def test_additional_options(sequences):
app1 = ClustalOmegaApp(sequences)
app1.start()
app2 = ClustalOmegaApp(sequences)
app2.add_additional_options(["--full"])
app2.start()
app1.join()
app2.join()
assert "--full" not in app1.get_command()
assert "--full" in app2.get_command()
assert app1.get_alignment() == app2.get_alignment()
def test_clustalo_tree(sequences):
leaves = [phylo.TreeNode(index=i) for i in range(len(sequences))]
inter1 = phylo.TreeNode([leaves[0], leaves[1]], [1.0, 1.0])
inter2 = phylo.TreeNode([leaves[2], leaves[3]], [2.5, 2.5])
root = phylo.TreeNode([inter1, inter2], [3.5, 2])
tree = phylo.Tree(root)
# You cannot simultaneously set and get a tree in ClustalOmega
# -> Test whether both is possible in separate calls
app = ClustalOmegaApp(sequences)
app.set_guide_tree(tree)
app.start()
app.join()
app = ClustalOmegaApp(sequences)
app.start()
app.join()
assert app.get_guide_tree() is not None
def test_additional_options(sequences):
bin_path = BIN_PATH[ClustalOmegaApp]
if is_not_installed(bin_path):
pytest.skip(f"'{bin_path}' is not installed")
app1 = ClustalOmegaApp(sequences)
app1.start()
app2 = ClustalOmegaApp(sequences)
app2.add_additional_options(["--full"])
app2.start()
app1.join()
app2.join()
assert "--full" not in app1.get_command()
assert "--full" in app2.get_command()
assert app1.get_alignment() == app2.get_alignment()
def test_clustalo_matrix(sequences):
ref_matrix = [[0, 1, 2, 3], [1, 0, 1, 2], [2, 1, 0, 1], [3, 2, 1, 0]]
app = ClustalOmegaApp(sequences)
app.full_matrix_calculation()
app.set_distance_matrix(np.array(ref_matrix))
app.start()
app.join()
test_matrix = app.get_distance_matrix()
assert np.allclose(ref_matrix, test_matrix)
def test_clustalo_matrix(sequences):
bin_path = BIN_PATH[ClustalOmegaApp]
if is_not_installed(bin_path):
pytest.skip(f"'{bin_path}' is not installed")
ref_matrix = [[0, 1, 2, 3], [1, 0, 1, 2], [2, 1, 0, 1], [3, 2, 1, 0]]
app = ClustalOmegaApp(sequences)
app.full_matrix_calculation()
app.set_distance_matrix(np.array(ref_matrix))
app.start()
app.join()
test_matrix = app.get_distance_matrix()
assert np.allclose(ref_matrix, test_matrix)