def test_standard_code_lookup(self): """GeneticCodes should hold codes keyed by id as string and number""" sgc_new = GeneticCode(*self.NcbiStandard) sgc_number = GeneticCodes[1] sgc_string = GeneticCodes["1"] for sgc in sgc_new, sgc_number, sgc_string: self.assertEqual(sgc.CodeSequence, "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG") self.assertEqual(sgc.StartCodonSequence, "---M---------------M---------------M----------------------------") self.assertEqual(sgc.StartCodons, {"TTG": "M", "CTG": "M", "ATG": "M"}) self.assertEqual(sgc.ID, 1) self.assertEqual(sgc.Name, "Standard Nuclear") self.assertEqual(sgc["TTT"], "F") self.assertEqual(sgc.isStart("ATG"), True) self.assertEqual(sgc.isStart("AAA"), False) self.assertEqual(sgc.isStop("TAA"), True) self.assertEqual(sgc.isStop("AAA"), False) mtgc = GeneticCodes[2] self.assertEqual(mtgc.Name, "Vertebrate Mitochondrial") self.assertEqual(mtgc.isStart("AUU"), True) self.assertEqual(mtgc.isStop("UGA"), False) self.assertEqual(sgc_new.changes(mtgc), {"AGA": "R*", "AGG": "R*", "ATA": "IM", "TGA": "*W"}) self.assertEqual(mtgc.changes(sgc_new), {"AGA": "*R", "AGG": "*R", "ATA": "MI", "TGA": "W*"}) self.assertEqual(mtgc.changes(mtgc), {}) self.assertEqual( mtgc.changes("FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG"), {"AGA": "*R", "AGG": "*R", "ATA": "MI", "TGA": "W*"}, )
def test_standard_code_lookup(self): """GeneticCodes should hold codes keyed by id as string and number""" sgc_new = GeneticCode(*self.NcbiStandard) sgc_number = GeneticCodes[1] sgc_string = GeneticCodes['1'] for sgc in sgc_new, sgc_number, sgc_string: self.assertEqual(sgc.CodeSequence, 'FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG') self.assertEqual(sgc.StartCodonSequence, '---M---------------M---------------M----------------------------') self.assertEqual(sgc.StartCodons, {'TTG':'M', 'CTG':'M', 'ATG':'M'}) self.assertEqual(sgc.ID, 1) self.assertEqual(sgc.Name, 'Standard Nuclear') self.assertEqual(sgc['TTT'], 'F') self.assertEqual(sgc.isStart('ATG'), True) self.assertEqual(sgc.isStart('AAA'), False) self.assertEqual(sgc.isStop('TAA'), True) self.assertEqual(sgc.isStop('AAA'), False) mtgc = GeneticCodes[2] self.assertEqual(mtgc.Name, 'Vertebrate Mitochondrial') self.assertEqual(mtgc.isStart('AUU'), True) self.assertEqual(mtgc.isStop('UGA'), False) self.assertEqual(sgc_new.changes(mtgc), {'AGA':'R*', 'AGG':'R*', 'ATA':'IM', 'TGA':'*W'}) self.assertEqual(mtgc.changes(sgc_new), {'AGA':'*R', 'AGG':'*R', 'ATA':'MI', 'TGA':'W*'}) self.assertEqual(mtgc.changes(mtgc), {}) self.assertEqual(mtgc.changes( 'FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG'), {'AGA':'*R', 'AGG':'*R', 'ATA':'MI', 'TGA':'W*'})