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Ancestral nodes from a founding generation can now be retained in simplify #781

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Ancestral nodes from a founding generation can now be retained in simplify #781

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13 changes: 13 additions & 0 deletions python/tests/simplify.py
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Original file line number Diff line number Diff line change
Expand Up @@ -108,6 +108,7 @@ def __init__(
filter_populations=True,
filter_individuals=True,
keep_unary=False,
founders=None,
):
self.ts = ts
self.n = len(sample)
Expand Down Expand Up @@ -140,6 +141,11 @@ def __init__(
self.position_lookup = None
if self.reduce_to_site_topology:
self.position_lookup = np.hstack([[0], position, [self.sequence_length]])
self.founders = founders
if self.founders is not None:
self.keep_founders = True
else:
self.keep_founders = False

def record_node(self, input_id, is_sample=False):
"""
Expand Down Expand Up @@ -263,6 +269,8 @@ def merge_labeled_ancestors(self, S, input_id):
"""
output_id = self.node_id_map[input_id]
is_sample = output_id != -1
if self.keep_founders:
is_founder = input_id in self.founders
if is_sample:
# Free up the existing ancestry mapping.
x = self.A_tail[input_id]
Expand All @@ -281,6 +289,11 @@ def merge_labeled_ancestors(self, S, input_id):
if output_id == -1:
output_id = self.record_node(input_id)
self.record_edge(left, right, output_id, ancestry_node)
elif self.keep_founders and is_founder:
if output_id == -1:
output_id = self.record_node(input_id)
self.record_edge(left, right, output_id, ancestry_node)

else:
if output_id == -1:
output_id = self.record_node(input_id)
Expand Down
79 changes: 79 additions & 0 deletions python/tests/test_topology.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4550,6 +4550,7 @@ def do_simplify(
filter_populations=True,
filter_individuals=True,
keep_unary=False,
founders=None,
):
"""
Runs the Python test implementation of simplify.
Expand All @@ -4563,6 +4564,7 @@ def do_simplify(
filter_populations=filter_populations,
filter_individuals=filter_individuals,
keep_unary=keep_unary,
founders=founders,
)
new_ts, node_map = s.simplify()
if compare_lib:
Expand Down Expand Up @@ -5413,6 +5415,83 @@ def test_many_trees_recurrent_mutations_internal_samples(self):
for keep in [True, False]:
self.verify_simplify_haplotypes(ts, samples, keep_unary=keep)

def test_keep_founders(self):

# 1.76┊ 14 ┊ 14 ┊ 14 ┊ 14 ┊ ┊
# ┊ ┏━━┻━┓ ┊ ┏━━┻━━━┓ ┊ ┏━━┻━━┓ ┊ ┏━━┻━━┓ ┊ ┊
# 1.51┊ ┃ ┃ ┊ ┃ 13 ┊ ┃ 13 ┊ ┃ 13 ┊ 13 ┊
# ┊ ┃ ┃ ┊ ┃ ┏━┻━┓ ┊ ┃ ┏┻━┓ ┊ ┃ ┏━┻━┓ ┊ ┏━━┻━━┓ ┊
# 1.27┊ ┃ ┃ ┊ ┃ ┃ ┃ ┊ ┃ ┃ ┃ ┊ ┃ 12 ┃ ┊ ┃ 12 ┊
# ┊ ┃ ┃ ┊ ┃ ┃ ┃ ┊ ┃ ┃ ┃ ┊ ┃ ┏┻┓ ┃ ┊ ┃ ┏┻┓ ┊
# 1.21┊ ┃ ┃ ┊ ┃ ┃ ┃ ┊ ┃ ┃ ┃ ┊ ┃ ┃ ┃ ┃ ┊ 11 ┃ ┃ ┊
# ┊ ┃ ┃ ┊ ┃ ┃ ┃ ┊ ┃ ┃ ┃ ┊ ┃ ┃ ┃ ┃ ┊ ┏━┻━┓ ┃ ┃ ┊
# 0.64┊ ┃ ┃ ┊ ┃ ┃ ┃ ┊ 10 ┃ ┃ ┊ ┃ ┃ ┃ ┃ ┊ ┃ ┃ ┃ ┃ ┊
# ┊ ┃ ┃ ┊ ┃ ┃ ┃ ┊ ┏┻━┓ ┃ ┃ ┊ ┃ ┃ ┃ ┃ ┊ ┃ ┃ ┃ ┃ ┊
# 0.49┊ ┃ 9 ┊ ┃ 9 ┃ ┊ ┃ ┃ ┃ ┃ ┊ ┃ ┃ ┃ ┃ ┊ ┃ ┃ ┃ ┃ ┊
# ┊ ┃ ┏━┻━┓ ┊ ┃ ┏━┻┓ ┃ ┊ ┃ ┃ ┃ ┃ ┊ ┃ ┃ ┃ ┃ ┊ ┃ ┃ ┃ ┃ ┊
# 0.31┊ ┃ ┃ 8 ┊ ┃ ┃ 8 ┃ ┊ ┃ ┃ 8 ┃ ┊ ┃ ┃ ┃ 8 ┊ ┃ 8 ┃ ┃ ┊
# ┊ ┃ ┃ ┏━┻┓ ┊ ┃ ┃ ┏┻┓ ┃ ┊ ┃ ┃ ┏┻┓ ┃ ┊ ┃ ┃ ┃ ┏┻┓ ┊ ┃ ┏┻┓ ┃ ┃ ┊
# 0.26┊ ┃ ┃ ┃ 7 ┊ ┃ ┃ ┃ ┃ ┃ ┊ ┃ ┃ ┃ ┃ ┃ ┊ ┃ ┃ ┃ ┃ ┃ ┊ ┃ ┃ ┃ ┃ ┃ ┊
# ┊ ┃ ┃ ┃ ┏┻┓ ┊ ┃ ┃ ┃ ┃ ┃ ┊ ┃ ┃ ┃ ┃ ┃ ┊ ┃ ┃ ┃ ┃ ┃ ┊ ┃ ┃ ┃ ┃ ┃ ┊
# 0.03┊ 6 ┃ ┃ ┃ ┃ ┊ 6 ┃ ┃ ┃ ┃ ┊ 6 ┃ ┃ ┃ ┃ ┊ 6 ┃ ┃ ┃ ┃ ┊ 6 ┃ ┃ ┃ ┃ ┊
# ┊ ┏┻┓ ┃ ┃ ┃ ┃ ┊ ┏┻┓ ┃ ┃ ┃ ┃ ┊ ┏┻┓ ┃ ┃ ┃ ┃ ┊ ┏┻┓ ┃ ┃ ┃ ┃ ┊ ┏┻┓ ┃ ┃ ┃ ┃ ┊
# 0.00┊ 0 5 1 2 3 4 ┊ 0 5 1 2 4 3 ┊ 0 5 1 2 4 3 ┊ 0 5 1 3 2 4 ┊ 0 5 2 4 1 3 ┊
# 0.00 0.18 0.37 0.75 0.91 1.00

nodes = io.StringIO(
"""\
id is_sample population time
0 1 -1 0.00000000000000
1 1 -1 0.00000000000000
2 0 -1 0.00000000000000
3 0 -1 0.00000000000000
4 0 -1 0.00000000000000
5 0 -1 0.00000000000000
6 0 -1 0.03000000000000
7 0 -1 0.26000000000000
8 0 -1 0.31000000000000
9 0 -1 0.49000000000000
10 0 -1 0.64000000000000
11 0 -1 1.21000000000000
12 0 -1 1.27000000000000
13 0 -1 1.51000000000000
14 0 -1 1.76000000000000
"""
)
edges = io.StringIO(
"""\
id left right parent child
0 0.00000000 1.00000000 6 0,5
1 0.00000000 0.18000000 7 3,4
2 0.00000000 1.00000000 8 2
3 0.18000000 1.00000000 8 4
4 0.00000000 0.18000000 8 7
5 0.00000000 0.37000000 9 1,8
6 0.37000000 0.75000000 10 1,6
7 0.91000000 1.00000000 11 6,8
8 0.75000000 1.00000000 12 1,3
9 0.18000000 0.75000000 13 3
10 0.37000000 0.91000000 13 8
11 0.18000000 0.37000000 13 9
12 0.91000000 1.00000000 13 11
13 0.75000000 1.00000000 13 12
14 0.00000000 0.37000000 14 6
15 0.75000000 0.91000000 14 6
16 0.00000000 0.18000000 14 9
17 0.37000000 0.75000000 14 10
18 0.18000000 0.91000000 14 13
"""
)
ts = tskit.load_text(nodes=nodes, edges=edges, strict=False)
ts.dump("founders.trees")
ts, node_map = self.do_simplify(
ts, samples=ts.samples(), founders=[14], compare_lib=False
)
# for t in ts.trees():
# print(t.draw(format="unicode"))
# t1 = ts.dump_tables()
# print(t1)


class TestMapToAncestors(unittest.TestCase):
"""
Expand Down