def test_minimize_depths_complex(self):
self.complexSetUp()
seqs = map(sub.parse_alignment, self.raw_reads)
expected_matrix = [[seqs[0], seqs[1], seqs[3]], [seqs[4]],
[seqs[6], seqs[7]]]
expected_list = [seqs[0], seqs[1], seqs[3], seqs[4], seqs[6], seqs[7]]
for seq in expected_list:
seq.pick()
expected_depths = np.array([3, 4, 6, 4, 3, 2, 2, 1])
self.matrix.min_depth = 3
self.matrix.minimize_depths()
actual_matrix = self.matrix.seq_matrix
for row in actual_matrix:
for seq in row:
if not seq.picked:
row.remove(seq)
self.assertEquals(expected_matrix, actual_matrix)
assert_equal(expected_depths, self.matrix.depth_array)
self.assertEquals([seq.string for seq in expected_list],
sub.flatten_and_filter_matrix(
self.matrix.seq_matrix))
def test_minimize_depths_complex_more_random(self, func):
#TODO: Refactor this so as not to duplicate code with non-random ecoli test
self.complexSetUp()
seqs = map(sub.parse_alignment, self.raw_reads)
expected_matrix = [[seqs[0], seqs[1], seqs[2], seqs[3]],
[seqs[4], seqs[5]], [seqs[6], seqs[7]]]
expected_list = seqs
for seq in expected_list:
seq.pick()
expected_depths = np.array([4, 6, 7, 4, 3, 2, 2, 1])
self.matrix.min_depth = 3
self.matrix.more_random = True
self.matrix.minimize_depths()
actual_matrix = self.matrix.seq_matrix
for row in actual_matrix:
for seq in row:
if not seq.picked:
row.remove(seq)
self.assertEquals(expected_matrix, actual_matrix)
assert_equal(expected_depths, self.matrix.depth_array)
self.assertEquals([seq.string for seq in expected_list],
sub.flatten_and_filter_matrix(
self.matrix.seq_matrix))
def test_minimize_depths_complex(self):
self.complexSetUp()
seqs = map(sub.parse_alignment, self.raw_reads)
expected_matrix = [
[seqs[0], seqs[1], seqs[3]],
[seqs[4]],
[seqs[6], seqs[7]]
]
expected_list = [ seqs[0], seqs[1], seqs[3], seqs[4], seqs[6], seqs[7] ]
for seq in expected_list:
seq.pick()
expected_depths = np.array([3, 4, 6, 4, 3, 2, 2, 1])
self.matrix.min_depth = 3
self.matrix.minimize_depths()
actual_matrix = self.matrix.seq_matrix
for row in actual_matrix:
for seq in row:
if not seq.picked:
row.remove(seq)
self.assertEquals(expected_matrix, actual_matrix)
assert_equal(expected_depths, self.matrix.depth_array)
self.assertEquals([seq.string for seq in expected_list], sub.flatten_and_filter_matrix(self.matrix.seq_matrix))
def test_minimize_depths_complex_more_random(self, func):
#TODO: Refactor this so as not to duplicate code with non-random ecoli test
self.complexSetUp()
seqs = map(sub.parse_alignment, self.raw_reads)
expected_matrix = [
[seqs[0], seqs[1], seqs[2], seqs[3]],
[seqs[4], seqs[5]],
[seqs[6], seqs[7]]
]
expected_list = seqs
for seq in expected_list:
seq.pick()
expected_depths = np.array([4, 6, 7, 4, 3, 2, 2, 1])
self.matrix.min_depth = 3
self.matrix.more_random = True
self.matrix.minimize_depths()
actual_matrix = self.matrix.seq_matrix
for row in actual_matrix:
for seq in row:
if not seq.picked:
row.remove(seq)
self.assertEquals(expected_matrix, actual_matrix)
assert_equal(expected_depths, self.matrix.depth_array)
self.assertEquals([seq.string for seq in expected_list], sub.flatten_and_filter_matrix(self.matrix.seq_matrix))
