def set_params(self):
"""Organize and format all input parameters into class variables to access
later. Specific instances of parameters are checked and set. All the parameters that are
set are logged. The target objects are set along with the paths.
Args:
None
Returns:
None
Raises:
None
"""
log_msgs = self.parse_opts() # Parse the config file and command line parameters into the self.opts dictionary.
utils.setup_logger(self.get_param('analysis_dir', True), 'breakmer') # Create logging object.
# Log the parameter setup after the logging object is created.
utils.log(self.logging_name, 'info', 'Setting up parameters')
# Setup the logger first before checking required params - log if there is a missing parameter.
self.check_required_params()
# Log all parameters passed in, warn for poor paths
for param_key, param_value in self.opts.items():
utils.log(self.logging_name, 'info', '%s = %s' % (param_key, param_value))
# Log parameter overwritten by configuration file input values.
for log_msg in log_msgs:
utils.log(self.logging_name, log_msg[0], log_msg[1])
self.set_targets()
self.gene_annotations = Anno()
self.gene_annotations.add_genes(self.get_param('gene_annotation_file'))
self.paths['ref_data'] = os.path.abspath(os.path.normpath(self.opts['reference_data_dir'])) # Path to target reference sequence fast files.
self.set_param('reference_fasta_dir', os.path.split(self.opts['reference_fasta'])[0]) # Path to genome fasta file.
# Setup directories
self.paths['analysis'] = os.path.abspath(os.path.normpath(self.opts['analysis_dir']))
self.paths['output'] = os.path.join(self.paths['analysis'], 'output')
if 'targets_dir' in self.opts:
self.paths['targets'] = os.path.abspath(os.path.normpath(self.opts['targets_dir']))
else:
self.paths['targets'] = os.path.join(self.paths['analysis'], 'targets')
# Create all the paths.
for path in self.paths:
utils.log(self.logging_name, 'info', 'Creating %s directory (%s)' % (path, self.paths[path]))
if not os.path.exists(self.paths[path]):
os.makedirs(self.paths[path])
# If starting the blat server then return.
if self.fnc_cmd == 'start_blat_server':
utils.log(self.logging_name, 'info', 'Starting the blat server.')
return
self.check_binaries() # Check if Jellyfish and Cutadapt work.
# self.filter = resultfilter.ResultFilter(self.get_param('filterList'), self) # Instantiate the filter class.
self.set_insertsize_thresh() # Set the expected insert size threshold from the properly mapped read
def set_params(self, arguments):
"""Organize and format all input parameters into class variables to access
later. Specific instances of parameters are checked and set. All parameters that are
set are logged. The target objects are set along with the paths.
Args:
arguments (dict): The argparse dictionary object from the command line options.
Returns:
None
Raises:
None
"""
self.parse_opts(arguments) # Parse the config file and command line parameters into the self.opts dictionary.
utils.setup_logger(self.get_param('analysis_dir', True), 'breakmer') # Create logging object.
utils.log(self.loggingName, 'info', 'Setting up parameters')
# Log all parameters passed in, warn for poor paths
for paramKey, paramValue in self.opts.items():
utils.log(self.loggingName, 'info', '%s = %s' % (paramKey, paramValue))
self.set_targets()
self.paths['ref_data'] = os.path.abspath(os.path.normpath(self.opts['reference_data_dir'])) # Path to target reference sequence fast files.
self.set_param('reference_fasta_dir', os.path.split(self.opts['reference_fasta'])[0]) # Path to genome fasta file.
# If only preseting the reference data no need to continue.
if self.fncCmd == 'prepare_reference_data':
self.set_insertsize_thresh() # Set the expected insert size threshold from the properly mapped read pairs.
utils.log(self.loggingName, 'info', 'Preset reference data option set! Only the reference data directory will be setup.')
return
# Setup directories
self.paths['analysis'] = os.path.abspath(os.path.normpath(self.opts['analysis_dir']))
self.paths['output'] = os.path.join(self.paths['analysis'], 'output')
if 'targets_dir' in self.opts:
self.paths['targets'] = os.path.abspath(os.path.normpath(self.opts['targets_dir']))
else:
self.paths['targets'] = os.path.join(self.paths['analysis'], 'targets')
# Create all the paths.
for path in self.paths:
utils.log(self.loggingName, 'info', 'Creating %s directory (%s)' % (path, self.paths[path]))
if not os.path.exists(self.paths[path]):
os.makedirs(self.paths[path])
# If starting the blat server then return.
if self.fncCmd == 'start_blat_server':
utils.log(self.loggingName, 'info', 'Starting the blat server.')
return
self.check_binaries() # Check if Jellyfish and Cutadapt work.
self.filter = resultfilter.ResultFilter(self.get_param('filterList'), self) # Instantiate the filter class.
self.set_insertsize_thresh() # Set the expected insert size threshold from the properly mapped read pairs.
def set_params(self):
"""Organize and format all input parameters into class variables to access
later. Specific instances of parameters are checked and set. All the parameters that are
set are logged. The target objects are set along with the paths.
Args:
None
Returns:
None
Raises:
None
"""
log_msgs = self.parse_opts(
) # Parse the config file and command line parameters into the self.opts dictionary.
utils.setup_logger(self.get_param('analysis_dir', True),
'breakmer') # Create logging object.
# Log the parameter setup after the logging object is created.
utils.log(self.logging_name, 'info', 'Setting up parameters')
# Setup the logger first before checking required params - log if there is a missing parameter.
self.check_required_params()
# Log all parameters passed in, warn for poor paths
for param_key, param_value in self.opts.items():
utils.log(self.logging_name, 'info',
'%s = %s' % (param_key, param_value))
# Log parameter overwritten by configuration file input values.
for log_msg in log_msgs:
utils.log(self.logging_name, log_msg[0], log_msg[1])
if self.get_param('targets_bed_file') is not None:
self.set_targets()
self.gene_annotations = Anno()
self.gene_annotations.add_genes(
self.get_param('gene_annotation_file'))
if 'reference_data_dir' in self.opts:
self.paths['ref_data'] = os.path.abspath(
os.path.normpath(self.opts['reference_data_dir'])
) # Path to target reference sequence fast files.
if 'reference_fasta' in self.opts:
self.set_param('reference_fasta_dir',
os.path.split(self.opts['reference_fasta'])
[0]) # Path to genome fasta file.
# Setup directories
self.paths['analysis'] = os.path.abspath(
os.path.normpath(self.opts['analysis_dir']))
self.paths['output'] = os.path.join(self.paths['analysis'], 'output')
if 'targets_dir' in self.opts:
self.paths['targets'] = os.path.abspath(
os.path.normpath(self.opts['targets_dir']))
else:
self.paths['targets'] = os.path.join(self.paths['analysis'],
'targets')
# Create all the paths.
for path in self.paths:
utils.log(self.logging_name, 'info',
'Creating %s directory (%s)' % (path, self.paths[path]))
if not os.path.exists(self.paths[path]):
os.makedirs(self.paths[path])
# If starting the blat server then return.
if self.fnc_cmd == 'start_blat_server':
utils.log(self.logging_name, 'info', 'Starting the blat server.')
return
if self.fnc_cmd == 'profile_data':
return
self.check_binaries() # Check if Jellyfish and Cutadapt work.
# self.filter = resultfilter.ResultFilter(self.get_param('filterList'), self) # Instantiate the filter class.
self.set_insertsize_thresh(
) # Set the expected insert size threshold from the properly mapped read
def set_params(self, arguments):
"""Organize and format all input parameters into class variables to access
later. Specific instances of parameters are checked and set. All parameters that are
set are logged. The target objects are set along with the paths.
Args:
arguments (dict): The argparse dictionary object from the command line options.
Returns:
None
Raises:
None
"""
self.parse_opts(
arguments
) # Parse the config file and command line parameters into the self.opts dictionary.
utils.setup_logger(self.get_param('analysis_dir', True),
'breakmer') # Create logging object.
utils.log(self.loggingName, 'info', 'Setting up parameters')
# Log all parameters passed in, warn for poor paths
for paramKey, paramValue in self.opts.items():
utils.log(self.loggingName, 'info',
'%s = %s' % (paramKey, paramValue))
self.set_targets()
self.paths['ref_data'] = os.path.abspath(
os.path.normpath(self.opts['reference_data_dir'])
) # Path to target reference sequence fast files.
self.set_param(
'reference_fasta_dir',
os.path.split(
self.opts['reference_fasta'])[0]) # Path to genome fasta file.
# If only preseting the reference data no need to continue.
if self.fncCmd == 'prepare_reference_data':
self.set_insertsize_thresh(
) # Set the expected insert size threshold from the properly mapped read pairs.
utils.log(
self.loggingName, 'info',
'Preset reference data option set! Only the reference data directory will be setup.'
)
return
# Setup directories
self.paths['analysis'] = os.path.abspath(
os.path.normpath(self.opts['analysis_dir']))
self.paths['output'] = os.path.join(self.paths['analysis'], 'output')
if 'targets_dir' in self.opts:
self.paths['targets'] = os.path.abspath(
os.path.normpath(self.opts['targets_dir']))
else:
self.paths['targets'] = os.path.join(self.paths['analysis'],
'targets')
# Create all the paths.
for path in self.paths:
utils.log(self.loggingName, 'info',
'Creating %s directory (%s)' % (path, self.paths[path]))
if not os.path.exists(self.paths[path]):
os.makedirs(self.paths[path])
# If starting the blat server then return.
if self.fncCmd == 'start_blat_server':
utils.log(self.loggingName, 'info', 'Starting the blat server.')
return
self.check_binaries() # Check if Jellyfish and Cutadapt work.
self.filter = resultfilter.ResultFilter(
self.get_param('filterList'),
self) # Instantiate the filter class.
self.set_insertsize_thresh(
) # Set the expected insert size threshold from the properly mapped read pairs.