def sites_count_dict(codon_transitions=codon_weighting(empirical_mutations())):
"""Count sites for each codon, weighted by a mutation distribution."""
codons = []
for a in 'ATCG':
for b in 'ATCG':
for c in 'ATCG':
codons.append(a + b + c)
d = dict()
for codon in codons:
a = 0
s = 0
for i in range(len(codon)):
bases = list('ATCG')
bases.remove(codon[i])
aa = sequtil.translate_orf(codon)
for base in bases:
new_codon = list(codon)
new_codon[i] = base
new_codon = "".join(new_codon)
new_aa = sequtil.translate_orf(new_codon)
if new_aa == aa:
s += 3 * codon_transitions[(codon, new_codon)]
else:
a += 3 * codon_transitions[(codon, new_codon)]
d[codon] = (a, s)
return d
def sites_count_dict(codon_transitions=codon_weighting(empirical_mutations())):
"""Count sites for each codon, weighted by a mutation distribution."""
codons = []
for a in 'ATCG':
for b in 'ATCG':
for c in 'ATCG':
codons.append(a + b + c)
d = dict()
for codon in codons:
a = 0
s = 0
for i in range(len(codon)):
bases = list('ATCG')
bases.remove(codon[i])
aa = sequtil.translate_orf(codon)
for base in bases:
new_codon = list(codon)
new_codon[i] = base
new_codon = "".join(new_codon)
new_aa = sequtil.translate_orf(new_codon)
if new_aa == aa:
s += 3 * codon_transitions[(codon, new_codon)]
else:
a += 3 * codon_transitions[(codon, new_codon)]
d[codon] = (a,s)
return d
def is_nonsyn(snp):
'test whether snp is non-synonymous, assuming frame 0 CDS annotation'
geneSNP = snp.geneSNP
ipos = geneSNP.start % 3
codonStart = geneSNP.start - ipos
codon = str(geneSNP.path.sequence[codonStart:codonStart + 3])
b = snp.alt # substitution letter
if geneSNP.sequence.orientation < 0: # must complement
b = rcDict[b.upper()]
codonAlt = codon[:ipos] + b + codon[ipos + 1:]
snp.aaRef = sequtil.translate_orf(codon)
snp.aaAlt = sequtil.translate_orf(codonAlt)
return snp.aaRef != snp.aaAlt
def test_simple_translate(self):
db = self.db
assert sequtil.translate_orf(str(db['methionine'])) == 'M'
assert sequtil.translate_orf(str(db['flim'])) == 'FLIM'
def test_simple_translate(self):
db = self.db
assert sequtil.translate_orf(str(db['methionine'])) == 'M'
assert sequtil.translate_orf(str(db['flim'])) == 'FLIM'
