def test_subset(self): # need to test exons
a = Entry(1, 5, 9, "x")
b = Entry(1, 10, 20, "b")
c = Entry(1, 10, 21, "x")
d = Entry(1, 30, 40, "d")
e = Entry(2, 10, 20, "x")
gr = Gr([a, b, c, d, e])
self.assertEqual(gr.subset(["x"]), Gr([a, c, e]))
def test_initialisation(self):
a = Entry(1, 5, 9, "c")
b = Entry(1, 10, 20, "d")
c = Entry(1, 10, 21, "c")
d = Entry(1, 30, 40, "a")
e = Entry(2, 10, 20, "b")
gr = Gr([e, d, c, b, a])
self.assertEqual(gr, Gr([a, b, c, d, e]))
self.assertEqual(list(gr), [a, b, c, d, e])
def test_combined_with(self):
a = Entry(1, 5, 9)
b = Entry(1, 10, 20)
c = Entry(1, 11, 15)
d = Entry(1, 17, 40)
e = Entry(1, 42, 60)
gr = Gr([a, b, c, d, e])
self.assertEqual(gr.combined_with(gr), Gr([a, b, c, d, e]*2))
self.assertEqual(Gr([a]).combined_with(Gr([b])), Gr([a, b]))
def test_inverted(self):
a = Entry(1, 5, 9, "c")
b = Entry(1, 10, 20, "d")
c = Entry(1, 10, 21, "c")
d = Entry(1, 30, 40, "a")
e = Entry(2, 10, 20, "b")
gr = Gr([a])
self.assertEqual(gr.inverted.inverted, gr)
self.assertEqual(gr.inverted.number_of_components, 26)
self.assertEqual(len(set(entry.chrom for entry in gr.inverted)), 25)
gr = Gr([e, d, c, b, a])
self.assertEqual(gr.inverted.inverted, gr.merged)
self.assertEqual(gr.inverted.number_of_components, 28)
def test_hash_eq(self): # test with variants
a = Entry(1, 5, 9, "c")
b = Entry(1, 10, 20, "d")
c = Entry(1, 10, 21, "c")
d = Entry(1, 30, 40, "a")
e = Entry(2, 10, 20, "b")
gr = Gr([e, d, c, b, a])
self.assertEqual(gr, Gr([a, b, c, d, e]))
self.assertNotEqual(gr, Gr([b, c, d, e]))
self.assertNotEqual(gr, Gr([a, a, b, c, d, e]))
self.assertIn(gr, set([Gr([a, b, c, d, e])]))
self.assertNotIn(gr, set([Gr([b, c, d, e])]))
self.assertNotIn(gr, set([Gr([a, a, b, c, d, e])]))
def test_properties(self):
a = Entry(1, 5, 9, "c")
b = Entry(1, 10, 20, "d")
c = Entry(1, 10, 21, "c")
d = Entry(1, 30, 40, "a")
e = Entry(2, 10, 20, "b")
gr = Gr([e, d, c, b, a])
self.assertEqual(gr.number_of_components, 5)
self.assertEqual(gr.bases, 50)
self.assertEqual(gr.is_empty, False)
self.assertEqual(Gr().is_empty, True)
self.assertEqual(gr.names, ["a", "b", "c", "d"])
self.assertEqual(gr.names_as_string, "a, b, c, d") # Need to test exons
self.assertEqual(gr.locations_as_string, "chr1:5-9, chr1:10-20, chr1:10-21, chr1:30-40, chr2:10-20")
self.assertEqual(list(gr.sorted_by_name), [d, e, a, c, b])
def test_bisect_left(self):
a = Entry(1, 5, 9)
b = Entry(1, 10, 14)
c = Entry(1, 20, 24)
d = Entry(1, 30, 34)
e = Entry(1, 40, 44)
array = Gr([e, d, c, b, a]).data[1]
self.assertEqual(bisect_left(array, 30, 0, len(array)), 3)
array = Gr([e, d, c, b, a, Entry(1, 100, 130)]).data[1]
self.assertEqual(bisect_left(array, 30, 0, len(array)), 0)
array = Gr([e, d, c, b, a, Entry(1, 100, 120)]).data[1]
self.assertEqual(bisect_left(array, 30, 0, len(array)), 1)
array = Gr([e, d, c, b, a, Entry(1, 100, 200)]).data[1]
self.assertEqual(bisect_left(array, 30, 0, len(array)), 0)
array = Gr([e, d, c, b, a, Entry(1, 100, 120)]).data[1]
self.assertEqual(bisect_left(array, 400, 0, len(array)), len(array))
def merged(self):
a = Entry(1, 5, 9, "c")
b = Entry(1, 10, 20, "d")
c = Entry(1, 11, 15, "c")
d = Entry(1, 17, 40, "a")
e = Entry(1, 42, 60, "b")
f = Entry(2, 42, 60, "e")
self.assertEqual(Gr([a, a, a]).merged, Gr([a]))
self.assertEqual(Gr([a, b, c, d, e, f]).merged, Gr([Entry(1, 5, 40), e, f]))
self.assertEqual(Gr([b, e]).merged, Gr([b, e]))
self.assertEqual(Gr([b, c]).merged, Gr([b]))
def test_subranges_covered_by(self):
a = Entry(1, 5, 9)
b = Entry(1, 10, 20)
c = Entry(1, 11, 15)
d = Entry(1, 17, 40)
e = Entry(1, 42, 60)
f = Entry(2, 42, 60)
x = Entry(1, 16, 30)
gr = Gr([a, x])
self.assertEqual(gr.subranges_covered_by(Gr([b])), Gr())
self.assertEqual(gr.subranges_covered_by(Gr([b, c, d])), Gr([x]))
self.assertEqual(gr.subranges_covered_by(Gr([b]*2)), Gr())
self.assertEqual(gr.subranges_covered_by(Gr([b, c, d]*2)), Gr([x]))
def test_iterate(self):
a = Entry(1, 5, 9)
b = Entry(1, 10, 14)
c = Entry(1, 20, 24)
d = Entry(1, 30, 34)
e = Entry(1, 40, 44)
array = Gr([e, d, c, b, a]).data[1]
self.assertEqual(list(Iterate(array).yield_overlapping(1, 4)), [])
self.assertEqual(list(Iterate(array).yield_overlapping(1, 5)), [a])
self.assertEqual(list(Iterate(array).yield_overlapping(24, 30)), [c, d])
self.assertEqual(list(Iterate(array).yield_overlapping(24, 40)), [c, d, e])
self.assertEqual(list(Iterate(array).yield_overlapping(24, 1000)), [c, d, e])
array = Gr([e, d, c, b, a, Entry(1, 1000, 2000)]).data[1]
self.assertEqual(list(Iterate(array).yield_overlapping(29, 35)), [d])
x = Entry(1, 9, 30)
array = Gr([e, d, c, b, a, x]).data[1]
self.assertEqual(list(Iterate(array).yield_overlapping(30, 30)), [x, d])
def test_overlapped_by(self):
a = Entry(1, 5, 9)
b = Entry(1, 10, 20)
c = Entry(1, 11, 15)
d = Entry(1, 17, 40)
e = Entry(1, 42, 60)
f = Entry(2, 42, 60)
gr = Gr([a, b, c, d, e, f])
gr2 = Gr([a, b, c, d, e, f]*2)
x = Entry(1, 12, 13)
self.assertEqual(gr.overlapped_by(Gr([Entry(1,2,3)])), Gr())
self.assertEqual(gr.overlapped_by(gr), gr)
self.assertEqual(gr.overlapped_by(gr2), gr)
self.assertEqual(gr2.overlapped_by(gr), gr2)
self.assertEqual(gr2.overlapped_by(gr2), gr2)
self.assertEqual(gr.overlapped_by(Gr([x])), Gr([x]*2))
self.assertEqual(gr.overlapped_by(Gr([Entry(1, 9, 10)])), Gr([Entry(1, 9, 9), Entry(1, 10, 10)]))
self.assertEqual(Gr([Entry(1, 2, 200)]).overlapped_by(gr), Gr([Entry(1, 5, 40), e]))
def test_repr(self):
gr = Gr([Entry(23, 10, 20), Entry(1, 56, 88, "?", "+")])
self.assertEqual(eval(repr(gr)), gr)
self.assertEqual(repr(gr), 'Gr([Entry("1", 56, 88, "?", "+"), Entry(Chrom(23), 10, 20, ".", ".")])')
def test_constructor(self):
self.assertEqual(Entry("1", 10, 20), Entry("chr1", 10, 20))
self.assertEqual(Entry("23", 10, 20), Entry("23", 10, 20))
self.assertEqual(Entry("23", 10, 20), Entry(23, 10, 20))
self.assertEqual(Entry(23, 10, 20), Entry("chrX", 10, 20))
self.assertEqual(Entry(23, 10, 20), Entry("X", 10, 20))
self.assertEqual(Entry(23, 10, 20), Entry("X", 10, 20, "?"))
self.assertEqual(Entry(23, 10, 20), Entry("X", 10, 20, "?", "+"))
self.assertEqual(Entry(23, 10, 20).name, ".")
self.assertEqual(Entry(23, 10, 20).strand, ".")
with self.assertRaises(KeyError):
Entry(0, 10, 20)
Entry(26, 10, 20)
Entry("?", 10, 20)
def test_eq_hash(self):
self.assertNotEqual(Entry(23, 10, 20), set([Entry(23, 10, 21)]))
self.assertNotEqual(Entry(23, 10, 20), set([Entry(23, 9, 2)]))
self.assertNotEqual(Entry(23, 10, 20), set([Entry(21, 10, 21)]))
self.assertIn(Entry(23, 10, 20, "?", "+"), set([Entry(23, 10, 20)]))
self.assertNotIn(Entry(23, 10, 20, "?", "+"), set([Entry(23, 11, 20, "?", "+")]))
def test_location(self):
self.assertEqual(Entry(23, 10, 20).location, "chrX:10-20")
def test_not_touched_by(self):
a = Entry(1, 5, 9)
b = Entry(1, 10, 20)
c = Entry(1, 11, 15)
d = Entry(1, 17, 40)
e = Entry(1, 42, 60)
f = Entry(2, 42, 60)
gr = Gr([a, b, c, d, e, f])
self.assertEqual(gr.not_touched_by(Gr([Entry(1, 3, 4)])), gr)
self.assertEqual(gr.not_touched_by(Gr([Entry(1, 5, 5)])), Gr([b, c, d, e, f]))
self.assertEqual(gr.not_touched_by(Gr([Entry(1, 1, 100)])), Gr([f]))
self.assertEqual(gr.not_touched_by(Gr([Entry(1, 16, 17)])), Gr([a, c, e, f]))
self.assertEqual(Gr([b]+[c]*1000+[d]).not_touched_by(Gr([Entry(1, 19, 19)])), Gr([c]*1000))
self.assertEqual(gr.not_touched_by(Gr([Entry(1, 3, 4)]*2)), gr)
self.assertEqual(gr.not_touched_by(Gr([Entry(1, 5, 5)]*2)), Gr([b, c, d, e, f]))
self.assertEqual(gr.not_touched_by(Gr([Entry(1, 1, 100)]*2)), Gr([f]))
self.assertEqual(gr.not_touched_by(Gr([Entry(1, 16, 17)]*2)), Gr([a, c, e, f]))
self.assertEqual(Gr([b]+[c]*1000+[d]).not_touched_by(Gr([Entry(1, 19, 19)]*2)), Gr([c]*1000))
def test_repr(self):
self.assertEqual(eval(repr(Entry(23, 10, 20))), Entry(23, 10, 20,))
self.assertEqual(repr(Entry(23, 10, 20, "?", "+")), 'Entry("chrX", 10, 20, "?", "+")')