def test_fastq_to_sequence_collection(self):
for valid_files, kwargs, components in self.valid_configurations:
for valid in valid_files:
for observed_kwargs in kwargs:
_drop_kwargs(observed_kwargs, 'seq_num')
constructor = observed_kwargs.get('constructor', Sequence)
# Can't use partials for this because the read
# function below can't operate on partials
expected_kwargs = {}
if hasattr(constructor, 'lowercase'):
expected_kwargs['lowercase'] = 'introns'
observed_kwargs['lowercase'] = 'introns'
expected = SequenceCollection(
[constructor(
c[2], metadata={'id': c[0], 'description': c[1]},
positional_metadata={'quality': np.array(c[3],
np.uint8)},
**expected_kwargs)
for c in components])
observed = _fastq_to_sequence_collection(valid,
**observed_kwargs)
self.assertEqual(observed, expected)
def test_fastq_to_sequence_collection(self):
for valid, kwargs, components in self.valid_files:
for kwarg in kwargs:
_drop_kwargs(kwarg, 'seq_num')
constructor = kwarg.get('constructor', BiologicalSequence)
expected = SequenceCollection(
[constructor(c[2], id=c[0], description=c[1], quality=c[3])
for c in components])
observed = _fastq_to_sequence_collection(valid, **kwarg)
# TODO remove when #656 is resolved
self.assertEqual(observed, expected)
for o, e in zip(observed, expected):
self.assertTrue(o.equals(e))
def test_fastq_to_sequence_collection(self):
for valid, kwargs, components in self.valid_files:
for kwarg in kwargs:
_drop_kwargs(kwarg, 'seq_num')
constructor = kwarg.get('constructor', BiologicalSequence)
expected = SequenceCollection([
constructor(c[2], id=c[0], description=c[1], quality=c[3])
for c in components
])
observed = _fastq_to_sequence_collection(valid, **kwarg)
# TODO remove when #656 is resolved
self.assertEqual(observed, expected)
for o, e in zip(observed, expected):
self.assertTrue(o.equals(e))
def test_fastq_to_sequence_collection(self):
for valid_files, kwargs, components in self.valid_configurations:
for valid in valid_files:
for kwarg in kwargs:
_drop_kwargs(kwarg, 'seq_num')
constructor = kwarg.get('constructor', Sequence)
expected = SequenceCollection(
[constructor(
c[2], metadata={'id': c[0], 'description': c[1]},
positional_metadata={'quality': np.array(c[3],
np.uint8)})
for c in components])
observed = _fastq_to_sequence_collection(valid, **kwarg)
self.assertEqual(observed, expected)
