Python setup_logging Examples

Example #1

File: empty_rg_header_seq_reads.py Project: uc-cdis/gdc-readgroups

 def setUp(self):
     self.parser = argparse.ArgumentParser()
     self.parser.set_defaults(level=logging.DEBUG)
     self.args = self.parser.parse_args([])
     self.logger = main.setup_logging(self.args)
     current_dir = os.path.dirname(os.path.realpath(__file__))
     sam = os.path.join(current_dir, 'data', SAMFILE)
     self.bam = util.subprocess_make_bam(sam, self.logger)

Example #2

File: rg_header_pu1dot.py Project: uc-cdis/gdc-readgroups

 def setUp(self):
     self.parser = argparse.ArgumentParser()
     self.parser.set_defaults(level=logging.DEBUG)
     self.args = self.parser.parse_args([])
     self.logger = main.setup_logging(self.args)
     current_dir = os.path.dirname(os.path.realpath(__file__))
     sam = os.path.join(current_dir, 'data', SAMFILE)
     expectedjson = os.path.join(current_dir, 'data', EXPECTEDJSON)
     with open(expectedjson, 'r') as f:
         self.expecteddata = json.load(f)
     self.bam = util.make_bam(sam)