def test_newick_to_tree_node_invalid_files(self):
for invalid, error_fragments in self.invalid_newicks:
fh = StringIO(invalid)
with self.assertRaises(NewickFormatError) as cm:
_newick_to_tree_node(fh)
for frag in error_fragments:
self.assertIn(frag, str(cm.exception))
fh.close()
def test_newick_to_tree_node_invalid_files(self):
for invalid, error_fragments in self.invalid_newicks:
fh = StringIO(invalid)
with self.assertRaises(NewickFormatError) as cm:
_newick_to_tree_node(fh)
for frag in error_fragments:
self.assertIn(frag, str(cm.exception))
fh.close()
def test_roundtrip(self):
for tree, newicks in self.trees_newick_lists:
newick = newicks[0]
fh = StringIO(newick)
tree = _newick_to_tree_node(fh)
fh2 = StringIO()
_tree_node_to_newick(tree, fh2)
fh2.seek(0)
tree2 = _newick_to_tree_node(fh2)
self.assertEqual(newick, fh2.getvalue())
self._assert_equal(tree, tree2)
fh.close()
fh2.close()
def test_roundtrip(self):
for tree, newicks in self.trees_newick_lists:
newick = newicks[0]
fh = StringIO(newick)
tree = _newick_to_tree_node(fh)
fh2 = StringIO()
_tree_node_to_newick(tree, fh2)
fh2.seek(0)
tree2 = _newick_to_tree_node(fh2)
self.assertEqual(newick, fh2.getvalue())
self._assert_equal(tree, tree2)
fh.close()
fh2.close()
def test_newick_to_tree_node_convert_underscores(self):
fh = StringIO('(_:0.1, _a, _b)__;')
tree = _newick_to_tree_node(fh, convert_underscores=False)
fh2 = StringIO()
_tree_node_to_newick(tree, fh2)
self.assertEquals(fh2.getvalue(), "('_':0.1,'_a','_b')'__';\n")
fh2.close()
fh.close()
def test_newick_to_tree_node_convert_underscores(self):
fh = StringIO('(_:0.1, _a, _b)__;')
tree = _newick_to_tree_node(fh, convert_underscores=False)
fh2 = StringIO()
_tree_node_to_newick(tree, fh2)
self.assertEquals(fh2.getvalue(), "('_':0.1,'_a','_b')'__';\n")
fh2.close()
fh.close()
def test_newick_to_tree_node_valid_files(self):
for tree, newicks in self.trees_newick_lists:
for newick in newicks:
fh = StringIO(newick)
read_tree = _newick_to_tree_node(fh)
self._assert_equal(tree, read_tree)
fh.close()
def test_newick_to_tree_node_valid_files(self):
for tree, newicks in self.trees_newick_lists:
for newick in newicks:
fh = StringIO(newick)
read_tree = _newick_to_tree_node(fh)
self._assert_equal(tree, read_tree)
fh.close()