def test_basic(self):
ibd_segs = find_ibd(self.ts, sample_pairs=[(0, 1)])
true_segs = {
(0, 1): [ibd.Segment(0.0, 0.4, 2),
ibd.Segment(0.4, 1.0, 3)]
}
assert ibd_is_equal(ibd_segs, true_segs)
def test_defaults(self):
ibd_segs = find_ibd(self.ts, sample_pairs=[(1, 2)])
true_segs = {
(1, 2): [ibd.Segment(0.0, 0.2, 4),
ibd.Segment(0.2, 1.0, 4)],
}
assert ibd_is_equal(ibd_segs, true_segs)
def test_input_sample_pairs(self):
ibd_segs = find_ibd(self.ts, sample_pairs=[(0, 1), (0, 3)])
true_segs = {
(0, 1): [ibd.Segment(0.0, 1.0, 4)],
(0, 3): [ibd.Segment(0.3, 1.0, 4),
ibd.Segment(0.0, 0.3, 5)],
}
assert ibd_is_equal(ibd_segs, true_segs)
def test_basic(self):
ibd_f = ibd.IbdFinder(self.ts)
ibd_segs = ibd_f.find_ibd_segments()
ibd_segs = convert_dict_of_segmentlists(ibd_segs)
true_segs = {
(0, 1): [ibd.Segment(0.0, 0.4, 2),
ibd.Segment(0.4, 1.0, 3)]
}
assert ibd_is_equal(ibd_segs, true_segs)
def test_defaults(self):
ibd_f = ibd.IbdFinder(self.ts)
ibd_segs = ibd_f.find_ibd_segments()
ibd_segs = convert_dict_of_segmentlists(ibd_segs)
true_segs = {
(0, 1): [ibd.Segment(0.0, 1.0, 3)],
(0, 2): [ibd.Segment(0.0, 1.0, 4)],
(1, 2): [ibd.Segment(0.0, 1.0, 4)],
}
assert ibd_is_equal(ibd_segs, true_segs)
def test_defaults(self):
ts = self.ts
ibd_f = ibd.IbdFinder(ts)
ibd_segs = ibd_f.find_ibd_segments()
true_segs = {
(0, 1): [
ibd.Segment(0.0, 0.2, 4),
ibd.Segment(0.7, 1.0, 4),
ibd.Segment(0.2, 0.7, 4),
]
}
ibd_segs = convert_dict_of_segmentlists(ibd_segs)
assert ibd_is_equal(ibd_segs, true_segs)
def test_basic(self):
ibd_segs = find_ibd(self.ts,
sample_pairs=[(0, 1), (0, 2), (0, 3), (1, 2),
(1, 3), (2, 3)])
true_segs = {
(0, 1): [],
(0, 2): [ibd.Segment(0.0, 1.0, 2)],
(0, 3): [],
(1, 2): [],
(1, 3): [ibd.Segment(0.0, 1.0, 3)],
(2, 3): [],
}
assert ibd_is_equal(ibd_segs, true_segs)
def test_time(self):
ts = self.ts
ibd_f = ibd.IbdFinder(ts, max_time=3)
ibd_segs = ibd_f.find_ibd_segments()
true_segs = {
(0, 1): [ibd.Segment(0, 1, 4)],
(0, 2): [ibd.Segment(0, 0.3, 4)],
(0, 3): [ibd.Segment(0.3, 1, 4)],
(1, 2): [ibd.Segment(0, 0.3, 4)],
(1, 3): [ibd.Segment(0.3, 1, 4)],
(2, 3): [],
}
ibd_segs = convert_dict_of_segmentlists(ibd_segs)
assert ibd_is_equal(ibd_segs, true_segs)
def test_time(self):
ibd_segs = find_ibd(
self.ts,
sample_pairs=[(0, 1), (0, 2), (0, 3), (1, 2), (1, 3), (2, 3)],
max_time=3,
)
true_segs = {
(0, 1): [ibd.Segment(0, 1, 4)],
(0, 2): [ibd.Segment(0, 0.3, 4)],
(0, 3): [ibd.Segment(0.3, 1, 4)],
(1, 2): [ibd.Segment(0, 0.3, 4)],
(1, 3): [ibd.Segment(0.3, 1, 4)],
(2, 3): [],
}
assert ibd_is_equal(ibd_segs, true_segs)
def test_length(self):
ts = self.ts
ibd_f = ibd.IbdFinder(ts, min_length=0.4)
ibd_segs = ibd_f.find_ibd_segments()
true_segs = {(0, 1): [ibd.Segment(0.2, 0.7, 4)]}
ibd_segs = convert_dict_of_segmentlists(ibd_segs)
assert ibd_is_equal(ibd_segs, true_segs)
def test_time(self):
ibd_segs = find_ibd(self.ts,
sample_pairs=[(0, 1)],
max_time=1.2,
compare_lib=True)
true_segs = {(0, 1): [ibd.Segment(0.0, 0.4, 2)]}
assert ibd_is_equal(ibd_segs, true_segs)
def test_length(self):
ibd_segs = find_ibd(self.ts,
sample_pairs=[(0, 1)],
min_length=0.5,
compare_lib=True)
true_segs = {(0, 1): [ibd.Segment(0.4, 1.0, 3)]}
assert ibd_is_equal(ibd_segs, true_segs)
def test_time(self):
ibd_f = ibd.IbdFinder(self.ts, max_time=1.5)
ibd_segs = ibd_f.find_ibd_segments()
ibd_segs = convert_dict_of_segmentlists(ibd_segs)
true_segs = {
(0, 1): [ibd.Segment(0.0, 1.0, 3)],
(0, 2): [],
(1, 2): []
}
assert ibd_is_equal(ibd_segs, true_segs)
def test_input_sample_pairs(self):
ibd_f = ibd.IbdFinder(self.ts, sample_pairs=[(0, 1), (2, 3), (1, 3)])
ibd_segs = ibd_f.find_ibd_segments()
ibd_segs = convert_ibd_output_to_seglists(ibd_segs)
true_segs = {
(0, 1): [
ibd.Segment(0.0, 0.2, 4),
ibd.Segment(0.7, 1.0, 4),
ibd.Segment(0.2, 0.7, 4),
],
(2, 3): [ibd.Segment(0.2, 0.7, 4)],
}
ibd_segs = find_ibd(
self.ts,
sample_pairs=[(0, 1), (2, 3)],
compare_lib=True,
print_c=False,
print_py=False,
)
assert ibd_is_equal(ibd_segs, true_segs)
def test_time(self):
ibd_segs = find_ibd(
self.ts,
sample_pairs=[(0, 1), (0, 2), (1, 2)],
max_time=1.5,
compare_lib=True,
)
true_segs = {
(0, 1): [ibd.Segment(0.0, 1.0, 3)],
(0, 2): [],
(1, 2): []
}
assert ibd_is_equal(ibd_segs, true_segs)
def convert_ibd_output_to_seglists(ibd_out):
"""
Converts the Python mock-up output back into lists of segments.
This is needed to use the ibd_is_equal function.
"""
for key in ibd_out.keys():
seg_list = []
num_segs = len(ibd_out[key]["left"])
for s in range(num_segs):
seg_list.append(
ibd.Segment(
left=ibd_out[key]["left"][s],
right=ibd_out[key]["right"][s],
node=ibd_out[key]["node"][s],
))
ibd_out[key] = seg_list
return ibd_out
def test_length(self):
ts = self.ts
ibd_f = ibd.IbdFinder(ts, min_length=0.5)
ibd_segs = ibd_f.find_ibd_segments()
true_segs = {
(0, 1): [ibd.Segment(0, 1, 4)],
(0, 2): [ibd.Segment(0.3, 1, 5)],
(0, 3): [ibd.Segment(0.3, 1, 4)],
(1, 2): [ibd.Segment(0.3, 1, 5)],
(1, 3): [ibd.Segment(0.3, 1, 4)],
(2, 3): [ibd.Segment(0.3, 1, 5)],
}
ibd_segs = convert_dict_of_segmentlists(ibd_segs)
assert ibd_is_equal(ibd_segs, true_segs)
def test_length(self):
ibd_segs = find_ibd(
self.ts,
sample_pairs=[(0, 1), (0, 2), (0, 3), (1, 2), (1, 3), (2, 3)],
min_length=0.5,
)
true_segs = {
(0, 1): [ibd.Segment(0, 1, 4)],
(0, 2): [ibd.Segment(0.3, 1, 5)],
(0, 3): [ibd.Segment(0.3, 1, 4)],
(1, 2): [ibd.Segment(0.3, 1, 5)],
(1, 3): [ibd.Segment(0.3, 1, 4)],
(2, 3): [ibd.Segment(0.3, 1, 5)],
}
assert ibd_is_equal(ibd_segs, true_segs)
def test_defaults(self):
ibd_segs = find_ibd(self.ts, sample_pairs=[(0, 2)])
true_segs = {
(0, 2): [ibd.Segment(0, 1, 3)],
}
assert ibd_is_equal(ibd_segs, true_segs)
def test_length(self):
ibd_f = ibd.IbdFinder(self.ts, min_length=0.5)
ibd_segs = ibd_f.find_ibd_segments()
ibd_segs = convert_dict_of_segmentlists(ibd_segs)
true_segs = {(0, 1): [ibd.Segment(0.4, 1.0, 3)]}
assert ibd_is_equal(ibd_segs, true_segs)
def test_defaults(self):
ts = self.ts
ibd_f = ibd.IbdFinder(ts)
ibd_segs = ibd_f.find_ibd_segments()
# print(ibd_segs[(0,1)])
true_segs = {
(0, 1): [ibd.Segment(0, 1, 4)],
(0, 2): [ibd.Segment(0, 0.3, 4),
ibd.Segment(0.3, 1, 5)],
(0, 3): [ibd.Segment(0, 0.3, 5),
ibd.Segment(0.3, 1, 4)],
(1, 2): [ibd.Segment(0, 0.3, 4),
ibd.Segment(0.3, 1, 5)],
(1, 3): [ibd.Segment(0, 0.3, 5),
ibd.Segment(0.3, 1, 4)],
(2, 3): [ibd.Segment(0.3, 1, 5),
ibd.Segment(0, 0.3, 5)],
}
ibd_segs = convert_dict_of_segmentlists(ibd_segs)
# print(ibd_segs)
assert ibd_is_equal(ibd_segs, true_segs)
def test_defaults(self):
ibd_segs = find_ibd(self.ts,
sample_pairs=[(0, 1), (0, 2), (0, 3), (1, 2),
(1, 3), (2, 3)])
true_segs = {
(0, 1): [ibd.Segment(0, 1, 4)],
(0, 2): [ibd.Segment(0, 0.3, 4),
ibd.Segment(0.3, 1, 5)],
(0, 3): [ibd.Segment(0, 0.3, 5),
ibd.Segment(0.3, 1, 4)],
(1, 2): [ibd.Segment(0, 0.3, 4),
ibd.Segment(0.3, 1, 5)],
(1, 3): [ibd.Segment(0, 0.3, 5),
ibd.Segment(0.3, 1, 4)],
(2, 3): [ibd.Segment(0.3, 1, 5),
ibd.Segment(0, 0.3, 5)],
}
assert ibd_is_equal(ibd_segs, true_segs)
def test_length(self):
ibd_segs = find_ibd(self.ts, sample_pairs=[(0, 1)], min_length=0.4)
true_segs = {(0, 1): [ibd.Segment(0.2, 0.7, 4)]}
assert ibd_is_equal(ibd_segs, true_segs)
def get_ibd(
sample0,
sample1,
treeSequence,
min_length=0,
max_time=None,
path_ibd=True,
mrca_ibd=True,
):
"""
Returns all IBD segments for a given pair of nodes in a tree
using a naive algorithm.
Note: This function probably looks more complicated than it needs to be --
This is because it also calculates other 'versions' of IBD (mrca_ibd=False,
path_ibd=False) that we have't implemented properly yet.
"""
ibd_list = []
ts, node_map = treeSequence.simplify(samples=[sample0, sample1],
keep_unary=True,
map_nodes=True)
node_map = node_map.tolist()
for n in ts.nodes():
if max_time is not None and n.time > max_time:
break
node_id = n.id
interval_list = []
if n.flags == 1:
continue
prev_dict = None
for t in ts.trees():
if len(list(t.nodes(n.id))) == 1 or t.num_samples(n.id) < 2:
continue
if mrca_ibd and n.id != t.mrca(0, 1):
continue
current_int = t.get_interval()
if len(interval_list) == 0:
interval_list.append(current_int)
else:
prev_int = interval_list[-1]
if not path_ibd and prev_int[1] == current_int[0]:
interval_list[-1] = (prev_int[0], current_int[1])
elif prev_dict is not None and subtrees_are_equal(
t, prev_dict, node_id):
interval_list[-1] = (prev_int[0], current_int[1])
else:
interval_list.append(current_int)
prev_dict = t.get_parent_dict()
for interval in interval_list:
if min_length == 0 or interval.right - interval.left > min_length:
orig_id = node_map.index(node_id)
ibd_list.append(ibd.Segment(interval[0], interval[1], orig_id))
return ibd_list
