def test_single_sample(self):
# test that if we provide a single sample, we get the same sample back
results = list(Sample.trim_samples(iter([self.samples[0]])))
self.assertEqual(len(results), 1)
got, is_last_in_contig, heuristic = results[0]
self.assertEqual(got, self.samples[0])
self.assertTrue(is_last_in_contig)
def test_gapped(self):
# check we get is_last_in_contig if we have a gap between samples
trimmed = list(Sample.trim_samples((s for s in self.samples[::2])))
for i, (expt, (got, is_last_in_contig,
heuristic)) in enumerate(zip(self.samples[::2],
trimmed)):
self.assertEqual(got, expt)
self.assertTrue(is_last_in_contig)
def test_works(self):
# test simple case of 3 chained samples
trimmed = list(Sample.trim_samples((s for s in self.samples)))
for i, (expt, (got, is_last_in_contig,
heuristic)) in enumerate(zip(self.sliced, trimmed)):
self.assertEqual(got, expt)
if i == len(self.sliced) - 1:
self.assertTrue(is_last_in_contig)
else:
self.assertFalse(is_last_in_contig)
def test_raises(self):
# test we get an exception if we e.g. provide samples from different
# refs or samples out of order
self.assertRaises(OverlapException,
lambda x: list(Sample.trim_samples(x)),
iter(self.samples[::-1]))