def test_valid_file(self):
"""Should not raise an exception when a valid file is provided"""
try:
grapple.sort_and_index(self._test_file)
except Exception as e:
self.fail(e)
def test_valid_file(self):
"""Should not raise an exception when a valid file is provided"""
try:
grapple.sort_and_index(self._test_file)
except Exception as e:
self.fail(e)
def test_none_prefix(self):
"""Should raise an exception when None is used as the prefix"""
with self.assertRaises(TypeError):
grapple.sort_and_index(self._test_file, prefix_id=None)
def test_bad_prefix(self):
"""Should raise an exception when a type that cannot be converted to a string is given for the prefix"""
with self.assertRaises(TypeError):
grapple.sort_and_index(self._test_file, prefix_id=0)
def test_none_file(self):
"""Should raise an exception when None is passed as the read file"""
with self.assertRaises(AttributeError):
grapple.sort_and_index(None)
def test_absent_file(self):
"""Should raise an exception when a read file does not exist"""
with self.assertRaises(CalledProcessError):
grapple.sort_and_index('this_file_does_not_exist.bam')
def test_invalid_file(self):
"""Should raise an exception when a file with the wrong format is used"""
with self.assertRaises(ValueError):
grapple.sort_and_index(os.path.join('test_files', 'lambda_ref.fa'))
def test_none_prefix(self):
"""Should raise an exception when None is used as the prefix"""
with self.assertRaises(TypeError):
grapple.sort_and_index(self._test_file, prefix_id=None)
def test_bad_prefix(self):
"""Should raise an exception when a type that cannot be converted to a string is given for the prefix"""
with self.assertRaises(TypeError):
grapple.sort_and_index(self._test_file, prefix_id=0)
def test_none_file(self):
"""Should raise an exception when None is passed as the read file"""
with self.assertRaises(AttributeError):
grapple.sort_and_index(None)
def test_absent_file(self):
"""Should raise an exception when a read file does not exist"""
with self.assertRaises(CalledProcessError):
grapple.sort_and_index('this_file_does_not_exist.bam')
def test_invalid_file(self):
"""Should raise an exception when a file with the wrong format is used"""
with self.assertRaises(ValueError):
grapple.sort_and_index(os.path.join('test_files', 'lambda_ref.fa'))