def test_file_prune():
lines = fileinput.input("tests/treefiles/basic.trees")
trees = NewickParser().consume(lines)
pruned = Prune(filename="tests/argfiles/taxa_abc.txt").consume(trees)
for t in pruned:
leaves = t.get_leaf_names()
assert not any((x in leaves for x in ("A", "B", "C")))
def test_inverse_annotation_prune(basictrees):
annotated = Annotate(filename="tests/argfiles/annotation.csv", key="taxon").consume(basictrees)
pruned = Prune(attribute="f1", values="0", inverse=True).consume(annotated)
for t in pruned:
leaves = t.get_leaf_names()
assert all((x in leaves for x in ("A", "B", "C")))
assert not any ((x in leaves for x in ("D", "E", "F")))
def test_prune():
lines = fileinput.input("tests/treefiles/basic.trees")
trees = NewickParser().consume(lines)
pruned = Prune(["A"]).consume(trees)
for t in pruned:
leaves = t.get_leaf_names()
assert "A" not in leaves
assert all((x in leaves for x in ("B", "C", "D", "E", "F")))
def test_inverse_prune():
lines = fileinput.input("tests/treefiles/basic.trees")
trees = NewickParser().consume(lines)
pruned = Prune(["A", "B"], inverse=True).consume(trees)
for t in pruned:
leaves = t.get_leaf_names()
assert all((x in leaves for x in ("A", "B")))
assert not any((x in leaves for x in ("C", "D", "E", "F")))
def test_annotation_prune():
lines = fileinput.input("tests/treefiles/basic.trees")
trees = NewickParser().consume(lines)
annotated = Annotate(filename="tests/argfiles/annotation.csv", key="taxon").consume(trees)
pruned = Prune(attribute="f1", value="0").consume(annotated)
for t in pruned:
leaves = t.get_leaf_names()
assert not any((x in leaves for x in ("A", "B", "C")))
def test_init_from_args(argfilepath):
prune = Prune.init_from_args("A,B,C")
assert prune.opts.filename == None
assert prune.opts.attribute == None
assert prune.opts.values == None
assert prune.opts.inverse == False
prune = Prune.init_from_args("A,B,C --inverse")
assert prune.opts.inverse == True
taxa_abc = argfilepath('taxa_abc.txt')
prune = Prune.init_from_args("--file {0}".format(taxa_abc))
assert prune.opts.filename == taxa_abc
assert prune.opts.attribute == None
assert prune.opts.values == None
prune = Prune.init_from_args("--attribute foo --values bar")
assert prune.opts.filename == None
assert prune.opts.attribute == "foo"
assert prune.opts.values == ["bar"]
def test_init_from_args():
prune = Prune.init_from_args("A,B,C")
assert prune.taxa == set(("A","B","C"))
assert prune.filename == None
assert prune.attribute == None
assert prune.value == None
assert prune.inverse == False
prune = Prune.init_from_args("A,B,C --inverse")
assert prune.inverse == True
prune = Prune.init_from_args("--file tests/argfiles/taxa_abc.txt")
assert prune.taxa == set(("A","B","C"))
assert prune.filename == "tests/argfiles/taxa_abc.txt"
assert prune.attribute == None
assert prune.value == None
prune = Prune.init_from_args("--attribute foo --value bar")
assert prune.taxa == []
assert prune.filename == None
assert prune.attribute == "foo"
assert prune.value == "bar"
def test_bad_init_no_args():
with pytest.raises(ValueError):
Prune()
def test_bad_init_empty_file(emptyargs):
with pytest.raises(ValueError):
Prune(filename=emptyargs)
def test_bad_init_no_value_only():
with pytest.raises(ValueError):
Prune(value="bar")
def test_inverse_prune(basictrees):
pruned = Prune(taxa=["A", "B"], inverse=True).consume(basictrees)
for t in pruned:
leaves = t.get_leaf_names()
assert all((x in leaves for x in ("A", "B")))
assert not any((x in leaves for x in ("C", "D", "E", "F")))
def test_prune(basictrees):
pruned = Prune(taxa=["A"]).consume(basictrees)
for t in pruned:
leaves = t.get_leaf_names()
assert "A" not in leaves
assert all((x in leaves for x in ("B", "C", "D", "E", "F")))
def test_bad_init_no_value_only():
Prune(value="bar")
def test_bad_init_empty_file():
Prune(filename="tests/argfiles/empty.txt")
def test_bad_init_no_attribute_only():
Prune(attribute="foo")
def test_bad_init_no_args():
Prune()
def test_bad_init_no_attribute_only():
with pytest.raises(ValueError):
Prune(attribute="foo")
def test_annotation_prune(basictrees, argfilepath):
annotated = Annotate(filename=argfilepath("annotation.csv"), key="taxon").consume(basictrees)
pruned = Prune(attribute="f1", values="0").consume(annotated)
for t in pruned:
leaves = t.get_leaf_names()
assert not any((x in leaves for x in ("A", "B", "C")))
def test_file_prune(basictrees):
pruned = Prune(filename="tests/argfiles/taxa_abc.txt").consume(basictrees)
for t in pruned:
leaves = t.get_leaf_names()
assert not any((x in leaves for x in ("A", "B", "C")))