def test_get_qual_stats(self):
""" Properly generates averages, std dev for bins """
qual_bins = [[1, 2, 6], [1, 2, 3], [2, 4], [4]]
expected_ave_bins = [3, 2, 3, 4]
expected_std_dev_bins = [2.16, 0.816, 1.0, 0]
expected_total_bases_bins = [3, 3, 2, 1]
score_min = 25
actual_ave_bins, actual_std_dev_bins, actual_total_bases_bins,\
suggested_trunc_pos = get_qual_stats(qual_bins, score_min)
# Should give correct suggested truncation position, where the quality
# score average went below 25, in this case, at base 0
expected_trunc_pos = 0
self.assertEqual(suggested_trunc_pos, expected_trunc_pos)
# Round standard deviation calculations
for n in range(len(actual_std_dev_bins)):
actual_std_dev_bins[n] = round(actual_std_dev_bins[n], 3)
self.assertEqual(actual_ave_bins, expected_ave_bins)
self.assertEqual(actual_std_dev_bins, expected_std_dev_bins)
self.assertEqual(actual_total_bases_bins, expected_total_bases_bins)
def test_get_qual_stats(self):
""" Properly generates averages, std dev for bins """
qual_bins = [[1, 2, 6], [1, 2, 3], [2, 4], [4]]
expected_ave_bins = [3, 2, 3, 4]
expected_std_dev_bins = [2.16, 0.816, 1.0, 0]
expected_total_bases_bins = [3, 3, 2, 1]
score_min = 25
actual_ave_bins, actual_std_dev_bins, actual_total_bases_bins,\
suggested_trunc_pos = get_qual_stats(qual_bins, score_min)
# Should give correct suggested truncation position, where the quality
# score average went below 25, in this case, at base 0
expected_trunc_pos = 0
self.assertEqual(suggested_trunc_pos, expected_trunc_pos)
# Round standard deviation calculations
for n in range(len(actual_std_dev_bins)):
actual_std_dev_bins[n] = round(actual_std_dev_bins[n], 3)
self.assertEqual(actual_ave_bins, expected_ave_bins)
self.assertEqual(actual_std_dev_bins, expected_std_dev_bins)
self.assertEqual(actual_total_bases_bins, expected_total_bases_bins)
