def esl_sfetch(sequence_file, name_iter, output_fp, use_temp=False):
"""
Fetch sequences named in name_iter from sequence_file, indexing if
necessary, writing to output_fp.
If ``use_temp`` is True, a temporary index is created and used.
"""
if not use_temp:
if not os.path.exists(sequence_file + '.ssi'):
logging.info("No index exists for %s. creating.", sequence_file)
peasel.create_ssi(sequence_file)
index = peasel.open_ssi(sequence_file)
sequences = (index[i] for i in name_iter)
count = peasel.write_fasta(sequences, output_fp)
else:
with peasel.temp_ssi(sequence_file) as index:
sequences = (index[i] for i in name_iter)
count = peasel.write_fasta(sequences, output_fp)
return count
def esl_sfetch(sequence_file, name_iter, output_fp, use_temp=False):
"""
Fetch sequences named in name_iter from sequence_file, indexing if
necessary, writing to output_fp.
If ``use_temp`` is True, a temporary index is created and used.
"""
if use_temp:
with peasel.temp_ssi(sequence_file) as index:
sequences = (index[i] for i in name_iter)
count = peasel.write_fasta(sequences, output_fp)
else:
try:
peasel.create_ssi(sequence_file)
except IOError:
logging.debug("An index already exists for %s", sequence_file)
index = peasel.open_ssi(sequence_file)
sequences = (index[i] for i in name_iter)
count = peasel.write_fasta(sequences, output_fp)
return count
def esl_sfetch(sequence_file, name_iter, output_fp, use_temp=False):
"""
Fetch sequences named in name_iter from sequence_file, indexing if
necessary, writing to output_fp.
If ``use_temp`` is True, a temporary index is created and used.
"""
if use_temp:
with peasel.temp_ssi(sequence_file) as index:
sequences = (index[i] for i in name_iter)
count = peasel.write_fasta(sequences, output_fp)
else:
try:
peasel.create_ssi(sequence_file)
except IOError:
logging.debug("An index already exists for %s", sequence_file)
index = peasel.open_ssi(sequence_file)
sequences = (index[i] for i in name_iter)
count = peasel.write_fasta(sequences, output_fp)
return count
def test_temp_ssi(self):
with peasel.temp_ssi(self.file_path) as ssi:
seq2 = ssi['sequence2']
self.assertTrue(seq2 is not None)
def test_temp_ssi(self):
with peasel.temp_ssi(self.file_path) as ssi:
seq2 = ssi['sequence2']
self.assertTrue(seq2 is not None)
