def test_is_aligned(self):
system = System(self.cfg, "T2SS", 10)
gene_ref = Gene(self.cfg, 'sctJ_FLG', system, self.profile_registry)
gene = Gene(self.cfg, 'sctJ', system, self.profile_registry)
homolog = Homolog( gene, gene_ref)
self.assertFalse( homolog.is_aligned() )
homolog = Homolog(gene, gene_ref, aligned = True )
self.assertTrue( homolog.is_aligned() )
def test_get_homologs(self):
system_foo = System(self.cfg, "foo", 10)
system_bar = System(self.cfg, "bar", 10)
gene = Gene(self.cfg, 'sctN', system_foo, self.profile_registry)
sctJ_FLG = Gene(self.cfg, 'sctJ_FLG', system_foo,
self.profile_registry)
sctJ = Gene(self.cfg, 'sctJ', system_bar, self.profile_registry)
homolog_1 = Homolog(sctJ_FLG, gene)
gene.add_homolog(homolog_1)
homolog_2 = Homolog(sctJ, gene)
gene.add_homolog(homolog_2)
self.assertEqual(gene.get_homologs(), [homolog_1, homolog_2])
def test_add_homolog(self):
system_foo = System(self.cfg, "foo", 10)
system_bar = System(self.cfg, "bar", 10)
gene = Gene(self.cfg, 'sctJ_FLG', system_foo, self.profile_registry)
gene_ref = Gene(self.cfg, 'sctJ', system_bar, self.profile_registry)
homolog = Homolog(self.cfg, gene, gene_ref)
gene.add_homolog(homolog)
self.assertEqual(len(gene.homologs), 1)
self.assertEqual(gene.homologs[0], homolog)
def test_is_aligned(self):
system = System(self.cfg, "T2SS", 10)
gene_ref = Gene(self.cfg, 'sctJ_FLG', system, self.profile_registry)
gene = Gene(self.cfg, 'sctJ', system, self.profile_registry)
homolog = Homolog(gene, gene_ref)
self.assertFalse(homolog.is_aligned())
homolog = Homolog(gene, gene_ref, aligned=True)
self.assertTrue(homolog.is_aligned())
def test_str(self):
"""
"""
system_foo = System(self.cfg, "foo", 10)
gene = Gene(self.cfg, 'sctJ_FLG', system_foo, self.profile_registry)
system_bar = System(self.cfg, "bar", 20)
gene_homolog = Gene(self.cfg, 'sctJ', system_bar,
self.profile_registry)
homolog = Homolog(gene_homolog, gene, self.cfg)
gene.add_homolog(homolog)
s = """name : sctJ_FLG
inter_gene_max_space: 10
homologs: sctJ"""
self.assertEqual(str(gene), s)
def test_get_gene_ref(self):
system = System(self.cfg, "foo", 10)
gene_name = 'sctJ_FLG'
gene_ref = Gene(self.cfg, gene_name, system, self.profile_registry)
homolog_name = 'sctJ'
gene_homolg = Gene(self.cfg, homolog_name, system,
self.profile_registry)
homolog = Homolog(gene_homolg, gene_ref)
gene_ref.add_homolog(homolog)
for meth in (system.add_forbidden_gene, system.add_accessory_gene,
system.add_mandatory_gene):
system._mandatory_genes = []
system._accessory_genes = []
system._forbidden_genes = []
meth(gene_ref)
self.assertEqual(gene_ref, system.get_gene_ref(homolog))
self.assertIsNone(system.get_gene_ref(gene_ref))
gene_ukn = Gene(self.cfg, 'abc', system, self.profile_registry)
self.assertRaises(KeyError, system.get_gene_ref, gene_ukn)
def test_get_gene(self):
system = System(self.cfg, "foo", 10)
gene_name = 'sctJ_FLG'
gene = Gene(self.cfg, gene_name, system, self.profile_registry)
for meth in (system.add_forbidden_gene, system.add_accessory_gene,
system.add_mandatory_gene):
system._mandatory_genes = []
system._accessory_genes = []
system._forbidden_genes = []
meth(gene)
self.assertEqual(gene, system.get_gene(gene_name))
self.assertRaises(KeyError, system.get_gene, 'bar')
homolog_name = 'sctJ'
gene_homolog = Gene(self.cfg, homolog_name, system,
self.profile_registry)
homolog = Homolog(gene_homolog, gene)
gene.add_homolog(homolog)
for meth in (system.add_forbidden_gene, system.add_accessory_gene,
system.add_mandatory_gene):
system._mandatory_genes = []
system._accessory_genes = []
system._forbidden_genes = []
meth(gene)
self.assertEqual(homolog, system.get_gene(homolog_name))
analog_name = 'sctC'
gene_analog = Gene(self.cfg, analog_name, system,
self.profile_registry)
analog = Analog(gene_analog, gene)
gene.add_analog(analog)
for meth in (system.add_forbidden_gene, system.add_accessory_gene,
system.add_mandatory_gene):
system._mandatory_genes = []
system._accessory_genes = []
system._forbidden_genes = []
meth(gene)
self.assertEqual(analog, system.get_gene(analog_name))
def test_delegation(self):
system = System(self.cfg, "T2SS", 10)
gene_ref = Gene(self.cfg, 'sctJ_FLG', system, self.profile_registry)
gene = Gene(self.cfg, 'sctJ', system, self.profile_registry)
homolog = Homolog(gene, gene_ref)
self.assertEqual(homolog.system, system)
def test_gene_ref(self):
system = System(self.cfg, "T2SS", 10)
gene_ref = Gene(self.cfg, 'sctJ_FLG', system, self.profile_registry)
gene = Gene(self.cfg, 'sctJ', system, self.profile_registry)
homolog_1 = Homolog(gene, gene_ref)
self.assertEqual(homolog_1.gene_ref, gene_ref)