def __call__(self, length):
"Retrieve a random sequence."
while True:
id, start, stop, orientation = self._choose_entry_point()
max_pos = stop-1-length
if max_pos > start:
pos = R.randint(start, max_pos)
segment = das.encode_segment(id, pos, pos+length)
id, start, stop, version, seq = das.fetch_dna(self.prefix, segment)
if seq.count('n') < length / 4: # make sure does not have too many 'N's
return seq
def __call__(self, length):
"Retrieve a random sequence."
while True:
id, start, stop, orientation = self._choose_entry_point()
max_pos = stop - 1 - length
if max_pos > start:
pos = R.randint(start, max_pos)
segment = das.encode_segment(id, pos, pos + length)
id, start, stop, version, seq = das.fetch_dna(
self.prefix, segment)
if seq.count(
'n'
) < length / 4: # make sure does not have too many 'N's
return seq
def get_dna_for_region(url, label, id_, start, end, padding_bases):
"@return: A Bio.Seq.SeqRecord for the specified region."
segment = '%s:%d,%d' % (id_, start-padding_bases, end+padding_bases)
_, _, _, _, sequence = das.fetch_dna(url, segment)
logging.debug('%s: DNA from %s for segment %s: %s' % (label, url, segment, sequence))
return SeqRecord(Seq(sequence, DNAAlphabet()), id=label, description='%s %s' % (url, segment))