Пример #1
0
    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])
Пример #2
0
    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)
Пример #3
0
    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)
Пример #4
0
    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")
Пример #5
0
    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)
Пример #6
0
 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])
Пример #7
0
 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])
Пример #8
0
 def test_reverse_complement_inplace(self):
     seq = easel.TextSequence(sequence="ATGC")
     seq.reverse_complement(inplace=True)
     self.assertEqual(seq.sequence, "GCAT")
Пример #9
0
 def test_reverse_complement(self):
     seq = easel.TextSequence(sequence="ATGC")
     rc = seq.reverse_complement()
     self.assertEqual(rc.sequence, "GCAT")
Пример #10
0
 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)
Пример #11
0
 def test_eq_not_seq(self):
     seq1 = easel.TextSequence(name=b"TEST", sequence="ATGC")
     self.assertNotEqual(seq1, 1)
     self.assertNotEqual(seq1, b"hello")
Пример #12
0
 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")
Пример #13
0
 def test_setter_name(self):
     seq = easel.TextSequence()
     self.assertEqual(seq.name, b"")
     seq.name = b"OTHER"
     self.assertEqual(seq.name, b"OTHER")
Пример #14
0
 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)
Пример #15
0
 def test_init_empty(self):
     seq = easel.TextSequence()
     self.assertEqual(seq.name, b"")
     self.assertEqual(seq.sequence, "")
     self.assertEqual(len(seq), 0)
Пример #16
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))
Пример #17
0
 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)
Пример #18
0
 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)