def set_ref_data(self):
"""Write the reference sequence to a fasta file for this specific target if it does not
exist.
Args:
None
Returns:
None
Raise:
None
"""
# Write reference fasta file if needed.
for i in range(len(self.files['target_ref_fn'])):
fn = self.files['target_ref_fn'][i]
direction = "forward" if fn.find("forward") != -1 else "reverse"
utils.log(self.loggingName, 'info', 'Extracting refseq sequence and writing %s' % fn)
utils.extract_refseq_fa(self.values, self.paths['ref_data'], self.params.get_param('reference_fasta'), direction, fn)
# If using blatn for target realignment, the db must be available.
blastn = self.params.get_param('blast')
if blastn is not None:
# Check if blast db files are available for each target.
if not os.path.isfile(self.files['target_ref_fn'][0] + '.nin'):
makedb = os.path.join(os.path.split(blastn)[0], 'makeblastdb') # Create blast db
cmd = "%s -in %s -dbtype 'nucl' -out %s" % (makedb, self.files['target_ref_fn'][0], self.files['target_ref_fn'][0])
utils.log(self.loggingName, 'info', 'Creating blast db files for target %s with reference file %s' % (self.name, self.files['target_ref_fn'][0]))
p = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True)
output, errors = p.communicate()
if errors != '':
utils.log(self.loggingName, 'debug', 'Failed to make blast db files using reference file %s' % self.files['target_ref_fn'][0])
def set_ref_data(self):
'''
'''
# Write rmask bed file if needed.
# if not self.params.opts['keep_repeat_regions'] and 'repeat_mask_file' in self.params.opts:
# self.logger.info('Extracting repeat mask regions for target gene %s.' % self.name)
# self.repeat_mask = setup_rmask(self.get_values(), self.paths['ref_data'], self.params.opts['repeat_mask_file'])
# Write reference fasta file if needed.
for target_refseq_fn in self.files['target_ref_fn']:
direction = "forward"
if target_refseq_fn.find("forward") == -1:
direction = "reverse"
utils.log(self.logging_name, 'info', 'Extracting refseq sequence and writing %s' % target_refseq_fn)
utils.extract_refseq_fa(self.get_values(), self.paths['ref_data'], self.params.get_param('reference_fasta'), direction, target_refseq_fn, self.params.get_param('buffer_size'))
def set_ref_data(self):
'''
'''
# Write rmask bed file if needed.
# if not self.params.opts['keep_repeat_regions'] and 'repeat_mask_file' in self.params.opts:
# self.logger.info('Extracting repeat mask regions for target gene %s.' % self.name)
# self.repeat_mask = setup_rmask(self.get_values(), self.paths['ref_data'], self.params.opts['repeat_mask_file'])
# Write reference fasta file if needed.
for target_refseq_fn in self.files['target_ref_fn']:
direction = "forward"
if target_refseq_fn.find("forward") == -1:
direction = "reverse"
utils.log(self.logging_name, 'info', 'Extracting refseq sequence and writing %s' % target_refseq_fn)
utils.extract_refseq_fa(self.get_values(), self.paths['ref_data'], self.params.get_param('reference_fasta'), direction, target_refseq_fn, self.params.get_param('buffer_size'))
def set_ref_data(self):
"""Write the reference sequence to a fasta file for this specific target if it does not
exist.
Args:
None
Returns:
None
Raise:
None
"""
# Write reference fasta file if needed.
for i in range(len(self.files['target_ref_fn'])):
fn = self.files['target_ref_fn'][i]
direction = "forward" if fn.find("forward") != -1 else "reverse"
utils.log(self.loggingName, 'info',
'Extracting refseq sequence and writing %s' % fn)
utils.extract_refseq_fa(self.values, self.paths['ref_data'],
self.params.get_param('reference_fasta'),
direction, fn)
# If using blatn for target realignment, the db must be available.
blastn = self.params.get_param('blast')
if blastn is not None:
# Check if blast db files are available for each target.
if not os.path.isfile(self.files['target_ref_fn'][0] + '.nin'):
makedb = os.path.join(os.path.split(blastn)[0],
'makeblastdb') # Create blast db
cmd = "%s -in %s -dbtype 'nucl' -out %s" % (
makedb, self.files['target_ref_fn'][0],
self.files['target_ref_fn'][0])
utils.log(
self.loggingName, 'info',
'Creating blast db files for target %s with reference file %s'
% (self.name, self.files['target_ref_fn'][0]))
p = subprocess.Popen(cmd,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
shell=True)
output, errors = p.communicate()
if errors != '':
utils.log(
self.loggingName, 'debug',
'Failed to make blast db files using reference file %s'
% self.files['target_ref_fn'][0])
