def test_input_errors(self):
with pytest.raises(ValueError):
ibd.IbdFinder(self.ts, sample_pairs=[0])
with pytest.raises(AssertionError):
ibd.IbdFinder(self.ts, sample_pairs=[(0, 1, 2)])
with pytest.raises(ValueError):
ibd.IbdFinder(self.ts, sample_pairs=[(0, 5)])
with pytest.raises(ValueError):
ibd.IbdFinder(self.ts, sample_pairs=[(0, 1), (1, 0)])
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 find_ibd(
ts,
sample_pairs,
min_length=0,
max_time=None,
compare_lib=True,
print_c=False,
print_py=False,
):
"""
Calculates IBD segments using Python and converts output to lists of segments.
Also compares result with C library.
"""
ibd_f = ibd.IbdFinder(ts,
sample_pairs=sample_pairs,
max_time=max_time,
min_length=min_length)
ibd_segs = ibd_f.find_ibd_segments()
ibd_segs = convert_ibd_output_to_seglists(ibd_segs)
if compare_lib:
c_out = ts.tables.find_ibd(sample_pairs,
max_time=max_time,
min_length=min_length)
c_out = convert_ibd_output_to_seglists(c_out)
if print_c:
print("C output:\n")
print(c_out)
if print_py:
print("Python output:\n")
print(ibd_segs)
assert ibd_is_equal(ibd_segs, c_out)
return ibd_segs
def verify_equal_ibd(treeSequence):
"""
Calculates IBD segments using both the 'naive' and sophisticated algorithms,
verifies that the same output is produced.
NB: May be good to expand this in the future so that many different combos
of IBD options are tested simultaneously (all the MRCA and path-IBD combos),
for example.
"""
ts = treeSequence
ibd0 = ibd.IbdFinder(ts, samples=ts.samples())
ibd0 = ibd0.find_ibd_segments()
ibd1 = get_ibd_all_pairs(ts, path_ibd=True, mrca_ibd=True)
# Convert each SegmentList object into a list of Segment objects.
ibd0_tolist = {}
for key, val in ibd0.items():
if val is not None:
ibd0_tolist[key] = convert_segmentlist_to_list(val)
# Check for equality.
for key0, val0 in ibd0_tolist.items():
assert key0 in ibd1.keys()
val1 = ibd1[key0]
val0.sort()
val1.sort()
def test_basic(self):
ts = self.ts
ibd_f = ibd.IbdFinder(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, 1)]}
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()
ibd_segs = convert_dict_of_segmentlists(ibd_segs)
true_segs = {
(0, 2): [ibd.Segment(0, 1, 3)],
}
assert ibd_is_equal(ibd_segs, true_segs)
def test_time(self):
ts = self.ts
ibd_f = ibd.IbdFinder(ts, max_time=1.8)
ibd_segs = ibd_f.find_ibd_segments()
true_segs = {(0, 1): []}
ibd_segs = convert_dict_of_segmentlists(ibd_segs)
assert ibd_is_equal(ibd_segs, true_segs)
ibd_f = ibd.IbdFinder(ts, max_time=2.8)
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_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_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_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_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_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_no_samples(self):
#
# 2
# / \
# / \
# / \
# (0) (1)
nodes = io.StringIO("""\
id is_sample time
0 0 0
1 0 0
2 0 1
3 0 1
""")
edges = io.StringIO("""\
left right parent child
0 1 2 0
0 1 3 1
""")
ts = tskit.load_text(nodes=nodes, edges=edges, strict=False)
with pytest.raises(ValueError):
ibd.IbdFinder(ts, sample_pairs=[(0, 1)])
def ibd_segments(
ts,
*,
within=None,
between=None,
min_span=0,
max_time=None,
compare_lib=True,
print_c=False,
print_py=False,
):
"""
Calculates IBD segments using Python and converts output to lists of segments.
Also compares result with C library.
"""
ibd_f = ibd.IbdFinder(ts,
within=within,
between=between,
max_time=max_time,
min_span=min_span)
ibd_segs = ibd_f.run()
if print_py:
print("Python output:\n")
print(ibd_segs)
# ibd_f.print_state()
if compare_lib:
c_out = ts.ibd_segments(
within=within,
between=between,
max_time=max_time,
min_span=min_span,
store_segments=True,
)
if print_c:
print("C output:\n")
print(c_out)
assert_ibd_equal(ibd_segs, c_out)
return ibd_segs
def test_length(self):
ibd_f = ibd.IbdFinder(self.ts, min_length=0.2)
ibd_segs = ibd_f.find_ibd_segments()
ibd_segs = convert_dict_of_segmentlists(ibd_segs)
true_segs = {(0, 1): []}
assert ibd_is_equal(ibd_segs, true_segs)
