def test_get_codon_optim_seq(self):
'''Tests get_codon_optim_seq method.'''
cod_opt = codon_utils.CodonOptimiser('83333')
aa_codes = codon_utils.AA_CODES
aa_codes.pop('Stop')
aa_seq = ''.join([random.choice(list(aa_codes.values()))
for _ in range(random.randint(100, 2500))])
max_repeat_nuc = 5
restr_enzyms = ['BsaI']
dna_seq = cod_opt.get_codon_optim_seq(aa_seq,
max_repeat_nuc=max_repeat_nuc,
restr_enzyms=restr_enzyms)
self.assertFalse(seq_utils.is_invalid(dna_seq, max_repeat_nuc,
restr_enzyms))
def __init__(self, dna, organism, filters):
self.__dna = dna_utils.get_dna(dna)
self.__dna['typ'] = dna_utils.SO_PART
self.__dna['parameters']['Type'] = 'PART'
self.__organism = organism
self.__filters = filters
self.__filters['restr_enzs'] = self.__filters.get('restr_enzs', [])
self.__filters['gc_min'] = float(self.__filters['gc_min'])
self.__filters['gc_max'] = float(self.__filters['gc_max'])
self.__calc = rbs_calculator.RbsCalculator(
organism['r_rna'], vienna_utils) \
if self.__organism else None
self.__cod_opt = codon_utils.CodonOptimiser(organism['taxonomy_id']) \
if self.__organism else None
self.__dna_new = None
def test_get_random_codon_fail(self):
'''Tests get_random_codon method.'''
cod_opt = codon_utils.CodonOptimiser('83333')
self.assertRaises(
ValueError, cod_opt.get_random_codon, 'M', ['ATG'])
def test_get_random_codon(self):
'''Tests get_random_codon method.'''
cod_opt = codon_utils.CodonOptimiser('83333')
self.assertEqual('CTA', cod_opt.get_random_codon('L', ['CTG', 'TTA',
'CTT', 'TTG',
'CTC']))
def test_get_codon_prob(self):
'''Tests get_codon_prob method.'''
cod_opt = codon_utils.CodonOptimiser('83333')
self.assertAlmostEqual(0.46, cod_opt.get_codon_prob('CTG'), 2)