def test_sampleContext(self):
self.assertEqual(
alg.sampleContext(
alg.factorByField(
sp.p_tree.parse("(B|a,(A|b,C|b,E|b),D|c);").tree, field=2),
keep=[],
maxTips=1,
),
sp.Node(kids=[
sp.Node(label="B|a", factor="a"),
sp.Node(label="A|b", factor="b"),
sp.Node(label="D|c", factor="c"),
]),
)
self.assertEqual(
alg.sampleContext(
alg.factorByField(
sp.p_tree.parse("(B|a,(A|b,C|b,E|b),D|c);").tree, field=2),
keep=[],
maxTips=2,
),
sp.Node(kids=[
sp.Node(label="B|a", factor="a"),
sp.Node(kids=[
sp.Node(label="A|b", factor="b"),
sp.Node(label="C|b", factor="b"),
]),
sp.Node(label="D|c", factor="c"),
]),
)
def test_node(self):
self.assertEqual(
sp.p_node.parse("(A[foo=boo,bar=baz]:0.42)Root"),
sp.Node(
kids=[
sp.Node(label="A",
form={
"foo": "boo",
"bar": "baz"
},
length=0.42)
],
label="Root",
),
)
def test_newick(self):
self.assertEqual(
sp.p_tree.parse("(A[foo=boo]:0.42)Root;").tree,
sp.Node(
kids=[sp.Node(label="A", form={"foo": "boo"}, length=0.42)],
label="Root",
),
)
self.assertEqual(
sp.p_tree.parse("(B,(A,C,E),D);").tree,
sp.Node(kids=[
sp.Node(label="B"),
sp.Node(kids=[
sp.Node(label="A"),
sp.Node(label="C"),
sp.Node(label="E"),
]),
sp.Node(label="D"),
]),
)
def test_treemap(self):
def _lower(x):
if x.label:
x.label = x.label.lower()
return x
self.assertEqual(
alg.treemap(sp.p_tree.parse("(B,(A,C,E),D);").tree, _lower),
sp.Node(kids=[
sp.Node(label="b"),
sp.Node(kids=[
sp.Node(label="a"),
sp.Node(label="c"),
sp.Node(label="e"),
]),
sp.Node(label="d"),
]),
)
def test_factorByLabel(self):
def _fun(name):
try:
return name.split("|")[1]
except:
return None
self.assertEqual(
alg.factorByLabel(
sp.p_tree.parse("(B|a,(A|b,C|b,E|b),D|c);").tree, _fun),
sp.Node(kids=[
sp.Node(label="B|a", factor="a"),
sp.Node(kids=[
sp.Node(label="A|b", factor="b"),
sp.Node(label="C|b", factor="b"),
sp.Node(label="E|b", factor="b"),
]),
sp.Node(label="D|c", factor="c"),
]),
)
def test_leaf(self):
self.assertEqual(
sp.p_leaf.parse("A[foo=boo]:0.42"),
sp.Node(label="A", form={"foo": "boo"}, length=0.42),
)