def test_for_two_cbox_error(self):
with self.assertRaises(WrongCDBoxOrderExeption):
CD_snoRNA(snor_id="test_snoRNA",
organism="hg",
chrom="chr1",
start=100,
end=170,
strand="+",
sequence="A" * 70,
snor_type="CD",
d_boxes="60..63",
c_boxes="30..36, 50..56")
raised = False
try:
cdsnor = CD_snoRNA(snor_id="test_snoRNA",
organism="hg",
chrom="chr1",
start=100,
end=170,
strand="+",
sequence="A" * 70,
snor_type="CD",
d_boxes="60..63",
c_boxes="30..36, 50..56",
switch_boxes=True)
except WrongCDBoxOrderExeption:
raised = True
self.assertFalse(
raised, "WrongCDBoxOrderExeption raised with swith_boxes=True")
self.assertEqual(cdsnor.c_box, (30, 36))
self.assertEqual(cdsnor.cprime_box, (50, 56))
def setUp(self):
self.snor = CD_snoRNA(snor_id="test_snoRNA",
organism="hg",
chrom="chr1",
start=100,
end=164,
strand="+",
sequence="C" * 5 + "T" * 20 + "C" * 10 +
"A" * 20 + "CATG" + "T" * 5,
snor_type="CD",
d_boxes="26..29,56..59",
c_boxes="49..55,5..13")
def test_for_non_dbox(self):
with self.assertRaises(NoBoxException):
cdsnor = CD_snoRNA(snor_id="test_snoRNA",
organism="hg",
chrom="chr1",
start=100,
end=170,
strand="+",
sequence="A" * 70,
snor_type="CD",
d_boxes=None)
def test_for_many_dbox_error(self):
with self.assertRaises(ToManyBoxesException):
cdsnor = CD_snoRNA(snor_id="test_snoRNA",
organism="hg",
chrom="chr1",
start=100,
end=170,
strand="+",
sequence="A" * 70,
snor_type="CD",
d_boxes="60..63, 20..23, 30..33")
def test_for_one_dbox_error(self):
with self.assertRaises(WrongCDBoxPlacementException):
cdsnor = CD_snoRNA(snor_id="test_snoRNA",
organism="hg",
chrom="chr1",
start=100,
end=170,
strand="+",
sequence="A" * 70,
snor_type="CD",
d_boxes="20..23")
def test_for_two_dbox(self):
cdsnor = CD_snoRNA(snor_id="test_snoRNA",
organism="hg",
chrom="chr1",
start=100,
end=170,
strand="+",
sequence="A" * 70,
snor_type="CD",
d_boxes="20..23, 60..63")
self.assertEqual(cdsnor.d_box, (60, 63))
self.assertEqual(cdsnor.dprime_box, (20, 23))
def test_for_two_cbox(self):
cdsnor = CD_snoRNA(snor_id="test_snoRNA",
organism="hg",
chrom="chr1",
start=100,
end=170,
strand="+",
sequence="A" * 70,
snor_type="CD",
d_boxes="60..63",
c_boxes="50..56,30..36")
self.assertEqual(cdsnor.c_box, (30, 36))
self.assertEqual(cdsnor.cprime_box, (50, 56))
class TestCD_snoRNA(unittest.TestCase):
"""Test CD_snoRNA class"""
def setUp(self):
self.snor = CD_snoRNA(snor_id="test_snoRNA",
organism="hg",
chrom="chr1",
start=100,
end=164,
strand="+",
sequence="C" * 5 + "T" * 20 + "C" * 10 +
"A" * 20 + "CATG" + "T" * 5,
snor_type="CD",
d_boxes="26..29,56..59",
c_boxes="49..55,5..13")
def test_for_non_dbox(self):
with self.assertRaises(NoBoxException):
cdsnor = CD_snoRNA(snor_id="test_snoRNA",
organism="hg",
chrom="chr1",
start=100,
end=170,
strand="+",
sequence="A" * 70,
snor_type="CD",
d_boxes=None)
def test_for_one_dbox_error(self):
with self.assertRaises(WrongCDBoxPlacementException):
cdsnor = CD_snoRNA(snor_id="test_snoRNA",
organism="hg",
chrom="chr1",
start=100,
end=170,
strand="+",
sequence="A" * 70,
snor_type="CD",
d_boxes="20..23")
def test_for_one_dbox(self):
cdsnor = CD_snoRNA(snor_id="test_snoRNA",
organism="hg",
chrom="chr1",
start=100,
end=170,
strand="+",
sequence="A" * 70,
snor_type="CD",
d_boxes="60..63")
self.assertEqual(cdsnor.d_box, (60, 63))
self.assertEqual(cdsnor.dprime_box, None)
def test_for_two_dbox(self):
cdsnor = CD_snoRNA(snor_id="test_snoRNA",
organism="hg",
chrom="chr1",
start=100,
end=170,
strand="+",
sequence="A" * 70,
snor_type="CD",
d_boxes="20..23, 60..63")
self.assertEqual(cdsnor.d_box, (60, 63))
self.assertEqual(cdsnor.dprime_box, (20, 23))
def test_for_two_dbox_error(self):
with self.assertRaises(WrongCDBoxOrderExeption):
CD_snoRNA(snor_id="test_snoRNA",
organism="hg",
chrom="chr1",
start=100,
end=170,
strand="+",
sequence="A" * 70,
snor_type="CD",
d_boxes="60..63, 20..23")
raised = False
try:
cdsnor = CD_snoRNA(snor_id="test_snoRNA",
organism="hg",
chrom="chr1",
start=100,
end=170,
strand="+",
sequence="A" * 70,
snor_type="CD",
d_boxes="60..63, 20..23",
switch_boxes=True)
except WrongCDBoxOrderExeption:
raised = True
self.assertFalse(
raised, "WrongCDBoxOrderExeption raised with swith_boxes=True")
self.assertEqual(cdsnor.d_box, (60, 63))
self.assertEqual(cdsnor.dprime_box, (20, 23))
def test_for_many_dbox_error(self):
with self.assertRaises(ToManyBoxesException):
cdsnor = CD_snoRNA(snor_id="test_snoRNA",
organism="hg",
chrom="chr1",
start=100,
end=170,
strand="+",
sequence="A" * 70,
snor_type="CD",
d_boxes="60..63, 20..23, 30..33")
def test_for_one_cbox(self):
cdsnor = CD_snoRNA(snor_id="test_snoRNA",
organism="hg",
chrom="chr1",
start=100,
end=170,
strand="+",
sequence="A" * 70,
snor_type="CD",
d_boxes="60..63",
c_boxes="30..36")
self.assertEqual(cdsnor.c_box, (30, 36))
self.assertEqual(cdsnor.cprime_box, None)
def test_for_two_cbox(self):
cdsnor = CD_snoRNA(snor_id="test_snoRNA",
organism="hg",
chrom="chr1",
start=100,
end=170,
strand="+",
sequence="A" * 70,
snor_type="CD",
d_boxes="60..63",
c_boxes="50..56,30..36")
self.assertEqual(cdsnor.c_box, (30, 36))
self.assertEqual(cdsnor.cprime_box, (50, 56))
def test_for_two_cbox_error(self):
with self.assertRaises(WrongCDBoxOrderExeption):
CD_snoRNA(snor_id="test_snoRNA",
organism="hg",
chrom="chr1",
start=100,
end=170,
strand="+",
sequence="A" * 70,
snor_type="CD",
d_boxes="60..63",
c_boxes="30..36, 50..56")
raised = False
try:
cdsnor = CD_snoRNA(snor_id="test_snoRNA",
organism="hg",
chrom="chr1",
start=100,
end=170,
strand="+",
sequence="A" * 70,
snor_type="CD",
d_boxes="60..63",
c_boxes="30..36, 50..56",
switch_boxes=True)
except WrongCDBoxOrderExeption:
raised = True
self.assertFalse(
raised, "WrongCDBoxOrderExeption raised with swith_boxes=True")
self.assertEqual(cdsnor.c_box, (30, 36))
self.assertEqual(cdsnor.cprime_box, (50, 56))
def test_for_many_cbox_error(self):
with self.assertRaises(ToManyBoxesException):
cdsnor = CD_snoRNA(snor_id="test_snoRNA",
organism="hg",
chrom="chr1",
start=100,
end=170,
strand="+",
sequence="A" * 70,
snor_type="CD",
d_boxes="60..63",
c_boxes="50..56, 20..26, 30..36")
def test_for_plexy_string(self):
cdsnor1 = CD_snoRNA(snor_id="test_snoRNA",
organism="hg",
chrom="chr1",
start=100,
end=170,
strand="+",
sequence="A" * 70,
snor_type="CD",
d_boxes="61..64",
c_boxes=None)
plexy1 = ">test_snoRNA-_NNNNNNN_10_AAAA_61\n%s\n" % ("A" * 70)
self.assertEqual(cdsnor1.get_plexy_string(), plexy1)
cdsnor2 = CD_snoRNA(snor_id="test_snoRNA",
organism="hg",
chrom="chr1",
start=100,
end=170,
strand="+",
sequence="A" * 70,
snor_type="CD",
d_boxes="30..33,60..63",
c_boxes=None)
plexy2 = ">test_snoRNA-_NNNNNNN_50_AAAA_30_NNNNNNN_10_AAAA_60\n%s\n" \
% ("A"*70)
self.assertEqual(cdsnor2.get_plexy_string(), plexy2)
cdsnor3 = CD_snoRNA(snor_id="test_snoRNA",
organism="hg",
chrom="chr1",
start=100,
end=170,
strand="+",
sequence="A" * 70,
snor_type="CD",
d_boxes="60..63",
c_boxes="21..27")
plexy3 = ">test_snoRNA-_AAAAAAA_21_AAAA_60\n%s\n" \
% ("A"*70)
self.assertEqual(cdsnor3.get_plexy_string(), plexy3)
cdsnor4 = CD_snoRNA(snor_id="test_snoRNA",
organism="hg",
chrom="chr1",
start=100,
end=170,
strand="+",
sequence="A" * 70,
snor_type="CD",
d_boxes="30..33,60..63",
c_boxes="21..27")
plexy4 = ">test_snoRNA-_NNNNNNN_50_AAAA_30_AAAAAAA_21_AAAA_60\n%s\n" \
% ("A"*70)
self.assertEqual(cdsnor4.get_plexy_string(), plexy4)
cdsnor5 = CD_snoRNA(snor_id="test_snoRNA",
organism="hg",
chrom="chr1",
start=100,
end=170,
strand="+",
sequence="A" * 70,
snor_type="CD",
d_boxes="60..63",
c_boxes="49..55,21..27")
plexy5 = ">test_snoRNA-_AAAAAAA_21_AAAA_60\n%s\n" \
% ("A"*70)
self.assertEqual(cdsnor5.get_plexy_string(), plexy5)
cdsnor6 = CD_snoRNA(snor_id="test_snoRNA",
organism="hg",
chrom="chr1",
start=100,
end=170,
strand="+",
sequence="A" * 70,
snor_type="CD",
d_boxes="30..33,60..63",
c_boxes="49..55,21..27")
plexy6 = ">test_snoRNA-_AAAAAAA_49_AAAA_30_AAAAAAA_21_AAAA_60\n%s\n" \
% ("A"*70)
self.assertEqual(cdsnor6.get_plexy_string(), plexy6)
def test_interaction_region_d_box(self):
inreg = self.snor.get_d_interaction_region(length=20)
self.assertEqual(type(inreg), type(Seq("AAAA")))
self.assertEqual(str(inreg), "A" * 20)
def test_interaction_region_dprime_box(self):
inreg = self.snor.get_dprime_interaction_region(length=20)
self.assertEqual(type(inreg), type(Seq("AAAA")))
self.assertEqual(str(inreg), "T" * 20)
def test_for_plexy_string(self):
cdsnor1 = CD_snoRNA(snor_id="test_snoRNA",
organism="hg",
chrom="chr1",
start=100,
end=170,
strand="+",
sequence="A" * 70,
snor_type="CD",
d_boxes="61..64",
c_boxes=None)
plexy1 = ">test_snoRNA-_NNNNNNN_10_AAAA_61\n%s\n" % ("A" * 70)
self.assertEqual(cdsnor1.get_plexy_string(), plexy1)
cdsnor2 = CD_snoRNA(snor_id="test_snoRNA",
organism="hg",
chrom="chr1",
start=100,
end=170,
strand="+",
sequence="A" * 70,
snor_type="CD",
d_boxes="30..33,60..63",
c_boxes=None)
plexy2 = ">test_snoRNA-_NNNNNNN_50_AAAA_30_NNNNNNN_10_AAAA_60\n%s\n" \
% ("A"*70)
self.assertEqual(cdsnor2.get_plexy_string(), plexy2)
cdsnor3 = CD_snoRNA(snor_id="test_snoRNA",
organism="hg",
chrom="chr1",
start=100,
end=170,
strand="+",
sequence="A" * 70,
snor_type="CD",
d_boxes="60..63",
c_boxes="21..27")
plexy3 = ">test_snoRNA-_AAAAAAA_21_AAAA_60\n%s\n" \
% ("A"*70)
self.assertEqual(cdsnor3.get_plexy_string(), plexy3)
cdsnor4 = CD_snoRNA(snor_id="test_snoRNA",
organism="hg",
chrom="chr1",
start=100,
end=170,
strand="+",
sequence="A" * 70,
snor_type="CD",
d_boxes="30..33,60..63",
c_boxes="21..27")
plexy4 = ">test_snoRNA-_NNNNNNN_50_AAAA_30_AAAAAAA_21_AAAA_60\n%s\n" \
% ("A"*70)
self.assertEqual(cdsnor4.get_plexy_string(), plexy4)
cdsnor5 = CD_snoRNA(snor_id="test_snoRNA",
organism="hg",
chrom="chr1",
start=100,
end=170,
strand="+",
sequence="A" * 70,
snor_type="CD",
d_boxes="60..63",
c_boxes="49..55,21..27")
plexy5 = ">test_snoRNA-_AAAAAAA_21_AAAA_60\n%s\n" \
% ("A"*70)
self.assertEqual(cdsnor5.get_plexy_string(), plexy5)
cdsnor6 = CD_snoRNA(snor_id="test_snoRNA",
organism="hg",
chrom="chr1",
start=100,
end=170,
strand="+",
sequence="A" * 70,
snor_type="CD",
d_boxes="30..33,60..63",
c_boxes="49..55,21..27")
plexy6 = ">test_snoRNA-_AAAAAAA_49_AAAA_30_AAAAAAA_21_AAAA_60\n%s\n" \
% ("A"*70)
self.assertEqual(cdsnor6.get_plexy_string(), plexy6)