Exemplos de mask em Python

Exemplo n.º 1

Arquivo: test_filter.py Projeto: misialq/q2-alignment

    def test_conservation_boundaries(self):
        alignment1 = skbio.TabularMSA([
            skbio.DNA('A', metadata={
                'id': 'seq1',
                'description': ''
            }),
            skbio.DNA('A', metadata={
                'id': 'seq2',
                'description': ''
            }),
            skbio.DNA('A', metadata={
                'id': 'seq3',
                'description': ''
            })
        ])
        alignment2 = skbio.TabularMSA([
            skbio.DNA('-', metadata={
                'id': 'seq1',
                'description': ''
            }),
            skbio.DNA('-', metadata={
                'id': 'seq2',
                'description': ''
            }),
            skbio.DNA('-', metadata={
                'id': 'seq3',
                'description': ''
            })
        ])

        actual = mask(alignment1, max_gap_frequency=1.0, min_conservation=1.0)
        self.assertEqual(actual, alignment1)

        actual = mask(alignment2, max_gap_frequency=1.0, min_conservation=0.0)
        self.assertEqual(actual, alignment2)

Exemplo n.º 2

Arquivo: test_filter.py Projeto: gregcaporaso/q2-alignment

 def test_invalid_conservation_threshold(self):
     alignment = skbio.TabularMSA(
         [skbio.DNA('-', metadata={'id': 'seq1', 'description': ''}),
          skbio.DNA('-', metadata={'id': 'seq2', 'description': ''}),
          skbio.DNA('-', metadata={'id': 'seq3', 'description': ''})]
     )
     eps = np.finfo(float).eps
     with self.assertRaises(ValueError):
         mask(alignment, min_conservation=0.0 - eps)
     with self.assertRaises(ValueError):
         mask(alignment, min_conservation=1.0 + eps)

Exemplo n.º 3

Arquivo: test_filter.py Projeto: qiime2/q2-alignment

 def test_invalid_conservation_threshold(self):
     alignment = skbio.TabularMSA(
         [skbio.DNA('-', metadata={'id': 'seq1', 'description': ''}),
          skbio.DNA('-', metadata={'id': 'seq2', 'description': ''}),
          skbio.DNA('-', metadata={'id': 'seq3', 'description': ''})]
     )
     eps = np.finfo(float).eps
     with self.assertRaises(ValueError):
         mask(alignment, min_conservation=0.0 - eps)
     with self.assertRaises(ValueError):
         mask(alignment, min_conservation=1.0 + eps)

Exemplo n.º 4

Arquivo: test_filter.py Projeto: gregcaporaso/q2-alignment

    def test_empty_input(self):
        alignment = skbio.TabularMSA(
            [skbio.DNA('', metadata={'id': 'seq1', 'description': ''}),
             skbio.DNA('', metadata={'id': 'seq2', 'description': ''}),
             skbio.DNA('', metadata={'id': 'seq3', 'description': ''})]
            )
        with self.assertRaises(ValueError):
            mask(alignment)

        alignment = skbio.TabularMSA([])
        with self.assertRaises(ValueError):
            mask(alignment)

Exemplo n.º 5

Arquivo: test_filter.py Projeto: qiime2/q2-alignment

    def test_empty_input(self):
        alignment = skbio.TabularMSA(
            [skbio.DNA('', metadata={'id': 'seq1', 'description': ''}),
             skbio.DNA('', metadata={'id': 'seq2', 'description': ''}),
             skbio.DNA('', metadata={'id': 'seq3', 'description': ''})]
            )
        with self.assertRaises(ValueError):
            mask(alignment)

        alignment = skbio.TabularMSA([])
        with self.assertRaises(ValueError):
            mask(alignment)

Exemplo n.º 6

Arquivo: test_filter.py Projeto: gregcaporaso/q2-alignment

    def test_conservation_boundaries(self):
        alignment1 = skbio.TabularMSA(
            [skbio.DNA('A', metadata={'id': 'seq1', 'description': ''}),
             skbio.DNA('A', metadata={'id': 'seq2', 'description': ''}),
             skbio.DNA('A', metadata={'id': 'seq3', 'description': ''})])
        alignment2 = skbio.TabularMSA(
            [skbio.DNA('-', metadata={'id': 'seq1', 'description': ''}),
             skbio.DNA('-', metadata={'id': 'seq2', 'description': ''}),
             skbio.DNA('-', metadata={'id': 'seq3', 'description': ''})])

        actual = mask(alignment1, max_gap_frequency=1.0, min_conservation=1.0)
        self.assertEqual(actual, alignment1)

        actual = mask(alignment2, max_gap_frequency=1.0, min_conservation=0.0)
        self.assertEqual(actual, alignment2)

Exemplo n.º 7

Arquivo: test_filter.py Projeto: misialq/q2-alignment

    def test_basic(self):
        alignment = skbio.TabularMSA([
            skbio.DNA('AGA', metadata={
                'id': 'seq1',
                'description': ''
            }),
            skbio.DNA('-GA', metadata={
                'id': 'seq2',
                'description': ''
            }),
            skbio.DNA('-GC', metadata={
                'id': 'seq3',
                'description': ''
            })
        ])

        actual = mask(alignment, max_gap_frequency=0.05, min_conservation=0.30)

        expected = skbio.TabularMSA([
            skbio.DNA('GA', metadata={
                'id': 'seq1',
                'description': ''
            }),
            skbio.DNA('GA', metadata={
                'id': 'seq2',
                'description': ''
            }),
            skbio.DNA('GC', metadata={
                'id': 'seq3',
                'description': ''
            })
        ])

        self.assertEqual(actual, expected)

Exemplo n.º 8

Arquivo: test_filter.py Projeto: gregcaporaso/q2-alignment

    def test_basic(self):
        alignment = skbio.TabularMSA(
            [skbio.DNA('AGA', metadata={'id': 'seq1', 'description': ''}),
             skbio.DNA('-GA', metadata={'id': 'seq2', 'description': ''}),
             skbio.DNA('-GC', metadata={'id': 'seq3', 'description': ''})]
        )

        actual = mask(alignment, max_gap_frequency=0.05, min_conservation=0.30)

        expected = skbio.TabularMSA(
            [skbio.DNA('GA', metadata={'id': 'seq1', 'description': ''}),
             skbio.DNA('GA', metadata={'id': 'seq2', 'description': ''}),
             skbio.DNA('GC', metadata={'id': 'seq3', 'description': ''})]
        )

        self.assertEqual(actual, expected)