def test_procreate_child_child_chromosome_set(self):
chromosome_m1, chromosome_f1 = 'AC', 'GA'
chromosome_m2, chromosome_f2 = 'CT', 'TG'
# set up father chromosome
father = a2.Male(build_id('m'))
father.set_by_pos(17, 42, chromosome_m1)
father.set_by_pos(10, 84, chromosome_m2)
self.assertEqual(chromosome_m1, father.get_by_pos(17, 42),
'Failed to set father chromosome "%s" to %d-%d.' % (chromosome_m1, 17, 42))
self.assertEqual(chromosome_m2, father.get_by_pos(10, 84),
'Failed to set father chromosome "%s" to %d-%d.' % (chromosome_m2, 10, 84))
# set up mother chromosome
mother = a2.Female(build_id('f'))
mother.set_by_pos(17, 42, chromosome_f1)
mother.set_by_pos(10, 84, chromosome_f2)
self.assertEqual(chromosome_f1, mother.get_by_pos(17, 42),
'Failed to set mother chromosome "%s" to %d-%d.' % (chromosome_f1, 17, 42))
self.assertEqual(chromosome_f2, mother.get_by_pos(10, 84),
'Failed to set mother chromosome "%s" to %d-%d.' % (chromosome_f2, 10, 84))
# set up binder chromosome
binder = a2.Binder()
binder.set_sex('F')
binder.set_by_pos(17, 42, 'RM')
binder.set_by_pos(10, 84, 'LM')
# procreate child
child = mother.procreate(father, binder)
self.assertIsNotNone(child, 'Failed to procreate child. No Female object is created.')
self.assertTrue(isinstance(child, a2.Female), 'Type check failed, procreated child should be a Female object.')
self.assertEqual('AA', child.get_by_pos(17, 42), 'Child chromosome at %d-%d is incorrect.' % (17, 42))
self.assertEqual('TT', child.get_by_pos(10, 84), 'Child chromosome at %d-%d is incorrect.' % (10, 84))
def test_set_by_pos_boundary_index_and_check_child_index(self):
chromosome_m1, chromosome_f1 = 'CT', 'AC'
chromosome_m2, chromosome_f2 = 'AG', 'GT'
# set up father chromosome
father = a2.Male(build_id('m'))
father.set_by_pos(0, 42, chromosome_m1)
father.set_by_pos(22, 84, chromosome_m2)
# self.assertEqual(chromosome_m1, father.get_by_pos(0, 42),
# 'Failed to set father chromosome "%s" to %d-%d.' % (chromosome_m1, 0, 42))
# self.assertEqual(chromosome_m2, father.get_by_pos(22, 84),
# 'Failed to set father chromosome "%s" to %d-%d.' % (chromosome_m2, 22, 84))
# set up mother chromosome
mother = a2.Female(build_id('f'))
mother.set_by_pos(0, 42, chromosome_f1)
mother.set_by_pos(22, 84, chromosome_f2)
# self.assertEqual(chromosome_f1, mother.get_by_pos(0, 42),
# 'Failed to set mother chromosome "%s" to %d-%d.' % (chromosome_f1, 0, 42))
# self.assertEqual(chromosome_f2, mother.get_by_pos(22, 84),
# 'Failed to set mother chromosome "%s" to %d-%d.' % (chromosome_f2, 22, 84))
# set up binder chromosome
binder = a2.Binder()
binder.set_sex('M')
binder.set_by_pos(0, 42, 'RM')
binder.set_by_pos(22, 84, 'LM')
# procreate child
child = mother.procreate(father, binder)
# self.assertIsNotNone(child, 'Failed to procreate child (Male). No Male object is created.')
# self.assertTrue(isinstance(child, a2.Male), 'Type check failed, procreated child should be a Male object.')
self.assertEqual('CC', child.get_by_pos(0, 42), 'Child chromosome at %d-%d is incorrect.' % (0, 42))
self.assertEqual('GG', child.get_by_pos(22, 84), 'Child chromosome at %d-%d is incorrect.' % (22, 84))
def test_procreate_no_child_chromosome_set(self):
father = a2.Male(build_id('m'))
mother = a2.Female(build_id('f'))
binder = a2.Binder()
binder.set_sex('F')
child = mother.procreate(father, binder)
self.assertIsNotNone(child, 'Failed to procreate child (Female). No Female object is created.')
self.assertFalse(isinstance(child, a2.Male), 'Type check failed, procreated child should be a Male object.')
self.assertTrue(isinstance(child, a2.Female), 'Type check failed, procreated child should not be a Female object.')
def test_query_diff_chromosome_same_pair_position(self):
chromosome1, chromosome2 = 'AG', 'CT'
# set up father
mother = a2.Female(build_id('f'))
mother.set_by_pos(17, 42, chromosome1)
# set up query
query = a2.Query()
query.set_by_pos(17, 42, chromosome2)
self.assertFalse(mother.test(query),
'Failed to test the query. Both chromosome is set to (%d-%d), but Mother chromosome is "%s", Query chromosome is "%s".'
% (17, 42, chromosome1, chromosome2))
def test_query_set_by_marker(self):
chromosome = random.choice(NUCLEOTIDE) + 'G'
marker = build_marker()
# setup mother
mother = a2.Female(build_id('f'))
mother.set_by_pos(9, 76, chromosome)
# set up query
query = a2.Query()
query.set_marker(marker, 9, 76)
query.set_by_marker(marker, '3G')
self.assertTrue(mother.test(query),
'Failed to test the query. Chromosome "%s" is set to (%d-%d)' % (chromosome, 9, 76))
def test_init(self):
self.assertIsNotNone(a2.Female(build_id('f')), 'Failed to create Female object.')
def setUp(self):
self.female = a2.Female(build_id('female'))