def test_generate_haplotype_mutation(self):
haplotype_original = generator.generate_haplotype(self.haplotype_length, generator.ModificationType.NONE)
haplotype = generator.generate_haplotype(self.haplotype_length, generator.ModificationType.MUTATION, haplotype_original)
self.assertIsNotNone(haplotype)
self.assertNotEqual(haplotype, haplotype_original)
for character in self.invalid_bases:
self.assertNotIn(character, haplotype)
for base in haplotype:
self.assertIn(base, self.bases)
def test_generate_haplotype_inexistent_modification_kind(self):
haplotype = generator.generate_haplotype(self.haplotype_length, "XPTO")
self.assertIsNone(haplotype)
haplotype = generator.generate_haplotype(self.haplotype_length, -1)
self.assertIsNone(haplotype)
haplotype = generator.generate_haplotype(self.haplotype_length, None)
self.assertIsNone(haplotype)
haplotype = generator.generate_haplotype(self.haplotype_length, True)
self.assertIsNone(haplotype)
def test_generate_haplotype_recombination(self):
haplotype_original_one = generator.generate_haplotype(self.haplotype_length, generator.ModificationType.NONE)
haplotype_original_other = generator.generate_haplotype(self.haplotype_length, generator.ModificationType.NONE)
while haplotype_original_one == haplotype_original_other:
haplotype_original_other = generator.generate_haplotype(self.haplotype_length, generator.ModificationType.NONE)
haplotype = generator.generate_haplotype(self.haplotype_length, generator.ModificationType.RECOMBINATION, haplotype_original_one, haplotype_original_other)
self.assertIsNotNone(haplotype)
self.assertNotEqual(haplotype, haplotype_original_one)
self.assertNotEqual(haplotype, haplotype_original_other)
for character in self.invalid_bases:
self.assertNotIn(character, haplotype)
for base in haplotype:
self.assertIn(base, self.bases)
def test_generate_haplotype_normal(self):
haplotype = generator.generate_haplotype(self.haplotype_length, generator.ModificationType.NONE)
self.assertIsNotNone(haplotype)
for character in self.invalid_bases:
self.assertNotIn(character, haplotype)
for base in haplotype:
self.assertIn(base, self.bases)
def test_generate_haplotype_mutation_excedent(self):
haplotype_original = generator.generate_haplotype(self.haplotype_length, generator.ModificationType.NONE)
haplotype = generator.generate_haplotype(self.haplotype_length, generator.ModificationType.MUTATION, haplotype_original, haplotype_original)
self.assertIsNone(haplotype)
def test_generate_haplotype_mutation_incomplete(self):
haplotype_original = generator.generate_haplotype(self.haplotype_length, generator.ModificationType.NONE)
haplotype = generator.generate_haplotype(self.haplotype_length, generator.ModificationType.MUTATION)
self.assertIsNone(haplotype)
def test_generate_haplotype_negative_size(self):
negative_sizes = [random.randint(-(sys.maxint) - 1,0) for x in range(0,1000)]
for negative_size in negative_sizes:
haplotype = generator.generate_haplotype(negative_size, generator.ModificationType.NONE)
self.assertIsNone(haplotype)
def test_generate_haplotype_zero_size(self):
haplotype = generator.generate_haplotype(0, generator.ModificationType.NONE)
self.assertIsNone(haplotype)
