def __init__(self,
analysis_dir,
pairs_sheet=None,
taskname='SnsWesPairsSnv',
config_file='SnsWesPairsSnv.yml',
extra_handlers=None,
**kwargs):
"""
"""
SnsTask.__init__(self,
analysis_dir=analysis_dir,
taskname=taskname,
extra_handlers=extra_handlers,
config_file=config_file)
# make sure the samples pairs sheet was passed
if not pairs_sheet:
raise self._exceptions.AnalysisFileMissing(
message='Samples pairs was not passed to task {0}'.format(
self),
errors='')
# copy the sample pairs sheet to the proper location
pairs_sheet_output = self.get_analysis_file_outpath(
file_basename="samples.pairs.csv")
self.logger.debug(
'Copying samples pairs sheet from\n{0}\nto\n{1}'.format(
pairs_sheet, pairs_sheet_output))
shutil.copy2(pairs_sheet, pairs_sheet_output)
def __init__(self,
analysis_dir,
taskname='DemoSnsTask',
extra_handlers=None,
**kwargs):
"""
"""
SnsTask.__init__(self,
analysis_dir=analysis_dir,
taskname=taskname,
extra_handlers=extra_handlers)
def __init__(self,
analysis_dir,
taskname='SnsRnaStar',
config_file='SnsRnaStar.yml',
extra_handlers=None,
**kwargs):
"""
"""
SnsTask.__init__(self,
analysis_dir=analysis_dir,
taskname=taskname,
extra_handlers=extra_handlers)
def __init__(self,
analysis_dir,
targets_bed=None,
fastq_dirs=None,
taskname='StartSns',
config_file='StartSns.yml',
extra_handlers=None,
**kwargs):
"""
"""
SnsTask.__init__(self,
analysis_dir=analysis_dir,
taskname=taskname,
extra_handlers=extra_handlers,
config_file=config_file)
if not fastq_dirs:
raise self._exceptions.AnalysisFileMissing(
message='Fastq directories were not passed to task {0}'.format(
self),
errors='')
if not targets_bed:
raise self._exceptions.AnalysisFileMissing(
message='Targets .bed file was not passed to task {0}'.format(
self),
errors='')
# fastq directories to be used
self.fastq_dirs = []
for fastq_dir in fastq_dirs:
self.fastq_dirs.append(os.path.realpath(fastq_dir))
# path to the input targets files
self.targets_bed = targets_bed
# list of items to validate before proceeding
setup_items = []
for item in self.fastq_dirs:
setup_items.append(item)
setup_items.append(self.targets_bed)
setup_items.append(self.output_dir)
self.validate_items(items=setup_items)
def __init__(self, analysis_dir, pairs_sheet = None, taskname = 'SnsSetupPairs', config_file = 'SnsSetupPairs.yml', extra_handlers = None, **kwargs):
"""
"""
SnsTask.__init__(self, analysis_dir = analysis_dir, taskname = taskname, extra_handlers = extra_handlers, config_file = config_file)
# make sure the samples pairs sheet was passed
if not pairs_sheet:
raise self._exceptions.AnalysisFileMissing(message = 'Samples pairs was not passed to task {0}'.format(self), errors = '')
# the basename of the file to create
pairs_sheet_basename = self.task_configs['pairs_sheet_basename'] # "samples.pairs.csv"
# path to expected/required output file
pairs_sheet_output = self.get_analysis_file_outpath(file_basename = pairs_sheet_basename)
# make sure it doesn't exist already
self.tools.backup_file(input_file = pairs_sheet_output, use_logger = self.logger)
# copy the sample pairs sheet to the proper location
self.logger.debug('Copying samples pairs sheet from\n{0}\nto\n{1}'.format(pairs_sheet, pairs_sheet_output))
shutil.copy2(pairs_sheet, pairs_sheet_output)
# make sure it really worked
self.validate_items([pairs_sheet_output])