Skip to content

Commit

Permalink
Final test fixups
Browse files Browse the repository at this point in the history
  • Loading branch information
@jeromekelleher
jeromekelleher committed Sep 6, 2024
1 parent 05d977d commit 63037e4
Show file tree
Hide file tree
Showing 2 changed files with 7 additions and 113 deletions.
12 changes: 7 additions & 5 deletions tests/test_inference.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -563,13 +563,14 @@ def test_first_day(self, tmp_path, fx_ts_map, fx_alignment_store, fx_metadata_db
assert list(ts.mutations_time) == [0, 0, 0]
assert list(ts.mutations_site) == [8632, 17816, 27786]
sc2ts_md = ts.node(2).metadata["sc2ts"]
assert len(sc2ts_md["mutations"]) == 3
for mut_md, mut in zip(sc2ts_md["mutations"], ts.mutations()):
hmm_md = sc2ts_md["hmm"][0]
assert hmm_md["direction"] == "forward"
assert len(hmm_md["mutations"]) == 3
for mut_md, mut in zip(hmm_md["mutations"], ts.mutations()):
assert mut_md["derived_state"] == mut.derived_state
assert mut_md["site_id"] == mut.site
assert mut_md["site_position"] == ts.sites_position[mut.site]
assert mut_md["inherited_state"] == ts.site(mut.site).ancestral_state
assert sc2ts_md["path"] == [{"left": 0, "parent": 1, "right": 29904}]
assert hmm_md["path"] == [{"left": 0, "parent": 1, "right": 29904}]
assert sc2ts_md["qc"] == {
"num_masked_sites": 133,
"original_base_composition": {
Expand Down Expand Up @@ -665,7 +666,8 @@ def test_exact_matches(self, fx_ts_map, node, strain, parent):
assert x.flags == (tskit.NODE_IS_SAMPLE | sc2ts.core.NODE_IS_EXACT_MATCH)
md = x.metadata
assert md["strain"] == strain
sc2ts_md = md["sc2ts"]
sc2ts_md = md["sc2ts"]["hmm"][0]
assert sc2ts_md["direction"] == "forward"
assert len(sc2ts_md["path"]) == 1
assert len(sc2ts_md["mutations"]) == 0
assert sc2ts_md["path"][0] == {
Expand Down
108 changes: 0 additions & 108 deletions tests/test_tree_hueristics.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -297,114 +297,6 @@ def test_two_sites_reversion_and_shared(self):
assert ts2.num_nodes == ts.num_nodes + 1


class TestInsertRecombinants:
def test_no_recombination(self):
ts1 = tskit.Tree.generate_balanced(4, arity=4).tree_sequence
ts2 = sc2ts.inference.insert_recombinants(ts1)
ts1.tables.assert_equals(ts2.tables)

def test_single_breakpoint_single_recombinant_no_mutations(self):
tables = tskit.TableCollection(10)
tables.nodes.add_row(flags=0, time=1)
tables.nodes.add_row(flags=0, time=1)
tables.nodes.add_row(flags=1, time=0)
tables.edges.add_row(0, 5, parent=0, child=2)
tables.edges.add_row(5, 10, parent=1, child=2)
ts = prepare(tables)

ts2 = sc2ts.inference.insert_recombinants(ts)
assert_sequences_equal(ts, ts2)
assert ts2.num_mutations == 0
assert ts2.num_nodes == ts.num_nodes + 1
assert ts2.num_edges == ts.num_edges + 1
assert_sequences_equal(ts, ts2)

def test_single_breakpoint_two_recombinants_no_mutations(self):
tables = tskit.TableCollection(10)
tables.nodes.add_row(flags=0, time=1)
tables.nodes.add_row(flags=0, time=1)
tables.nodes.add_row(flags=1, time=0)
tables.nodes.add_row(flags=1, time=0)
tables.edges.add_row(0, 5, parent=0, child=2)
tables.edges.add_row(5, 10, parent=1, child=2)
tables.edges.add_row(0, 5, parent=0, child=3)
tables.edges.add_row(5, 10, parent=1, child=3)
ts = prepare(tables)

ts2 = sc2ts.inference.insert_recombinants(ts)
assert_sequences_equal(ts, ts2)
assert ts2.num_mutations == 0
assert ts2.num_nodes == ts.num_nodes + 1
assert ts2.num_edges == ts.num_edges
assert_sequences_equal(ts, ts2)

def test_single_breakpoint_single_recombinant_one_mutation(self):
tables = tskit.TableCollection(10)
tables.nodes.add_row(flags=0, time=1)
tables.nodes.add_row(flags=0, time=1)
tables.nodes.add_row(flags=1, time=0)
tables.edges.add_row(0, 5, parent=0, child=2)
tables.edges.add_row(5, 10, parent=1, child=2)
tables.sites.add_row(4, "A")
tables.mutations.add_row(site=0, node=2, derived_state="T")
ts = prepare(tables)

ts2 = sc2ts.inference.insert_recombinants(ts)
md = ts2.node(3).metadata
assert md["mutations"] == [[2, [[0, "A", "T"]]]]
assert_sequences_equal(ts, ts2)
assert ts2.num_mutations == 1
assert ts2.num_nodes == ts.num_nodes + 1
assert ts2.num_edges == ts.num_edges + 1
assert np.all(ts2.mutations_node == 3)

def test_single_breakpoint_single_recombinant_two_mutations(self):
tables = tskit.TableCollection(10)
tables.nodes.add_row(flags=0, time=1)
tables.nodes.add_row(flags=0, time=1)
tables.nodes.add_row(flags=1, time=0)
tables.edges.add_row(0, 5, parent=0, child=2)
tables.edges.add_row(5, 10, parent=1, child=2)
tables.sites.add_row(4, "A")
tables.sites.add_row(5, "G")
tables.mutations.add_row(site=0, node=2, derived_state="T")
tables.mutations.add_row(site=1, node=2, derived_state="C")
ts = prepare(tables)

ts2 = sc2ts.inference.insert_recombinants(ts)
md = ts2.node(3).metadata
assert md["mutations"] == [[2, [[0, "A", "T"], [1, "G", "C"]]]]
assert_sequences_equal(ts, ts2)
assert ts2.num_mutations == 2
assert ts2.num_nodes == ts.num_nodes + 1
assert ts2.num_edges == ts.num_edges + 1
assert np.all(ts2.mutations_node == 3)

def test_single_breakpoint_two_recombinants_different_mutations(self):
tables = tskit.TableCollection(10)
tables.sites.add_row(4, "A")
tables.sites.add_row(5, "G")
tables.nodes.add_row(flags=0, time=1)
tables.nodes.add_row(flags=0, time=1)
for j in [2, 3]:
tables.nodes.add_row(flags=1, time=0)
tables.edges.add_row(0, 5, parent=0, child=j)
tables.edges.add_row(5, 10, parent=1, child=j)
# Share the mutation at site 0
tables.mutations.add_row(site=0, node=j, derived_state="T")
# Different mutations at site 1
tables.mutations.add_row(site=1, node=2, derived_state="C")
tables.mutations.add_row(site=1, node=3, derived_state="T")
ts = prepare(tables)

ts2 = sc2ts.inference.insert_recombinants(ts)
assert_sequences_equal(ts, ts2)
md = ts2.node(4).metadata
assert ts2.num_mutations == 3
assert ts2.num_nodes == ts.num_nodes + 1
assert ts2.num_edges == ts.num_edges


class TestTrimBranches:
def test_one_mutation_three_children(self):
# 3.00┊ 6 ┊
Expand Down

0 comments on commit 63037e4

Please sign in to comment.