def test_valid_files(self): for valid, kwargs, components in self.valid_files: for kwarg in kwargs: _drop_kwargs(kwarg, 'seq_num') constructor = kwarg.get('constructor', Sequence) expected = [ constructor(c['sequence'], metadata={ 'id': c['id'], 'machine_name': c['machine_name'], 'run_number': c['run_number'], 'lane_number': c['lane_number'], 'tile_number': c['tile_number'], 'x': c['x'], 'y': c['y'], 'index': c['index'], 'read_number': c['read_number'] }, positional_metadata={ 'quality': np.array(c['quality'], dtype=np.uint8) }) for c in components ] observed = list(_qseq_to_generator(valid, **kwarg)) self.assertEqual(len(expected), len(observed)) for o, e in zip(observed, expected): self.assertEqual(o, e)
def test_valid_files(self): for valid, kwargs, components in self.valid_files: for kwarg in kwargs: _drop_kwargs(kwarg, 'seq_num') constructor = kwarg.get('constructor', Sequence) expected = [ constructor( c['sequence'], metadata={'id': c['id'], 'machine_name': c['machine_name'], 'run_number': c['run_number'], 'lane_number': c['lane_number'], 'tile_number': c['tile_number'], 'x': c['x'], 'y': c['y'], 'index': c['index'], 'read_number': c['read_number']}, positional_metadata={ 'quality': np.array(c['quality'], dtype=np.uint8)}) for c in components] observed = list(_qseq_to_generator(valid, **kwarg)) self.assertEqual(len(expected), len(observed)) for o, e in zip(observed, expected): self.assertEqual(o, e)
def test_invalid_files(self): for invalid, kwargs, errors, etype in self.invalid_files: with self.assertRaises(etype) as cm: for kwarg in kwargs: _drop_kwargs(kwarg, 'seq_num') list(_qseq_to_generator(invalid, **kwarg)) for e in errors: self.assertIn(e, str(cm.exception))