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_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_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_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_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_read_write(self):
for reader_fn, writer_fn, fhs in (
(_lsmat_to_dissimilarity_matrix, _dissimilarity_matrix_to_lsmat, self.dissim_fhs),
(_lsmat_to_distance_matrix, _distance_matrix_to_lsmat, self.dist_fhs),
):
for fh in fhs:
# Read.
fh.seek(0)
lsmat1 = reader_fn(fh)
# Write.
out_fh = StringIO()
writer_fn(lsmat1, out_fh)
out_fh.seek(0)
# Read.
lsmat2 = reader_fn(out_fh)
out_fh.close()
self.assertEqual(lsmat1, lsmat2)
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_read_write(self):
for reader_fn, writer_fn, fhs in ((_lsmat_to_dissimilarity_matrix,
_dissimilarity_matrix_to_lsmat,
self.dissim_fhs),
(_lsmat_to_distance_matrix,
_distance_matrix_to_lsmat,
self.dist_fhs)):
for fh in fhs:
# Read.
fh.seek(0)
lsmat1 = reader_fn(fh)
# Write.
out_fh = StringIO()
writer_fn(lsmat1, out_fh)
out_fh.seek(0)
# Read.
lsmat2 = reader_fn(out_fh)
out_fh.close()
self.assertEqual(lsmat1, lsmat2)
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_newick_sniffer_invalid_files(self):
for invalid, _ in self.invalid_newicks:
fh = StringIO(invalid)
self.assertEqual(_newick_sniffer(fh), (False, {}))
fh.close()
def test_newick_sniffer_valid_files(self):
for _, newicks in self.trees_newick_lists:
for newick in newicks:
fh = StringIO(newick)
self.assertEqual(_newick_sniffer(fh), (True, {}))
fh.close()