def test_file_collapse():
lines = fileinput.input("tests/treefiles/basic.trees")
trees = list(NewickParser().consume(lines))
collapsed = Collapse(filename="tests/argfiles/collapse.txt").consume(trees)
# These groups are monophyletic in the first 5 of the 6 basic trees, so...
for n, t in enumerate(collapsed):
assert len(t.get_leaves()) == (2 if n < 5 else 6)
def test_collapse():
lines = fileinput.input("tests/treefiles/basic.trees")
trees = list(NewickParser().consume(lines))
collapsed = Collapse({"left":("A","B","C"), "right":("D","E","F")}).consume(trees)
# These groups are monophyletic in the first 5 of the 6 basic trees, so...
for n, t in enumerate(collapsed):
assert len(t.get_leaves()) == (2 if n < 5 else 6)
def test_attribute_collapse(basictrees):
annotated = Annotate(
filename="tests/argfiles/annotation.csv", key="taxon").consume(basictrees)
# f1 in the annotations applied above corresponds to the same left/right
# split as the other tests above
collapsed = Collapse(attribute="f1").consume(annotated)
# These groups are monophyletic in the first 5 of the 6 basic trees, so...
for n, t in enumerate(collapsed):
assert len(t.get_leaves()) == (2 if n < 5 else 6)
def test_attribute_collapse():
lines = fileinput.input("tests/treefiles/basic.trees")
trees = list(NewickParser().consume(lines))
annotated = Annotate("tests/argfiles/annotation.csv", "taxon").consume(trees)
# f1 in the annotations applied above corresponds to the same left/right
# split as the other tests above
collapsed = Collapse(attribute="f1").consume(annotated)
# These groups are monophyletic in the first 5 of the 6 basic trees, so...
for n, t in enumerate(collapsed):
assert len(t.get_leaves()) == (2 if n < 5 else 6)
def test_init():
collapse = Collapse.init_from_args("--translate tests/argfiles/collapse.txt")
assert collapse.filename == "tests/argfiles/collapse.txt"
collapse = Collapse.init_from_args("--attribute collapsibility")
assert collapse.attribute == "collapsibility"
def test_attribute_non_collapse():
lines = fileinput.input("tests/treefiles/basic.trees")
trees = list(NewickParser().consume(lines))
collapsed = Collapse(attribute="foo").consume(trees)
for t1, t2 in zip(trees, collapsed):
assert t1.write() == t2.write()
def test_non_collapse():
lines = fileinput.input("tests/treefiles/basic.trees")
trees = list(NewickParser().consume(lines))
collapsed = Collapse({"non-existent":("X","Y","Z")}).consume(trees)
for t1, t2 in zip(trees, collapsed):
assert t1.write() == t2.write()
def test_bad_init_no_args():
Collapse()
def test_init(argfilepath):
collapse = Collapse.init_from_args("--translate {0}".format(argfilepath('collapse.txt')))
assert collapse.opts.filename == argfilepath('collapse.txt')
collapse = Collapse.init_from_args("--attribute collapsibility")
assert collapse.opts.attribute == "collapsibility"
def test_attribute_non_collapse(basictrees):
trees = list(basictrees)
collapsed = Collapse(attribute="foo").consume(trees)
for t1, t2 in zip(trees, collapsed):
assert t1.write() == t2.write()
def test_non_collapse(basictrees):
trees = list(basictrees)
collapsed = Collapse({"non-existent":("X","Y","Z")}).consume(trees)
for t1, t2 in zip(trees, collapsed):
assert t1.write() == t2.write()
def test_file_collapse(basictrees, argfilepath):
collapsed = Collapse(filename=argfilepath("collapse.txt")).consume(basictrees)
# These groups are monophyletic in the first 5 of the 6 basic trees, so...
for n, t in enumerate(collapsed):
assert len(t.get_leaves()) == (2 if n < 5 else 6)
def test_collapse(basictrees):
collapsed = Collapse(
clades={"left":("A","B","C"), "right":("D","E","F")}).consume(basictrees)
# These groups are monophyletic in the first 5 of the 6 basic trees, so...
for n, t in enumerate(collapsed):
assert len(t.get_leaves()) == (2 if n < 5 else 6)
def test_bad_init_no_args():
with pytest.raises(ValueError):
Collapse()