Exemplos de ClusterConsensus.load_fasta_file em Python

Exemplo n.º 1

Arquivo: ClusterConsensus_test.py Projeto: aslett1/BioPericles

  def test_get_all_sequences(self):
    test_folder = os.path.abspath(os.path.dirname(__file__))
    test_data_path = os.path.join(test_folder, 'data', 'cluster_A_multifasta.aln')

    cluster = ClusterConsensus()
    with open(test_data_path, 'r') as input_file:
      cluster.load_fasta_file(input_file)
      sequences = cluster._get_all_sequences(cluster.sequences)

    expected = ["AAAAACAAAAA-", "ATGAACAAAA--"]
    self.assertEqual(sequences, expected)

Exemplo n.º 2

    def test_get_all_sequences(self):
        test_folder = os.path.abspath(os.path.dirname(__file__))
        test_data_path = os.path.join(test_folder, 'data',
                                      'cluster_A_multifasta.aln')

        cluster = ClusterConsensus()
        with open(test_data_path, 'r') as input_file:
            cluster.load_fasta_file(input_file)
            sequences = cluster._get_all_sequences(cluster.sequences)

        expected = ["AAAAACAAAAA-", "ATGAACAAAA--"]
        self.assertEqual(sequences, expected)

Exemplo n.º 3

Arquivo: ClusterConsensus_test.py Projeto: aslett1/BioPericles

  def test_load_fasta_file(self, seqio_mock):
    cluster = ClusterConsensus()

    fake_file = StringIO("Some sequences")

    fake_sequence_generator = GeneratorMock(['AG', 'AG', 'AG'])

    seqio_mock.parse.return_value = fake_sequence_generator

    cluster.load_fasta_file(fake_file)
    seqio_mock.parse.assert_called_once_with(fake_file, 'fasta')
    self.assertEqual(cluster.sequences, fake_sequence_generator)
    self.assertEqual(fake_sequence_generator.call_count, 0)

    self.assertEqual(cluster.get_consensus(), 'AG')
    self.assertEqual(fake_sequence_generator.call_count, 3)

Exemplo n.º 4

    def test_load_fasta_file(self, seqio_mock):
        cluster = ClusterConsensus()

        fake_file = StringIO("Some sequences")

        fake_sequence_generator = GeneratorMock(['AG', 'AG', 'AG'])

        seqio_mock.parse.return_value = fake_sequence_generator

        cluster.load_fasta_file(fake_file)
        seqio_mock.parse.assert_called_once_with(fake_file, 'fasta')
        self.assertEqual(cluster.sequences, fake_sequence_generator)
        self.assertEqual(fake_sequence_generator.call_count, 0)

        self.assertEqual(cluster.get_consensus(), 'AG')
        self.assertEqual(fake_sequence_generator.call_count, 3)

Exemplo n.º 5

Arquivo: ClusterConsensus_test.py Projeto: aslett1/BioPericles

  def test_real_file(self):
    test_folder = os.path.abspath(os.path.dirname(__file__))
    test_data_path = os.path.join(test_folder, 'data', 'cluster_A_multifasta.aln')

    cluster = ClusterConsensus()
    cluster.output_file = StringIO()
    cluster.output_file.name = "fake_filename.aln"
    with open(test_data_path, 'r') as input_file:
      cluster.load_fasta_file(input_file)
      cluster.write_consensus()

    expected_response = """\
>fake_filename
ANNAACAAAANN
"""
    cluster.output_file.seek(0)
    self.assertEqual(cluster.output_file.read(), expected_response)

Exemplo n.º 6

    def test_real_file(self):
        test_folder = os.path.abspath(os.path.dirname(__file__))
        test_data_path = os.path.join(test_folder, 'data',
                                      'cluster_A_multifasta.aln')

        cluster = ClusterConsensus()
        cluster.output_file = StringIO()
        cluster.output_file.name = "fake_filename.aln"
        with open(test_data_path, 'r') as input_file:
            cluster.load_fasta_file(input_file)
            cluster.write_consensus()

        expected_response = """\
>fake_filename
ANNAACAAAANN
"""
        cluster.output_file.seek(0)
        self.assertEqual(cluster.output_file.read(), expected_response)