def test_beast_vector_annotated_nexus_output_cat():
lines = fileinput.input("tests/treefiles/beast_output_geo_annotations.nex")
trees = ComplexNewickParser().consume(lines)
trees = Cat().consume(trees)
for t in trees:
for n in t.traverse():
assert hasattr(n, "location")
def test_init():
# Test defaults
cat = Cat.init_from_args("")
assert cat.burnin == 0
assert cat.subsample == 1
assert cat.annotations == True
# Test burnin
cat = Cat.init_from_args("--burnin 10")
assert cat.burnin == 10
# Test subsample
cat = Cat.init_from_args("--subsample 10")
assert cat.subsample == 10
# Test no annotations
cat = Cat.init_from_args("--no-annotations")
assert cat.annotations == False
def test_beast_annotated_nexus_output_cat():
lines = fileinput.input(
"tests/treefiles/beast_output_rate_annotations.nex")
trees = ComplexNewickParser().consume(lines)
trees = Cat().consume(trees)
for t in trees:
for n in t.traverse():
assert hasattr(n, "rate")
assert len(t.get_leaves()) == 26
def test_beast_nexus_output_cat(treefilenewick):
trees = Cat().consume(treefilenewick('beast_output.nex'))
for t in trees:
assert len(t.get_leaves()) == 26
def test_basic_cat(basictrees):
trees = Cat().consume(basictrees)
assert sum((1 for _ in trees)) == 6
def test_mr_bayes_nexus_output_cat(treefilenewick):
trees = Cat().consume(treefilenewick('mr_bayes_output.nex'))
for t in trees:
assert len(t.get_leaves()) == 12
def test_beast_vector_annotated_nexus_output_cat(treefilenewick):
trees = Cat().consume(treefilenewick('beast_output_geo_annotations.nex'))
for t in trees:
for n in t.traverse():
assert hasattr(n, "location")
def test_beast_annotated_nexus_output_cat(treefilenewick):
trees = Cat().consume(treefilenewick('beast_output_rate_annotations.nex'))
for t in trees:
for n in t.traverse():
assert hasattr(n, "rate")
assert len(t.get_leaves()) == 26
def test_command_bad_args():
with pytest.raises(SystemExit):
run_command('sibling')
with pytest.raises(SystemExit):
_ = Cat.init_from_args("cat --foobar")
def test_command_bad_args():
cat = Cat.init_from_args("cat --foobar")
def test_mr_bayes_nexus_output_cat():
lines = fileinput.input("tests/treefiles/mr_bayes_output.nex")
trees = ComplexNewickParser().consume(lines)
trees = Cat().consume(trees)
for t in trees:
assert len(t.get_leaves()) == 12
def test_burnin():
lines = fileinput.input("tests/treefiles/basic.trees")
trees = NewickParser().consume(lines)
burntin = Cat(burnin=50).consume(trees)
assert sum((1 for t in burntin)) == 3
def test_basic_cat():
lines = fileinput.input("tests/treefiles/basic.trees")
trees = NewickParser().consume(lines)
subsampled = Cat(subsample=2).consume(trees)
assert sum((1 for t in subsampled)) == 3