def testAdd(self):
# strict
self.assertRaises(sequence.SequenceError, self.ali.add,
sequence.Sequence('sn', 'sn', 'TOO-LONG-SEQ'))
self.assertRaises(sequence.DuplicateSequenceError, self.ali.add,
sequence.Sequence('s1', 's1', 'AB-CD'))
def setUp(self):
super(TestSequenceCollection, self).setUp()
s1 = sequence.Sequence('id1', '>id1 desc', 'AB-CD',
sequence.SequenceTypes.Protein)
s2 = sequence.Sequence('id2', '>id2 desc', 'ABCDE',
sequence.SequenceTypes.Protein)
self.collection = sequence.SequenceCollection([s1, s2])
self.data = '>id1 desc\nAB-CD\n>id2 desc\nABCDE'
def setUp(self):
super(TestSequence, self).setUp()
self.data = '>id desc\nAB-CD'
self.sequence = sequence.Sequence('id', '>id desc', 'AB-CD',
sequence.SequenceTypes.Protein)
assert str(self.sequence) == self.data
def setUp(self):
super(TestSequenceAlignment, self).setUp()
seq1 = sequence.Sequence('s1', 's1 desc1', 'AB-CD',
sequence.SequenceTypes.Protein)
seq2 = sequence.RichSequence('s2', 's2 desc2', list('ABX-D'),
sequence.SequenceTypes.Protein)
self.ali = self._factory([seq1, seq2])
self.ali2 = self._factory([seq1, seq2, seq2, seq2], strict=False)
def testFromSequence(self):
seq = sequence.Sequence('testA',
'test seq',
'ABCDE',
type=sequence.SequenceTypes.Protein)
chain = structure.Chain.from_sequence(seq, 'Z')
self.assertEqual(chain.sequence, 'ABCDE')
self.assertEqual(chain.id, 'Z')
self.assertEqual(chain.residues[2].sequence_number, 2)
self.assertEqual(chain.residues[2].rank, 2)
self.assertEqual(chain.residues[2].type, sequence.ProteinAlphabet.ASX)