def test_eq(self):
s1 = easel.DigitalSequence(self.alphabet, name=b"seq1", sequence=bytearray([1, 2, 3, 4]))
s2 = easel.DigitalSequence(self.alphabet, name=b"seq2", sequence=bytearray([1, 2, 3, 3]))
msa = easel.DigitalMSA(self.alphabet, sequences=[s1, s2])
msa2 = easel.DigitalMSA(self.alphabet, sequences=[s1, s2])
self.assertEqual(msa, msa2)
msa2.name = b"other"
self.assertNotEqual(msa, msa2)
self.assertNotEqual(msa, 1)
self.assertNotEqual(msa, [s1, s2])
def test_eq(self):
arr = bytearray([0, 1, 2, 3])
seq1 = easel.DigitalSequence(self.abc, name=b"TEST", sequence=arr)
self.assertEqual(seq1, seq1)
self.assertNotEqual(seq1, object())
seq2 = easel.DigitalSequence(self.abc, name=b"TEST", sequence=arr)
self.assertEqual(seq1, seq2)
seq3 = easel.DigitalSequence(self.abc, name=b"OTHER", sequence=arr)
self.assertNotEqual(seq1, seq3)
arr2 = bytearray([0, 1, 2, 0])
seq4 = easel.DigitalSequence(self.abc, name=b"TEST", sequence=arr2)
self.assertNotEqual(seq1, seq4)
def test_digitize_roundtrip(self):
arr = bytearray([0, 1, 2, 3])
dsq1 = easel.DigitalSequence(self.abc, name=b"TEST", sequence=arr)
tsq1 = dsq1.textize()
self.assertEqual(tsq1.name, dsq1.name)
dsq2 = tsq1.digitize(self.abc)
self.assertEqual(dsq1.name, dsq2.name)
self.assertEqual(list(dsq1.sequence), list(dsq2.sequence))
self.assertEqual(dsq1, dsq2)
def test_copy(self):
arr = bytearray([0, 1, 2, 3])
seq = easel.DigitalSequence(self.abc, name=b"TEST", sequence=arr)
# copy the sequence
cpy = seq.copy()
# check the copy is equal and attributes are equal
self.assertEqual(seq, cpy)
self.assertEqual(seq.name, cpy.name)
self.assertEqual(seq.checksum(), cpy.checksum())
# check attributes can be read even after the original object
# is (hopefully) deallocated, to make sure internal strings were copied
del seq
gc.collect()
self.assertEqual(cpy.name, b"TEST")
# check `copy.copy` works too
cpy2 = copy.copy(cpy)
self.assertEqual(cpy, cpy2)
self.assertEqual(cpy.name, cpy2.name)
def test_init_duplicate_names(self):
s1 = easel.DigitalSequence(self.alphabet, name=b"seq1", sequence=bytearray([1, 2, 3, 4]))
s2 = easel.DigitalSequence(self.alphabet, name=b"seq1", sequence=bytearray([1, 2, 3, 3]))
self.assertRaises(ValueError, easel.DigitalMSA, self.alphabet, sequences=[s1, s2])
def test_init_length_mismatch(self):
s1 = easel.DigitalSequence(self.alphabet, name=b"seq1", sequence=bytearray([1, 2, 3, 4]))
s2 = easel.DigitalSequence(self.alphabet, name=b"seq2", sequence=bytearray([1, 2]))
self.assertRaises(ValueError, easel.DigitalMSA, self.alphabet, sequences=[s1, s2])
def test_init_sequences(self):
s1 = easel.DigitalSequence(self.alphabet, name=b"seq1", sequence=bytearray([1, 2, 3, 4]))
msa = easel.DigitalMSA(self.alphabet, sequences=[s1])
self.assertEqual(len(msa), 4)
self.assertEqual(len(msa.sequences), 1)
self.assertTrue(msa)
def test_eq_copy(self):
s1 = easel.DigitalSequence(self.alphabet, name=b"seq1", sequence=bytearray([1, 2, 3, 4]))
s2 = easel.DigitalSequence(self.alphabet, name=b"seq2", sequence=bytearray([1, 2, 3, 3]))
msa = easel.DigitalMSA(self.alphabet, sequences=[s1, s2])
self.assertEqual(msa, msa.copy())
self.assertEqual(msa, copy.copy(msa))
def test_eq_not_seq(self):
arr = bytearray([0, 1, 2, 3])
seq1 = easel.DigitalSequence(self.abc, name=b"TEST", sequence=arr)
self.assertNotEqual(seq1, 1)
self.assertNotEqual(seq1, b"hello")
def test_setter_description(self):
seq = easel.DigitalSequence(self.abc)
self.assertIs(seq.description, b"")
seq.description = b"a test sequence"
self.assertEqual(seq.description, b"a test sequence")
def test_setter_name(self):
seq = easel.DigitalSequence(self.abc)
self.assertEqual(seq.name, b"")
seq.name = b"OTHER"
self.assertEqual(seq.name, b"OTHER")
def test_init_kwargs(self):
arr = bytearray([0, 1, 2, 3])
seq = easel.DigitalSequence(self.abc, name=b"TEST", sequence=arr)
self.assertEqual(seq.name, b"TEST")
self.assertEqual(bytearray(seq.sequence), arr)
self.assertEqual(len(seq), 4)
def test_init_empty(self):
seq = easel.DigitalSequence(self.abc)
self.assertEqual(seq.name, b"")
self.assertEqual(seq.sequence, bytearray())
self.assertEqual(len(seq), 0)