def setUp(self):
self.sub_seq_extractor = SubSeqExtractor(
"AAAAAAAAAACCCCCCCCCCGGGGGGGGGGTTTATTT",
coordinate_start=0,
include_pos=True)
class TestSubSeqExtractor2(unittest.TestCase):
"""Testing with
- a 0-based coordinate system
- the query base included in the extracted sequence
"""
def setUp(self):
self.sub_seq_extractor = SubSeqExtractor(
"AAAAAAAAAACCCCCCCCCCGGGGGGGGGGTTTATTT",
coordinate_start=0,
include_pos=True)
def test_extract_single_pos(self):
self.assertEqual(self.sub_seq_extractor.extract(9), "A")
self.assertEqual(self.sub_seq_extractor.extract(10), "C")
self.assertEqual(self.sub_seq_extractor.extract(19), "C")
self.assertEqual(self.sub_seq_extractor.extract(20), "G")
def test_extract_upstream_seq(self):
self.assertEqual(self.sub_seq_extractor.extract(9, upstream=9),
"AAAAAAAAAA")
self.assertEqual(
len(self.sub_seq_extractor.extract(9, upstream=9)), 10)
self.assertEqual(self.sub_seq_extractor.extract(19, upstream=9),
"CCCCCCCCCC")
self.assertEqual(self.sub_seq_extractor.extract(24, upstream=9),
"CCCCCGGGGG")
def test_extract_downstream_seq(self):
self.assertEqual(
self.sub_seq_extractor.extract(10, downstream=9),
"CCCCCCCCCC")
self.assertEqual(
self.sub_seq_extractor.extract(20, downstream=9),
"GGGGGGGGGG")
def test_extract_down_and_upstream_seq(self):
self.assertEqual(self.sub_seq_extractor.extract(
33, upstream=3, downstream=3), "TTTATTT")
self.assertEqual(self.sub_seq_extractor.extract(
9, upstream=5, downstream=5), "AAAAAACCCCC")
def test_extract_single_pos_revese(self):
self.assertEqual(
self.sub_seq_extractor.extract(9, rev_strand=True), "T")
self.assertEqual(
self.sub_seq_extractor.extract(10, rev_strand=True), "G")
self.assertEqual(
self.sub_seq_extractor.extract(19, rev_strand=True), "G")
self.assertEqual(
self.sub_seq_extractor.extract(20, rev_strand=True), "C")
def test_extract_upstream_seq_reverse(self):
self.assertEqual(
self.sub_seq_extractor.extract(
10, upstream=9, rev_strand=True),
"GGGGGGGGGG")
self.assertEqual(
self.sub_seq_extractor.extract(
9, upstream=9, rev_strand=True),
"GGGGGGGGGT")
def test_extract_downstream_seq_reverse(self):
self.assertEqual(
self.sub_seq_extractor.extract(
19, downstream=9, rev_strand=True), "GGGGGGGGGG")
self.assertEqual(
self.sub_seq_extractor.extract(
10, downstream=9, rev_strand=True), "GTTTTTTTTT")
def test_extract_down_and_upstream_seq_reverse(self):
self.assertEqual(self.sub_seq_extractor.extract(
33, upstream=3, downstream=3, rev_strand=True),
"AAATAAA")
self.assertEqual(self.sub_seq_extractor.extract(
9, upstream=5, downstream=5, rev_strand=True),
"GGGGGTTTTTT")
class TestSubSeqExtractor3(unittest.TestCase):
"""Testing with
- a 1-based coordinate system
- the query base NOT included in the extracted sequence
"""
def setUp(self):
self.sub_seq_extractor = SubSeqExtractor(
"AAAAAAAAAACCCCCCCCCCGGGGGGGGGGTTTATTT",
coordinate_start=1,
include_pos=False)
def test_extract_single_pos(self):
self.assertEqual(self.sub_seq_extractor.extract(10), "")
self.assertEqual(self.sub_seq_extractor.extract(11), "")
self.assertEqual(self.sub_seq_extractor.extract(20), "")
self.assertEqual(self.sub_seq_extractor.extract(21), "")
def test_extract_upstream_seq(self):
self.assertEqual(self.sub_seq_extractor.extract(10, upstream=9),
"AAAAAAAAA")
self.assertEqual(
len(self.sub_seq_extractor.extract(10, upstream=9)), 9)
self.assertEqual(self.sub_seq_extractor.extract(20, upstream=9),
"CCCCCCCCC")
self.assertEqual(self.sub_seq_extractor.extract(25, upstream=9),
"CCCCCGGGG")
def test_extract_downstream_seq(self):
self.assertEqual(
self.sub_seq_extractor.extract(
11, downstream=9),
"CCCCCCCCC")
self.assertEqual(
self.sub_seq_extractor.extract(21, downstream=9),
"GGGGGGGGG")
self.assertEqual(
self.sub_seq_extractor.extract(30, downstream=5),
"TTTAT")
def test_extract_down_and_upstream_seq(self):
self.assertEqual(self.sub_seq_extractor.extract(
34, upstream=3, downstream=3), "TTTATTT")
self.assertEqual(self.sub_seq_extractor.extract(
10, upstream=5, downstream=5), "AAAAAACCCCC")
def test_extract_single_pos_revese(self):
self.assertEqual(
self.sub_seq_extractor.extract(10, rev_strand=True), "")
self.assertEqual(
self.sub_seq_extractor.extract(11, rev_strand=True), "")
self.assertEqual(
self.sub_seq_extractor.extract(20, rev_strand=True), "")
self.assertEqual(
self.sub_seq_extractor.extract(21, rev_strand=True), "")
def test_extract_upstream_seq_reverse(self):
self.assertEqual(
self.sub_seq_extractor.extract(
11, upstream=9, rev_strand=True),
"GGGGGGGGG")
self.assertEqual(
self.sub_seq_extractor.extract(
11, upstream=9, rev_strand=True),
"GGGGGGGGG")
def test_extract_downstream_seq_reverse(self):
self.assertEqual(
self.sub_seq_extractor.extract(
20, downstream=9, rev_strand=True), "GGGGGGGGG")
self.assertEqual(
self.sub_seq_extractor.extract(
11, downstream=9, rev_strand=True), "TTTTTTTTT")
self.assertEqual(
self.sub_seq_extractor.extract(
37, downstream=9, rev_strand=True), "AATAAACCC")
def test_extract_down_and_upstream_seq_reverse(self):
self.assertEqual(self.sub_seq_extractor.extract(
34, upstream=3, downstream=3, rev_strand=True),
"AAATAAA")
self.assertEqual(self.sub_seq_extractor.extract(
10, upstream=5, downstream=5, rev_strand=True),
"GGGGGTTTTTT")
def setUp(self):
self.sub_seq_extractor = SubSeqExtractor(
"AAAAAAAAAACCCCCCCCCCGGGGGGGGGGTTTATTT",
coordinate_start=0,
include_pos=True)
class TestSubSeqExtractor2(unittest.TestCase):
"""Testing with
- a 0-based coordinate system
- the query base included in the extracted sequence
"""
def setUp(self):
self.sub_seq_extractor = SubSeqExtractor(
"AAAAAAAAAACCCCCCCCCCGGGGGGGGGGTTTATTT",
coordinate_start=0,
include_pos=True)
def test_extract_single_pos(self):
self.assertEqual(self.sub_seq_extractor.extract(9), "A")
self.assertEqual(self.sub_seq_extractor.extract(10), "C")
self.assertEqual(self.sub_seq_extractor.extract(19), "C")
self.assertEqual(self.sub_seq_extractor.extract(20), "G")
def test_extract_upstream_seq(self):
self.assertEqual(self.sub_seq_extractor.extract(9, upstream=9),
"AAAAAAAAAA")
self.assertEqual(len(self.sub_seq_extractor.extract(9, upstream=9)),
10)
self.assertEqual(self.sub_seq_extractor.extract(19, upstream=9),
"CCCCCCCCCC")
self.assertEqual(self.sub_seq_extractor.extract(24, upstream=9),
"CCCCCGGGGG")
def test_extract_downstream_seq(self):
self.assertEqual(self.sub_seq_extractor.extract(10, downstream=9),
"CCCCCCCCCC")
self.assertEqual(self.sub_seq_extractor.extract(20, downstream=9),
"GGGGGGGGGG")
def test_extract_down_and_upstream_seq(self):
self.assertEqual(
self.sub_seq_extractor.extract(33, upstream=3, downstream=3),
"TTTATTT")
self.assertEqual(
self.sub_seq_extractor.extract(9, upstream=5, downstream=5),
"AAAAAACCCCC")
def test_extract_single_pos_revese(self):
self.assertEqual(self.sub_seq_extractor.extract(9, rev_strand=True),
"T")
self.assertEqual(self.sub_seq_extractor.extract(10, rev_strand=True),
"G")
self.assertEqual(self.sub_seq_extractor.extract(19, rev_strand=True),
"G")
self.assertEqual(self.sub_seq_extractor.extract(20, rev_strand=True),
"C")
def test_extract_upstream_seq_reverse(self):
self.assertEqual(
self.sub_seq_extractor.extract(10, upstream=9, rev_strand=True),
"GGGGGGGGGG")
self.assertEqual(
self.sub_seq_extractor.extract(9, upstream=9, rev_strand=True),
"GGGGGGGGGT")
def test_extract_downstream_seq_reverse(self):
self.assertEqual(
self.sub_seq_extractor.extract(19, downstream=9, rev_strand=True),
"GGGGGGGGGG")
self.assertEqual(
self.sub_seq_extractor.extract(10, downstream=9, rev_strand=True),
"GTTTTTTTTT")
def test_extract_down_and_upstream_seq_reverse(self):
self.assertEqual(
self.sub_seq_extractor.extract(33,
upstream=3,
downstream=3,
rev_strand=True), "AAATAAA")
self.assertEqual(
self.sub_seq_extractor.extract(9,
upstream=5,
downstream=5,
rev_strand=True), "GGGGGTTTTTT")
class TestSubSeqExtractor3(unittest.TestCase):
"""Testing with
- a 1-based coordinate system
- the query base NOT included in the extracted sequence
"""
def setUp(self):
self.sub_seq_extractor = SubSeqExtractor(
"AAAAAAAAAACCCCCCCCCCGGGGGGGGGGTTTATTT",
coordinate_start=1,
include_pos=False)
def test_extract_single_pos(self):
self.assertEqual(self.sub_seq_extractor.extract(10), "")
self.assertEqual(self.sub_seq_extractor.extract(11), "")
self.assertEqual(self.sub_seq_extractor.extract(20), "")
self.assertEqual(self.sub_seq_extractor.extract(21), "")
def test_extract_upstream_seq(self):
self.assertEqual(self.sub_seq_extractor.extract(10, upstream=9),
"AAAAAAAAA")
self.assertEqual(len(self.sub_seq_extractor.extract(10, upstream=9)),
9)
self.assertEqual(self.sub_seq_extractor.extract(20, upstream=9),
"CCCCCCCCC")
self.assertEqual(self.sub_seq_extractor.extract(25, upstream=9),
"CCCCCGGGG")
def test_extract_downstream_seq(self):
self.assertEqual(self.sub_seq_extractor.extract(11, downstream=9),
"CCCCCCCCC")
self.assertEqual(self.sub_seq_extractor.extract(21, downstream=9),
"GGGGGGGGG")
self.assertEqual(self.sub_seq_extractor.extract(30, downstream=5),
"TTTAT")
def test_extract_down_and_upstream_seq(self):
self.assertEqual(
self.sub_seq_extractor.extract(34, upstream=3, downstream=3),
"TTTATTT")
self.assertEqual(
self.sub_seq_extractor.extract(10, upstream=5, downstream=5),
"AAAAAACCCCC")
def test_extract_single_pos_revese(self):
self.assertEqual(self.sub_seq_extractor.extract(10, rev_strand=True),
"")
self.assertEqual(self.sub_seq_extractor.extract(11, rev_strand=True),
"")
self.assertEqual(self.sub_seq_extractor.extract(20, rev_strand=True),
"")
self.assertEqual(self.sub_seq_extractor.extract(21, rev_strand=True),
"")
def test_extract_upstream_seq_reverse(self):
self.assertEqual(
self.sub_seq_extractor.extract(11, upstream=9, rev_strand=True),
"GGGGGGGGG")
self.assertEqual(
self.sub_seq_extractor.extract(11, upstream=9, rev_strand=True),
"GGGGGGGGG")
def test_extract_downstream_seq_reverse(self):
self.assertEqual(
self.sub_seq_extractor.extract(20, downstream=9, rev_strand=True),
"GGGGGGGGG")
self.assertEqual(
self.sub_seq_extractor.extract(11, downstream=9, rev_strand=True),
"TTTTTTTTT")
self.assertEqual(
self.sub_seq_extractor.extract(37, downstream=9, rev_strand=True),
"AATAAACCC")
def test_extract_down_and_upstream_seq_reverse(self):
self.assertEqual(
self.sub_seq_extractor.extract(34,
upstream=3,
downstream=3,
rev_strand=True), "AAATAAA")
self.assertEqual(
self.sub_seq_extractor.extract(10,
upstream=5,
downstream=5,
rev_strand=True), "GGGGGTTTTTT")