def test_transform(self):
wk = SequenceIterator(['aattgg'], transform=self.rev_f)
wk.state = self.seqqual_ok.copy()
self.assertEqual(wk.state['Sequence'], self.seqqual_ok['Sequence'])
wk.transform()
self.assertEqual(wk.state['Sequence'],
self.seqqual_ok['Sequence'][::-1])
self.assertTrue((wk.state['Qual'] ==
self.seqqual_ok['Qual'][::-1]).all())
def test_transform(self):
wk = SequenceIterator(['aattgg'], transform=self.rev_f)
wk.state = self.seqqual_ok.copy()
self.assertEqual(wk.state['Sequence'], self.seqqual_ok['Sequence'])
wk.transform()
self.assertEqual(wk.state['Sequence'],
self.seqqual_ok['Sequence'][::-1])
self.assertTrue(
(wk.state['Qual'] == self.seqqual_ok['Qual'][::-1]).all())
def test_validate_lengths_false(self):
wk = SequenceIterator(['aattgg'], valid_length=False)
wk.state = self.seq_ok.copy()
wk.valid_lengths()
self.assertFalse(wk.failed)
wk.state = self.seqqual_ok.copy()
wk.valid_lengths()
self.assertFalse(wk.failed)
wk.state = self.seqqual_bad_qual.copy()
wk.valid_lengths()
self.assertFalse(wk.failed)
def test_validate_ids_true(self):
wk = SequenceIterator(['aattgg'], valid_id=True)
wk.state = self.seq_ok.copy()
wk.validate_ids()
self.assertFalse(wk.failed)
wk.state = self.seqqual_ok.copy()
wk.validate_ids()
self.assertFalse(wk.failed)
wk.state = self.seqqual_bad_id.copy()
wk.validate_ids()
self.assertTrue(wk.failed)
def test_validate_lengths_true(self):
wk = SequenceIterator(['aattgg'], valid_length=True)
wk.state = self.seq_ok.copy()
wk.valid_lengths()
self.assertFalse(wk.failed)
wk.state = self.seqqual_ok.copy()
wk.valid_lengths()
self.assertFalse(wk.failed)
wk.state = self.seqqual_bad_qual.copy()
wk.valid_lengths()
self.assertTrue(wk.failed)
def test_validate_ids_false(self):
wk = SequenceIterator(['aattgg'], valid_id=False)
wk.state = self.seq_ok.copy()
wk.validate_ids()
self.assertFalse(wk.failed)
wk.state = self.seqqual_ok.copy()
wk.validate_ids()
self.assertFalse(wk.failed)
wk.state = self.seqqual_bad_id.copy()
wk.validate_ids()
self.assertFalse(wk.failed)
def test_passing_none_for_seqs(self):
with self.assertRaises(ValueError):
SequenceIterator(None)