class TestCoreGene(MacsyTest):
def setUp(self):
args = argparse.Namespace()
args.sequence_db = self.find_data("base", "test_1.fasta")
args.db_type = 'gembase'
args.models_dir = self.find_data('models')
args.res_search_dir = tempfile.gettempdir()
args.log_level = 30
self.cfg = Config(MacsyDefaults(), args)
self.model_name = 'foo'
self.model_location = ModelLocation(path=os.path.join(args.models_dir, self.model_name))
self.profile_factory = ProfileFactory(self.cfg)
def tearDown(self):
try:
shutil.rmtree(self.cfg.working_dir())
except:
pass
def test_core_gene(self):
model_fqn = "foo/bar"
model = Model(model_fqn, 10)
gene_name = 'toto'
cg = CoreGene(self.model_location, gene_name, self.profile_factory)
self.assertEqual(cg.name, gene_name)
self.assertEqual(cg.model_family_name, model.family_name)
self.assertEqual(cg.profile, self.profile_factory.get_profile(cg, self.model_location))
cg2 = CoreGene(self.model_location, gene_name, self.profile_factory)
self.assertTrue(isinstance(hash(cg), int))
self.assertEqual(hash(cg), hash(cg2))
gene_name = 'totote'
cg3 = CoreGene(self.model_location, gene_name, self.profile_factory)
self.assertNotEqual(hash(cg), hash(cg3))
class TestProfileFactory(MacsyTest):
def setUp(self):
args = argparse.Namespace()
args.sequence_db = self.find_data("base", "test_1.fasta")
args.db_type = 'gembase'
args.models_dir = self.find_data('models')
args.res_search_dir = tempfile.gettempdir()
args.log_level = 30
self.cfg = Config(MacsyDefaults(), args)
self.model_name = 'foo'
self.models_location = ModelLocation(
path=os.path.join(args.models_dir, self.model_name))
self.profile_factory = ProfileFactory(self.cfg)
def tearDown(self):
try:
shutil.rmtree(self.cfg.working_dir)
except:
pass
def test_get_profile(self):
gene_name = 'sctJ_FLG'
gene = CoreGene(self.models_location, gene_name, self.profile_factory)
profile = self.profile_factory.get_profile(gene, self.models_location)
self.assertTrue(isinstance(profile, Profile))
self.assertEqual(profile.gene.name, gene_name)
def test_get_uniq_object(self):
gene_name = 'sctJ_FLG'
gene = CoreGene(self.models_location, gene_name, self.profile_factory)
profile1 = self.profile_factory.get_profile(gene, self.models_location)
profile2 = self.profile_factory.get_profile(gene, self.models_location)
self.assertEqual(profile1, profile2)
def test_unknow_profile(self):
gene_name = 'sctJ_FLG'
gene = CoreGene(self.models_location, gene_name, self.profile_factory)
gene._name = "bar"
with self.assertRaises(MacsypyError) as ctx:
self.profile_factory.get_profile(gene, self.models_location)
self.assertEqual(str(ctx.exception),
f"'{self.model_name}/{gene.name}': No such profile")