def test_init(self):
with self.assertRaises(ValueError):
prom = pt.BindingSite("promoter", -1, 10, dict())
with self.assertRaises(ValueError):
site = pt.BindingSite("promoter", -1, -10, dict())
with self.assertRaises(ValueError):
site = pt.BindingSite("promoter", 1, -10, dict())
with self.assertRaises(ValueError):
site = pt.BindingSite("promoter", 1, 10, {"rnapol": -2})
with self.assertRaises(ValueError):
site = pt.BindingSite("promoter", 1, 10, {
"rnapol": -2, "ecolipol": 1})
def test_coverings(self):
site = pt.BindingSite("promoter", 1, 10, {"rnapol": 1.0})
self.assertFalse(site.was_covered())
self.assertFalse(site.is_covered())
self.assertFalse(site.was_uncovered())
site.cover()
self.assertTrue(site.is_covered())
self.assertTrue(site.was_covered())
self.assertFalse(site.was_uncovered())
site.reset_state()
self.assertTrue(site.is_covered())
self.assertFalse(site.was_covered())
self.assertFalse(site.was_uncovered())
site.uncover()
self.assertFalse(site.is_covered())
self.assertFalse(site.was_covered())
self.assertTrue(site.was_uncovered())
site.reset_state()
self.assertFalse(site.is_covered())
self.assertFalse(site.was_covered())
self.assertFalse(site.was_uncovered())
def test_clone(self):
# Clone should create explicit copy
site = pt.BindingSite("promoter", 1, 10, {"rnapol": 1.0})
new_site = site.clone()
self.assertNotEqual(site, new_site)
site.cover()
self.assertTrue(site.is_covered())
self.assertFalse(new_site.is_covered())
def test_exposure(self):
# This is really just testing if the bindings are set up correctly
site = pt.BindingSite("promoter", 1, 10, {"rnapol": 1.0})
self.assertFalse(site.first_exposure)
site.first_exposure = True
self.assertTrue(site.first_exposure)
def test_interaction(self):
site = pt.BindingSite("promoter", 1, 10, {"rnapol": 1.0})
self.assertTrue(site.check_interaction("rnapol"))
self.assertFalse(site.check_interaction("otherpol"))