def test_poly_a_clipper():
# Define Object
poly_a_clipper = PolyAClipper()
# Test: If there is no poly a stretch the sequence is not changed
seq_no_stretch = result_seq = "ATAGTAGGAGATTTAGACCAGATGACGATGACACAC"
"AATGGTTAGGTACAGATAG"
assert poly_a_clipper.clip_poly_a_stretch(seq_no_stretch) == result_seq
# Test: If the sequence is empty the sequence is not changed
empty_seq = result_seq = ""
assert poly_a_clipper.clip_poly_a_stretch(empty_seq) == result_seq
# Test: Clip a terminal 10 fold A stretch
test_seq = "ATAGTAGGAGATTTAGACCAGATGACGATGACACAAAAAAAAAATTTAGACGACG"
result_seq = "ATAGTAGGAGATTTAGACCAGATGACGATGACAC"
assert poly_a_clipper.clip_poly_a_stretch(test_seq) == result_seq
# Test: If there is less than a 10 fold terminal stretch don't clip
test_seq = result_seq = "ATAGTAGGAGATTTAGACCAGATGACGATGACACAAAAAAAAA"
"TTTAGACGACG"
assert poly_a_clipper.clip_poly_a_stretch(test_seq) == result_seq
# Test: All A sequence
test_seq = "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"
result_seq = ""
assert poly_a_clipper.clip_poly_a_stretch(test_seq) == result_seq
# Test: Sequence with an starting 'AAAA' substring
test_seq = "TTTAAAATTTTTTTTAAAACCCCCCCCCCAAAAC"
assert list(poly_a_clipper._aaaa_starting_substrings(
test_seq, 11)) == [['AAAATTTTTTT', 3], ['AAAACCCCCCC', 15]]
# Test: If there is no terminal A stretch, there is no clipping
test_seq = result_seq = "AAAAATTTTCCGCCCGGGAAATTTT"
assert poly_a_clipper.remove_3_prime_a(test_seq) == result_seq
# Test: Removal of one terminal A
test_seq = "AAAAATTTTCCGCCCGGGAAATTTTA"
result_seq = "AAAAATTTTCCGCCCGGGAAATTTT"
assert poly_a_clipper.remove_3_prime_a(test_seq) == result_seq
# Test: Removal of multiple terminal As
test_seq = "AAAAATTTTCCGCCCGGGAAATTTTAAAAAA"
result_seq = "AAAAATTTTCCGCCCGGGAAATTTT"
assert poly_a_clipper.remove_3_prime_a(test_seq) == result_seq
class TestPolyAClipper(unittest.TestCase):
def setUp(self):
self.poly_a_clipper = PolyAClipper()
def test_clip_poly_a_strech_no_change(self):
"""If there is no poly a strech the sequence is not changed."""
test_seq = "ATAGTAGGAGATTTAGACCAGATGACGATGACACACAATGGTTAGGTACAGATAG"
result_seq = test_seq
self.assertEqual(self.poly_a_clipper.clip_poly_a_strech(test_seq),
result_seq)
def test_clip_poly_a_strech_empt(self):
"""If there the sequence is empty the sequence is not changed."""
test_seq = ""
result_seq = test_seq
self.assertEqual(self.poly_a_clipper.clip_poly_a_strech(test_seq),
result_seq)
def test_clip_poly_a_strech_terminal_10_a(self):
"""Clipp terminal A strech if it is 10 A."""
test_seq = "ATAGTAGGAGATTTAGACCAGATGACGATGACACAAAAAAAAAAA"
result_seq = "ATAGTAGGAGATTTAGACCAGATGACGATGACAC"
self.assertEqual(self.poly_a_clipper.clip_poly_a_strech(test_seq),
result_seq)
def test_clip_poly_a_strech_internal_10_a(self):
"""Clip before a 10 A long internal strech."""
test_seq = "ATAGTAGGAGATTTAGACCAGATGACGATGACACAAAAAAAAAATTTAGACGACG"
result_seq = "ATAGTAGGAGATTTAGACCAGATGACGATGACAC"
self.assertEqual(self.poly_a_clipper.clip_poly_a_strech(test_seq),
result_seq)
def test_clip_poly_a_strech_terminal_09_a(self):
"""If there less than 10 A don't clip."""
test_seq = "ATAGTAGGAGATTTAGACCAGATGACGATGACACAAAAAAAAAA"
result_seq = test_seq
self.assertEqual(self.poly_a_clipper.clip_poly_a_strech(test_seq),
result_seq)
def test_clip_poly_a_strecht_internal_(self):
"""If there less than 10 A don't clip."""
test_seq = "ATAGTAGGAGATTTAGACCAGATGACGATGACACAAAAAAAAATTTAGACGACG"
result_seq = test_seq
self.assertEqual(self.poly_a_clipper.clip_poly_a_strech(test_seq),
result_seq)
def test_clip_poly_a_strecht_internal_09_a(self):
"""Test all A string"""
test_seq = "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"
result_seq = ""
self.assertEqual(self.poly_a_clipper.clip_poly_a_strech(test_seq),
result_seq)
def test_aaaa_starting_substrings(self):
test_seq = "TTTAAAATTTTTTTTAAAACCCCCCCCCCAAAAC"
self.assertEqual(
list(self.poly_a_clipper._aaaa_starting_substrings(test_seq, 11)),
[["AAAATTTTTTT", 3], ["AAAACCCCCCC", 15]],
)
def test_remove_3_prime_a_no_change(self):
"""If there are no terminal As, there is no clipping."""
test_seq = "AAAAATTTTCCGCCCGGGAAATTTT"
result_seq = test_seq
self.assertEqual(self.poly_a_clipper.remove_3_prime_a(test_seq),
result_seq)
def test_remove_3_prime_a_one_a(self):
"""Remove terminal A"""
test_seq = "AAAAATTTTCCGCCCGGGAAATTTTA"
result_seq = "AAAAATTTTCCGCCCGGGAAATTTT"
self.assertEqual(self.poly_a_clipper.remove_3_prime_a(test_seq),
result_seq)
def test_remove_3_prime_a_multiple_as(self):
"""Remove terminal stretch of multiple As"""
test_seq = "AAAAATTTTCCGCCCGGGAAATTTTAAAAAA"
result_seq = "AAAAATTTTCCGCCCGGGAAATTTT"
self.assertEqual(self.poly_a_clipper.remove_3_prime_a(test_seq),
result_seq)
class TestPolyAClipper(unittest.TestCase):
def setUp(self):
self.poly_a_clipper = PolyAClipper()
def test_clip_poly_a_strech_no_change(self):
"""If there is no poly a strech the sequence is not changed."""
test_seq = "ATAGTAGGAGATTTAGACCAGATGACGATGACACACAATGGTTAGGTACAGATAG"
result_seq = test_seq
self.assertEqual(
self.poly_a_clipper.clip_poly_a_strech(test_seq),
result_seq)
def test_clip_poly_a_strech_empt(self):
"""If there the sequence is empty the sequence is not changed."""
test_seq = ""
result_seq = test_seq
self.assertEqual(
self.poly_a_clipper.clip_poly_a_strech(test_seq),
result_seq)
def test_clip_poly_a_strech_terminal_10_a(self):
"""Clipp terminal A strech if it is 10 A."""
test_seq = "ATAGTAGGAGATTTAGACCAGATGACGATGACACAAAAAAAAAAA"
result_seq = "ATAGTAGGAGATTTAGACCAGATGACGATGACAC"
self.assertEqual(
self.poly_a_clipper.clip_poly_a_strech(test_seq),
result_seq)
def test_clip_poly_a_strech_internal_10_a(self):
"""Clip before a 10 A long internal strech."""
test_seq = "ATAGTAGGAGATTTAGACCAGATGACGATGACACAAAAAAAAAATTTAGACGACG"
result_seq = "ATAGTAGGAGATTTAGACCAGATGACGATGACAC"
self.assertEqual(
self.poly_a_clipper.clip_poly_a_strech(test_seq),
result_seq)
def test_clip_poly_a_strech_terminal_09_a(self):
"""If there less than 10 A don't clip."""
test_seq = "ATAGTAGGAGATTTAGACCAGATGACGATGACACAAAAAAAAAA"
result_seq = test_seq
self.assertEqual(
self.poly_a_clipper.clip_poly_a_strech(test_seq),
result_seq)
def test_clip_poly_a_strecht_internal_(self):
"""If there less than 10 A don't clip."""
test_seq = "ATAGTAGGAGATTTAGACCAGATGACGATGACACAAAAAAAAATTTAGACGACG"
result_seq = test_seq
self.assertEqual(
self.poly_a_clipper.clip_poly_a_strech(test_seq),
result_seq)
def test_clip_poly_a_strecht_internal_09_a(self):
"""Test all A string"""
test_seq = "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"
result_seq = ""
self.assertEqual(
self.poly_a_clipper.clip_poly_a_strech(test_seq),
result_seq)
def test_aaaa_starting_substrings(self):
test_seq = "TTTAAAATTTTTTTTAAAACCCCCCCCCCAAAAC"
self.assertEqual(
list(self.poly_a_clipper._aaaa_starting_substrings(test_seq, 11)),
[['AAAATTTTTTT', 3], ['AAAACCCCCCC', 15]])
def test_remove_3_prime_a_no_change(self):
"""If there are no terminal As, there is no clipping."""
test_seq = "AAAAATTTTCCGCCCGGGAAATTTT"
result_seq = test_seq
self.assertEqual(
self.poly_a_clipper.remove_3_prime_a(test_seq), result_seq)
def test_remove_3_prime_a_one_a(self):
"""Remove terminal A"""
test_seq = "AAAAATTTTCCGCCCGGGAAATTTTA"
result_seq = "AAAAATTTTCCGCCCGGGAAATTTT"
self.assertEqual(
self.poly_a_clipper.remove_3_prime_a(test_seq), result_seq)
def test_remove_3_prime_a_multiple_as(self):
"""Remove terminal stretch of multiple As"""
test_seq = "AAAAATTTTCCGCCCGGGAAATTTTAAAAAA"
result_seq = "AAAAATTTTCCGCCCGGGAAATTTT"
self.assertEqual(
self.poly_a_clipper.remove_3_prime_a(test_seq), result_seq)
