def test_create_primer_with_zero_length(self):
"""
Scenario desc: We initialize primer with 0 length.
We should get value error.
"""
with self.assertRaises(ValueError) as context:
Primer("ACGT", Primer.REVERSE, 0, 0)
self.assertTrue(
'Length must be greater than zero' in str(context.exception))
with self.assertRaises(ValueError) as context:
Primer("ACGT", Primer.FORWARD, 2, 0)
self.assertTrue(
'Length must be greater than zero' in str(context.exception))
def test_create_primer_without_length(self):
"""
Scenario desc: We initialize Primer without
length. We should get value error.
"""
with self.assertRaises(ValueError) as context:
Primer("ACGT", Primer.REVERSE, 1, None)
self.assertTrue(
'Primer length must be specified' in str(context.exception))
with self.assertRaises(ValueError) as context:
Primer("ACGT", Primer.FORWARD, 1, None)
self.assertTrue(
'Primer length must be specified' in str(context.exception))
def test_primer_compute_gc_content(self):
"""
Scenario desc : Test gc content computation
"""
self.assertEqual(
100.0,
Primer("GCGCGCGCG", Primer.FORWARD, 0, 9).get_gc_content())
self.assertEqual(
0,
Primer("ATATATATA", Primer.FORWARD, 0, 9).get_gc_content())
self.assertEqual(
50.0,
Primer("CGCGAAAA", Primer.REVERSE, 7, 8).get_gc_content())
self.assertEqual(
75.0,
Primer("CCCCCCAA", Primer.REVERSE, 7, 8).get_gc_content())
def test_primer_normal_order_sequence(self):
"""
Scenario desc : We provide parent sequence, direction, start of the primer
and length of the primer. We expect valid primer with correct normal order sequence.
"""
self.assertEqual(
"A",
Primer("ACGT", Primer.FORWARD, 0, 1).normal_order_sequence)
self.assertEqual(
"ACGT",
Primer("ACGT", Primer.FORWARD, 0, 4).normal_order_sequence)
self.assertEqual(
"CG",
Primer("ACGT", Primer.FORWARD, 1, 2).normal_order_sequence)
self.assertEqual(
"T",
Primer("ACGT", Primer.FORWARD, 3, 1).normal_order_sequence)
#TODO sure it should not be reversed?
self.assertEqual(
"T",
Primer("ACGT", Primer.REVERSE, 3, 1).normal_order_sequence)
self.assertEqual(
"ACGT",
Primer("ACGT", Primer.REVERSE, 3, 4).normal_order_sequence)
self.assertEqual(
"CG",
Primer("ACGT", Primer.REVERSE, 2, 2).normal_order_sequence)
def test_create_primer_without_direction(self):
"""
Scenario desc: We initialize Primer without
direction. We should get value error.
"""
with self.assertRaises(ValueError) as context:
Primer("ACGT", None, 0, 1)
self.assertTrue(
'Primer direction must be specified' in str(context.exception))
def test_create_primer_with_invalid_direction(self):
"""
Scenario desc: We initialize Primer with invalid
direction. We should get value error.
"""
with self.assertRaises(ValueError) as context:
Primer("ACGT", "", 0, 1)
self.assertTrue('Direction must be either forward or reverse' in str(
context.exception))
def test_create_primer_without_parent_seq(self):
"""
Scenario desc: We initialize Primer without
parent sequence. We should get value error.
"""
with self.assertRaises(ValueError) as context:
Primer(None, Primer.FORWARD, 0, 1)
self.assertTrue('Parent sequence must be defined to create primer' in
str(context.exception))
def step_create_primer(context):
try:
context.primer = Primer(getattr(context, "parent_sequence", None),
getattr(context, "direction", None),
getattr(context, "start", None),
getattr(context, "length", None))
context.error = None
except Exception as e:
context.error = e
context.primer = None
def test_primer_get_3_end_seq(self):
"""
Scenario desc : Test getting 3 end sequence.
"""
self.assertEqual(
"CGCGCG",
Primer("GCGCGCGCG", Primer.FORWARD, 0,
9).get_three_end_sequence(ConcreteTripletMutation(0, "")))
self.assertEqual(
"ATAT",
Primer("ATATATATA", Primer.REVERSE, 8,
9).get_three_end_sequence(ConcreteTripletMutation(4, "")))
self.assertEqual(
"AAA",
Primer("CGCGAAAA", Primer.FORWARD, 0,
8).get_three_end_sequence(ConcreteTripletMutation(2, "")))
self.assertEqual(
"CCCCCCA",
Primer("CCCCCCAA", Primer.REVERSE, 7,
8).get_three_end_sequence(ConcreteTripletMutation(7, "")))
def test_primer_get_mutated_seq(self):
"""
Scenario desc : Test mutation of primer.
"""
self.assertEqual(
"GGTAAAAAA",
Primer("AAAAAAAAA", Primer.FORWARD, 0,
9).get_mutated_sequence(0, "GGT"))
self.assertEqual(
"AAGGTAAAA",
Primer("AAAAAAAAA", Primer.FORWARD, 0,
9).get_mutated_sequence(2, "GGT"))
self.assertEqual(
"AAAAGTTAA",
Primer("AAAAAAAAA", Primer.REVERSE, 8,
9).get_mutated_sequence(4, "GTT"))
self.assertEqual(
"AAAAAAGTT",
Primer("AAAAAAAAA", Primer.REVERSE, 8,
9).get_mutated_sequence(6, "GTT"))
def test_create_rv_primer_with_invalid_length_start(self):
"""
Scenario desc: We initialize reverse primer with invalid
combination of length and start. We should get value error.
"""
with self.assertRaises(ValueError) as context:
Primer("ACGT", Primer.REVERSE, 0, 2)
self.assertTrue(
'Primer end is not in sequence' in str(context.exception))
with self.assertRaises(ValueError) as context:
Primer("ACGT", Primer.REVERSE, 0, 3)
self.assertTrue(
'Primer end is not in sequence' in str(context.exception))
with self.assertRaises(ValueError) as context:
Primer("ACGT", Primer.REVERSE, 1, 3)
self.assertTrue(
'Primer end is not in sequence' in str(context.exception))
with self.assertRaises(ValueError) as context:
Primer("ACGT", Primer.REVERSE, 1, 4)
self.assertTrue(
'Primer end is not in sequence' in str(context.exception))
with self.assertRaises(ValueError) as context:
Primer("ACGT", Primer.REVERSE, 4, 13)
self.assertTrue(
'Primer start is not in sequence' in str(context.exception))
with self.assertRaises(ValueError) as context:
Primer("ACGT", Primer.REVERSE, 3, 5)
self.assertTrue(
'Primer end is not in sequence' in str(context.exception))
def test_primer_compute_5_end_seq_size(self):
"""
Scenario desc : Test computation of five end size from mutation.
"""
self.assertEqual(
1,
Primer("ACGTACGTA", Primer.FORWARD, 0,
5).get_five_end_size_from_mutation(
ConcreteTripletMutation(1, "")))
self.assertEqual(
1,
Primer("ACGTACGTA", Primer.FORWARD, 0,
6).get_five_end_size_from_mutation(
ConcreteTripletMutation(1, "")))
self.assertEqual(
1,
Primer("ACGTACGTA", Primer.FORWARD, 1,
6).get_five_end_size_from_mutation(
ConcreteTripletMutation(2, "")))
self.assertEqual(
2,
Primer("ACGTACGTA", Primer.FORWARD, 1,
7).get_five_end_size_from_mutation(
ConcreteTripletMutation(3, "")))
self.assertEqual(
1,
Primer("ACGTACGTA", Primer.REVERSE, 7,
5).get_five_end_size_from_mutation(
ConcreteTripletMutation(4, "")))
self.assertEqual(
1,
Primer("ACGTACGTA", Primer.REVERSE, 7,
6).get_five_end_size_from_mutation(
ConcreteTripletMutation(4, "")))
self.assertEqual(
1,
Primer("ACGTACGTA", Primer.REVERSE, 6,
6).get_five_end_size_from_mutation(
ConcreteTripletMutation(3, "")))
self.assertEqual(
2,
Primer("AAAAAAAAA", Primer.REVERSE, 7,
6).get_five_end_size_from_mutation(
ConcreteTripletMutation(3, "")))
#TODO get overlap tests
def test_create_primer_with_invalid_start(self):
"""
Scenario desc: We initialize Primer with invalid
start values. We should get value error.
"""
"""Negative value"""
with self.assertRaises(ValueError) as context:
Primer("ACGT", Primer.REVERSE, -1, 1)
self.assertTrue(
'Primer start is not in sequence' in str(context.exception))
with self.assertRaises(ValueError) as context:
Primer("ACGT", Primer.FORWARD, -1, 1)
self.assertTrue(
'Primer start is not in sequence' in str(context.exception))
"""Start is bigger than length"""
with self.assertRaises(ValueError) as context:
Primer("ACGT", Primer.REVERSE, 4, 1)
self.assertTrue(
'Primer start is not in sequence' in str(context.exception))
with self.assertRaises(ValueError) as context:
Primer("ACGT", Primer.FORWARD, 4, 1)
self.assertTrue(
'Primer start is not in sequence' in str(context.exception))
def test_primer_normal_order_end(self):
"""
Scenario desc : We provide parent sequence, direction, start of the primer
and length of the primer. We expect valid primer with correct normal order end.
"""
self.assertEqual(1, Primer("ACGT", Primer.FORWARD, 0, 1).normal_end)
self.assertEqual(4, Primer("ACGT", Primer.FORWARD, 0, 4).normal_end)
self.assertEqual(3, Primer("ACGT", Primer.FORWARD, 1, 2).normal_end)
self.assertEqual(4, Primer("ACGT", Primer.FORWARD, 3, 1).normal_end)
self.assertEqual(4, Primer("ACGT", Primer.REVERSE, 3, 1).normal_end)
self.assertEqual(4, Primer("ACGT", Primer.REVERSE, 3, 4).normal_end)
self.assertEqual(3, Primer("ACGT", Primer.REVERSE, 2, 2).normal_end)
def test_create_valid_primers(self):
"""
Scenario desc : We provide parent sequence, direction, start of the primer
and length of the primer. We expect valid primer.
"""
Primer("ACGT", Primer.FORWARD, 0, 1)
Primer("ACGT", Primer.FORWARD, 0, 4)
Primer("ACGT", Primer.FORWARD, 1, 2)
Primer("ACGT", Primer.REVERSE, 3, 1)
Primer("ACGT", Primer.REVERSE, 3, 4)
Primer("ACGT", Primer.REVERSE, 2, 2)
self.assertTrue(True)
def test_primer_compute_3_end_seq_size(self):
"""
Scenario desc : Test computation of three end size from mutation.
"""
self.assertEqual(
1,
Primer("ACGTACGTA", Primer.FORWARD, 0,
5).get_three_end_size_from_mutation(
ConcreteTripletMutation(1, "")))
self.assertEqual(
2,
Primer("ACGTACGTA", Primer.FORWARD, 0,
6).get_three_end_size_from_mutation(
ConcreteTripletMutation(1, "")))
self.assertEqual(
2,
Primer("ACGTACGTA", Primer.FORWARD, 1,
6).get_three_end_size_from_mutation(
ConcreteTripletMutation(2, "")))
self.assertEqual(
1,
Primer("ACGTACGTA", Primer.REVERSE, 7,
5).get_three_end_size_from_mutation(
ConcreteTripletMutation(4, "")))
self.assertEqual(
2,
Primer("ACGTACGTA", Primer.REVERSE, 7,
6).get_three_end_size_from_mutation(
ConcreteTripletMutation(4, "")))
self.assertEqual(
2,
Primer("ACGTACGTA", Primer.REVERSE, 6,
6).get_three_end_size_from_mutation(
ConcreteTripletMutation(3, "")))
self.assertEqual(
4,
Primer("AAAAAAAAA", Primer.REVERSE, 8,
9).get_three_end_size_from_mutation(
ConcreteTripletMutation(4, "")))