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)