def test_compare_bases(self):
cluster = ClusterConsensus()
self.assertEqual(cluster._compare_bases(['A', 'A']), 'A')
self.assertEqual(cluster._compare_bases(['A', 'T']), 'N')
self.assertEqual(cluster._compare_bases(['A', 'N']), 'N')
self.assertEqual(cluster._compare_bases(['N', 'N']), 'N')
self.assertEqual(cluster._compare_bases(['A', '-']), 'N')
self.assertEqual(cluster._compare_bases(['-', '-']), 'N')
def test_compare_bases(self):
cluster = ClusterConsensus()
self.assertEqual(cluster._compare_bases(['A', 'A']), 'A')
self.assertEqual(cluster._compare_bases(['A', 'T']), 'N')
self.assertEqual(cluster._compare_bases(['A', 'N']), 'N')
self.assertEqual(cluster._compare_bases(['N', 'N']), 'N')
self.assertEqual(cluster._compare_bases(['A', '-']), 'N')
self.assertEqual(cluster._compare_bases(['-', '-']), 'N')
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)
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)
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)
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)
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')
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_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_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_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')
def test_get_length_of_longest(self):
cluster = ClusterConsensus()
sequence_strings = ["AAAAA", "ATGAACAAAA--"]
longest = cluster._get_length_of_longest(sequence_strings)
self.assertEqual(longest, 12)
def test_get_length_of_longest(self):
cluster = ClusterConsensus()
sequence_strings = ["AAAAA", "ATGAACAAAA--"]
longest = cluster._get_length_of_longest(sequence_strings)
self.assertEqual(longest, 12)
