def test_get_cluster_name(self, random_mock): cluster = ClusterConsensus() cluster.output_file = StringIO() random_mock.return_value = 10000 self.assertEqual(cluster._get_cluster_name(), 'cluster_10000') cluster.output_file = MagicMock() cluster.output_file.name = 'foo/bar.baz.mfa' self.assertEqual(cluster._get_cluster_name(), 'bar.baz') cluster.cluster_name = 'foo' self.assertEqual(cluster._get_cluster_name(), 'foo')
def test_get_cluster_name(self, random_mock): cluster = ClusterConsensus() cluster.output_file = StringIO() random_mock.return_value = 10000 self.assertEqual(cluster._get_cluster_name(), 'cluster_10000') cluster.output_file = MagicMock() cluster.output_file.name = 'foo/bar.baz.mfa' self.assertEqual(cluster._get_cluster_name(), 'bar.baz') cluster.cluster_name = 'foo' self.assertEqual(cluster._get_cluster_name(), 'foo')
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)
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)
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)
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)