def test_copy(self):
a = PacBioBam.GenomicInterval("foo", 10, 20)
b = PacBioBam.GenomicInterval(a)
c = a
self.assertEqual(a, a)
self.assertEqual(a, b)
self.assertEqual(a, c)
def test_ctors(self):
empty = PacBioBam.GenomicInterval()
normal = PacBioBam.GenomicInterval("foo", 100, 200)
self.assertEqual("", empty.Name())
self.assertEqual(0, empty.Start())
self.assertEqual(0, empty.Stop())
self.assertEqual("foo", normal.Name())
self.assertEqual(100, normal.Start())
self.assertEqual(200, normal.Stop())
def test_modifiers(self):
a = PacBioBam.GenomicInterval("foo", 10, 20)
b = PacBioBam.GenomicInterval(a)
b.Name("bar").Start(2).Stop(10)
c = PacBioBam.GenomicInterval(a)
c.Interval(b.Interval())
self.assertNotEqual(a, b)
self.assertEqual("bar", b.Name())
self.assertEqual(2, b.Start())
self.assertEqual(10, b.Stop())
self.assertEqual(a.Name(), c.Name())
self.assertEqual(b.Interval(), c.Interval())
def test_cover(self):
a = PacBioBam.GenomicInterval("foo", 2, 4)
b = PacBioBam.GenomicInterval("foo", 3, 5)
c = PacBioBam.GenomicInterval("foo", 6, 8)
d = PacBioBam.GenomicInterval("foo", 1, 7)
e = PacBioBam.GenomicInterval("foo", 5, 8)
f = PacBioBam.GenomicInterval("bar", 3, 5) # same as b, different ref
# 0123456789
# a --
# b --
# c --
# d ------
# e ---
# self-cover
self.assertTrue(a.Covers(a))
self.assertTrue(a.CoveredBy(a))
# basic covers/covered
self.assertTrue(b.CoveredBy(d))
self.assertTrue(d.Covers(b))
self.assertNotEqual(b, d)
self.assertFalse(b.Covers(d))
# same coords as b, but different ref
self.assertFalse(f.CoveredBy(d))
self.assertFalse(d.Covers(f))
self.assertNotEqual(f, d)
self.assertFalse(f.Covers(d))
# obvious disjoint
self.assertFalse(b.Covers(c))
self.assertFalse(c.Covers(b))
self.assertFalse(b.CoveredBy(c))
self.assertFalse(c.CoveredBy(b))
# b.stop == e.start (intervals are right-open, so disjoint)
self.assertFalse(b.Covers(e))
self.assertFalse(b.CoveredBy(e))
# shared endpoint, start contained
self.assertTrue(e.Covers(c))
self.assertTrue(c.CoveredBy(e))
def test_validity(self):
a = PacBioBam.GenomicInterval() # default
b = PacBioBam.GenomicInterval("foo", 0,
0) # valid id, start == stop (zero)
c = PacBioBam.GenomicInterval("foo", 4,
4) # valid id, start == stop (non-zero)
d = PacBioBam.GenomicInterval(
"foo", 0, 1) # valid id, start < stop (start == zero) OK
e = PacBioBam.GenomicInterval(
"foo", 4, 5) # valid id, start < stop (start > zero) OK
f = PacBioBam.GenomicInterval("foo", 5, 4) # valid id, start > stop
g = PacBioBam.GenomicInterval("", 0,
0) # invalid id, start == stop (zero)
h = PacBioBam.GenomicInterval(
"", 4, 4) # invalid id, start == stop (non-zero)
i = PacBioBam.GenomicInterval(
"", 0, 1) # invalid id, start < stop (start == zero)
j = PacBioBam.GenomicInterval(
"", 4, 5) # invalid id, start < stop (start > zero)
k = PacBioBam.GenomicInterval("", 5, 4) # invalid id, start > stop
self.assertTrue(d.IsValid())
self.assertTrue(e.IsValid())
self.assertFalse(a.IsValid())
self.assertFalse(b.IsValid())
self.assertFalse(c.IsValid())
self.assertFalse(f.IsValid())
self.assertFalse(g.IsValid())
self.assertFalse(h.IsValid())
self.assertFalse(i.IsValid())
self.assertFalse(j.IsValid())
self.assertFalse(k.IsValid())