def test_write_output(self):
builder = TreeBuilder()
builder.sequences = {"seq1": "a sequence object"}
builder.tree = "Tree"
builder.sequences_output_file = StringIO()
builder.tree_output_file = StringIO()
builder._write_tree = MagicMock()
builder._write_sequences = MagicMock()
builder.write_output()
builder._write_tree.assert_called_with("Tree",
builder.tree_output_file)
builder._write_sequences.assert_called_with(
["a sequence object"], builder.sequences_output_file)
def test_write_output(self):
builder = TreeBuilder()
builder.sequences = {"seq1": "a sequence object"}
builder.tree = "Tree"
builder.sequences_output_file = StringIO()
builder.tree_output_file = StringIO()
builder._write_tree = MagicMock()
builder._write_sequences = MagicMock()
builder.write_output()
builder._write_tree.assert_called_with("Tree",
builder.tree_output_file)
builder._write_sequences.assert_called_with(["a sequence object"],
builder.sequences_output_file)
def test_add_hereditary_nodes(self, temp_mock):
builder = TreeBuilder()
output_directory = tempfile.mkdtemp()
temp_mock.mkdtemp.return_value = output_directory
temp_mock.NamedTemporaryFile.side_effect = \
(tempfile.NamedTemporaryFile(dir=output_directory, delete=False) for i in xrange(10))
fasta_filename = os.path.join(test_data(), 'animals.mfa')
with open(fasta_filename) as fasta_file:
builder.load_fasta_sequences(fasta_file)
tree_filename = os.path.join(test_data(), 'animals.terminal_nodes.newick')
builder.tree = Bio.Phylo.read(tree_filename, 'newick')
builder.add_hereditary_nodes()
self.assertIsInstance(builder.tree, Bio.Phylo.Newick.Tree)
tree_nodes = sorted([node.name for node in builder.tree.find_clades()])
self.assertItemsEqual(tree_nodes, builder.sequences.keys())
self.assertEqual(len(tree_nodes), 19)
self.assertFalse(os.path.isdir(output_directory))
def test_add_hereditary_nodes(self, temp_mock):
builder = TreeBuilder()
output_directory = tempfile.mkdtemp()
temp_mock.mkdtemp.return_value = output_directory
temp_mock.NamedTemporaryFile.side_effect = \
(tempfile.NamedTemporaryFile(dir=output_directory, delete=False) for i in xrange(10))
fasta_filename = os.path.join(test_data(), 'animals.mfa')
with open(fasta_filename) as fasta_file:
builder.load_fasta_sequences(fasta_file)
tree_filename = os.path.join(test_data(),
'animals.terminal_nodes.newick')
builder.tree = Bio.Phylo.read(tree_filename, 'newick')
builder.add_hereditary_nodes()
self.assertIsInstance(builder.tree, Bio.Phylo.Newick.Tree)
tree_nodes = sorted([node.name for node in builder.tree.find_clades()])
self.assertItemsEqual(tree_nodes, builder.sequences.keys())
self.assertEqual(len(tree_nodes), 19)
self.assertFalse(os.path.isdir(output_directory))
