_search_dir': self.tmp_dir
}
self.assertRaises(ValueError, Config, **kwargs)
def test_inter_gene_max_space(self):
inter_gene_max_space = (["T2SS", 32], ['Flagellum', 64])
self.cfg = Config(cfg_file="nimportnaoik",
sequence_db=os.path.join(self._data_dir, "base",
"test_base.fa"),
db_type='gembase',
def_dir=os.path.join(self._data_dir, 'DEF'),
profile_dir=os.path.join(self._data_dir, 'profiles'),
inter_gene_max_space=inter_gene_max_space,
res_search_dir=self.tmp_dir)
self.assertEqual(self.cfg.inter_gene_max_space('T2SS'), 32)
self.assertEqual(self.cfg.inter_gene_max_space('Flagellum'), 64)
self.assertIsNone(self.cfg.inter_gene_max_space('Foo'))
def test_min_genes_required(self):
min_genes_required = (["T2SS", 32], ['Flagellum', 64])
self.cfg = Config(cfg_file="nimportnaoik",
sequence_db=os.path.join(self._data_dir, "base",
"test_base.fa"),
db_type='gembase',
def_dir=os.path.join(self._data_dir, 'DEF'),
profile_dir=os.path.join(self._data_dir, 'profiles'),
min_genes_required=min_genes_required,
res_search_dir=self.tmp_dir)
self.assertEqual(self.cfg.min_genes_required('T2SS'), 32)
self.assertEqual(self.cfg.min_genes_required('Flagellum'), 64)
self.assertIsNone(self.cfg.min_genes_required('Foo'))
def test_max_nb_genes(self):
max_nb_genes = (["T2SS", 32], ['Flagellum', 64])
self.cfg = Config(cfg_file="nimportnaoik",
sequence_db=os.path.join(self._data_dir, "base",
"test_base.fa"),
db_type='gembase',
def_dir=os.path.join(self._data_dir, 'DEF'),
profile_dir=os.path.join(self._data_dir, 'profiles'),
max_nb_genes=max_nb_genes,
res_search_dir=self.tmp_dir)
self.assertEqual(self.cfg.max_nb_genes('T2SS'), 32)
self.assertEqual(self.cfg.max_nb_genes('Flagellum'), 64)
self.assertIsNone(self.cfg.max_nb_genes('Foo'))
def test_min_mandatory_genes_required(self):
min_mandatory_genes_required = (["T2SS", 32], ['Flagellum', 64])
self.cfg = Config(
cfg_file="nimportnaoik",
sequence_db=os.path.join(self._data_dir, "base", "test_base.fa"),
db_type='gembase',
def_dir=os.path.join(self._data_dir, 'DEF'),
profile_dir=os.path.join(self._data_dir, 'profiles'),
min_mandatory_genes_required=min_mandatory_genes_required,
res_search_dir=self.tmp_dir)
self.assertEqual(self.cfg.min_mandatory_genes_required('T2SS'), 32)
self.assertEqual(self.cfg.min_mandatory_genes_required('Flagellum'),
64)
self.assertIsNone(self.cfg.min_mandatory_genes_required('Foo'))
def test_multi_loci(self):
multi_loci = "T2SS,Flagellum"
self.cfg = Config(cfg_file="nimportnaoik",
sequence_db=os.path.join(self._data_dir, "base",
"test_base.fa"),
db_type='gembase',
def_dir=os.path.join(self._data_dir, 'DEF'),
profile_dir=os.path.join(self._data_dir, 'profiles'),
multi_loci=multi_loci,
res_search_dir=self.tmp_dir)
self.assertTrue(self.cfg.multi_loci('T2SS'))
self.assertTrue(self.cfg.multi_loci('Flagellum'))
self.assertFalse(self.cfg.multi_loci('Foo'))
def test_res_extract_suffix(self):
self.cfg = Config(cfg_file="nimportnaoik",
sequence_db=os.path.join(self._data_dir, "base",
"test_base.fa"),
db_type='gembase',
def_dir=os.path.join(self._data_dir, 'DEF'),
profile_dir=os.path.join(self._data_dir, 'profiles'),
res_search_dir=self.tmp_dir)
self.assertEqual(self.cfg.res_extract_suffix, '.res_hmm_extract')
self.tearDown()
res_extract_suffix = 'foo'
self.cfg = Config(cfg_file="nimportnaoik",
sequence_db=os.path.join(self._data_dir, "base",
"test_base.fa"),
db_type='gembase',
def_dir=os.path.join(self._data_dir, 'DEF'),
profile_dir=os.path.join(self._data_dir, 'profiles'),
res_extract_suffix=res_extract_suffix,
res_search_dir=self.tmp_dir)
self.assertEqual(self.cfg.res_extract_suffix, res_extract_suffix)
def test_res_search_dir(self):
kwargs = {
'cfg_file': "nimportnaoik",
'sequence_db': os.path.join(self._data_dir, "base",
"test_base.fa"),
'db_type': 'gembase',
'def_dir': os.path.join(self._data_dir, 'DEF'),
'profile_dir': os.path.join(self._data_dir, 'profiles'),
'res_search_dir': 'foo',
'log_file':
'NUL' if platform.system() == 'Windows' else '/dev/null'
}
self.assertRaises(ValueError, Config, **kwargs)
self.tearDown()
res_search_dir = os.path.join(os.path.dirname(__file__), 'datatest')
self.cfg = Config(
cfg_file="nimportnaoik",
sequence_db=os.path.join(self._data_dir, "base", "test_base.fa"),
db_type='gembase',
def_dir=os.path.join(self._data_dir, 'DEF'),
profile_dir=os.path.join(self._data_dir, 'profiles'),
res_search_dir=res_search_dir,
log_file='NUL' if platform.system() == 'Windows' else '/dev/null')
self.assertEqual(self.cfg.res_search_dir, res_search_dir)
def test_out_dir(self):
out_dir = os.path.join(self.tmp_dir, 'macsy_test_config')
try:
shutil.rmtree(out_dir)
except:
pass
os.makedirs(out_dir, 0775)
f = open(os.path.join(out_dir, 'fake'), 'w')
f.close()
kwargs = {
'cfg_file': "nimportnaoik",
'sequence_db': os.path.join(self._data_dir, "base",
"test_base.fa"),
'db_type': 'gembase',
'def_dir': os.path.join(self._data_dir, 'DEF'),
'profile_dir': os.path.join(self._data_dir, 'profiles'),
'out_dir': out_dir,
'log_file':
'NUL' if platform.system() == 'Windows' else '/dev/null'
}
self.assertRaises(ValueError, Config, **kwargs)
shutil.rmtree(out_dir)
self.tearDown()
os.makedirs(out_dir, 0775)
self.cfg = Config(
cfg_file="nimportnaoik",
sequence_db=os.path.join(self._data_dir, "base", "test_base.fa"),
db_type='gembase',
def_dir=os.path.join(self._data_dir, 'DEF'),
profile_dir=os.path.join(self._data_dir, 'profiles'),
out_dir=out_dir,
log_file='NUL' if platform.system() == 'Windows' else '/dev/null')
self.assertEqual(self.cfg.working_dir, out_dir)
def test_res_search_suffix(self):
self.cfg = Config(cfg_file="nimportnaoik",
sequence_db=os.path.join(self._data_dir, "base",
"test_base.fa"),
db_type='gembase',
def_dir=os.path.join(os.path.dirname(__file__), '..',
'data', 'DEF'),
profile_dir=os.path.join(self._data_dir, 'profiles'),
res_search_dir=self.tmp_dir)
self.assertEqual(self.cfg.res_search_suffix, '.search_hmm.out')
self.tearDown()
res_search_suffix = 'foo'
self.cfg = Config(cfg_file="nimportnaoik",
sequence_db=os.path.join(self._data_dir, "base",
"test_base.fa"),
db_type='gembase',
def_dir=os.path.join(self._data_dir, 'DEF'),
profile_dir=os.path.join(self._data_dir, 'profiles'),
res_search_suffix=res_search_suffix,
res_search_dir=self.tmp_dir)
self.assertEqual(self.cfg.res_search_suffix, res_search_suffix)
def test_sequence_db(self):
kwargs = {
'cfg_file': "nimportnaoik",
'db_type': 'gembase',
'def_dir': os.path.join(self._data_dir, 'DEF'),
'profile_dir': os.path.join(self._data_dir, 'profiles'),
'worker_nb': '2.3',
'res_search_dir': self.tmp_dir,
'log_file':
'NUL' if platform.system() == 'Windows' else '/dev/null'
}
self.assertRaises(ValueError, Config, **kwargs)
kwargs = {
'cfg_file': "nimportnaoik",
'sequence_db': "foo",
'db_type': 'gembase',
'def_dir': os.path.join(self._data_dir, 'DEF'),
'profile_dir': os.path.join(self._data_dir, 'profiles'),
'worker_nb': '2.3',
'res_search_dir': self.tmp_dir,
'log_file':
'NUL' if platform.system() == 'Windows' else '/dev/null'
}
self.assertRaises(ValueError, Config, **kwargs)
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa")
self.cfg = Config(
cfg_file="nimportnaoik",
sequence_db=sequence_db,
db_type='gembase',
def_dir=os.path.join(self._data_dir, 'DEF'),
profile_dir=os.path.join(self._data_dir, 'profiles'),
res_search_dir=self.tmp_dir,
log_file='NUL' if platform.system() == 'Windows' else '/dev/null')
self.assertEqual(self.cfg.sequence_db, sequence_db)
def test_worker_nb(self):
self.cfg = Config(cfg_file="nimportnaoik",
sequence_db=os.path.join(self._data_dir, "base",
"test_base.fa"),
db_type='gembase',
def_dir=os.path.join(self._data_dir, 'DEF'),
profile_dir=os.path.join(self._data_dir, 'profiles'),
res_search_dir=self.tmp_dir)
self.assertEqual(self.cfg.worker_nb, 1)
self.tearDown()
self.cfg = Config(cfg_file="nimportnaoik",
sequence_db=os.path.join(self._data_dir, "base",
"test_base.fa"),
db_type='gembase',
def_dir=os.path.join(self._data_dir, 'DEF'),
profile_dir=os.path.join(self._data_dir, 'profiles'),
res_search_dir=self.tmp_dir,
worker_nb=2)
self.assertEqual(self.cfg.worker_nb, 2)
self.tearDown()
kwargs = {
'cfg_file': "nimportnaoik",
'sequence_db': os.path.join(self._data_dir, "base",
"test_base.fa"),
'db_type': 'gembase',
'def_dir': os.path.join(self._data_dir, 'DEF'),
'profile_dir': os.path.join(self._data_dir, 'profiles'),
'res_search_dir': self.tmp_dir,
'worker_nb': '2.3'
}
self.assertRaises(ValueError, Config, **kwargs)
class Test(unittest.TestCase):
_data_dir = os.path.join(os.path.dirname(__file__), "datatest")
def setUp(self):
l = logging.getLogger()
l.manager.loggerDict.clear()
if hasattr(self, 'tmp_dir'):
try:
shutil.rmtree(self.cfg.working_dir)
except Exception as err:
pass
self.tmp_dir = tempfile.gettempdir()
def tearDown(self):
logging.shutdown()
l = logging.getLogger()
l.manager.loggerDict.clear()
if hasattr(self, 'cfg'):
try:
shutil.rmtree(self.cfg.working_dir)
except Exception as err:
pass
def test_build_indexes(self):
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = self.tmp_dir
)
self.assertFalse(self.cfg.build_indexes)
self.tearDown()
kwargs = {'cfg_file' : "nimportnaoik",
'sequence_db' : os.path.join(self._data_dir, "base", "test_base.fa"),
'db_type' : 'gembase',
'def_dir' : os.path.join(self._data_dir, 'DEF'),
'profile_dir' : os.path.join(self._data_dir, 'profiles'),
'build_indexes' : True
}
config = Config(
cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = self.tmp_dir,
build_indexes = True
)
self.assertTrue(config.build_indexes)
def test_default(self):
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = self.tmp_dir
)
self.assertEqual(self.cfg.hmmer_exe, 'hmmsearch')
def test_coverage_profile(self):
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = self.tmp_dir,
)
self.assertEqual( self.cfg.coverage_profile, 0.5 )
self.tearDown()
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
coverage_profile = 0.6,
res_search_dir = self.tmp_dir,
)
self.assertEqual( self.cfg.coverage_profile, 0.6 )
self.tearDown()
#coverage_profile must be a float
kwargs = {'cfg_file' : "nimportnaoik",
'sequence_db' : os.path.join(self._data_dir, "base", "test_base.fa"),
'db_type' : 'gembase',
'def_dir' : os.path.join(self._data_dir, 'DEF'),
'profile_dir' : os.path.join(self._data_dir, 'profiles'),
'coverage_profile' : "foo",
'res_search_dir' : self.tmp_dir
}
self.assertRaises(ValueError, Config, **kwargs)
def test_def_dir(self):
kwargs = {'cfg_file' : "nimportnaoik",
'sequence_db' : os.path.join(self._data_dir, "base", "test_base.fa"),
'db_type' : 'gembase',
'profile_dir' : os.path.join(self._data_dir, 'profiles'),
'def_dir': '/kjhdsjkg938268235764kjdsg',
'res_search_dir' : self.tmp_dir
}
real_def_dir = os.path.join(os.path.dirname(__file__), '..', 'data', 'DEF'),
self.assertRaises(ValueError, Config, **kwargs)
def_dir = os.path.join(tempfile.gettempdir(), 'macsyfinder_DEF')
if not os.path.exists(def_dir):
os.mkdir(def_dir)
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = def_dir,
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = self.tmp_dir
)
self.assertEqual(def_dir, self.cfg.def_dir)
shutil.rmtree(def_dir)
self.tearDown()
def_dir = os.path.join(os.path.dirname(__file__),'..', 'data', 'DEF')
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = def_dir,
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = self.tmp_dir
)
self.assertEqual(def_dir, self.cfg.def_dir)
def test_e_value_res(self):
kwargs = {'cfg_file' : "nimportnaoik",
'sequence_db' : os.path.join(self._data_dir, "base", "test_base.fa"),
'db_type' : 'gembase',
'def_dir' : os.path.join(self._data_dir, 'DEF'),
'profile_dir' : os.path.join(self._data_dir, 'profiles'),
'e_value_res' : 'foo',
'res_search_dir' : self.tmp_dir
}
self.assertRaises(ValueError, Config, **kwargs)
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = self.tmp_dir
)
self.assertEqual(self.cfg.e_value_res, 1)
self.tearDown()
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
e_value_res = 0.7,
res_search_dir = self.tmp_dir
)
self.assertEqual(self.cfg.e_value_res, 0.7)
self.tearDown()
kwargs = {'cfg_file' : "nimportnaoik",
'sequence_db' : os.path.join(self._data_dir, "base", "test_base.fa"),
'db_type' : 'gembase',
'def_dir' : os.path.join(self._data_dir, 'DEF'),
'profile_dir' : os.path.join(self._data_dir, 'profiles'),
'e_value_res' : 0.7,
'i_evalue_sel' : 1,
'res_search_dir' : self.tmp_dir
}
self.assertRaises(ValueError, Config, **kwargs)
def test_hmmer_exe(self):
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = self.tmp_dir
)
self.assertEqual(self.cfg.hmmer_exe, 'hmmsearch')
self.tearDown()
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
hmmer_exe = 'truc',
res_search_dir = self.tmp_dir
)
self.assertEqual(self.cfg.hmmer_exe, 'truc')
def test_index_db_exe(self):
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = self.tmp_dir
)
self.assertEqual(self.cfg.index_db_exe, 'makeblastdb')
self.tearDown()
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
index_db_exe = 'truc',
res_search_dir = self.tmp_dir
)
self.assertEqual(self.cfg.index_db_exe, 'truc')
def test_i_value_sel(self):
kwargs = {'cfg_file' : "nimportnaoik",
'sequence_db' : os.path.join(self._data_dir, "base", "test_base.fa"),
'db_type' : 'gembase',
'def_dir' : os.path.join(self._data_dir, 'DEF'),
'profile_dir' : os.path.join(self._data_dir, 'profiles'),
'i_evalue_sel' : 'foo',
'res_search_dir' : self.tmp_dir
}
self.assertRaises(ValueError, Config, **kwargs)
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = self.tmp_dir
)
self.assertEqual(self.cfg.i_evalue_sel, 0.001)
self.tearDown()
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
i_evalue_sel = 0.7,
res_search_dir = self.tmp_dir
)
self.assertEqual(self.cfg.i_evalue_sel, 0.7)
self.tearDown()
kwargs = {'cfg_file' : "nimportnaoik",
'sequence_db' : os.path.join(self._data_dir, "base", "test_base.fa"),
'db_type' : 'gembase',
'def_dir' : os.path.join(self._data_dir, 'DEF'),
'profile_dir' : os.path.join(self._data_dir, 'profiles'),
'e_value_res' : 0.7,
'i_evalue_sel' : 1,
'res_search_dir' : self.tmp_dir
}
self.assertRaises(ValueError, Config, **kwargs)
def test_db_type(self):
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = self.tmp_dir
)
self.assertEqual( self.cfg.db_type, 'gembase')
self.tearDown()
kwargs = {'cfg_file' : "nimportnaoik",
'sequence_db' : os.path.join(self._data_dir, "base", "test_base.fa"),
'db_type' : 'foo',
'def_dir' : os.path.join(self._data_dir, 'DEF'),
'profile_dir' : os.path.join(self._data_dir, 'profiles'),
'res_search_dir' : self.tmp_dir
}
self.assertRaises(ValueError, Config, **kwargs)
def test_previous_run(self):
kwargs = {'cfg_file' : "nimportnaoik",
'sequence_db' : os.path.join(self._data_dir, "base", "test_base.fa"),
'db_type' : 'gembase',
'def_dir' : os.path.join(self._data_dir, 'DEF'),
'profile_dir' : os.path.join(self._data_dir, 'profiles'),
'previous_run' : 'foo',
'res_search_dir' : self.tmp_dir
}
self.assertRaises(ValueError, Config, **kwargs)
try:
cfg_base = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = self.tmp_dir
)
self.assertIsNone(cfg_base.previous_run)
cfg_base.save( cfg_base.working_dir )
#wait
time.sleep(1)
new_cfg = Config(previous_run = cfg_base.working_dir)
self.assertEqual(new_cfg.previous_run, cfg_base.working_dir)
finally:
# close loggers filehandles, so they don't block file deletion
# in shutil.rmtree calls in Windows
logging.shutdown()
try:
shutil.rmtree(new_cfg.working_dir)
except:
pass
def test_profile_dir(self):
kwargs = {'cfg_file' : "nimportnaoik",
'sequence_db' : os.path.join(self._data_dir, "base", "test_base.fa"),
'db_type' : 'gembase',
'def_dir' : os.path.join(self._data_dir, 'DEF'),
'profile_dir' : 'foo',
'res_search_dir' : self.tmp_dir
}
self.assertRaises(ValueError, Config, **kwargs)
profile_dir = os.path.join(os.path.dirname(__file__), '..', 'data', 'profiles')
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = profile_dir,
res_search_dir = self.tmp_dir
)
self.assertEqual(self.cfg.profile_dir, profile_dir)
def test_profile_suffix(self):
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = self.tmp_dir
)
self.assertEqual(self.cfg.profile_suffix, '.hmm')
self.tearDown()
profile_suffix = 'foo'
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
profile_suffix = profile_suffix,
res_search_dir = self.tmp_dir
)
self.assertEqual(self.cfg.profile_suffix, profile_suffix)
def test_replicon_topology(self):
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = self.tmp_dir
)
self.assertEqual(self.cfg.replicon_topology, 'circular')
self.tearDown()
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
replicon_topology = 'linear',
res_search_dir = self.tmp_dir
)
self.assertEqual(self.cfg.replicon_topology, 'linear')
self.tearDown()
kwargs = {'cfg_file' : "nimportnaoik",
'sequence_db' : os.path.join(self._data_dir, "base", "test_base.fa"),
'db_type' : 'gembase',
'def_dir' : os.path.join(self._data_dir, 'DEF'),
'profile_dir' : os.path.join(self._data_dir, 'profiles'),
'replicon_topology' : 'foo',
'res_search_dir' : self.tmp_dir
}
self.assertRaises(ValueError, Config, **kwargs)
def test_inter_gene_max_space(self):
inter_gene_max_space = (["T2SS", 32], ['Flagellum', 64])
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
inter_gene_max_space = inter_gene_max_space,
res_search_dir = self.tmp_dir
)
self.assertEqual(self.cfg.inter_gene_max_space('T2SS'), 32)
self.assertEqual(self.cfg.inter_gene_max_space('Flagellum'), 64)
self.assertIsNone(self.cfg.inter_gene_max_space('Foo'))
def test_min_genes_required(self):
min_genes_required = (["T2SS", 32], ['Flagellum', 64])
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
min_genes_required = min_genes_required,
res_search_dir = self.tmp_dir
)
self.assertEqual(self.cfg.min_genes_required('T2SS'), 32)
self.assertEqual(self.cfg.min_genes_required('Flagellum'), 64)
self.assertIsNone(self.cfg.min_genes_required('Foo'))
def test_max_nb_genes(self):
max_nb_genes = (["T2SS", 32], ['Flagellum', 64])
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
max_nb_genes = max_nb_genes,
res_search_dir = self.tmp_dir
)
self.assertEqual(self.cfg.max_nb_genes('T2SS'), 32)
self.assertEqual(self.cfg.max_nb_genes('Flagellum'), 64)
self.assertIsNone(self.cfg.max_nb_genes('Foo'))
def test_min_mandatory_genes_required(self):
min_mandatory_genes_required = (["T2SS", 32], ['Flagellum', 64])
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
min_mandatory_genes_required = min_mandatory_genes_required,
res_search_dir = self.tmp_dir
)
self.assertEqual(self.cfg.min_mandatory_genes_required('T2SS'), 32)
self.assertEqual(self.cfg.min_mandatory_genes_required('Flagellum'), 64)
self.assertIsNone(self.cfg.min_mandatory_genes_required('Foo'))
def test_multi_loci(self):
multi_loci = "T2SS,Flagellum"
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
multi_loci = multi_loci,
res_search_dir = self.tmp_dir
)
self.assertTrue(self.cfg.multi_loci('T2SS'))
self.assertTrue(self.cfg.multi_loci('Flagellum'))
self.assertFalse(self.cfg.multi_loci('Foo'))
def test_res_extract_suffix(self):
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = self.tmp_dir
)
self.assertEqual(self.cfg.res_extract_suffix, '.res_hmm_extract')
self.tearDown()
res_extract_suffix = 'foo'
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_extract_suffix = res_extract_suffix,
res_search_dir = self.tmp_dir
)
self.assertEqual(self.cfg.res_extract_suffix, res_extract_suffix)
def test_res_search_dir(self):
kwargs = {'cfg_file' : "nimportnaoik",
'sequence_db' : os.path.join(self._data_dir, "base", "test_base.fa"),
'db_type' : 'gembase',
'def_dir' : os.path.join(self._data_dir, 'DEF'),
'profile_dir' : os.path.join(self._data_dir, 'profiles'),
'res_search_dir' : 'foo',
'log_file' : 'NUL' if platform.system() == 'Windows' else '/dev/null'
}
self.assertRaises(ValueError, Config, **kwargs)
self.tearDown()
res_search_dir = os.path.join(os.path.dirname(__file__), 'datatest')
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = res_search_dir,
log_file = 'NUL' if platform.system() == 'Windows' else '/dev/null'
)
self.assertEqual(self.cfg.res_search_dir, res_search_dir)
def test_res_search_suffix(self):
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(os.path.dirname(__file__),'..', 'data', 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = self.tmp_dir
)
self.assertEqual(self.cfg.res_search_suffix, '.search_hmm.out')
self.tearDown()
res_search_suffix = 'foo'
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_suffix = res_search_suffix,
res_search_dir = self.tmp_dir
)
self.assertEqual(self.cfg.res_search_suffix, res_search_suffix)
def test_sequence_db(self):
kwargs = {'cfg_file' : "nimportnaoik",
'db_type' : 'gembase',
'def_dir' : os.path.join(self._data_dir, 'DEF'),
'profile_dir' : os.path.join(self._data_dir, 'profiles'),
'worker_nb' : '2.3' ,
'res_search_dir' : self.tmp_dir,
'log_file' : 'NUL' if platform.system() == 'Windows' else '/dev/null'
}
self.assertRaises(ValueError, Config, **kwargs)
kwargs = {'cfg_file' : "nimportnaoik",
'sequence_db' : "foo",
'db_type' : 'gembase',
'def_dir' : os.path.join(self._data_dir, 'DEF'),
'profile_dir' : os.path.join(self._data_dir, 'profiles'),
'worker_nb' : '2.3',
'res_search_dir' : self.tmp_dir,
'log_file' : 'NUL' if platform.system() == 'Windows' else '/dev/null'
}
self.assertRaises(ValueError, Config, **kwargs)
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa")
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = sequence_db,
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = self.tmp_dir,
log_file = 'NUL' if platform.system() == 'Windows' else '/dev/null'
)
self.assertEqual(self.cfg.sequence_db, sequence_db)
def test_worker_nb(self):
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = self.tmp_dir
)
self.assertEqual(self.cfg.worker_nb, 1)
self.tearDown()
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = self.tmp_dir,
worker_nb = 2
)
self.assertEqual(self.cfg.worker_nb, 2)
self.tearDown()
kwargs = {'cfg_file' : "nimportnaoik",
'sequence_db' : os.path.join(self._data_dir, "base", "test_base.fa"),
'db_type' : 'gembase',
'def_dir' : os.path.join(self._data_dir, 'DEF'),
'profile_dir' : os.path.join(self._data_dir, 'profiles'),
'res_search_dir' : self.tmp_dir,
'worker_nb' : '2.3'
}
self.assertRaises(ValueError, Config, **kwargs)
class Test(unittest.TestCase):
_data_dir = os.path.join(os.path.dirname(__file__), "datatest")
def tearDown(self):
try:
shutil.rmtree(self.cfg.working_dir)
except:
pass
def test_build_indexes(self):
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = '/tmp'
)
self.assertFalse(self.cfg.build_indexes)
self.tearDown()
kwargs = {'cfg_file' : "nimportnaoik",
'sequence_db' : os.path.join(self._data_dir, "base", "test_base.fa"),
'db_type' : 'gembase',
'def_dir' : os.path.join(self._data_dir, 'DEF'),
'profile_dir' : os.path.join(self._data_dir, 'profiles'),
'build_indexes' : True
}
config = Config(
cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = '/tmp',
build_indexes = True
)
self.assertTrue(config.build_indexes)
def test_default(self):
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = '/tmp'
)
self.assertEqual(self.cfg.hmmer_exe, 'hmmsearch')
def test_coverage_profile(self):
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = '/tmp',
)
self.assertEqual( self.cfg.coverage_profile, 0.5 )
self.tearDown()
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
coverage_profile = 0.6,
res_search_dir = '/tmp',
)
self.assertEqual( self.cfg.coverage_profile, 0.6 )
self.tearDown()
#coverage_profile must be a float
kwargs = {'cfg_file' : "nimportnaoik",
'sequence_db' : os.path.join(self._data_dir, "base", "test_base.fa"),
'db_type' : 'gembase',
'def_dir' : os.path.join(self._data_dir, 'DEF'),
'profile_dir' : os.path.join(self._data_dir, 'profiles'),
'coverage_profile' : "foo",
'res_search_dir' : '/tmp'
}
self.assertRaises(ValueError, Config, **kwargs)
def test_def_dir(self):
kwargs = {'cfg_file' : "nimportnaoik",
'sequence_db' : os.path.join(self._data_dir, "base", "test_base.fa"),
'db_type' : 'gembase',
'profile_dir' : os.path.join(self._data_dir, 'profiles'),
'def_dir': '/kjhdsjkg938268235764kjdsg',
'res_search_dir' : '/tmp',
}
real_def_dir = os.path.join(os.path.dirname(__file__), '..', 'data', 'DEF'),
self.assertRaises(ValueError, Config, **kwargs)
def_dir = os.path.join('/tmp', 'macsyfinder_DEF')
if not os.path.exists(def_dir):
os.mkdir(def_dir)
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = def_dir,
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = '/tmp',
)
self.assertEqual(def_dir, self.cfg.def_dir)
shutil.rmtree(def_dir)
self.tearDown()
def_dir = os.path.join(os.path.dirname(__file__),'..', 'data', 'DEF')
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = def_dir,
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = '/tmp',
)
self.assertEqual( def_dir, self.cfg.def_dir)
def test_e_value_res(self):
kwargs = {'cfg_file' : "nimportnaoik",
'sequence_db' : os.path.join(self._data_dir, "base", "test_base.fa"),
'db_type' : 'gembase',
'def_dir' : os.path.join(self._data_dir, 'DEF'),
'profile_dir' : os.path.join(self._data_dir, 'profiles'),
'e_value_res' : 'foo',
'res_search_dir' : '/tmp'
}
self.assertRaises(ValueError, Config, **kwargs)
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = '/tmp'
)
self.assertEqual(self.cfg.e_value_res, 1)
self.tearDown()
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
e_value_res = 0.7,
res_search_dir = '/tmp',
)
self.assertEqual(self.cfg.e_value_res, 0.7)
self.tearDown()
kwargs = {'cfg_file' : "nimportnaoik",
'sequence_db' : os.path.join(self._data_dir, "base", "test_base.fa"),
'db_type' : 'gembase',
'def_dir' : os.path.join(self._data_dir, 'DEF'),
'profile_dir' : os.path.join(self._data_dir, 'profiles'),
'e_value_res' : 0.7,
'i_evalue_sel' : 1,
'res_search_dir' : '/tmp',
}
self.assertRaises(ValueError, Config, **kwargs)
def test_hmmer_exe(self):
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = '/tmp'
)
self.assertEqual(self.cfg.hmmer_exe, 'hmmsearch')
self.tearDown()
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
hmmer_exe = 'truc',
res_search_dir = '/tmp',
)
self.assertEqual(self.cfg.hmmer_exe, 'truc')
def test_index_db_exe(self):
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = '/tmp'
)
self.assertEqual(self.cfg.index_db_exe, 'makeblastdb')
self.tearDown()
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
index_db_exe = 'truc',
res_search_dir = '/tmp',
)
self.assertEqual(self.cfg.index_db_exe, 'truc')
def test_i_value_sel(self):
kwargs = {'cfg_file' : "nimportnaoik",
'sequence_db' : os.path.join(self._data_dir, "base", "test_base.fa"),
'db_type' : 'gembase',
'def_dir' : os.path.join(self._data_dir, 'DEF'),
'profile_dir' : os.path.join(self._data_dir, 'profiles'),
'i_evalue_sel' : 'foo',
'res_search_dir' : '/tmp',
}
self.assertRaises(ValueError, Config, **kwargs)
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = '/tmp'
)
self.assertEqual(self.cfg.i_evalue_sel, 0.001)
self.tearDown()
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
i_evalue_sel = 0.7,
res_search_dir = '/tmp',
)
self.assertEqual(self.cfg.i_evalue_sel, 0.7)
self.tearDown()
kwargs = {'cfg_file' : "nimportnaoik",
'sequence_db' : os.path.join(self._data_dir, "base", "test_base.fa"),
'db_type' : 'gembase',
'def_dir' : os.path.join(self._data_dir, 'DEF'),
'profile_dir' : os.path.join(self._data_dir, 'profiles'),
'e_value_res' : 0.7,
'i_evalue_sel' : 1,
'res_search_dir' : '/tmp',
}
self.assertRaises(ValueError, Config, **kwargs)
def test_db_type(self):
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = '/tmp',
)
self.assertEqual( self.cfg.db_type, 'gembase')
self.tearDown()
kwargs = {'cfg_file' : "nimportnaoik",
'sequence_db' : os.path.join(self._data_dir, "base", "test_base.fa"),
'db_type' : 'foo',
'def_dir' : os.path.join(self._data_dir, 'DEF'),
'profile_dir' : os.path.join(self._data_dir, 'profiles'),
'res_search_dir' : '/tmp',
}
self.assertRaises(ValueError, Config, **kwargs)
def test_previous_run(self):
kwargs = {'cfg_file' : "nimportnaoik",
'sequence_db' : os.path.join(self._data_dir, "base", "test_base.fa"),
'db_type' : 'gembase',
'def_dir' : os.path.join(self._data_dir, 'DEF'),
'profile_dir' : os.path.join(self._data_dir, 'profiles'),
'previous_run' : 'foo',
'res_search_dir' : '/tmp',
}
self.assertRaises(ValueError, Config, **kwargs)
try:
cfg_base = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = '/tmp',
)
self.assertIsNone(cfg_base.previous_run)
cfg_base.save( cfg_base.working_dir )
#wait
time.sleep(1)
new_cfg = Config(previous_run = cfg_base.working_dir)
self.assertEqual(new_cfg.previous_run, cfg_base.working_dir)
finally:
try:
shutil.rmtree(cfg_base.working_dir)
except:
pass
try:
shutil.rmtree(new_cfg.working_dir)
except:
pass
def test_profile_dir(self):
kwargs = {'cfg_file' : "nimportnaoik",
'sequence_db' : os.path.join(self._data_dir, "base", "test_base.fa"),
'db_type' : 'gembase',
'def_dir' : os.path.join(self._data_dir, 'DEF'),
'profile_dir' : 'foo',
'res_search_dir' : '/tmp',
}
self.assertRaises(ValueError, Config, **kwargs)
profile_dir = os.path.join(os.path.dirname(__file__), '..', 'data', 'profiles')
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = profile_dir,
res_search_dir = '/tmp',
)
self.assertEqual(self.cfg.profile_dir , profile_dir)
def test_profile_suffix(self):
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = '/tmp'
)
self.assertEqual(self.cfg.profile_suffix, '.hmm')
self.tearDown()
profile_suffix = 'foo'
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
profile_suffix = profile_suffix,
res_search_dir = '/tmp',
)
self.assertEqual(self.cfg.profile_suffix, profile_suffix)
def test_replicon_topology(self):
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = '/tmp',
)
self.assertEqual(self.cfg.replicon_topology, 'circular')
self.tearDown()
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
replicon_topology = 'linear',
res_search_dir = '/tmp',
)
self.assertEqual(self.cfg.replicon_topology, 'linear')
self.tearDown()
kwargs = {'cfg_file' : "nimportnaoik",
'sequence_db' : os.path.join(self._data_dir, "base", "test_base.fa"),
'db_type' : 'gembase',
'def_dir' : os.path.join(self._data_dir, 'DEF'),
'profile_dir' : os.path.join(self._data_dir, 'profiles'),
'replicon_topology' : 'foo'
}
self.assertRaises(ValueError, Config, **kwargs)
def test_inter_gene_max_space(self):
inter_gene_max_space = (["T2SS", 32], ['Flagellum', 64])
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
inter_gene_max_space = inter_gene_max_space,
res_search_dir = '/tmp',
)
self.assertEqual(self.cfg.inter_gene_max_space('T2SS'), 32)
self.assertEqual(self.cfg.inter_gene_max_space('Flagellum'), 64)
self.assertIsNone(self.cfg.inter_gene_max_space('Foo'))
def test_min_genes_required(self):
min_genes_required = (["T2SS", 32], ['Flagellum', 64])
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
min_genes_required = min_genes_required,
res_search_dir = '/tmp',
)
self.assertEqual(self.cfg.min_genes_required('T2SS'), 32)
self.assertEqual(self.cfg.min_genes_required('Flagellum'), 64)
self.assertIsNone(self.cfg.min_genes_required('Foo'))
def test_max_nb_genes(self):
max_nb_genes = (["T2SS", 32], ['Flagellum', 64])
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
max_nb_genes = max_nb_genes,
res_search_dir = '/tmp',
)
self.assertEqual(self.cfg.max_nb_genes('T2SS'), 32)
self.assertEqual(self.cfg.max_nb_genes('Flagellum'), 64)
self.assertIsNone(self.cfg.max_nb_genes('Foo'))
def test_min_mandatory_genes_required(self):
min_mandatory_genes_required = (["T2SS", 32], ['Flagellum', 64])
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
min_mandatory_genes_required = min_mandatory_genes_required,
res_search_dir = '/tmp',
)
self.assertEqual(self.cfg.min_mandatory_genes_required('T2SS'), 32)
self.assertEqual(self.cfg.min_mandatory_genes_required('Flagellum'), 64)
self.assertIsNone(self.cfg.min_mandatory_genes_required('Foo'))
def test_multi_loci(self):
multi_loci = "T2SS,Flagellum"
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
multi_loci = multi_loci,
res_search_dir = '/tmp',
)
self.assertTrue(self.cfg.multi_loci('T2SS'))
self.assertTrue(self.cfg.multi_loci('Flagellum'))
self.assertFalse(self.cfg.multi_loci('Foo'))
def test_res_extract_suffix(self):
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = '/tmp',
)
self.assertEqual(self.cfg.res_extract_suffix, '.res_hmm_extract')
self.tearDown()
res_extract_suffix = 'foo'
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_extract_suffix = res_extract_suffix,
res_search_dir = '/tmp',
)
self.assertEqual(self.cfg.res_extract_suffix, res_extract_suffix)
def test_res_search_dir(self):
kwargs = {'cfg_file' : "nimportnaoik",
'sequence_db' : os.path.join(self._data_dir, "base", "test_base.fa"),
'db_type' : 'gembase',
'def_dir' : os.path.join(self._data_dir, 'DEF'),
'profile_dir' : os.path.join(self._data_dir, 'profiles'),
'res_search_dir' : 'foo',
}
self.assertRaises(ValueError, Config, **kwargs)
res_search_dir = os.path.join(os.path.dirname(__file__), 'datatest')
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = res_search_dir
)
self.assertEqual(self.cfg.res_search_dir , res_search_dir)
def test_res_search_suffix(self):
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(os.path.dirname(__file__),'..', 'data', 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = '/tmp',
)
self.assertEqual(self.cfg.res_search_suffix, '.search_hmm.out')
self.tearDown()
res_search_suffix = 'foo'
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_suffix = res_search_suffix,
res_search_dir = '/tmp',
)
self.assertEqual(self.cfg.res_search_suffix, res_search_suffix)
# def test_save(self):
# pass
#
def test_sequence_db(self):
kwargs = {'cfg_file' : "nimportnaoik",
'db_type' : 'gembase',
'def_dir' : os.path.join(self._data_dir, 'DEF'),
'profile_dir' : os.path.join(self._data_dir, 'profiles'),
'worker_nb' : '2.3' ,
'res_search_dir' : '/tmp',
}
self.assertRaises(ValueError, Config, **kwargs)
kwargs = {'cfg_file' : "nimportnaoik",
'sequence_db' : "foo",
'db_type' : 'gembase',
'def_dir' : os.path.join(self._data_dir, 'DEF'),
'profile_dir' : os.path.join(self._data_dir, 'profiles'),
'worker_nb' : '2.3',
'res_search_dir' : '/tmp',
}
self.assertRaises(ValueError, Config, **kwargs)
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa")
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = sequence_db,
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = '/tmp',
)
self.assertEqual(self.cfg.sequence_db, sequence_db)
def test_worker_nb(self):
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = '/tmp'
)
self.assertEqual(self.cfg.worker_nb, 1)
self.tearDown()
self.cfg = Config(cfg_file = "nimportnaoik",
sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"),
db_type = 'gembase',
def_dir = os.path.join(self._data_dir, 'DEF'),
profile_dir = os.path.join(self._data_dir, 'profiles'),
res_search_dir = '/tmp',
worker_nb = 2
)
self.assertEqual(self.cfg.worker_nb, 2)
self.tearDown()
kwargs = {'cfg_file' : "nimportnaoik",
'sequence_db' : os.path.join(self._data_dir, "base", "test_base.fa"),
'db_type' : 'gembase',
'def_dir' : os.path.join(self._data_dir, 'DEF'),
'profile_dir' : os.path.join(self._data_dir, 'profiles'),
'res_search_dir' : '/tmp',
'worker_nb' : '2.3'
}
self.assertRaises(ValueError, Config, **kwargs)
