def test_screw_formats_inplace_ui(capsys, pb_odd_resources):
temp_file = br.TempFile()
with open(pb_odd_resources["compare"], "r") as ifile:
temp_file.write(ifile.read())
test_in_args = deepcopy(in_args)
test_in_args.screw_formats = "nexus"
test_in_args.in_place = True
test_in_args.trees[0] = temp_file.path
tester = Pb.PhyloBuddy(temp_file.path)
Pb.command_line_ui(test_in_args, tester, skip_exit=True)
out, err = capsys.readouterr()
assert "File overwritten at:" in err
check_file = os.path.isfile("%s.nex" % temp_file.path)
assert check_file
test_in_args.trees[0] = "%s.nex" % temp_file.path
test_in_args.screw_formats = "newick"
tester = Pb.PhyloBuddy("%s.nex" % temp_file.path)
Pb.command_line_ui(test_in_args, tester, skip_exit=True)
out, err = capsys.readouterr()
assert "File overwritten at:" in err
check_file = os.path.isfile("%s.nwk" % temp_file.path)
assert check_file
def test_show_unique(pb_odd_resources, pb_resources, hf):
tester = Pb.PhyloBuddy(pb_odd_resources['compare'])
Pb.show_unique(tester)
assert hf.buddy2hash(tester) == "396e27e3c7c5aa126ec07f31307a288e"
with pytest.raises(AssertionError): # If only a single tree is present
tester = Pb.PhyloBuddy(pb_resources.get_one("m k"))
Pb.show_unique(tester)
def test_show_unique(pb_odd_resources, pb_resources, hf):
tester = Pb.PhyloBuddy(pb_odd_resources['compare'])
Pb.show_unique(tester)
assert hf.buddy2hash(tester) == "ea5b0d1fcd7f39cb556c0f5df96281cf"
with pytest.raises(AssertionError): # If only a single tree is present
tester = Pb.PhyloBuddy(pb_resources.get_one("m k"))
Pb.show_unique(tester)
def test_collapse_polytomies_ui(capsys, pb_odd_resources, hf):
test_in_args = deepcopy(in_args)
test_in_args.collapse_polytomies = [[20]]
Pb.command_line_ui(test_in_args, Pb.PhyloBuddy(pb_odd_resources['support']), skip_exit=True)
out, err = capsys.readouterr()
assert hf.string2hash(out) == "1b0979265205b17ca7f34abbd02f6e26"
test_in_args.collapse_polytomies = [[0.1, 'length']]
Pb.command_line_ui(test_in_args, Pb.PhyloBuddy(pb_odd_resources['support']), skip_exit=True)
out, err = capsys.readouterr()
assert hf.string2hash(out) == "252572f7b9566c62df24d57065412240"
def test_split_polytomies_ui(capsys):
test_in_args = deepcopy(in_args)
test_in_args.split_polytomies = True
Pb.command_line_ui(test_in_args, Pb.PhyloBuddy(Pb.PhyloBuddy('(A,(B,C,D));')), skip_exit=True)
out, err = capsys.readouterr()
assert out in ['(A:1.0,(B:1.0,(C:1.0,D:1.0):1e-06):1.0):1.0;\n',
'(A:1.0,(B:1.0,(D:1.0,C:1.0):1e-06):1.0):1.0;\n',
'(A:1.0,(C:1.0,(B:1.0,D:1.0):1e-06):1.0):1.0;\n',
'(A:1.0,(C:1.0,(D:1.0,B:1.0):1e-06):1.0):1.0;\n',
'(A:1.0,(D:1.0,(B:1.0,C:1.0):1e-06):1.0):1.0;\n',
'(A:1.0,(D:1.0,(C:1.0,B:1.0):1e-06):1.0):1.0;\n']
def test_collapse_polytomies(pb_odd_resources, hf):
tester = Pb.PhyloBuddy(pb_odd_resources['support'])
tester = Pb.collapse_polytomies(tester, 20)
assert hf.buddy2hash(tester) == "1b0979265205b17ca7f34abbd02f6e26"
tester = Pb.PhyloBuddy(pb_odd_resources['support'])
tester = Pb.collapse_polytomies(tester, threshold=0.1, mode='length')
assert hf.buddy2hash(tester) == "252572f7b9566c62df24d57065412240"
with pytest.raises(NameError) as err:
Pb.collapse_polytomies(tester, threshold=0.1, mode='foo')
assert "Mode must be 'support' or 'length'" in str(err)
def __init__(self):
base_dict_structure = {'single': {}, 'multi': {}}
self.resources = deepcopy(base_dict_structure)
self.resources['single'] = {file_format: name.format(path=RESOURCE_PATH) for file_format, name in [
("newick", "{path}single_tree.newick"),
("nexus", "{path}single_tree.nex"),
("nexml", "{path}single_tree.xml")]}
self.resources['multi'] = {file_format: name.format(path=RESOURCE_PATH) for file_format, name in [
("newick", "{path}multi_tree.newick"),
("nexus", "{path}multi_tree.nex"),
("nexml", "{path}multi_tree.xml")]}
# Create new PhyloBuddy objects for each resrouce file
self.pb_objs = deepcopy(base_dict_structure)
for num in self.resources:
for file_format in self.resources[num]:
self.pb_objs[num][file_format] = Pb.PhyloBuddy(self.resources[num][file_format])
self.code_dict = {"num_trees": {"o": "single", "m": "multi"},
"format": {"k": "newick", "n": "nexus", "l": "nexml"}}
self.single_letter_codes = {"o": "single", "m": "multi",
"k": "newick", "n": "nexus", "l": "nexml"}
def test_unroot_ui(capsys, pb_odd_resources, hf):
test_in_args = deepcopy(in_args)
test_in_args.unroot = True
Pb.command_line_ui(test_in_args, Pb.PhyloBuddy(pb_odd_resources["figtree"]), skip_exit=True)
out, err = capsys.readouterr()
assert hf.string2hash(out) == "10e9024301b3178cdaed0b57ba33f615"
def test_show_unique_unrooted(monkeypatch, pb_odd_resources, hf):
def mock_treeerror(*args):
raise TreeError(args)
tester = Pb.PhyloBuddy(pb_odd_resources['compare'])
Pb.unroot(tester)
Pb.show_unique(tester)
assert hf.buddy2hash(tester) == "50f1d86072989ac61dcf95ee5fc19f7e"
def test_split_polytomies():
tester = Pb.PhyloBuddy('(A,(B,C,D));')
Pb.split_polytomies(tester)
assert str(tester) in ['(A:1.0,(B:1.0,(C:1.0,D:1.0):1e-06):1.0):1.0;\n',
'(A:1.0,(B:1.0,(D:1.0,C:1.0):1e-06):1.0):1.0;\n',
'(A:1.0,(C:1.0,(B:1.0,D:1.0):1e-06):1.0):1.0;\n',
'(A:1.0,(C:1.0,(D:1.0,B:1.0):1e-06):1.0):1.0;\n',
'(A:1.0,(D:1.0,(B:1.0,C:1.0):1e-06):1.0):1.0;\n',
'(A:1.0,(D:1.0,(C:1.0,B:1.0):1e-06):1.0):1.0;\n']
def test_show_unique_ui(capsys, pb_resources, hf, pb_odd_resources):
test_in_args = deepcopy(in_args)
test_in_args.show_unique = True
Pb.command_line_ui(test_in_args, Pb.PhyloBuddy(pb_odd_resources["compare"]), skip_exit=True)
out, err = capsys.readouterr()
assert hf.string2hash(out) == "ea5b0d1fcd7f39cb556c0f5df96281cf"
with pytest.raises(AssertionError) as err:
Pb.command_line_ui(test_in_args, pb_resources.get_one("m k"), pass_through=True)
assert "PhyloBuddy object should have exactly 2 trees." in str(err)
def test_error(monkeypatch, capsys, pb_resources, pb_odd_resources):
test_in_args = deepcopy(in_args)
test_in_args.show_unique = [True]
Pb.command_line_ui(test_in_args, pb_resources.get_one("o k"), skip_exit=True)
out, err = capsys.readouterr()
assert "PhyloBuddy object should have exactly 2 trees." in err
monkeypatch.setattr(Pb, "_convert_to_ete", mock_assertionerror)
with pytest.raises(AssertionError):
Pb.command_line_ui(test_in_args, Pb.PhyloBuddy(pb_odd_resources["compare"]), skip_exit=True)
def test_show_unique_unrooted(monkeypatch, pb_odd_resources, hf):
def mock_treeerror(*args):
raise TreeError(args)
tester = Pb.PhyloBuddy(pb_odd_resources['compare'])
Pb.unroot(tester)
Pb.show_unique(tester)
assert hf.buddy2hash(tester) == "2bba16e2c77102ba150adecc352407a9"
monkeypatch.setattr(Pb.ete3.TreeNode, 'robinson_foulds', mock_treeerror)
with pytest.raises(TreeError):
Pb.show_unique(tester)
def test_hash_ids_edges(monkeypatch, pb_resources, hf, pb_odd_resources):
class MockRandom(object):
def __init__(self):
self.values = [
"YCva8wcKxN", "r5iHz5XItJ", "b0dfUBWelI", "Tv0XxZziIQ",
"hkwU50UQfq", "Jbn4JWgxXy", "OeGgev9Mdu", "pQRpDbjomQ",
"z9JvFAa1vZ", "vHwNvExi6A", "i6tluyP88x", "mXvIO8GYAg",
"clDGuGrku8", "atmvoy1uN6", "0R59tE6LgP", "eOUHJPbVaf",
"2U0FarU2Lv", "4tITUmacIV", "UND58iKTiH", "aqQWMJnjeu",
"rOFRXh4ftJ", "HeAcnkJ8LV", "bdWtyB4OP4", "L0aFqF3oMc",
"4HN9dP8uqL", "TtdeGIxxY6", "s4S1RfO9sO", "mIScdjmMzq",
"ohGB7fpJGq", "CtLTzCg6RB", "QufRP2p8jN", "NA98oE9g9u",
"6IbtWWrdDr", "ZqnxsFXwpT", "hZd46Bc15s", "iL936ARfV9",
"iOcjJIWv7Y", "yVkDeDhFpK", "d2amahGHzt", "H9VzjZZdbW",
"kxFL0xMfFx", "glhRhmReup", "kxFL0xMfFx"
]
self.current_value = self.values.pop()
def choice(self, *args):
if not self.current_value:
self.current_value = self.values.pop()
next_char = self.current_value[0]
self.current_value = self.current_value[1:]
return next_char
with pytest.raises(TypeError) as e:
Pb.hash_ids(Pb.PhyloBuddy, hash_length="foo")
assert "Hash length argument must be an integer, not <class 'str'>" in str(
e)
with pytest.raises(ValueError) as e:
Pb.hash_ids(Pb.PhyloBuddy, hash_length=0)
assert "Hash length must be greater than 0" in str(e)
with pytest.raises(ValueError) as e:
Pb.hash_ids(pb_resources.get_one("m n"), hash_length=1)
assert "Insufficient number of hashes available to cover all sequences." in str(
e)
tester = Pb.PhyloBuddy(pb_odd_resources['node_lables'])
test_hash = hf.buddy2hash(tester)
tester = Pb.hash_ids(tester, hash_length=5, nodes=True)
assert hf.buddy2hash(tester) != test_hash
monkeypatch.setattr(Pb.random, "Random", MockRandom)
tester = Pb.hash_ids(pb_resources.get_one("o n"))
assert hf.buddy2hash(tester) == "48b1b2b0e1f7012ea1a964269300ac6b"
def test_list_ids_ui(capsys, pb_resources, hf):
test_in_args = deepcopy(in_args)
test_in_args.list_ids = [True]
Pb.command_line_ui(test_in_args, pb_resources.get_one("m k"), skip_exit=True)
out, err = capsys.readouterr()
assert hf.string2hash(out) == "4f0857e0211ff0cd058d0cf7cbaf64d5"
test_in_args.list_ids = [4]
Pb.command_line_ui(test_in_args, pb_resources.get_one("m k"), skip_exit=True)
out, err = capsys.readouterr()
assert hf.string2hash(out) == "bf2fbfe1bd52e9b27ae21f5c06e7763a"
test_in_args.list_ids = [4]
Pb.command_line_ui(test_in_args, Pb.PhyloBuddy("(, );"), skip_exit=True)
out, err = capsys.readouterr()
assert out == "#### tree_1 ####\nNone\n\n"
def test_unroot(pb_odd_resources, hf):
tester = Pb.PhyloBuddy(pb_odd_resources['figtree'])
Pb.unroot(tester)
assert hf.buddy2hash(tester) == "10e9024301b3178cdaed0b57ba33f615"
def test_rename_nodes(pb_odd_resources, hf):
tester = Pb.PhyloBuddy(pb_odd_resources["node_lables"])
Pb.rename(tester, "Equus|Ruminantiamorpha|Canis", "Family")
assert hf.buddy2hash(tester) == "46ba6ce0f3a1859b4c7326a6f5e69263"
