def test_eq(self):
s1 = easel.TextSequence(name=b"seq1", sequence="ATGC")
s2 = easel.TextSequence(name=b"seq2", sequence="ATGG")
msa = easel.TextMSA(sequences=[s1, s2])
msa2 = easel.TextMSA(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):
seq1 = easel.TextSequence(name=b"TEST", sequence="ATGC")
self.assertEqual(seq1, seq1)
self.assertNotEqual(seq1, object())
seq2 = easel.TextSequence(name=b"TEST", sequence="ATGC")
self.assertEqual(seq1, seq2)
seq3 = easel.TextSequence(name=b"OTHER", sequence="ATGC")
self.assertNotEqual(seq1, seq3)
seq4 = easel.TextSequence(name=b"TEST", sequence="ATGT")
self.assertNotEqual(seq1, seq4)
def test_digitize_roundtrip(self):
seq1 = easel.TextSequence(name=b"TEST", sequence="ATGC")
dsq1 = seq1.digitize(easel.Alphabet.dna())
self.assertEqual(seq1.name, dsq1.name)
seq2 = dsq1.textize()
self.assertEqual(seq1.name, seq2.name)
self.assertEqual(seq1, seq2)
def test_reverse_complement_protein(self):
seq = easel.TextSequence(sequence="MEMLP")
with warnings.catch_warnings():
warnings.simplefilter('error')
self.assertRaises(Warning, seq.reverse_complement)
with warnings.catch_warnings():
warnings.simplefilter('ignore')
rc = seq.reverse_complement()
self.assertEqual(rc.sequence, "NNKNK")
def test_copy(self):
seq = easel.TextSequence(name=b"TEST", sequence="ATGC")
# 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.TextSequence(name=b"seq1", sequence="ATGC")
s2 = easel.TextSequence(name=b"seq1", sequence="ATTC")
self.assertRaises(ValueError, easel.TextMSA, sequences=[s1, s2])
def test_init_length_mismatch(self):
s1 = easel.TextSequence(name=b"seq1", sequence="ATGC")
s2 = easel.TextSequence(name=b"seq2", sequence="AT")
self.assertRaises(ValueError, easel.TextMSA, sequences=[s1, s2])
def test_reverse_complement_inplace(self):
seq = easel.TextSequence(sequence="ATGC")
seq.reverse_complement(inplace=True)
self.assertEqual(seq.sequence, "GCAT")
def test_reverse_complement(self):
seq = easel.TextSequence(sequence="ATGC")
rc = seq.reverse_complement()
self.assertEqual(rc.sequence, "GCAT")
def test_write_roundtrip(self):
seq = easel.TextSequence(name=b"ecoRI", sequence="GAATTC")
with io.BytesIO() as buffer:
seq.write(buffer)
seq2 = easel.SequenceFile.parse(buffer.getvalue(), "fasta")
self.assertEqual(seq, seq2)
def test_eq_not_seq(self):
seq1 = easel.TextSequence(name=b"TEST", sequence="ATGC")
self.assertNotEqual(seq1, 1)
self.assertNotEqual(seq1, b"hello")
def test_setter_description(self):
seq = easel.TextSequence()
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.TextSequence()
self.assertEqual(seq.name, b"")
seq.name = b"OTHER"
self.assertEqual(seq.name, b"OTHER")
def test_init_kwargs(self):
seq = easel.TextSequence(name=b"TEST", sequence="ATGC")
self.assertEqual(seq.name, b"TEST")
self.assertEqual(seq.sequence, "ATGC")
self.assertEqual(len(seq), 4)
def test_init_empty(self):
seq = easel.TextSequence()
self.assertEqual(seq.name, b"")
self.assertEqual(seq.sequence, "")
self.assertEqual(len(seq), 0)
def test_eq_copy(self):
s1 = easel.TextSequence(name=b"seq1", sequence="ATGC")
s2 = easel.TextSequence(name=b"seq2", sequence="ATGG")
msa = easel.TextMSA(sequences=[s1, s2])
self.assertEqual(msa, msa.copy())
self.assertEqual(msa, copy.copy(msa))
def test_init_sequences(self):
s1 = easel.TextSequence(name=b"seq1", sequence="ATGC")
msa = easel.TextMSA(sequences=[s1])
self.assertEqual(len(msa), 4)
self.assertEqual(len(msa.sequences), 1)
self.assertTrue(msa)
def test_reverse_complement_protein(self):
abc = easel.Alphabet.amino()
seq = easel.TextSequence(sequence="MEMLP").digitize(abc)
self.assertRaises(ValueError, seq.reverse_complement)
self.assertRaises(ValueError, seq.reverse_complement, inplace=True)
