def test_choice_with_alleles(self):
""" test that choice_with_alleles() works correctly.
"""
# if you add a choice with alleles, then check that we get back alleles,
# and that they are the same
choices = WeightedChoice()
choices.add_choice(1, 1, "A", "T")
self.assertEqual(choices.choice_with_alleles(),
{'alt': 'T', 'ref': 'A', 'pos': 1, 'offset': 0})
self.assertEqual(choices.choice(), 1)
# if you add choices without alleles, then default the alleles to "N"
choices = WeightedChoice()
choices.add_choice(1, 1)
self.assertEqual(choices.choice_with_alleles(),
{'alt': 'N', 'ref': 'N', 'pos': 1, 'offset': 0})
# make sure you can't add multi-base alleles to the choices
with self.assertRaises(TypeError):
choices.add_choice(1, 1, "AA", "A")
choices.add_choice(1, 1, "A", "AG")
# make sure non-zero offsets are returned corectly
choices = WeightedChoice()
choices.add_choice(1, 1, "A", "T", 3)
self.assertEqual(choices.choice_with_alleles(),
{'alt': 'T', 'ref': 'A', 'pos': 1, 'offset': 3})
self.assertEqual(choices.choice(), 1)
def test_choice_with_alleles(self):
""" test that choice_with_alleles() works correctly.
"""
# if you add a choice with alleles, then check that we get back alleles,
# and that they are the same
choices = WeightedChoice()
choices.add_choice(1, 1, "A", "T")
self.assertEqual(choices.choice_with_alleles(), {
'alt': 'T',
'ref': 'A',
'pos': 1,
'offset': 0
})
self.assertEqual(choices.choice(), 1)
# if you add choices without alleles, then default the alleles to "N"
choices = WeightedChoice()
choices.add_choice(1, 1)
self.assertEqual(choices.choice_with_alleles(), {
'alt': 'N',
'ref': 'N',
'pos': 1,
'offset': 0
})
# make sure you can't add multi-base alleles to the choices
with self.assertRaises(TypeError):
choices.add_choice(1, 1, "AA", "A")
choices.add_choice(1, 1, "A", "AG")
# make sure non-zero offsets are returned corectly
choices = WeightedChoice()
choices.add_choice(1, 1, "A", "T", 3)
self.assertEqual(choices.choice_with_alleles(), {
'alt': 'T',
'ref': 'A',
'pos': 1,
'offset': 3
})
self.assertEqual(choices.choice(), 1)