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))
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))
