def nonsyn(self, frame):
nsyn, nnon = 0, 0
nsam = len(self.DNAdata.sequences)
syn_seqs, nonsyn_seqs = ['' for n in range(nsam)], ['' for n in range(nsam)]
for codons in loopByColumn(self.DNAdata.sequences, start = frame, size = 3):
nmiss = sum([len(set(i) - set('ATGCatgc')) for i in codons])
if nmiss > 0:
# contains non-ATGC data
pass
elif len(codons[0]) != 3:
# number of bases in codon != 3
pass
else:
ucodons = list(set(codons))
nucodons = len(ucodons)
if nucodons > 2:
# > 1 segregating site in codon
pass
elif nucodons == 1:
# monomorphic site
nsp, nnp = synNonsynProbs(ucodons[0])
nsyn += 3 * nsp
nnon += 3 * nnp
else:
codon1, codon2 = ucodons[0], ucodons[1]
codon_count = [(codons.count(codon1), codon1), (codons.count(codon2), codon2)]
codon_count.sort(reverse = True)
major = codon_count[0][1]
nsp, nnp = synNonsynProbs(major)
nsyn += 3 * nsp
nnon += 3 * nnp
sindex = [i for i in range(len(codon1)) if codon1[i] != codon2[i]][0]
for s in range(len(codons)):
aa1, aa2 = dna_to_amino[ucodons[0]], dna_to_amino[ucodons[1]]
if aa1 == aa2:
syn_seqs[s] += codons[s][sindex]
else:
nonsyn_seqs[s] += codons[s][sindex]
SynClass = type(self)(syn_seqs, self.DNAdata.ids)
NonSynClass = type(self)(nonsyn_seqs, self.DNAdata.ids)
SynClass.validSites = nsyn
NonSynClass.validSites = nnon
return SynClass, NonSynClass
def nonsyn(self, frame):
nsyn, nnon = 0, 0
nsam = len(self.DNAdata.sequences)
syn_seqs, nonsyn_seqs = ['' for n in range(nsam)], ['' for n in range(nsam)]
for codons in loopByColumn(self.DNAdata.sequences, start = frame, size = 3):
nmiss = sum([len(set(i) - set('ATGCatgc')) for i in codons])
if nmiss > 0:
# contains non-ATGC data
pass
elif len(codons[0]) != 3:
# number of bases in codon != 3
pass
else:
ucodons = list(set(codons))
nucodons = len(ucodons)
if nucodons > 2:
# > 1 segregating site in codon
pass
elif nucodons == 1:
# monomorphic site
nsp, nnp = synNonsynProbs(ucodons[0])
nsyn += 3 * nsp
nnon += 3 * nnp
else:
codon1, codon2 = ucodons[0], ucodons[1]
codon_count = [(codons.count(codon1), codon1), (codons.count(codon2), codon2)]
codon_count.sort(reverse = True)
major = codon_count[0][1]
nsp, nnp = synNonsynProbs(major)
nsyn += 3 * nsp
nnon += 3 * nnp
sindex = [i for i in range(len(codon1)) if codon1[i] != codon2[i]][0]
for s in range(len(codons)):
aa1, aa2 = dna_to_amino[ucodons[0]], dna_to_amino[ucodons[1]]
if aa1 == aa2:
syn_seqs[s] += codons[s][sindex]
else:
nonsyn_seqs[s] += codons[s][sindex]
SynClass = type(self)(syn_seqs, self.DNAdata.ids)
NonSynClass = type(self)(nonsyn_seqs, self.DNAdata.ids)
SynClass.validSites = nsyn
NonSynClass.validSites = nnon
return SynClass, NonSynClass
def iter_sites(self):
for site in loopByColumn(self.sequences):
yield site
def iter_sites(self):
for site in loopByColumn(self.sequences):
yield site
