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.assertEqual(fh2.getvalue(), "('_':0.1,'_a','_b')'__';\n")
fh2.close()
fh.close()
def test_tree_node_to_newick(self):
for tree, newicks in self.trees_newick_lists:
newick = newicks[0]
fh = StringIO()
_tree_node_to_newick(tree, fh)
self.assertEqual(newick, fh.getvalue())
fh.close()
def test_write(self):
for fn, objs, strs in ((_dissimilarity_matrix_to_lsmat,
self.dissim_objs, self.dissim_strs),
(_distance_matrix_to_lsmat, self.dist_objs,
self.dist_strs)):
for obj, str_ in zip(objs, strs):
fh = StringIO()
fn(obj, fh)
obs = fh.getvalue()
fh.close()
self.assertEqual(obs, str_)
# Test writing CSV (TSV is written above).
for fn, cls in ((_dissimilarity_matrix_to_lsmat, DissimilarityMatrix),
(_distance_matrix_to_lsmat, DistanceMatrix)):
obj = cls(self.lsmat_3x3_data, ['a', 'b', 'c'])
fh = StringIO()
fn(obj, fh, delimiter=',')
obs = fh.getvalue()
fh.close()
self.assertEqual(obs, LSMat_3x3_CSV)
def test_write(self):
for fn, objs, strs in (
(_dissimilarity_matrix_to_lsmat, self.dissim_objs, self.dissim_strs),
(_distance_matrix_to_lsmat, self.dist_objs, self.dist_strs),
):
for obj, str_ in zip(objs, strs):
fh = StringIO()
fn(obj, fh)
obs = fh.getvalue()
fh.close()
self.assertEqual(obs, str_)
# Test writing CSV (TSV is written above).
for fn, cls in (
(_dissimilarity_matrix_to_lsmat, DissimilarityMatrix),
(_distance_matrix_to_lsmat, DistanceMatrix),
):
obj = cls(self.lsmat_3x3_data, ["a", "b", "c"])
fh = StringIO()
fn(obj, fh, delimiter=",")
obs = fh.getvalue()
fh.close()
self.assertEqual(obs, LSMat_3x3_CSV)
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()
