def main():
"""
:return:
"""
parser = argparse.ArgumentParser(
description='Convert BAM Read Groups to GDC Read Group Nodes')
subparsers = parser.add_subparsers(dest='command')
parser.add_argument('-d',
'--debug',
action='store_const',
const=logging.DEBUG,
dest='level',
help='Enable debug logging.')
parser.set_defaults(level=logging.INFO)
parser.add_argument('-v',
'--version',
action='store_true',
required=False,
help='Output program version.')
parser_bam = subparsers.add_parser(
'bam-mode', help='using a BAM file, write GDC Read Group nodes')
parser_bam.add_argument('-b',
'--bam-path',
action='store',
required=True,
help='BAM file')
parser_bam.add_argument('-f',
'--output-format',
action='store',
choices=['json', 'tsv'],
default='json',
required=False)
parser_template = subparsers.add_parser(
'template-mode', help='write template with two Read Groups')
parser_template.add_argument('-f',
'--output-format',
action='store',
choices=['json', 'tsv'],
default='json',
required=False)
args = parser.parse_args()
logger = setup_logging(args)
if args.command:
if args.command == 'bam-mode':
validate_input(args.bam_path, logger)
out_file = extract_readgroup(args.bam_path, args.output_format,
logger)
logger.info('\nwrote {}'.format(out_file))
elif args.command == 'template-mode':
out_file = generate_template(args.output_format, logger)
logger.info('\nwrote {}'.format(out_file))
elif args.version:
output_version(logger)
else:
parser.print_help()
return
def test(self):
try:
self.testjson = extract_readgroup.extract_readgroup(self.bam, 'json', self.logger)
except NotABamError:
pass
else:
self.logger.error('Input File\n\t{}\ndid not raise `NotABamError`'.format(self.bam))
raise RuntimeError
def test(self):
self.testjson = extract_readgroup.extract_readgroup(
self.bam, 'json', self.logger)
with open(self.testjson, 'r') as f:
testdata = json.load(f)
self.assertEqual(self.expecteddata, testdata)