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_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_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_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)
