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Merged
merged 1 commit into from
Jan 26, 2022
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Add support for reference sequences #59

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2 changes: 2 additions & 0 deletions CHANGELOG.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,8 @@

- Fix for `time_units` in tskit 0.4.0 (benjeffery, #54, #55)

- Add support for reference sequence (benjeffery, #59)

--------------------
[0.2.0] - 2021-11-08
--------------------
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15 changes: 14 additions & 1 deletion tests/test_compression.py
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Expand Up @@ -188,6 +188,19 @@ def test_small_msprime_complex_mutations(self):
)
self.verify(tables.tree_sequence())

def test_ref_seq(self):
ts = msprime.simulate(10, recombination_rate=1, mutation_rate=2, random_seed=2)
tables = ts.tables
tables.reference_sequence.metadata_schema = (
tskit.MetadataSchema.permissive_json()
)
tables.reference_sequence.metadata = {"some": "data"}
tables.reference_sequence.data = "ACTG"
# NOTE: it's unclear whether we'll want to have this set at the same time as
# 'data', but it's useful to have something in all columns for now.
tables.reference_sequence.url = "http://example.com/a_reference"
self.verify(tables.tree_sequence())
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I assume verify calls tables.assert_equals() somewhere along the line? Otherwise we won't actually be testing much here I think.

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I have verified that verify actually verifies. I changed to use assert_equals anyway as it gives better errors.


def test_mutation_parent_example(self):
tables = tskit.TableCollection(1)
tables.nodes.add_row(flags=tskit.NODE_IS_SAMPLE, time=0)
Expand Down Expand Up @@ -263,7 +276,7 @@ def verify(self, ts):
path = pathlib.Path(tmpdir) / "treeseq.tsz"
tszip.compress(ts, path)
other_ts = tszip.decompress(path)
self.assertEqual(ts.tables, other_ts.tables)
ts.tables.assert_equals(other_ts.tables)


class TestMetadata(unittest.TestCase):
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14 changes: 11 additions & 3 deletions tszip/compression.py
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Expand Up @@ -194,7 +194,11 @@ def compress_zarr(ts, root, variants_only=False):

# Schemas, metadata and units need to be converted to arrays
for name in columns:
if name.endswith("metadata_schema") or name == "time_units":
if name.endswith("metadata_schema") or name in [
"time_units",
"reference_sequence/data",
"reference_sequence/url",
]:
columns[name] = np.frombuffer(columns[name].encode("utf-8"), np.int8)
if name.endswith("metadata"):
columns[name] = np.frombuffer(columns[name], np.int8)
Expand Down Expand Up @@ -296,10 +300,15 @@ def decompress_zarr(root):
for sub_key, sub_value in value.items():
if f"{key}/{sub_key}" in quantised_arrays:
dict_repr.setdefault(key, {})[sub_key] = coordinates[sub_value]
elif sub_key.endswith("metadata_schema"):
elif sub_key.endswith("metadata_schema") or (key, sub_key) in [
("reference_sequence", "data"),
("reference_sequence", "url"),
]:
dict_repr.setdefault(key, {})[sub_key] = bytes(sub_value).decode(
"utf-8"
)
elif (key, sub_key) == ("reference_sequence", "metadata"):
dict_repr.setdefault(key, {})[sub_key] = bytes(sub_value)
else:
dict_repr.setdefault(key, {})[sub_key] = sub_value
elif key.endswith("metadata_schema") or key == "time_units":
Expand All @@ -308,7 +317,6 @@ def decompress_zarr(root):
dict_repr[key] = bytes(value)
else:
dict_repr[key] = value

return tskit.TableCollection.fromdict(dict_repr).tree_sequence()


Expand Down