def _attach_data(self, sequences, ids):
self.DNAdata = SeqTable(sequences, ids)
self.IOdata = self._get_IOdata(self.DNAdata)
def _attach_data(self, sequences, ids):
self.DNAdata = SeqTable(sequences, ids)
self.IOdata = self._get_IOdata(self.DNAdata)
class DnaPopulationData(IOstats):
"""
Class representation of DNA sequences from multiple
samples.
"""
def __init__(self, *args):
if len(args) == 1:
seqs, ids = self._from_sequence(args[0])
elif len(args) == 2:
seqs, ids = self._from_sequence(args[0], args[1])
else:
raise TypeError, "Wrong number of arguments"
self._attach_data(seqs, ids)
def _from_sequence(self, seqs, ids = None):
if isinstance(seqs, list) is False:
raise TypeError, 'List expected.'
n = len(seqs)
if isinstance(ids, list) is False:
if ids is None:
ids = create_ids(n, "seq")
else:
raise TypeError, 'List expected.'
return seqs, ids
def _attach_data(self, sequences, ids):
self.DNAdata = SeqTable(sequences, ids)
self.IOdata = self._get_IOdata(self.DNAdata)
######
def __getitem__(self, item):
if isinstance(item, str):
seq = DNAequence(self.DNAdata[item], item)
elif isinstance(item, int):
seq = DNAequence(self.DNAdata[item], self.DNAdata.ids[item])
else:
raise TypeError, "String or integer required"
return seq
def __len__(self):
return len(self.DNAdata)
######
def _get_IOdata(self, seqs):
self.validSites = 0
io = []
for site in seqs.iter_sites():
SiteClass = Site(site)
if SiteClass.has_missing_data():
pass
elif SiteClass.number_of_alleles() > 2:
pass
elif SiteClass.number_of_alleles() == 1:
self.validSites += 1
else:
self.validSites += 1
siteIO = booleanDNA(SiteClass.alleles())
io.append(siteIO)
IO = IOtable(io)
return IO
######
def iter_sites(self):
for site in self.DNAdata.iter_sites():
yield site
######
def ids(self):
return self.DNAdata.ids
def nsamples(self):
return self.__len__()
def sequences(self):
return self.DNAdata.sequences
def length(self):
return self.validSites
######
def index(self, key):
return self.DNAdata.index(key)
def pop(self, index = None):
seq, seqid = self.DNAdata.pop(index)
self.IOdata = self._get_IOdata(self.DNAdata)
return DNAsequence(seq, seqid)
def sample(self, n, replace = False):
rids = random.sample(self.ids(), n)
rseqs = []
seqs = self.sequences()
for rid in rids:
i = self.index(rid)
rseqs.append(seqs[i])
return type(self)(rseqs, rids)
def sort(self):
new_ids = sorted(self.ids())
new_seqs = []
for i in new_ids:
new_seqs.append(self[i].sequence)
self._attach_data(new_seqs, new_ids)
def subset(self, ids):
allids = self.ids()
allseqs = self.sequences()
seqs = []
for i in xrange(self.nsamples()):
if allids[i] in ids:
seqs.append(allseqs[i])
return type(self)(seqs, ids)
######
def coding(self, refseq):
dna = ['A', 'T', 'G', 'C', 'a', 't', 'g', 'c']
nsam = self.nsamples()
inc = (i for i in xrange(len(refseq)) if refseq[i] in dna)
cds_seqs = ['' for j in xrange(nsam)]
for site in inc:
for ind in xrange(nsam):
cds_seqs[ind] += self.DNAdata.sequences[ind][site]
return type(self)(cds_seqs, self.DNAdata.ids)
######
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
class DnaPopulationData(IOstats):
"""
Class representation of DNA sequences from multiple
samples.
"""
def __init__(self, *args):
if len(args) == 1:
seqs, ids = self._from_sequence(args[0])
elif len(args) == 2:
seqs, ids = self._from_sequence(args[0], args[1])
else:
raise TypeError, "Wrong number of arguments"
self._attach_data(seqs, ids)
def _from_sequence(self, seqs, ids = None):
if isinstance(seqs, list) is False:
raise TypeError, 'List expected.'
n = len(seqs)
if isinstance(ids, list) is False:
if ids is None:
ids = create_ids(n, "seq")
else:
raise TypeError, 'List expected.'
return seqs, ids
def _attach_data(self, sequences, ids):
self.DNAdata = SeqTable(sequences, ids)
self.IOdata = self._get_IOdata(self.DNAdata)
######
def __len__(self):
return len(self.DNAdata)
######
def _get_IOdata(self, seqs):
self.validSites = 0
io = []
for site in seqs.iter_sites():
SiteClass = Site(site)
if SiteClass.has_missing_data():
pass
elif SiteClass.number_of_alleles() > 2:
pass
elif SiteClass.number_of_alleles() == 1:
self.validSites += 1
else:
self.validSites += 1
siteIO = booleanDNA(SiteClass.alleles())
io.append(siteIO)
IO = IOtable(io)
return IO
######
def iter_sites(self):
for site in self.DNAdata.iter_sites():
yield site
######
def ids(self):
return self.DNAdata.ids
def nsamples(self):
return self.__len__()
def sequences(self):
return self.DNAdata.sequences
def length(self):
return self.validSites
######
def index(self, key):
return self.DNAdata.index(key)
def pop(self, index = None):
seq, seqid = self.DNAdata.pop(index)
self.IOdata = self._get_IOdata(self.DNAdata)
return DNAsequence(seq, seqid)
######
def coding(self, refseq):
dna = ['A', 'T', 'G', 'C', 'a', 't', 'g', 'c']
nsam = self.nsamples()
inc = (i for i in xrange(len(refseq)) if refseq[i] in dna)
cds_seqs = ['' for j in xrange(nsam)]
for site in inc:
for ind in xrange(nsam):
cds_seqs[ind] += self.DNAdata.sequences[ind][site]
return type(self)(cds_seqs, self.DNAdata.ids)
######
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