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working towards a slice that will work on intervals #261

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merged 7 commits into from
Aug 13, 2019
Merged

working towards a slice that will work on intervals #261

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f47d4cb
working towards a slice that will work on intervals
andrewkern Jul 11, 2019
abad059
created a numpy implementation of the interval slice with Peter
andrewkern Jul 12, 2019
7db7c72
Add TableCollection.copy()
jeromekelleher Jul 14, 2019
820fa47
Add 'dice' method
jeromekelleher Jul 14, 2019
6df17fc
python version of fast dice
petrelharp Aug 5, 2019
b1c8f0c
Add keep_intervals and delete_intervals.
jeromekelleher Aug 7, 2019
e0b85c9
Move interval and packing code to util.py
jeromekelleher Aug 10, 2019
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3 changes: 1 addition & 2 deletions python/tests/test_genotypes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -410,9 +410,8 @@ def test_jukes_cantor_n20(self):

def test_zero_edge_missing_data(self):
ts = msprime.simulate(10, random_seed=2, mutation_rate=2)
ts = ts.slice(0.25, 0.75, reset_coordinates=False)
tables = ts.tables.keep_intervals([[0.25, 0.75]])
# add some sites in the deleted regions
tables = ts.dump_tables()
tables.sites.add_row(0.1, "A")
tables.sites.add_row(0.2, "A")
tables.sites.add_row(0.8, "A")
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35 changes: 34 additions & 1 deletion python/tests/test_tables.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1600,7 +1600,22 @@ def test_asdict(self):
"provenances": t.provenances.asdict()}
d2 = t.asdict()
self.assertEqual(set(d1.keys()), set(d2.keys()))
# TODO test the fromdict constructor

def test_from_dict(self):
ts = msprime.simulate(10, mutation_rate=1, random_seed=1)
t1 = ts.tables
d = {
"sequence_length": t1.sequence_length,
"individuals": t1.individuals.asdict(),
"populations": t1.populations.asdict(),
"nodes": t1.nodes.asdict(),
"edges": t1.edges.asdict(),
"sites": t1.sites.asdict(),
"mutations": t1.mutations.asdict(),
"migrations": t1.migrations.asdict(),
"provenances": t1.provenances.asdict()}
t2 = tskit.TableCollection.fromdict(d)
self.assertEquals(t1, t2)

def test_iter(self):
def test_iter(table_collection):
Expand All @@ -1621,6 +1636,21 @@ def test_equals_sequence_length(self):
tskit.TableCollection(sequence_length=1),
tskit.TableCollection(sequence_length=2))

def test_copy(self):
pop_configs = [msprime.PopulationConfiguration(5) for _ in range(2)]
migration_matrix = [[0, 1], [1, 0]]
t1 = msprime.simulate(
population_configurations=pop_configs,
migration_matrix=migration_matrix,
mutation_rate=1,
record_migrations=True,
random_seed=100).dump_tables()
t2 = t1.copy()
self.assertIsNot(t1, t2)
self.assertEqual(t1, t2)
t1.edges.clear()
self.assertNotEqual(t1, t2)

def test_equals(self):
pop_configs = [msprime.PopulationConfiguration(5) for _ in range(2)]
migration_matrix = [[0, 1], [1, 0]]
Expand All @@ -1637,6 +1667,9 @@ def test_equals(self):
record_migrations=True,
random_seed=1).dump_tables()
self.assertEqual(t1, t1)
self.assertEqual(t1, t1.copy())
self.assertEqual(t1.copy(), t1)

# The provenances may or may not be equal depending on the clock
# precision for record. So clear them first.
t1.provenances.clear()
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