def test_between_0_12(self):
true_segs = {
(0, 1): [tskit.IdentitySegment(0.0, 1.0, 3)],
(0, 2): [tskit.IdentitySegment(0.0, 1.0, 4)],
}
ibd_segs = ibd_segments(self.ts(), between=[[0], [1, 2]])
assert_ibd_equal(ibd_segs, true_segs)
def test_input_within(self):
ibd_segs = ibd_segments(self.ts(), within=[0, 2, 3, 5])
true_segs = {
(0, 2): [tskit.IdentitySegment(0.0, 1.0, 2)],
(3, 5): [tskit.IdentitySegment(0.0, 1.0, 5)],
}
assert_ibd_equal(ibd_segs, true_segs)
def naive_ibd(ts, a, b):
"""
Returns the IBD segments along the genome for a and b.
"""
def path(tree, u, v):
ret = [u]
while u != v:
u = tree.parent(u)
ret.append(u)
return ret
tree = ts.first()
mrca = tree.mrca(a, b)
last_paths = [path(tree, a, mrca), path(tree, b, mrca)]
last_mrca = mrca
left = 0.0
segs = []
while tree.next():
mrca = tree.mrca(a, b)
paths = [path(tree, a, mrca), path(tree, b, mrca)]
if paths != last_paths:
segs.append(
tskit.IdentitySegment(left, tree.interval.left, last_mrca))
last_paths = paths
left = tree.interval.left
last_mrca = mrca
segs.append(tskit.IdentitySegment(left, ts.sequence_length, last_mrca))
# Filter out segments with no mrca
return [seg for seg in segs if seg.node != -1]
def test_defaults(self):
ibd_segs = ibd_segments(self.ts())
true_segs = {
(0, 1):
[tskit.IdentitySegment(0, 5, 4),
tskit.IdentitySegment(5, 10, 4)],
}
assert_ibd_equal(ibd_segs, true_segs)
def test_defaults(self):
true_segs = {
(0, 1): [tskit.IdentitySegment(0.0, 1.0, 3)],
(0, 2): [tskit.IdentitySegment(0.0, 1.0, 4)],
(1, 2): [tskit.IdentitySegment(0.0, 1.0, 4)],
}
ibd_segs = ibd_segments(self.ts(), within=[0, 1, 2])
assert_ibd_equal(ibd_segs, true_segs)
def test_basic(self):
ibd_segs = ibd_segments(self.ts())
true_segs = {
(0, 2): [tskit.IdentitySegment(0.0, 1.0, 2)],
(1, 3): [tskit.IdentitySegment(0.0, 1.0, 3)],
}
assert_ibd_equal(ibd_segs, true_segs)
def test_defaults(self):
ibd_segs = ibd_segments(self.ts(), within=[1, 2])
true_segs = {
(1, 2): [
tskit.IdentitySegment(0.0, 0.2, 4),
tskit.IdentitySegment(0.2, 1.0, 4),
],
}
assert_ibd_equal(ibd_segs, true_segs)
def test_basic(self):
ibd_segs = ibd_segments(self.ts())
true_segs = {
(0, 1): [
tskit.IdentitySegment(0.0, 0.4, 2),
tskit.IdentitySegment(0.4, 1.0, 3),
]
}
assert_ibd_equal(ibd_segs, true_segs)
def test_defaults(self):
ibd_segs = ibd_segments(self.ts())
true_segs = {
(0, 1): [
tskit.IdentitySegment(0.0, 0.2, 4),
tskit.IdentitySegment(0.7, 1.0, 4),
tskit.IdentitySegment(0.2, 0.7, 4),
]
}
assert_ibd_equal(ibd_segs, true_segs)
def test_time(self):
ibd_segs = ibd_segments(self.ts(), max_time=3)
true_segs = {
(0, 1): [tskit.IdentitySegment(0, 1, 4)],
(0, 2): [tskit.IdentitySegment(0, 0.3, 4)],
(0, 3): [tskit.IdentitySegment(0.3, 1, 4)],
(1, 2): [tskit.IdentitySegment(0, 0.3, 4)],
(1, 3): [tskit.IdentitySegment(0.3, 1, 4)],
}
assert_ibd_equal(ibd_segs, true_segs)
def test_basic(self):
# FIXME
ibd_segs = ibd_segments(self.ts(), compare_lib=False)
true_segs = {
(0, 1): [tskit.IdentitySegment(0.0, 1.0, 1)],
(0, 2): [tskit.IdentitySegment(0.0, 1.0, 2)],
(1, 2): [tskit.IdentitySegment(0.0, 1.0, 2)],
}
assert_ibd_equal(ibd_segs, true_segs)
def test_input_within(self):
ibd_segs = ibd_segments(self.ts(), within=[0, 1, 2])
true_segs = {
(0, 1): [tskit.IdentitySegment(0, 1, 4)],
(0, 2): [
tskit.IdentitySegment(0, 0.3, 4),
tskit.IdentitySegment(0.3, 1, 5),
],
(1, 2): [
tskit.IdentitySegment(0, 0.3, 4),
tskit.IdentitySegment(0.3, 1, 5),
],
}
assert_ibd_equal(ibd_segs, true_segs)
def test_specified_samples(self):
ibd_segs = ibd_segments(self.ts(), within=[0, 1])
true_segs = {
(0, 1): [
tskit.IdentitySegment(0.0, 1, 2),
]
}
assert_ibd_equal(ibd_segs, true_segs)
def test_time(self):
ibd_segs = ibd_segments(
self.ts(),
max_time=1.5,
compare_lib=True,
)
true_segs = {(0, 1): [tskit.IdentitySegment(0.0, 1.0, 3)]}
assert_ibd_equal(ibd_segs, true_segs)
def test_length(self):
ibd_segs = ibd_segments(self.ts(), min_span=0.5)
true_segs = {
(0, 1): [tskit.IdentitySegment(0, 1, 4)],
(0, 2): [tskit.IdentitySegment(0.3, 1, 5)],
(0, 3): [tskit.IdentitySegment(0.3, 1, 4)],
(1, 2): [tskit.IdentitySegment(0.3, 1, 5)],
(1, 3): [tskit.IdentitySegment(0.3, 1, 4)],
(2, 3): [tskit.IdentitySegment(0.3, 1, 5)],
}
(ibd_segs, true_segs)
def test_all_samples(self):
# FIXME
ibd_segs = ibd_segments(self.ts(), within=range(6), compare_lib=False)
true_segs = {
(0, 2): [tskit.IdentitySegment(0.0, 1.0, 2)],
(0, 4): [tskit.IdentitySegment(0.0, 1.0, 4)],
(2, 4): [tskit.IdentitySegment(0.0, 1.0, 4)],
(1, 3): [tskit.IdentitySegment(0.0, 1.0, 3)],
(1, 5): [tskit.IdentitySegment(0.0, 1.0, 5)],
(3, 5): [tskit.IdentitySegment(0.0, 1.0, 5)],
}
assert_ibd_equal(ibd_segs, true_segs)
def test_within(self):
true_segs = {
(0, 1): [tskit.IdentitySegment(0.0, 1.0, 3)],
}
ibd_segs = ibd_segments(self.ts(), within=[0, 1])
assert_ibd_equal(ibd_segs, true_segs)
def test_defaults(self):
ibd_segs = ibd_segments(self.ts())
true_segs = {
(0, 1): [tskit.IdentitySegment(0, 1, 4)],
(0, 2): [
tskit.IdentitySegment(0, 0.3, 4),
tskit.IdentitySegment(0.3, 1, 5),
],
(0, 3): [
tskit.IdentitySegment(0, 0.3, 5),
tskit.IdentitySegment(0.3, 1, 4),
],
(1, 2): [
tskit.IdentitySegment(0, 0.3, 4),
tskit.IdentitySegment(0.3, 1, 5),
],
(1, 3): [
tskit.IdentitySegment(0, 0.3, 5),
tskit.IdentitySegment(0.3, 1, 4),
],
(2, 3): [
tskit.IdentitySegment(0.3, 1, 5),
tskit.IdentitySegment(0, 0.3, 5),
],
}
assert_ibd_equal(ibd_segs, true_segs)
def test_equal_to_length(self):
ibd_segs = ibd_segments(self.ts(), min_span=0.4)
true_segs = {(0, 1): [tskit.IdentitySegment(0.4, 1.0, 3)]}
assert_ibd_equal(ibd_segs, true_segs)
def add_segment(self, a, b, seg):
key = (a, b) if a < b else (b, a)
self.segments[key].append(tskit.IdentitySegment(seg.left, seg.right, seg.node))
