def test_init():
rename = Rename.init_from_args("--file tests/argfiles/rename.txt")
assert rename.remove == False
rename = Rename.init_from_args(
"--file tests/argfiles/rename.txt --remove-missing")
assert rename.remove == True
def test_rename_from_file(basictrees):
renamed = Rename(filename="tests/argfiles/rename.txt", from_="old", to_="new").consume(basictrees)
for t in renamed:
leaves = t.get_leaf_names()
assert "A" not in leaves
assert "X" in leaves
assert all((x in leaves for x in ("B", "C", "D", "E", "F")))
def test_rename(basictrees):
renamed = Rename(rename={"A":"X"}).consume(basictrees)
for t in renamed:
leaves = t.get_leaf_names()
assert "A" not in leaves
assert "X" in leaves
assert all((x in leaves for x in ("B", "C", "D", "E", "F")))
def test_rename_from_file():
lines = fileinput.input("tests/treefiles/basic.trees")
trees = NewickParser().consume(lines)
renamed = Rename(filename="tests/argfiles/rename.txt").consume(trees)
for t in renamed:
leaves = t.get_leaf_names()
assert "A" not in leaves
assert "X" in leaves
assert all((x in leaves for x in ("B", "C", "D", "E", "F")))
def test_rename_with_remove(basictrees):
renamed = Rename(rename={
"A":"X",
"B":"Y",
"C":"Z" }, remove=True).consume(basictrees)
for t in renamed:
leaves = t.get_leaf_names()
assert all((x in leaves for x in ("X", "Y", "Z")))
assert not any((x in leaves for x in ("A", "B", "C", "D", "E", "F")))
def test_rename_with_remove():
lines = fileinput.input("tests/treefiles/basic.trees")
trees = NewickParser().consume(lines)
renamed = Rename({
"A": "X",
"B": "Y",
"C": "Z"
}, remove=True).consume(trees)
for t in renamed:
leaves = t.get_leaf_names()
assert all((x in leaves for x in ("X", "Y", "Z")))
assert not any((x in leaves for x in ("A", "B", "C", "D", "E", "F")))
def test_bad_init_no_args():
Rename()
def test_init(argfilepath):
rename = Rename.init_from_args("--file {0} --from old --to new".format(argfilepath("rename.txt")))
assert rename.opts.remove == False
rename = Rename.init_from_args("--file {0} --from old --to new --remove-missing".format(argfilepath("rename.txt")))
assert rename.opts.remove == True
def test_bad_init_no_args():
with pytest.raises(ValueError):
Rename()