self.chunks_list = RefDataArray.read(
mainInitializer.refdata_file_name).get_parsed_list()
@staticmethod
def _run_pipeline(refdata: RefDataLine):
handler = PipelineHandler(refdata)
handler.run()
def run(self):
Utilities.single_core_queue(func=self._run_pipeline,
queue=self.chunks_list)
if __name__ == '__main__':
mainInitializer = Initializer()
launchTime = Utilities.get_time()
nodeName = subprocess.getoutput("hostname").strip()
mainLogFile = "{a}nBee_{b}_{c}.log".format(
a=mainInitializer.logs_directory, b=nodeName, c=launchTime)
print("Started main workflow with log file: '{}'".format(mainLogFile))
logging.basicConfig(
format=u'%(levelname)-8s [%(asctime)s] %(message)s',
level=logging.DEBUG,
handlers=[logging.FileHandler(mainLogFile),
logging.StreamHandler()])
sampleDataParser = SampleDataParser(mainInitializer.sampledata_file_name)
sampleFilesList = sampleDataParser.get_parsed_list()
if len(sampleFilesList) == 0:
Utilities.log_and_raise(
"No files to process, exiting: '{}'".format(sampleFilesList))
chunksHandler = ChunksHandler()
def __init__(self):
self._namespace = self._parse_args()
self.sampledata = self._namespace.input
self.target_length = CoveragesVerifier.get_wc_l(self._namespace.genome) + 1
self.prefix = self._namespace.prefix
self.suffix = self._namespace.suffix
self.debugging_bool = self._namespace.debug
self.output = self._namespace.output
if len(self.output) == 0:
self.output = "{}sampledata/{}.sampledata".format(Utilities.ends_with_slash(os.path.dirname(self.prefix)), Utilities.get_time())