def test_fastq_to_alignment(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 = Alignment(
[constructor(
c[2], metadata={'id': c[0],
'description': c[1]},
positional_metadata={'quality': np.array(c[3],
dtype=np.uint8)},
**expected_kwargs)
for c in components])
observed = _fastq_to_alignment(valid, **observed_kwargs)
self.assertEqual(observed, expected)
def test_fastq_to_alignment(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)
expected_kwargs = {}
expected_kwargs['lowercase'] = 'introns'
observed_kwargs['lowercase'] = 'introns'
expected = Alignment([
constructor(c[2],
metadata={
'id': c[0],
'description': c[1]
},
positional_metadata={
'quality': np.array(c[3],
dtype=np.uint8)
},
**expected_kwargs) for c in components
])
observed = _fastq_to_alignment(valid, **observed_kwargs)
self.assertEqual(observed, expected)
def test_fastq_to_alignment(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 = Alignment([
constructor(c[2],
metadata={
'id': c[0],
'description': c[1]
},
positional_metadata={
'quality': np.array(c[3],
dtype=np.uint8)
},
**expected_kwargs) for c in components
])
observed = _fastq_to_alignment(valid, **observed_kwargs)
self.assertEqual(observed, expected)
def test_fastq_to_alignment(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)
expected_kwargs = {}
expected_kwargs['lowercase'] = 'introns'
observed_kwargs['lowercase'] = 'introns'
expected = Alignment(
[constructor(
c[2], metadata={'id': c[0],
'description': c[1]},
positional_metadata={'quality': np.array(c[3],
dtype=np.uint8)},
**expected_kwargs)
for c in components])
observed = _fastq_to_alignment(valid, **observed_kwargs)
self.assertEqual(observed, expected)
