def test_overlap_indices(self):
# check we get right thing for overlap and abutting major and minor
# and that we get an exception if we give it any other case.
slices = [
slice(0, 3), # (0,0) -> (1,0) in self.samples[0]
slice(3, 5), # (2,0) -> (2,1) in self.samples[0]
slice(5, 8), # (2,2) -> (4,0) in self.samples[0]
slice(8, 11) # (4.1) -> (4.3) in self.samples[0]
]
sliced = [self.samples[0].slice(sl) for sl in slices]
samples_expt = [
(
self.samples[:2], (9, 1, False)
), # overlap of minor inds with odd number of overlapping positions
(
self.samples[1:], (6, 2, False)
), # overlap of major inds with even number of overlapping positions
(sliced[:2], (None, None, False)), # abuts
(sliced[1:3], (None, None, False)), # abuts
(sliced[2:], (None, None, False)), # abuts
]
for samples, expt in samples_expt:
self.assertEqual(Sample.overlap_indices(*samples), expt)
self.assertRaises(OverlapException, Sample.overlap_indices, samples[1],
samples[0])
def test_messy_overlap(self):
dtype = [('major', int), ('minor', int)]
pos = [
np.array([
(0, 0),
(1, 0),
(2, 0),
(2, 1),
(2, 2),
(3, 0),
(4, 0),
(4, 1),
(4, 2),
(4, 3),
(5, 0),
(6, 0),
(7, 0),
(8, 0),
(8, 1),
(9, 0),
],
dtype=dtype),
np.array(
[
(3, 0),
(4, 0),
(4, 1),
(4, 2), # (4,3) missing
(5, 0),
(6, 0),
(7, 0),
(8, 0),
(8, 1),
(9, 0),
(10, 0),
(10, 1),
(10, 2),
],
dtype=dtype),
np.array([
(3, 0),
(4, 0),
(4, 1),
(4, 2),
(5, 0),
(6, 0),
(6, 1),
(7, 0),
(7, 1),
(8, 0),
(8, 1),
(9, 0),
(10, 0),
(10, 1),
(10, 2),
],
dtype=dtype),
np.array(
[
(3, 0),
(4, 0),
(4, 1),
(4, 2), # (4,3) missing
(5, 0),
(5, 1),
(6, 0),
(6, 1),
(7, 0),
(7, 1),
(8, 0),
(8, 1),
(9, 0),
(10, 0),
(10, 1),
(10, 2),
],
dtype=dtype),
np.array(
[
(3, 0),
(4, 0),
(4, 1),
(4, 2), # (4,3) missing
(5, 0),
(5, 1),
(6, 0),
(6, 1),
(7, 0),
(7, 1),
(8, 0),
(9, 0),
(10, 0),
(10, 1),
(10, 2),
],
dtype=dtype),
]
sample = [
Sample(ref_name='contig1',
features=None,
ref_seq=None,
labels=None,
positions=p,
label_probs=None) for p in pos
]
expected = [
(12, 6), # (7, 0) is junction
(10, 4), # (5, 0) is junction
(13, 10), # (8, 0) is junction
(15, 11), # (9, 0) is junction
]
for other, exp in enumerate(expected, 1):
end, start, heuristic = Sample.overlap_indices(
sample[0], sample[other])
self.assertTrue(heuristic)
self.assertEqual((end, start), exp)
self.assertEqual(pos[0][exp[0]], pos[other][exp[1]])