def test008(self):
"""zero-length nucleotides"""
s = ""
c = [cod for cod in translate.codons(s)]
self.assertTrue(len(c) == 0)
self.assertTrue(translate.translate(s) == "")
self.assertTrue(translate.translateRaw(s) == "")
def test005(self):
"""codons"""
s = "ATGCatTCTNNNTAAAGA"
c = [cod for cod in translate.codons(s)]
self.assertTrue(c[0] == "ATG")
self.assertTrue(c[1] == "Cat")
self.assertTrue(c[-1] == "AGA")
def test008(self):
"""zero-length nucleotides"""
s = ''
c = [cod for cod in translate.codons(s)]
self.assertTrue(len(c) == 0)
self.assertTrue(translate.translate(s) == '')
self.assertTrue(translate.translateRaw(s) == '')
def test005(self):
"""codons"""
s = 'ATGCatTCTNNNTAAAGA'
c = [cod for cod in translate.codons(s)]
self.assertTrue(c[0] == 'ATG')
self.assertTrue(c[1] == 'Cat')
self.assertTrue(c[-1] == 'AGA')
def test009(self):
"""odd-length coding sequence"""
s = "TCTCGTAAGTACGCAGC"
c = [cod for cod in translate.codons(s)]
self.assertTrue(len(c) == 5)
self.assertTrue(c[-1] == "GCA")
self.assertTrue(translate.translate(s) is None)
self.assertTrue(translate.translateRaw(s) == "SRKYA")
def test009(self):
"""odd-length coding sequence"""
s = 'TCTCGTAAGTACGCAGC'
c = [cod for cod in translate.codons(s)]
self.assertTrue(len(c) == 5)
self.assertTrue(c[-1] == 'GCA')
self.assertTrue(translate.translate(s) is None)
self.assertTrue(translate.translateRaw(s) == 'SRKYA')
def makeMutantFromSequence(target_protein_seq, base_dna_seq): codons = [x for x in translate.codons(base_dna_seq)] base_prot_seq = translate.translate(base_dna_seq) assert len(base_prot_seq) == len(target_protein_seq) mutant_dna_seq = '' for (i, aa) in enumerate(target_protein_seq): if aa == base_prot_seq[i]: mutant_dna_seq += codons[i] else: mutant_dna_seq += translate.randomReverseTranslate(aa) assert translate.translate(mutant_dna_seq) == target_protein_seq return mutant_dna_seq
def test006(self):
"""zero-length codons"""
s = "AT"
c = [cod for cod in translate.codons(s)]
self.assertTrue(len(c) == 0)
info_outs.write(line)
# If optimization is desired, do it.
if options.optimize:
info_outs.write("# Optimizing sequences...\n")
gc = translate.geneticCode(rna=False)
codons = {}
opt_codon_dict = dict([(gc[c], c) for c in opt_codons])
opt_codon_dict['W'] = 'TGG'
opt_codon_dict['M'] = 'ATG'
opt_headers = []
opt_seqs = []
# optimize the codon sequences
for (id, seq) in seqs:
orig_codons = [c for c in translate.codons(seq)]
prot_seq = translate.translate(seq)
if not prot_seq is None:
for aa in translate.AAs():
codons[aa] = [
c for c in translate.getCodonsForAA(aa, rna=False)
if relad_dict[c] >= options.min_rel_adapt
]
opt_seq = ''
for (aai, aa) in enumerate(prot_seq):
#opt_seq += opt_codon_dict[aa] #random.choice(codons[aa])
codons_to_choose_from = codons[aa]
# If avoiding codons and we have a choice, eliminate the avoided codon.
if options.avoid_sequence and len(
codons_to_choose_from) > 1:
try:
def test006(self):
"""zero-length codons"""
s = 'AT'
c = [cod for cod in translate.codons(s)]
self.assertTrue(len(c) == 0)
info_outs.write(line)
# If optimization is desired, do it.
if options.optimize:
info_outs.write("# Optimizing sequences...\n")
gc = translate.geneticCode(rna=False)
codons = {}
opt_codon_dict = dict([(gc[c],c) for c in opt_codons])
opt_codon_dict['W'] = 'TGG'
opt_codon_dict['M'] = 'ATG'
opt_headers = []
opt_seqs = []
# optimize the codon sequences
for (id, seq) in seqs:
orig_codons = [c for c in translate.codons(seq)]
prot_seq = translate.translate(seq)
if not prot_seq is None:
for aa in translate.AAs():
codons[aa] = [c for c in translate.getCodonsForAA(aa, rna=False) if relad_dict[c] >= options.min_rel_adapt]
opt_seq = ''
for (aai, aa) in enumerate(prot_seq):
#opt_seq += opt_codon_dict[aa] #random.choice(codons[aa])
codons_to_choose_from = codons[aa]
# If avoiding codons and we have a choice, eliminate the avoided codon.
if options.avoid_sequence and len(codons_to_choose_from)>1:
try:
codons_to_choose_from.remove(orig_codons[aai])
except ValueError: # codon to be avoided not among codon choices anyway
pass
opt_seq += random.choice(codons_to_choose_from)
