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)