class TestConfig(MacsyTest):
def setUp(self):
self.defaults = MacsyDefaults()
self.parsed_args = Namespace()
def test_str_2_tuple(self):
s = 'set_1/Flagellum 12 set_1/t4ss 13'
expected = [('set_1/Flagellum', '12'), ('set_1/t4ss', '13')]
cfg = Config(self.defaults, self.parsed_args)
self.assertListEqual(cfg._str_2_tuple(s), expected)
with self.assertRaises(ValueError) as ctx:
s = 'set_1/Flagellum 12 set_1/t4ss'
cfg._str_2_tuple(s)
self.assertEqual(
str(ctx.exception),
f"You must provide a list of model name and value separated by spaces: {s}"
)
def test_config_file_2_dict(self):
cfg = Config(self.defaults, self.parsed_args)
res = cfg._config_file_2_dict(self.defaults, ['nimportnaoik'])
self.assertDictEqual({}, res)
cfg_file = self.find_data(
os.path.join('conf_files', 'macsy_test_conf.conf'))
res = cfg._config_file_2_dict(self.defaults, [cfg_file])
expected = {
'db_type': 'gembase',
'inter_gene_max_space': 'set_1/T2SS 2 set_1/Flagellum 4',
'min_mandatory_genes_required': 'set_1/T2SS 5 set_1/Flagellum 9',
'replicon_topology': 'circular',
'sequence_db': '/path/to/sequence/bank/fasta_file',
'topology_file': '/the/path/to/the/topology/to/use'
}
self.assertDictEqual(expected, res)
bad_cfg_file = self.find_data(
os.path.join('conf_files', 'macsy_test_bad_conf.conf'))
with self.assertRaises(ParsingError):
cfg._config_file_2_dict(self.defaults, [bad_cfg_file])
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_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_file_bad_values(self):
ori_conf_file = self.find_data(
os.path.join('conf_files', 'macsy_models.conf'))
config_parser = ConfigParser()
config_parser.read(ori_conf_file)
config_parser.add_section('general')
config_parser.set('general', 'worker', 'foo')
with tempfile.TemporaryDirectory() as tmpdirname:
dest_conf_file = os.path.join(tmpdirname, 'macsyfinder.conf')
with open(dest_conf_file, 'w') as cfg_file:
config_parser.write(cfg_file)
import macsypy.config
macsyconf = macsypy.config.__MACSY_CONF__
macsypy.config.__MACSY_CONF__ = tmpdirname
with self.assertRaises(ValueError) as ctx:
Config(self.defaults, self.parsed_args)
self.assertEqual(
str(ctx.exception),
"Invalid value in config_file for option 'worker': "
"invalid literal for int() with base 10: 'foo'")
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)
import macsypy.config
macsyconf = macsypy.config.__MACSY_CONF__
macsypy.config.__MACSY_CONF__ = tmpdirname
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)
else:
self.assertEqual(getattr(cfg, opt)(), val)
finally:
macsypy.config.__MACSY_CONF__ = macsyconf
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))
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))
else:
self.assertEqual(getattr(cfg, opt)(), exp_val)
def test_bad_values(self):
invalid_syntax = {
'inter_gene_max_space': 'set_1/Flagellum 4 2',
'max_nb_genes': 'set_1/Flagellum set_1/T3SS 3',
'min_genes_required': 'set_1/Flagellum set_1/T4SS 4',
'min_mandatory_genes_required': '12 set_1/T6SS 6',
}
for opt, val in invalid_syntax.items():
args = Namespace()
setattr(args, opt, val)
with self.assertRaises(ValueError) as ctx:
Config(self.defaults, args)
self.assertEqual(
str(ctx.exception),
f"Invalid syntax for '{opt}': You must provide a list of model name "
f"and value separated by spaces: {val}.")
int_error = {
'inter_gene_max_space': 'set_1/Flagellum 4.2 set_1/T2SS 2',
'max_nb_genes': 'set_1/Flagellum 4 set_1/T3SS FOO',
'min_genes_required': 'set_1/Flagellum FOO set_1/T4SS 4',
'min_mandatory_genes_required':
'set_1/Flagellum 12 set_1/T6SS 6.4',
}
for opt, val in int_error.items():
args = Namespace()
setattr(args, opt, val)
with self.assertRaises(ValueError):
Config(self.defaults, args)
def test_bad_db_type(self):
self.parsed_args.db_type = "FOO"
with self.assertRaises(ValueError) as ctx:
Config(self.defaults, self.parsed_args)
self.assertEqual(str(ctx.exception),
"db_type as unauthorized value : 'FOO'.")
def test_bad_topology(self):
self.parsed_args.replicon_topology = "FOO"
with self.assertRaises(ValueError) as ctx:
Config(self.defaults, self.parsed_args)
self.assertEqual(str(ctx.exception),
"replicon_topology as unauthorized value : 'FOO'.")
def test_bad_topology_file(self):
self.parsed_args.topology_file = "FOO"
with self.assertRaises(ValueError) as ctx:
Config(self.defaults, self.parsed_args)
self.assertEqual(
str(ctx.exception),
"topology_file 'FOO' does not exists or is not a file.")
def test_bad_sequence_db(self):
self.parsed_args.sequence_db = "FOO"
with self.assertRaises(ValueError) as ctx:
Config(self.defaults, self.parsed_args)
self.assertEqual(
str(ctx.exception),
"sequence_db 'FOO' does not exists or is not a file.")
def test_bad_models_dir(self):
self.parsed_args.models_dir = "FOO"
with self.assertRaises(ValueError) as ctx:
Config(self.defaults, self.parsed_args)
self.assertEqual(
str(ctx.exception),
"models_dir 'FOO' does not exists or is not a directory.")
def test_save(self):
self.parsed_args.max_nb_genes = [['Set_1/T2SS', 5],
['set_1/Flagelum', 12]]
self.parsed_args.multi_loci = 'Set_1/T2SS,set_1/Flagelum'
self.parsed_args.models = [['Set_1', 'T9SS', 'T3SS', 'T4SS_typeI']]
cfg = Config(self.defaults, self.parsed_args)
expected = {k: v for k, v in cfg._options.items() if v is not None}
expected['max_nb_genes'] = 'Set_1/T2SS 5 set_1/Flagelum 12'
expected['models'] = [('models_1', 'Set_1 T9SS T3SS T4SS_typeI')]
with tempfile.TemporaryDirectory() as tmpdirname:
cfg_path = os.path.join(tmpdirname, 'macsyfinder.conf')
cfg.save(path_or_buf=cfg_path)
saved_opt = cfg._config_file_2_dict(self.defaults, [cfg_path])
saved_opt['multi_loci'] = {
v
for v in
[v.strip() for v in saved_opt['multi_loci'].split(',')] if v
}
self.maxDiff = None
self.assertDictEqual(saved_opt, expected)
def test_out_dir(self):
cfg = Config(self.defaults, self.parsed_args)
self.assertEqual(
cfg.out_dir(),
os.path.join(cfg.res_search_dir(),
f'macsyfinder-{strftime("%Y%m%d_%H-%M-%S")}'))
self.parsed_args.out_dir = 'foo'
cfg = Config(self.defaults, self.parsed_args)
self.assertEqual(cfg.out_dir(), 'foo')
def test_working_dir(self):
cfg = Config(self.defaults, self.parsed_args)
self.assertEqual(cfg.out_dir(), cfg.working_dir())
def test_previous_n_sequence_db(self):
self.parsed_args.previous_run = self.find_data(
os.path.join('data_set', 'results'))
self.parsed_args.sequence_db = self.find_data(
os.path.join('base', 'test_1.fasta'))
with self.catch_log() as log:
cfg = Config(self.defaults, self.parsed_args)
catch_msg = log.get_value().strip()
self.assertEqual(cfg.sequence_db(), 'tests/data/base/test_1.fasta')
self.assertEqual(
f"ignore sequence_db '{self.parsed_args.sequence_db}' "
f"use sequence_db from previous_run '{self.parsed_args.previous_run}'.",
catch_msg)
def test_previous_wo_cfg(self):
self.parsed_args.previous_run = self.find_data(
os.path.join('data_set'))
with self.assertRaises(ValueError) as ctx:
Config(self.defaults, self.parsed_args)
self.assertEqual(
str(ctx.exception),
f"No config file found in dir {self.parsed_args.previous_run}")
def test_no_cut_ga(self):
cfg = Config(self.defaults, self.parsed_args)
self.assertFalse(cfg.no_cut_ga())
self.parsed_args.no_cut_ga = True
cfg = Config(self.defaults, self.parsed_args)
self.assertTrue(cfg.no_cut_ga())
def test_e_value_search(self):
cfg = Config(self.defaults, self.parsed_args)
self.assertEqual(self.defaults.e_value_search, cfg.e_value_search())
self.parsed_args.e_value_search = 1.0
cfg = Config(self.defaults, self.parsed_args)
self.assertEqual(cfg.e_value_search(), 1.0)
def test_hit_weights(self):
cfg = Config(self.defaults, self.parsed_args)
default = {
k: self.defaults[f"{k}_weight"]
for k in ('mandatory', 'accessory', 'neutral', 'itself',
'exchangeable', 'loner_multi_system')
}
self.assertDictEqual(default, cfg.hit_weights())
self.parsed_args.mandatory_weight = 2
self.parsed_args.accessory_weight = 1
self.parsed_args.exchangeable_weight = 0.5
self.parsed_args.loner_multi_system_weight = 0.2
cfg = Config(self.defaults, self.parsed_args)
expected = {
'mandatory': 2,
'accessory': 1,
'neutral': self.defaults.neutral_weight,
'itself': self.defaults.itself_weight,
'exchangeable': .5,
'loner_multi_system': .2
}
self.assertDictEqual(cfg.hit_weights(), expected)
class TestConfig(MacsyTest):
def setUp(self):
self._current_dir = os.getcwd()
self.tmp_dir = os.path.join(tempfile.gettempdir(),
'test_macsyfinder_Config')
if os.path.exists(self.tmp_dir):
shutil.rmtree(self.tmp_dir)
os.mkdir(self.tmp_dir)
self.defaults = MacsyDefaults()
self.parsed_args = Namespace()
def tearDown(self):
os.chdir(self._current_dir)
try:
shutil.rmtree(self.tmp_dir)
#pass
except Exception as err:
pass
def test_str_2_tuple(self):
s = 'set_1/Flagellum 12 set_1/t4ss 13'
expected = [('set_1/Flagellum', '12'), ('set_1/t4ss', '13')]
cfg = Config(self.defaults, self.parsed_args)
self.assertListEqual(cfg._str_2_tuple(s), expected)
with self.assertRaises(ValueError) as ctx:
s = 'set_1/Flagellum 12 set_1/t4ss'
cfg._str_2_tuple(s)
self.assertEqual(
str(ctx.exception),
f"You must provide a list of model name and value separated by spaces: {s}"
)
def test_set_option(self):
cfg = Config(self.defaults, self.parsed_args)
opts = {'GOOD': "GOOD", "BAD": None}
self.assertFalse('GOOD' in cfg._options)
self.assertFalse('BAD' in cfg._options)
cfg._set_options(opts)
self.assertTrue('GOOD' in cfg._options)
self.assertEqual(cfg._options['GOOD'], 'GOOD')
self.assertFalse('BAD' in cfg._options)
def test_set_log_level(self):
cfg = Config(self.defaults, self.parsed_args)
cfg._set_log_level(20)
self.assertEqual(cfg.log_level(), 20)
cfg._set_log_level('WARNING')
self.assertEqual(cfg.log_level(), 30)
with self.assertRaises(ValueError) as ctx:
cfg._set_log_level('FOO')
self.assertEqual(str(ctx.exception),
"Invalid value for log_level: FOO.")
def test_config_file_2_dict(self):
cfg = Config(self.defaults, self.parsed_args)
res = cfg._config_file_2_dict('nimportnaoik')
self.assertDictEqual({}, res)
cfg_file = self.find_data(
os.path.join('conf_files', 'macsy_test_conf.conf'))
res = cfg._config_file_2_dict(cfg_file)
expected = {
'db_type': 'gembase',
'inter_gene_max_space': 'set_1/T2SS 2 set_1/Flagellum 4',
'min_mandatory_genes_required': 'set_1/T2SS 5 set_1/Flagellum 9',
'replicon_topology': 'circular',
'sequence_db': '/path/to/sequence/bank/fasta_file',
'topology_file': '/the/path/to/the/topology/to/use'
}
self.assertDictEqual(expected, res)
bad_cfg_file = self.find_data(
os.path.join('conf_files', 'macsy_test_bad_conf.conf'))
with self.assertRaises(ParsingError):
cfg._config_file_2_dict(bad_cfg_file)
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}"
)
elif opt == 'models_dir':
val = self.defaults['system_models_dir']
self.assertEqual(
getattr(cfg, opt)(),
val,
msg=
f"test of '{opt}' failed : expected {getattr(cfg, opt)()} != got {val}"
)
else:
self.assertEqual(
getattr(cfg, opt)(),
val,
msg=
f"test of '{opt}' failed : expected {getattr(cfg, opt)()} != got {val}"
)
def test_cmd_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)
elif opt == 'models_dir':
self.assertEqual(
getattr(cfg, opt)(), self.defaults['system_models_dir'])
else:
self.assertEqual(getattr(cfg, opt)(),
val,
msg=f"error with {opt}")
self.parsed_args.cfg_file = 'niportnaoik'
with self.assertRaises(ValueError) as ctx:
Config(self.defaults, self.parsed_args)
self.assertEqual(str(ctx.exception),
"Config file niportnaoik not found.")
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)
def test_Config_file_bad_values(self):
ori_conf_file = self.find_data(
os.path.join('conf_files', 'macsy_models.conf'))
config_parser = ConfigParser()
config_parser.read(ori_conf_file)
config_parser.add_section('general')
config_parser.set('general', 'worker', 'foo')
with tempfile.TemporaryDirectory() as tmpdirname:
dest_conf_file = os.path.join(tmpdirname, 'macsyfinder.conf')
with open(dest_conf_file, 'w') as cfg_file:
config_parser.write(cfg_file)
self.parsed_args.cfg_file = dest_conf_file
with self.assertRaises(ValueError) as ctx:
Config(self.defaults, self.parsed_args)
self.assertEqual(
str(ctx.exception),
"Invalid value in config_file for option 'worker': "
"invalid literal for int() with base 10: 'foo'")
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_Config_conf_file_virtualenv(self):
methods_needing_args = {
'inter_gene_max_space': [('set_1/Flagellum', 4),
('set_1/T2SS', 2)],
'min_mandatory_genes_required': [('set_1/Flagellum', 9),
('set_1/T2SS', 5)]
}
modified_args = {
'db_type': 'gembase',
'coverage_profile': 0.1,
'replicon_topology': 'circular'
}
with tempfile.TemporaryDirectory() as tmpdirname:
ori_conf_file = self.find_data(
os.path.join('conf_files', 'macsy_virtualenv_test.conf'))
conf_dir = os.path.join(tmpdirname, 'etc', 'macsyfinder')
os.makedirs(conf_dir)
dest_conf_file = os.path.join(conf_dir, 'macsyfinder.conf')
shutil.copy(ori_conf_file, dest_conf_file)
virtual_env = os.environ.get("VIRTUAL_ENV")
os.environ['VIRTUAL_ENV'] = tmpdirname
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)
expected_values.update(modified_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 in ('max_nb_genes', 'min_genes_required',
'multi_loci'): # not set in cfg file
pass
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:
if virtual_env:
os.environ["VIRTUAL_ENV"] = virtual_env
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_model_conf(self):
self.parsed_args.models_dir = self.find_data('models')
self.parsed_args.models = "Model_w_conf all"
cfg = Config(self.defaults, self.parsed_args)
expected_weights = {
'mandatory': 13.0,
'accessory': 14.0,
'neutral': 0.0,
'itself': 11.0,
'exchangeable': 12.0,
'out_of_cluster': 10.0
}
self.assertDictEqual(cfg.hit_weights(), expected_weights)
self.assertEqual(cfg.i_evalue_sel(), 0.012)
self.assertEqual(cfg.e_value_search(), 0.12)
self.assertEqual(cfg.coverage_profile(), 0.55)
self.assertTrue(cfg.no_cut_ga())
def test_bad_values(self):
invalid_syntax = {
'inter_gene_max_space': 'set_1/Flagellum 4 2',
'max_nb_genes': 'set_1/Flagellum set_1/T3SS 3',
'min_genes_required': 'set_1/Flagellum set_1/T4SS 4',
'min_mandatory_genes_required': '12 set_1/T6SS 6',
}
for opt, val in invalid_syntax.items():
args = Namespace()
setattr(args, opt, val)
with self.assertRaises(ValueError) as ctx:
Config(self.defaults, args)
self.assertEqual(
str(ctx.exception),
f"Invalid syntax for '{opt}': You must provide a list of model name "
f"and value separated by spaces: {val}.")
int_error = {
'inter_gene_max_space': 'set_1/Flagellum 4.2 set_1/T2SS 2',
'max_nb_genes': 'set_1/Flagellum 4 set_1/T3SS FOO',
'min_genes_required': 'set_1/Flagellum FOO set_1/T4SS 4',
'min_mandatory_genes_required':
'set_1/Flagellum 12 set_1/T6SS 6.4',
}
for opt, val in int_error.items():
args = Namespace()
setattr(args, opt, val)
with self.assertRaises(ValueError):
Config(self.defaults, args)
def test_bad_db_type(self):
self.parsed_args.db_type = "FOO"
with self.assertRaises(ValueError) as ctx:
Config(self.defaults, self.parsed_args)
self.assertEqual(str(ctx.exception),
"db_type as unauthorized value : 'FOO'.")
def test_bad_topology(self):
self.parsed_args.replicon_topology = "FOO"
with self.assertRaises(ValueError) as ctx:
Config(self.defaults, self.parsed_args)
self.assertEqual(str(ctx.exception),
"replicon_topology as unauthorized value : 'FOO'.")
def test_bad_topology_file(self):
self.parsed_args.topology_file = "FOO"
with self.assertRaises(ValueError) as ctx:
Config(self.defaults, self.parsed_args)
self.assertEqual(
str(ctx.exception),
"topology_file 'FOO' does not exists or is not a file.")
def test_bad_sequence_db(self):
self.parsed_args.sequence_db = "FOO"
with self.assertRaises(ValueError) as ctx:
Config(self.defaults, self.parsed_args)
self.assertEqual(
str(ctx.exception),
"sequence_db 'FOO' does not exists or is not a file.")
def test_bad_models_dir(self):
self.parsed_args.models_dir = "FOO"
with self.assertRaises(ValueError) as ctx:
Config(self.defaults, self.parsed_args)
self.assertEqual(
str(ctx.exception),
"models_dir 'FOO' does not exists or is not a directory.")
def test_save(self):
self.parsed_args.max_nb_genes = [['Set_1/T2SS', 5],
['set_1/Flagelum', 12]]
self.parsed_args.multi_loci = 'Set_1/T2SS,set_1/Flagelum'
self.parsed_args.models = ['Set_1', 'T9SS', 'T3SS', 'T4SS_typeI']
cfg = Config(self.defaults, self.parsed_args)
expected = {k: v for k, v in cfg._options.items() if v is not None}
expected['max_nb_genes'] = 'Set_1/T2SS 5 set_1/Flagelum 12'
expected['models'] = 'Set_1 T9SS T3SS T4SS_typeI'
# save in file 'macsyfinder.conf'
with tempfile.TemporaryDirectory() as tmpdirname:
cfg_path = os.path.join(tmpdirname, 'macsyfinder.conf')
cfg.save(path_or_buf=cfg_path)
cfg.save(path_or_buf='/tmp/macsyfinder.conf')
new_args = Namespace()
new_args.cfg_file = cfg_path
restored_cfg = Config(self.defaults, new_args)
self.maxDiff = None
# the option cfg-file differ from the 2 configs
# None in cfg
# cfg_path in restored_cfg
self.assertEqual(restored_cfg._options['cfg_file'], cfg_path)
del (cfg._options['cfg_file'])
del (restored_cfg._options['cfg_file'])
self.assertDictEqual(cfg._options, restored_cfg._options)
def test_out_dir(self):
cfg = Config(self.defaults, self.parsed_args)
self.assertEqual(
cfg.out_dir(),
os.path.join(cfg.res_search_dir(),
f'macsyfinder-{strftime("%Y%m%d_%H-%M-%S")}'))
self.parsed_args.out_dir = 'foo'
cfg = Config(self.defaults, self.parsed_args)
self.assertEqual(cfg.out_dir(), 'foo')
def test_working_dir(self):
cfg = Config(self.defaults, self.parsed_args)
self.assertEqual(cfg.out_dir(), cfg.working_dir())
def test_models_dir(self):
self.parsed_args.models_dir = self.tmp_dir
cfg = Config(self.defaults, self.parsed_args)
self.assertEqual(cfg.models_dir(), [self.tmp_dir])
def test_previous_n_sequence_db(self):
self.parsed_args.previous_run = self.find_data(
os.path.join('data_set', 'results_1'))
sequence_db = self.find_data(os.path.join('base', 'test_1.fasta'))
self.parsed_args.sequence_db = sequence_db
with self.catch_log() as log:
cfg = Config(self.defaults, self.parsed_args)
# The config set the parsed_args.sequence_db to None
catch_msg = log.get_value().strip()
self.assertEqual(cfg.sequence_db(),
'tests/data/base/VICH001.B.00001.C001.prt')
self.maxDiff = None
self.assertEqual(
f"ignore sequence_db '{sequence_db}' use sequence_db from previous_run "
f"'{os.path.abspath(cfg.previous_run())}'.", catch_msg)
def test_previous_wo_cfg(self):
self.parsed_args.previous_run = self.find_data(
os.path.join('data_set'))
with self.assertRaises(ValueError) as ctx:
Config(self.defaults, self.parsed_args)
self.assertEqual(
str(ctx.exception),
f"No config file found in dir {self.parsed_args.previous_run}")
def test_no_cut_ga(self):
cfg = Config(self.defaults, self.parsed_args)
self.assertFalse(cfg.no_cut_ga())
self.parsed_args.no_cut_ga = True
cfg = Config(self.defaults, self.parsed_args)
self.assertTrue(cfg.no_cut_ga())
def test_e_value_search(self):
cfg = Config(self.defaults, self.parsed_args)
self.assertEqual(self.defaults.e_value_search, cfg.e_value_search())
self.parsed_args.e_value_search = 1.0
cfg = Config(self.defaults, self.parsed_args)
self.assertEqual(cfg.e_value_search(), 1.0)
def test_hit_weights(self):
cfg = Config(self.defaults, self.parsed_args)
default = {
k: self.defaults[f"{k}_weight"]
for k in ('mandatory', 'accessory', 'neutral', 'itself',
'exchangeable', 'out_of_cluster')
}
self.assertDictEqual(default, cfg.hit_weights())
self.parsed_args.mandatory_weight = 2
self.parsed_args.accessory_weight = 1
self.parsed_args.exchangeable_weight = 0.5
self.parsed_args.out_of_cluster_weight = 0.2
cfg = Config(self.defaults, self.parsed_args)
expected = {
'mandatory': 2,
'accessory': 1,
'neutral': self.defaults.neutral_weight,
'itself': self.defaults.itself_weight,
'exchangeable': .5,
'out_of_cluster': .2
}
self.assertDictEqual(cfg.hit_weights(), expected)