def testDnaRoundTrip(self):
ape_c = ape.as_ape_object(self.dna_chars)
dp_c = ape.as_dendropy_object(ape_c,
taxon_set=self.dna_chars.taxon_set)
self.assertDistinctButEqual(self.dna_chars,
dp_c,
distinct_taxa=False)
def is_binary_tree(tree):
"""
Determines if a tree is binary
@param tree: dendropy tree
@return: true/false
@rtype: bool
"""
r_tree = ape.as_ape_object(tree)
return robjects.r['is.binary.tree'](r_tree)[0]
def testTreeListRoundTrip(self):
ape_t = ape.as_ape_object(self.trees)
rt = ape.as_dendropy_object(ape_t, taxon_set=self.trees.taxon_set)
self.assertTrue(isinstance(rt, dendropy.TreeList), type(rt))
self.assertDistinctButEqual(self.trees, rt, distinct_taxa=False)
def testTreeRoundTrip(self):
for i, t1 in enumerate(self.trees):
ape_t = ape.as_ape_object(t1)
rt = ape.as_dendropy_object(ape_t, taxon_set=t1.taxon_set)
self.assertTrue(isinstance(rt, dendropy.Tree), type(rt))
self.assertDistinctButEqual(t1, rt, distinct_taxa=False)
def testDnaRoundTrip(self):
ape_c = ape.as_ape_object(self.dna_chars)
dp_c = ape.as_dendropy_object(ape_c, taxon_set=self.dna_chars.taxon_set)
self.assertDistinctButEqual(self.dna_chars, dp_c, distinct_taxa=False)
def testTreeListRoundTrip(self):
ape_t = ape.as_ape_object(self.trees)
rt = ape.as_dendropy_object(ape_t, taxon_set=self.trees.taxon_set)
self.assertTrue(isinstance(rt, dendropy.TreeList), type(rt))
self.assertDistinctButEqual(self.trees, rt, distinct_taxa=False)
def testTreeRoundTrip(self):
for i, t1 in enumerate(self.trees):
ape_t = ape.as_ape_object(t1)
rt = ape.as_dendropy_object(ape_t, taxon_set=t1.taxon_set)
self.assertTrue(isinstance(rt, dendropy.Tree), type(rt))
self.assertDistinctButEqual(t1, rt, distinct_taxa=False)