def test_toy_smith_waterman(self, decorator, tol):
smith_waterman_fn = tf_ops.hard_sw_affine
if decorator is not None:
smith_waterman_fn = decorator(smith_waterman_fn)
values, paths = smith_waterman_fn(self._w, tol)
paths_squeeze = alignment.path_label_squeeze(paths)
all_matches = tf.where(
alignment.paths_to_state_indicators(paths, 'match'))
values_test = tf.constant([5.0, 3.0, 2.94, 3.0], dtype=tf.float32)
self.assertAllClose(values, values_test, atol=2 * tol)
paths_squeeze_test = tf.constant(
[[[1., 0., 0., 0., 0.], [0., 2., 0., 0., 0.], [0., 0., 2., 0., 0.],
[0., 0., 0., 2., 0.], [0., 0., 0., 0., 2.]],
[[0., 0., 0., 0., 0.], [0., 0., 0., 0., 0.], [0., 0., 1., 0., 0.],
[0., 0., 0., 2., 0.], [0., 0., 0., 0., 2.]],
[[0., 0., 0., 0., 0.], [0., 1., 5., 0., 0.], [0., 0., 8., 0., 0.],
[0., 0., 0., 4., 0.], [0., 0., 0., 0., 2.]],
[[0., 0., 0., 0., 0.], [0., 1., 0., 0., 0.], [0., 0., 2., 0., 0.],
[0., 0., 0., 2., 0.], [0., 0., 0., 0., 0.]]],
dtype=tf.float32)
self.assertAllEqual(paths_squeeze, paths_squeeze_test)
all_matches_test = tf.constant(
[[0, 0, 0], [0, 1, 1], [0, 2, 2], [0, 3, 3], [0, 4, 4], [1, 2, 2],
[1, 3, 3], [1, 4, 4], [2, 1, 1], [2, 3, 3], [2, 4, 4], [3, 1, 1],
[3, 2, 2], [3, 3, 3]],
dtype=tf.int32)
self.assertAllEqual(all_matches, all_matches_test)
def test_alignments_to_paths(self):
exp_out = tf.convert_to_tensor(
[[[1., 0., 0., 0., 0., 0., 0.], [0., 2., 5., 0., 0., 0., 0.],
[0., 0., 0., 3., 0., 0., 0.], [0., 0., 0., 7., 0., 0., 0.],
[0., 0., 0., 9., 0., 0., 0.], [0., 0., 0., 0., 4., 0., 0.],
[0., 0., 0., 0., 0., 2., 0.], [0., 0., 0., 0., 0., 0., 2.]]],
tf.float32)
paths = alignment.alignments_to_paths(self.alignments, self.len_x,
self.len_y)
sq_paths = alignment.path_label_squeeze(paths)
self.assertAllEqual(sq_paths, exp_out)
# Invariance to padding.
padded_alignments = tf.concat(
[self.alignments, tf.zeros([1, 3, 3], tf.int32)], 2)
paths = alignment.alignments_to_paths(padded_alignments, self.len_x,
self.len_y)
sq_paths = alignment.path_label_squeeze(paths)
self.assertAllEqual(sq_paths, exp_out)
# Pads correctly via length arguments.
paths = alignment.alignments_to_paths(self.alignments, self.len_x + 3,
self.len_y + 3)
sq_paths = alignment.path_label_squeeze(paths)
self.assertAllEqual(sq_paths[:, :self.len_x, :self.len_y], exp_out)
self.assertAllEqual(sq_paths[:, self.len_x:, :],
tf.zeros([1, 3, self.len_y + 3], tf.float32))
self.assertAllEqual(sq_paths[Ellipsis, self.len_y:],
tf.zeros([1, self.len_x + 3, 3], tf.float32))
# Deals with empty ground-truth alignments.
paths = alignment.alignments_to_paths(tf.zeros_like(self.alignments),
self.len_x, self.len_y)
sq_paths = alignment.path_label_squeeze(paths)
self.assertAllEqual(sq_paths, tf.zeros_like(exp_out))
def test_smith_waterman_empty(self, decorator):
smith_waterman_fn = tf_ops.hard_sw_affine
if decorator is not None:
smith_waterman_fn = decorator(smith_waterman_fn)
tol = 1e-6
single_sub = - 5*tf.ones((5, 5))
toy_sub = tf.expand_dims(single_sub, 0)
toy_gap_open = 0.03 * tf.ones((toy_sub.shape[0],))
toy_gap_extend = 0.02 * tf.ones((toy_sub.shape[0],))
w = alignment.weights_from_sim_mat(toy_sub, toy_gap_open, toy_gap_extend)
values, paths = smith_waterman_fn(w, tol=tol)
paths_squeeze = alignment.path_label_squeeze(paths)
self.assertAllClose(values, [0.0], atol=2 * tol)
self.assertAllEqual(paths_squeeze, tf.zeros([1, 5, 5], tf.float32))
def test_smith_waterman_termination(self, decorator):
smith_waterman_fn = tf_ops.hard_sw_affine
if decorator is not None:
smith_waterman_fn = decorator(smith_waterman_fn)
tol = 1e-6
single_sub = tf.concat([- 5*tf.ones((3, 1)),
6*tf.eye(3) - 5*tf.ones((3, 3))], 1)
toy_sub = tf.expand_dims(single_sub, 0)
toy_gap_open = 0.03 * tf.ones((toy_sub.shape[0],))
toy_gap_extend = 0.02 * tf.ones((toy_sub.shape[0],))
w = alignment.weights_from_sim_mat(toy_sub, toy_gap_open, toy_gap_extend)
values, paths = smith_waterman_fn(w, tol=tol)
paths_squeeze = alignment.path_label_squeeze(paths)
self.assertAllClose(values, [3.0], atol=2 * tol)
paths_squeeze_test = tf.convert_to_tensor([[[0., 1., 0., 0.],
[0., 0., 2., 0.],
[0., 0., 0., 2.]]], tf.float32)
self.assertAllEqual(paths_squeeze, paths_squeeze_test)