Exemplos de ClusterConsensus._calculate_consensus em Python

Exemplo n.º 1

Arquivo: ClusterConsensus_test.py Projeto: aslett1/BioPericles

  def test_calculate_consensus(self):
    cluster = ClusterConsensus()

    sequence_generator = (FakeSequence(s) for s in ['AG', 'AG', 'A'])
    self.assertRaises(ValueError, cluster._calculate_consensus, sequence_generator)

    sequence_generator = (FakeSequence(s) for s in ['AG', 'AG', 'AG'])
    self.assertEqual(cluster._calculate_consensus(sequence_generator), 'AG')

    sequence_generator = (FakeSequence(s) for s in ['AG', 'AG', 'TG'])
    self.assertEqual(cluster._calculate_consensus(sequence_generator), 'NG')

    sequence_generator = (FakeSequence(s) for s in ['AG', 'AT', 'TG'])
    self.assertEqual(cluster._calculate_consensus(sequence_generator), 'NN')

    sequence_generator = (FakeSequence(s) for s in ['AG', 'A-', 'AG'])
    self.assertEqual(cluster._calculate_consensus(sequence_generator), 'AN')

Exemplo n.º 2

    def test_calculate_consensus(self):
        cluster = ClusterConsensus()

        sequence_generator = (FakeSequence(s) for s in ['AG', 'AG', 'A'])
        self.assertRaises(ValueError, cluster._calculate_consensus,
                          sequence_generator)

        sequence_generator = (FakeSequence(s) for s in ['AG', 'AG', 'AG'])
        self.assertEqual(cluster._calculate_consensus(sequence_generator),
                         'AG')

        sequence_generator = (FakeSequence(s) for s in ['AG', 'AG', 'TG'])
        self.assertEqual(cluster._calculate_consensus(sequence_generator),
                         'NG')

        sequence_generator = (FakeSequence(s) for s in ['AG', 'AT', 'TG'])
        self.assertEqual(cluster._calculate_consensus(sequence_generator),
                         'NN')

        sequence_generator = (FakeSequence(s) for s in ['AG', 'A-', 'AG'])
        self.assertEqual(cluster._calculate_consensus(sequence_generator),
                         'AN')

Exemplo n.º 3

Arquivo: ClusterConsensus_test.py Projeto: aslett1/BioPericles

  def test_write_consensus(self):
    cluster = ClusterConsensus()

    cluster.output_file = StringIO()
    cluster.cluster_name = 'cluster_1000'
    cluster._calculate_consensus = MagicMock(return_value='NNANTGUNCN')

    cluster.write_consensus()

    expected_results = """\
>cluster_1000
NNANTGUNCN
"""
    cluster.output_file.seek(0)
    self.assertEqual(cluster.output_file.read(), expected_results)

Exemplo n.º 4

    def test_write_consensus(self):
        cluster = ClusterConsensus()

        cluster.output_file = StringIO()
        cluster.cluster_name = 'cluster_1000'
        cluster._calculate_consensus = MagicMock(return_value='NNANTGUNCN')

        cluster.write_consensus()

        expected_results = """\
>cluster_1000
NNANTGUNCN
"""
        cluster.output_file.seek(0)
        self.assertEqual(cluster.output_file.read(), expected_results)