def test_back_translate(self):
prot = "ACDEFGHIKLMNPQRSTVWY*"
t = GeneticCode.std()
t.table["CGA"]
s = t.back_translate(prot)
self.assertEqual(prot, str(t.translate(s)))
GeneticCode.std().back_table
def test_translate_std(self):
dna = "GCCATTGTAATGGGCCGCTGAAAGGGTGCCCGA"
t = GeneticCode.std()
s = t.translate(dna)
self.assertEqual(str(s), "AIVMGR*KGAR")
for t in GeneticCode.std_list():
t.translate(dna)
def test_translate(self):
# Ref: http://lists.open-bio.org/pipermail/biopython/2006-March/002960.html
cft = (
("Vertebrate Mitochondrial", 'GCCATTGTAATGGGCCGCTGAAAGGGTGCCCGA',
'AIVMGRWKGAR'),
(11, 'CAAGGCGTCGAAYAGCTTCAGGAACAGGAC', 'QGVE?LQEQD'),
(1, 'GCCATTGTAATGGGCCGCTGAAAGGGTGCCCGA', 'AIVMGR*KGAR'),
)
for code, dna, protein in cft:
c = GeneticCode.by_name(code)
trans = c.translate(dna)
self.assertEqual(str(trans), protein)
self.assertRaises(ValueError, GeneticCode.by_name, 'not_a_name')
def test_repr(self):
for t in GeneticCode.std_list():
r = repr(t)
gc = eval(r)
self.assertEqual(r, repr(gc))
self.assertEqual(str(gc), str(t))