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*'})
