def test_parse_arguments(self):
# test the stages are returned correctly
args = DummyArgs()
_, _, _, _, _, _, stages = stools.parseArguments(args)
self.assertEqual(stages, ['1', '2', '3', '4'])
# test bad args
with self.assertRaises(SystemExit):
args = DummyArgs()
args.email = None
stools.parseArguments(args)
with self.assertRaises(SystemExit):
args = DummyArgs()
args.threads = -10
stools.parseArguments(args)
with self.assertRaises(SystemExit):
args = DummyArgs()
args.stages = '1-8'
stools.parseArguments(args)
with self.assertRaises(SystemExit):
args = DummyArgs()
args.stages = '4-1'
stools.parseArguments(args)
def test_parse_arguments(self):
# test the stages are returned correctly
args = DummyArgs()
_, _, _, _, _, _, stages = stools.parseArguments(args)
self.assertEqual(stages, ['1', '2', '3', '4'])
# test bad args
with self.assertRaises(SystemExit):
args = DummyArgs()
args.email = None
stools.parseArguments(args)
with self.assertRaises(SystemExit):
args = DummyArgs()
args.threads = -10
stools.parseArguments(args)
with self.assertRaises(SystemExit):
args = DummyArgs()
args.stages = '1-8'
stools.parseArguments(args)
with self.assertRaises(SystemExit):
args = DummyArgs()
args.stages = '4-1'
stools.parseArguments(args)
email=email, verbose=verbose, debug=debug,
logger=base_logger, retry=False)
runner.setup()
base_logger.info('Done.')
# pickle runner for restart
with open(argspath, 'w') as file:
pickle.dump((nworkers, threads_per_worker, folders, email,
threads, verbose, debug, stages), file)
# run stages
runner.run()
if __name__ == '__main__':
# make sure pglt knows about deps
if not mafft or not raxml or not blastn:
print('WARNING: Missing essential dependencies -- use `pglt_set_dependencies.py`')
# parse args
restart, retry, email, threads, verbose, debug, stages = \
stools.parseArguments()
# create base logger -- messages in parent folder log.txt
base_logger = stools.setUpLogging(verbose, debug, 'base')
try:
main(restart, retry, email, threads, verbose, debug, stages,
base_logger)
except KeyboardInterrupt:
base_logger.info('Execution halted by user')
if verbose:
sys.exit()
else:
sys.exit('Execution halted by user')
