def sequence(self, per_exon=False):
"""
if per-exon is True, return an array of exon sequences
NOTE: this is never reverse-complemented. TODO??
"""
db = self.db
if not per_exon:
start = self.txStart + 1
return _sequence(db, self.chrom, start, self.txEnd)
else:
# TODO: use same strategy as cds_sequence to reduce # of requests.
seqs = []
for start, end in self.exons:
seqs.append(_sequence(db, self.chrom, start + 1, end))
return seqs
def sequence(self, per_exon=False):
"""
if per-exon is True, return an array of exon sequences
NOTE: this is never reverse-complemented. TODO??
"""
db = self.db
if not per_exon:
start = self.txStart + 1
return _sequence(db, self.chrom, start, self.txEnd)
else:
# TODO: use same strategy as cds_sequence to reduce # of requests.
seqs = []
for start, end in self.exons:
seqs.append(_sequence(db, self.chrom, start + 1, end))
return seqs
def cds_sequence(self):
seqs = []
cds = self.cds
# grab all the sequences at once to reduce number of requests.
all_seq = _sequence(self.db, self.chrom, cds[0][0] + 1, cds[-1][1])
lowest = cds[0][0]
cds0 = [(s - lowest, e - lowest) for s, e in cds]
for cstart, cend in cds0:
seqs.append(all_seq[cstart:cend])
return seqs
def _cds_sequence(self, cds):
seqs = []
if len(cds) == 0: return []
# grab all the sequences at once to reduce number of requests.
all_seq = _sequence(self.db, self.chrom, cds[0][0] + 1, cds[-1][1])
if len(cds) == 1:
return all_seq
lowest = cds[0][0]
cds0 = [(s - lowest, e - lowest) for s, e in cds]
for cstart, cend in cds0:
seqs.append(all_seq[cstart:cend])
return seqs
def _cds_sequence(self, cds):
seqs = []
if len(cds) == 0: return []
# grab all the sequences at once to reduce number of requests.
all_seq = _sequence(self.db, self.chrom, cds[0][0] + 1, cds[-1][1])
if len(cds) == 1:
return all_seq
lowest = cds[0][0]
cds0 = [(s - lowest, e - lowest) for s, e in cds]
for cstart, cend in cds0:
seqs.append(all_seq[cstart:cend])
return seqs
