def test_none_prefix(self):
"""Should raise an exception when None is used as the prefix"""
with self.assertRaises(TypeError):
grapple.call_variants(self._test_file,
self._ref_file,
prefix_id=None)
def test_valid_files(self):
"""Should not raise an exception when supplying valid files"""
try:
grapple.call_variants(self._test_file, self._ref_file)
except Exception as e:
self.fail(e)
def test_valid_files(self):
"""Should not raise an exception when supplying valid files"""
try:
grapple.call_variants(self._test_file, self._ref_file)
except Exception as e:
self.fail(e)
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.call_variants(self._test_file, self._ref_file, prefix_id=0)
def test_none_prefix(self):
"""Should raise an exception when None is used as the prefix"""
with self.assertRaises(TypeError):
grapple.call_variants(self._test_file, self._ref_file, prefix_id=None)
def test_absent_ref_file(self):
"""Should raise an exception when the reference file doesn't exist"""
with self.assertRaises(CalledProcessError):
grapple.call_variants(self._test_file, 'this_file_does_not_exist.fa')
def test_none_ref_file(self):
"""Should raise an exception when None is passed as the reference file"""
with self.assertRaises(AttributeError):
grapple.call_variants(self._test_file, None)
def test_none_read_file(self):
"""Should raise an exception when None is used as the read file"""
with self.assertRaises(AttributeError):
grapple.call_variants(None, self._ref_file)
def test_invalid_ref_file(self):
"""Should raise an exception when the reference file is not in the right format"""
with self.assertRaises(ValueError):
grapple.call_variants(self._test_file, os.path.join('test_files', 'lambda_reads.fq'))
def test_invalid_read_file(self):
"""Should raise an exception when supplying a read file with the wrong format"""
with self.assertRaises(ValueError):
grapple.call_variants(self._ref_file, self._ref_file)
def test_absent_read_file(self):
"""Should raise an exception when supplying a read file that doesn't exist"""
with self.assertRaises(CalledProcessError):
grapple.call_variants('this_file_does_not_exist.bam', self._ref_file)
def test_absent_read_file(self):
"""Should raise an exception when supplying a read file that doesn't exist"""
with self.assertRaises(CalledProcessError):
grapple.call_variants('this_file_does_not_exist.bam',
self._ref_file)
def test_invalid_read_file(self):
"""Should raise an exception when supplying a read file with the wrong format"""
with self.assertRaises(ValueError):
grapple.call_variants(self._ref_file, self._ref_file)
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.call_variants(self._test_file, self._ref_file, prefix_id=0)
def test_none_ref_file(self):
"""Should raise an exception when None is passed as the reference file"""
with self.assertRaises(AttributeError):
grapple.call_variants(self._test_file, None)
def test_absent_ref_file(self):
"""Should raise an exception when the reference file doesn't exist"""
with self.assertRaises(CalledProcessError):
grapple.call_variants(self._test_file,
'this_file_does_not_exist.fa')
def test_invalid_ref_file(self):
"""Should raise an exception when the reference file is not in the right format"""
with self.assertRaises(ValueError):
grapple.call_variants(
self._test_file, os.path.join('test_files', 'lambda_reads.fq'))
def test_none_read_file(self):
"""Should raise an exception when None is used as the read file"""
with self.assertRaises(AttributeError):
grapple.call_variants(None, self._ref_file)