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_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 = 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_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_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 = 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)