def test_getoptions_bad_subcommand_error(self, mock_stderr):
# sub-module must be specified
with self.assertRaises(SystemExit):
qapa.getoptions(['bad'])
self.assertIn('argument subcommand: invalid choice:',
mock_stderr.getvalue())
self.assertIn("choose from 'build', 'fasta', 'quant'",
mock_stderr.getvalue())
def test_quant(self, mock_sys):
# should call create_merged_data.R and compute_pau.R
db = NamedTemporaryFile()
args = qapa.getoptions(
['quant', '--db', db.name, 'test_1.sf', 'test_2.sf'])
qapa.quant(args)
self.assertRegex(mock_sys.call_args_list[0][0][0],
r'create_merged_data.R')
self.assertRegex(mock_sys.call_args_list[1][0][0], r'compute_pau.R')
def test_getoptions_no_subcommand_error(self, mock_stderr):
with self.assertRaises(SystemExit):
qapa.getoptions([])
self.assertIn("Specify sub-command: 'build', 'fasta', 'quant'",
mock_stderr.getvalue())