def __init__(self):
if self.task_name is None:
raise Exception("{}.task_name must by set".format(
self.__class__.__name__))
self.directory()
self.context = Context.instance()
self.sample = self.context.sample
self.config = self.context.config
self._prepare()
def _prepare(self):
self.mode = self.config['phigaro']['mode']
self.finder = V2Finder(
window_len=self.config['phigaro']['window_len'],
threshold_min=self.config['phigaro']['threshold_min_%s' %
self.mode],
threshold_max=self.config['phigaro']['threshold_max_%s' %
self.mode],
mode=self.mode)
self._print_vogs = self.config['phigaro'].get('print_vogs', False)
self._filename = self.config['phigaro'].get('filename', False)
self._no_html = self.config['phigaro'].get('no_html', False)
self._not_open = self.config['phigaro'].get('not_open', False)
self._save_fasta = self.config['phigaro'].get('save_fasta', False)
self._output = self.config['phigaro'].get('output', False)
self._uuid = self.config['phigaro'].get('uuid', False)
self.context = Context.instance()
def __init__(self, input):
super().__init__()
self.input = input
self.context = Context.instance()