def test_read_var_length_filters(tmp_path):
uri = os.path.join(tmp_path, 'dataset')
ds = tiledbvcf.Dataset(uri, mode='w')
samples = [
os.path.join(TESTS_INPUT_DIR, s) for s in ['varLenFilter.vcf.gz']
]
ds.ingest_samples(samples)
ds = tiledbvcf.Dataset(uri, mode='r')
df = ds.read(['pos_start', 'filters'])
expected_df = pd.DataFrame({
'pos_start':
pd.Series([
12141, 12546, 13354, 13375, 13396, 13414, 13452, 13520, 13545,
17319, 17480
],
dtype=np.int32),
'filters':
pd.Series(
map(lambda lst: np.array(lst, dtype=np.object),
[['PASS'], ['PASS'], ['ANEUPLOID', 'LowQual'], ['PASS'],
['PASS'], ['ANEUPLOID', 'LOWQ', 'LowQual'], ['PASS'],
['PASS'], ['PASS'], ['LowQual'], ['PASS']]))
})
_check_dfs(expected_df, df)
def test_read_multiple_alleles(tmp_path):
uri = os.path.join(tmp_path, "dataset")
ds = tiledbvcf.Dataset(uri, mode="w")
samples = [os.path.join(TESTS_INPUT_DIR, s) for s in ["small3.bcf", "small.bcf"]]
ds.create_dataset()
ds.ingest_samples(samples)
ds = tiledbvcf.Dataset(uri, mode="r")
df = ds.read(
attrs=["sample_name", "pos_start", "alleles", "id", "filters"],
regions=["1:70100-1300000"],
)
expected_df = pd.DataFrame(
{
"sample_name": pd.Series(["HG00280", "HG00280"]),
"pos_start": pd.Series([866511, 1289367], dtype=np.int32),
"alleles": pd.Series(
map(
lambda lst: np.array(lst, dtype=np.object),
[["T", "CCCCTCCCT", "C", "CCCCTCCCTCCCT", "CCCCT"], ["CTG", "C"]],
)
),
"id": pd.Series([".", "rs1497816"]),
"filters": pd.Series(
map(
lambda lst: np.array(lst, dtype=np.object),
[["LowQual"], ["LowQual"]],
)
),
}
).sort_values(ignore_index=True, by=["sample_name", "pos_start"])
_check_dfs(
expected_df, df.sort_values(ignore_index=True, by=["sample_name", "pos_start"])
)
def test_sample_and_region_partitioned_read():
uri = os.path.join(TESTS_INPUT_DIR, 'arrays/v3/ingested_2samples')
cfg = tiledbvcf.ReadConfig(region_partition=(0, 2),
sample_partition=(0, 2))
ds = tiledbvcf.Dataset(uri, mode='r', cfg=cfg)
df = ds.read(attrs=['sample_name', 'pos_start', 'pos_end'],
regions=['1:12000-13000', '1:17000-18000'])
assert len(df) == 2
assert (df.sample_name == 'HG00280').all()
cfg = tiledbvcf.ReadConfig(region_partition=(0, 2),
sample_partition=(1, 2))
ds = tiledbvcf.Dataset(uri, mode='r', cfg=cfg)
df = ds.read(attrs=['sample_name', 'pos_start', 'pos_end'],
regions=['1:12000-13000', '1:17000-18000'])
assert len(df) == 2
assert (df.sample_name == 'HG01762').all()
cfg = tiledbvcf.ReadConfig(region_partition=(1, 2),
sample_partition=(0, 2))
ds = tiledbvcf.Dataset(uri, mode='r', cfg=cfg)
df = ds.read(attrs=['sample_name', 'pos_start', 'pos_end'],
regions=['1:12000-13000', '1:17000-18000'])
assert len(df) == 2
assert (df.sample_name == 'HG00280').all()
cfg = tiledbvcf.ReadConfig(region_partition=(1, 2),
sample_partition=(1, 2))
ds = tiledbvcf.Dataset(uri, mode='r', cfg=cfg)
df = ds.read(attrs=['sample_name', 'pos_start', 'pos_end'],
regions=['1:12000-13000', '1:17000-18000'])
assert len(df) == 0
def test_read_multiple_alleles(tmp_path):
uri = os.path.join(tmp_path, 'dataset')
ds = tiledbvcf.Dataset(uri, mode='w')
samples = [
os.path.join(TESTS_INPUT_DIR, s) for s in ['small3.bcf', 'small.bcf']
]
ds.ingest_samples(samples)
ds = tiledbvcf.Dataset(uri, mode='r')
df = ds.read(
attrs=['sample_name', 'pos_start', 'alleles', 'id', 'filters'],
regions=['1:70100-1300000'])
expected_df = pd.DataFrame({
'sample_name':
pd.Series(['HG00280', 'HG00280']),
'pos_start':
pd.Series([866511, 1289367], dtype=np.int32),
'alleles':
pd.Series(
map(lambda lst: np.array(lst, dtype=np.object),
[['T', 'CCCCTCCCT', 'C', 'CCCCTCCCTCCCT', 'CCCCT'],
['CTG', 'C']])),
'id':
pd.Series(['.', 'rs1497816']),
'filters':
pd.Series(
map(lambda lst: np.array(lst, dtype=np.object),
[['LowQual'], ['LowQual']]))
})
_check_dfs(expected_df, df)
def test_region_partitioned_read():
uri = os.path.join(TESTS_INPUT_DIR, "arrays/v3/ingested_2samples")
cfg = tiledbvcf.ReadConfig(region_partition=(0, 2))
ds = tiledbvcf.Dataset(uri, mode="r", cfg=cfg)
df = ds.read(
attrs=["sample_name", "pos_start", "pos_end"],
regions=["1:12000-13000", "1:17000-18000"],
)
assert len(df) == 4
cfg = tiledbvcf.ReadConfig(region_partition=(1, 2))
ds = tiledbvcf.Dataset(uri, mode="r", cfg=cfg)
df = ds.read(
attrs=["sample_name", "pos_start", "pos_end"],
regions=["1:12000-13000", "1:17000-18000"],
)
assert len(df) == 2
# Too many partitions still produces results
cfg = tiledbvcf.ReadConfig(region_partition=(1, 3))
ds = tiledbvcf.Dataset(uri, mode="r", cfg=cfg)
df = ds.read(
attrs=["sample_name", "pos_start", "pos_end"],
regions=["1:12000-13000", "1:17000-18000"],
)
assert len(df) == 2
# Error: index >= num partitions
cfg = tiledbvcf.ReadConfig(region_partition=(2, 2))
with pytest.raises(RuntimeError):
ds = tiledbvcf.Dataset(uri, mode="r", cfg=cfg)
def test_sample_partitioned_read():
uri = os.path.join(TESTS_INPUT_DIR, "arrays/v3/ingested_2samples")
cfg = tiledbvcf.ReadConfig(sample_partition=(0, 2))
ds = tiledbvcf.Dataset(uri, mode="r", cfg=cfg)
df = ds.read(attrs=["sample_name", "pos_start", "pos_end"],
regions=["1:12000-18000"])
assert len(df) == 11
assert (df.sample_name == "HG00280").all()
cfg = tiledbvcf.ReadConfig(sample_partition=(1, 2))
ds = tiledbvcf.Dataset(uri, mode="r", cfg=cfg)
df = ds.read(attrs=["sample_name", "pos_start", "pos_end"],
regions=["1:12000-18000"])
assert len(df) == 3
assert (df.sample_name == "HG01762").all()
# Error: too many partitions
cfg = tiledbvcf.ReadConfig(sample_partition=(1, 3))
ds = tiledbvcf.Dataset(uri, mode="r", cfg=cfg)
with pytest.raises(RuntimeError):
df = ds.read(attrs=["sample_name", "pos_start", "pos_end"],
regions=["1:12000-18000"])
# Error: index >= num partitions
cfg = tiledbvcf.ReadConfig(sample_partition=(2, 2))
with pytest.raises(RuntimeError):
ds = tiledbvcf.Dataset(uri, mode="r", cfg=cfg)
def test_tbb_threads_config():
uri = os.path.join(TESTS_INPUT_DIR, "arrays/v3/ingested_2samples")
cfg = tiledbvcf.ReadConfig(tiledb_config=["sm.num_tbb_threads=3"])
ds = tiledbvcf.Dataset(uri, mode="r", cfg=cfg)
cfg = tiledbvcf.ReadConfig(tiledb_config=["sm.num_tbb_threads=4"])
with pytest.raises(RuntimeError):
ds = tiledbvcf.Dataset(uri, mode="r", cfg=cfg)
def test_incremental_ingest(tmp_path):
uri = os.path.join(tmp_path, 'dataset')
ds = tiledbvcf.Dataset(uri, mode='w')
ds.ingest_samples([os.path.join(TESTS_INPUT_DIR, 'small.bcf')])
ds.ingest_samples([os.path.join(TESTS_INPUT_DIR, 'small2.bcf')])
# Open it back in read mode and check some queries
ds = tiledbvcf.Dataset(uri, mode='r')
assert ds.count() == 14
assert ds.count(regions=['1:12700-13400']) == 6
assert ds.count(samples=['HG00280'], regions=['1:12700-13400']) == 4
def test_incremental_ingest(tmp_path):
uri = os.path.join(tmp_path, "dataset")
ds = tiledbvcf.Dataset(uri, mode="w")
ds.create_dataset()
ds.ingest_samples([os.path.join(TESTS_INPUT_DIR, "small.bcf")])
ds.ingest_samples([os.path.join(TESTS_INPUT_DIR, "small2.bcf")])
# Open it back in read mode and check some queries
ds = tiledbvcf.Dataset(uri, mode="r")
assert ds.count() == 14
assert ds.count(regions=["1:12700-13400"]) == 6
assert ds.count(samples=["HG00280"], regions=["1:12700-13400"]) == 4
def test_read_var_length_filters(tmp_path):
uri = os.path.join(tmp_path, "dataset")
ds = tiledbvcf.Dataset(uri, mode="w")
samples = [
os.path.join(TESTS_INPUT_DIR, s) for s in ["varLenFilter.vcf.gz"]
]
ds.create_dataset()
ds.ingest_samples(samples)
ds = tiledbvcf.Dataset(uri, mode="r")
df = ds.read(["pos_start", "filters"])
expected_df = pd.DataFrame({
"pos_start":
pd.Series(
[
12141,
12546,
13354,
13375,
13396,
13414,
13452,
13520,
13545,
17319,
17480,
],
dtype=np.int32,
),
"filters":
pd.Series(
map(
lambda lst: np.array(lst, dtype=np.object),
[
["PASS"],
["PASS"],
["ANEUPLOID", "LowQual"],
["PASS"],
["PASS"],
["ANEUPLOID", "LOWQ", "LowQual"],
["PASS"],
["PASS"],
["PASS"],
["LowQual"],
["PASS"],
],
)),
}).sort_values(ignore_index=True, by=["pos_start"])
_check_dfs(expected_df, df.sort_values(ignore_index=True,
by=["pos_start"]))
def test_read_config():
uri = os.path.join(TESTS_INPUT_DIR, 'arrays/v3/ingested_2samples')
cfg = tiledbvcf.ReadConfig()
ds = tiledbvcf.Dataset(uri, mode='r', cfg=cfg)
cfg = tiledbvcf.ReadConfig(
memory_budget_mb=512,
region_partition=(0, 3),
tiledb_config=['sm.tile_cache_size=0', 'sm.num_reader_threads=1'])
ds = tiledbvcf.Dataset(uri, mode='r', cfg=cfg)
with pytest.raises(TypeError):
cfg = tiledbvcf.ReadConfig(abc=123)
def test_basic_ingest(tmp_path):
# Create the dataset
uri = os.path.join(tmp_path, "dataset")
ds = tiledbvcf.Dataset(uri, mode="w")
samples = [os.path.join(TESTS_INPUT_DIR, s) for s in ["small.bcf", "small2.bcf"]]
ds.create_dataset()
ds.ingest_samples(samples)
# Open it back in read mode and check some queries
ds = tiledbvcf.Dataset(uri, mode="r")
assert ds.count() == 14
assert ds.count(regions=["1:12700-13400"]) == 6
assert ds.count(samples=["HG00280"], regions=["1:12700-13400"]) == 4
def test_read_null_attrs(tmp_path):
uri = os.path.join(tmp_path, 'dataset')
ds = tiledbvcf.Dataset(uri, mode='w')
samples = [
os.path.join(TESTS_INPUT_DIR, s) for s in ['small3.bcf', 'small.bcf']
]
ds.ingest_samples(samples)
ds = tiledbvcf.Dataset(uri, mode='r')
df = ds.read(attrs=[
'sample_name', 'pos_start', 'pos_end', 'info_BaseQRankSum', 'info_DP',
'fmt_DP', 'fmt_MIN_DP'
],
regions=['1:12700-13400', '1:69500-69800'])
expected_df = pd.DataFrame({
'sample_name':
pd.Series([
'HG00280', 'HG01762', 'HG00280', 'HG01762', 'HG00280', 'HG00280',
'HG00280', 'HG00280', 'HG00280', 'HG00280', 'HG00280', 'HG00280'
]),
'pos_start':
pd.Series([
12546, 12546, 13354, 13354, 13375, 13396, 69371, 69511, 69512,
69761, 69762, 69771
],
dtype=np.int32),
'pos_end':
pd.Series([
12771, 12771, 13374, 13389, 13395, 13413, 69510, 69511, 69760,
69761, 69770, 69834
],
dtype=np.int32),
'info_BaseQRankSum':
pd.Series([
None, None, None, None, None, None, None,
np.array([-0.787], dtype=np.float32), None,
np.array([1.97], dtype=np.float32), None, None
]),
'info_DP':
pd.Series([
None, None, None, None, None, None, None,
np.array([89], dtype=np.int32), None,
np.array([24], dtype=np.int32), None, None
]),
'fmt_DP':
pd.Series([0, 0, 15, 64, 6, 2, 180, 88, 97, 24, 23, 21],
dtype=np.int32),
'fmt_MIN_DP':
pd.Series([0, 0, 14, 30, 3, 1, 20, None, 24, None, 23, 19])
})
_check_dfs(expected_df, df)
def test_basic_ingest(tmp_path):
# Create the dataset
uri = os.path.join(tmp_path, 'dataset')
ds = tiledbvcf.Dataset(uri, mode='w')
samples = [
os.path.join(TESTS_INPUT_DIR, s) for s in ['small.bcf', 'small2.bcf']
]
ds.ingest_samples(samples)
# Open it back in read mode and check some queries
ds = tiledbvcf.Dataset(uri, mode='r')
assert ds.count() == 14
assert ds.count(regions=['1:12700-13400']) == 6
assert ds.count(samples=['HG00280'], regions=['1:12700-13400']) == 4
def test_read_write_mode_exceptions():
ds = tiledbvcf.Dataset(
os.path.join(TESTS_INPUT_DIR, 'arrays/v3/ingested_2samples'))
samples = [
os.path.join(TESTS_INPUT_DIR, s) for s in ['small.bcf', 'small2.bcf']
]
with pytest.raises(Exception):
ds.ingest_samples(samples)
ds = tiledbvcf.Dataset(os.path.join(TESTS_INPUT_DIR,
'arrays/v3/ingested_2samples'),
mode='w')
with pytest.raises(Exception):
ds.count()
def test_read_config():
uri = os.path.join(TESTS_INPUT_DIR, "arrays/v3/ingested_2samples")
cfg = tiledbvcf.ReadConfig()
ds = tiledbvcf.Dataset(uri, mode="r", cfg=cfg)
cfg = tiledbvcf.ReadConfig(
memory_budget_mb=512,
region_partition=(0, 3),
tiledb_config=["sm.tile_cache_size=0", "sm.compute_concurrency_level=1"],
)
ds = tiledbvcf.Dataset(uri, mode="r", cfg=cfg)
with pytest.raises(TypeError):
cfg = tiledbvcf.ReadConfig(abc=123)
def test_ingest_merging_separate(tmp_path):
# Create the dataset
uri = os.path.join(tmp_path, "dataset_merging_separate")
ds = tiledbvcf.Dataset(uri, mode="w")
samples = [
os.path.join(TESTS_INPUT_DIR, s) for s in ["v2-DjrIAzkP-downsampled.vcf.gz"]
]
ds.create_dataset()
ds.ingest_samples(samples, contigs_to_keep_separate=["chr1"])
# Open it back in read mode and check some queries
ds = tiledbvcf.Dataset(uri, mode="r")
assert ds.count() == 246
assert ds.count(regions=["chrX:9032893-9032893"]) == 1
def test_read_write_mode_exceptions():
ds = tiledbvcf.Dataset(os.path.join(TESTS_INPUT_DIR, "arrays/v3/ingested_2samples"))
samples = [os.path.join(TESTS_INPUT_DIR, s) for s in ["small.bcf", "small2.bcf"]]
with pytest.raises(Exception):
ds.create_dataset()
with pytest.raises(Exception):
ds.ingest_samples(samples)
ds = tiledbvcf.Dataset(
os.path.join(TESTS_INPUT_DIR, "arrays/v3/ingested_2samples"), mode="w"
)
with pytest.raises(Exception):
ds.count()
def test_incomplete_reads():
# Using undocumented "0 MB" budget to test incomplete reads.
uri = os.path.join(TESTS_INPUT_DIR, "arrays/v3/ingested_2samples")
cfg = tiledbvcf.ReadConfig(memory_budget_mb=0)
test_ds = tiledbvcf.Dataset(uri, mode="r", cfg=cfg)
df = test_ds.read(attrs=["pos_end"], regions=["1:12700-13400"])
assert not test_ds.read_completed()
assert len(df) == 2
_check_dfs(
pd.DataFrame.from_dict(
{"pos_end": np.array([12771, 12771], dtype=np.int32)}),
df,
)
df = test_ds.continue_read()
assert not test_ds.read_completed()
assert len(df) == 2
_check_dfs(
pd.DataFrame.from_dict(
{"pos_end": np.array([13374, 13389], dtype=np.int32)}),
df,
)
df = test_ds.continue_read()
assert test_ds.read_completed()
assert len(df) == 2
_check_dfs(
pd.DataFrame.from_dict(
{"pos_end": np.array([13395, 13413], dtype=np.int32)}),
df,
)
def test_large_export_correctness():
uri = "s3://tiledb-inc-demo-data/tiledbvcf-arrays/v4/vcf-samples-20"
ds = tiledbvcf.Dataset(uri, mode="r", verbose=True)
df = ds.read(
attrs=[
"sample_name",
"contig",
"pos_start",
"pos_end",
"query_bed_start",
"query_bed_end",
],
samples=["v2-DjrIAzkP", "v2-YMaDHIoW", "v2-usVwJUmo", "v2-ZVudhauk"],
bed_file=os.path.join(
TESTS_INPUT_DIR, "E001_15_coreMarks_dense_filtered.bed.gz"
),
)
# total number of exported records
assert df.shape[0] == 1172081
# number of unique exported records
record_index = ["sample_name", "contig", "pos_start"]
assert df[record_index].drop_duplicates().shape[0] == 1168430
def test_read_limit():
uri = os.path.join(TESTS_INPUT_DIR, 'arrays/v3/ingested_2samples')
cfg = tiledbvcf.ReadConfig(limit=3)
ds = tiledbvcf.Dataset(uri, mode='r', cfg=cfg)
df = ds.read(
attrs=['sample_name', 'pos_start', 'pos_end', 'fmt_DP', 'fmt_PL'],
regions=['1:12100-13360', '1:13500-17350'])
assert len(df) == 3
def test_read_limit():
uri = os.path.join(TESTS_INPUT_DIR, "arrays/v3/ingested_2samples")
cfg = tiledbvcf.ReadConfig(limit=3)
ds = tiledbvcf.Dataset(uri, mode="r", cfg=cfg)
df = ds.read(
attrs=["sample_name", "pos_start", "pos_end", "fmt_DP", "fmt_PL"],
regions=["1:12100-13360", "1:13500-17350"],
)
assert len(df) == 3
def test_sample_and_region_partitioned_read():
uri = os.path.join(TESTS_INPUT_DIR, "arrays/v3/ingested_2samples")
cfg = tiledbvcf.ReadConfig(region_partition=(0, 2),
sample_partition=(0, 2))
ds = tiledbvcf.Dataset(uri, mode="r", cfg=cfg)
df = ds.read(
attrs=["sample_name", "pos_start", "pos_end"],
regions=["1:12000-13000", "1:17000-18000"],
)
assert len(df) == 2
assert (df.sample_name == "HG00280").all()
cfg = tiledbvcf.ReadConfig(region_partition=(0, 2),
sample_partition=(1, 2))
ds = tiledbvcf.Dataset(uri, mode="r", cfg=cfg)
df = ds.read(
attrs=["sample_name", "pos_start", "pos_end"],
regions=["1:12000-13000", "1:17000-18000"],
)
assert len(df) == 2
assert (df.sample_name == "HG01762").all()
cfg = tiledbvcf.ReadConfig(region_partition=(1, 2),
sample_partition=(0, 2))
ds = tiledbvcf.Dataset(uri, mode="r", cfg=cfg)
df = ds.read(
attrs=["sample_name", "pos_start", "pos_end"],
regions=["1:12000-13000", "1:17000-18000"],
)
assert len(df) == 2
assert (df.sample_name == "HG00280").all()
cfg = tiledbvcf.ReadConfig(region_partition=(1, 2),
sample_partition=(1, 2))
ds = tiledbvcf.Dataset(uri, mode="r", cfg=cfg)
df = ds.read(
attrs=["sample_name", "pos_start", "pos_end"],
regions=["1:12000-13000", "1:17000-18000"],
)
assert len(df) == 0
def test_ingest_disable_merging(tmp_path):
# Create the dataset
uri = os.path.join(tmp_path, "dataset_disable_merging")
cfg = tiledbvcf.ReadConfig(memory_budget_mb=1024)
attrs = ["sample_name", "contig", "pos_start", "pos_end"]
ds = tiledbvcf.Dataset(uri, mode="w")
samples = [
os.path.join(TESTS_INPUT_DIR, s) for s in ["v2-DjrIAzkP-downsampled.vcf.gz"]
]
ds.create_dataset()
ds.ingest_samples(samples, contig_fragment_merging=False)
# Open it back in read mode and check some queries
ds = tiledbvcf.Dataset(uri, cfg=cfg, mode="r", verbose=False)
df = ds.read(attrs=attrs)
assert ds.count() == 246
assert ds.count(regions=["chrX:9032893-9032893"]) == 1
# Create the dataset
uri = os.path.join(tmp_path, "dataset_merging_separate")
ds2 = tiledbvcf.Dataset(uri, mode="w", verbose=True)
samples = [
os.path.join(TESTS_INPUT_DIR, s) for s in ["v2-DjrIAzkP-downsampled.vcf.gz"]
]
ds2.create_dataset()
ds2.ingest_samples(samples, contigs_to_keep_separate=["chr1"])
# Open it back in read mode and check some queries
ds2 = tiledbvcf.Dataset(uri, cfg=cfg, mode="r", verbose=True)
df2 = ds2.read(attrs=attrs)
print(df.equals(df2))
assert df.equals(df2)
assert ds.count() == 246
assert ds.count(regions=["chrX:9032893-9032893"]) == 1
def test_incomplete_reads():
# Using undocumented "0 MB" budget to test incomplete reads.
uri = os.path.join(TESTS_INPUT_DIR, 'arrays/v3/ingested_2samples')
cfg = tiledbvcf.ReadConfig(memory_budget_mb=0)
test_ds = tiledbvcf.Dataset(uri, mode='r', cfg=cfg)
expected_df = pd.DataFrame(
{'sample_name': pd.Series(
['HG00280', 'HG01762', 'HG00280', 'HG01762', 'HG00280',
'HG01762', 'HG00280', 'HG00280', 'HG00280', 'HG00280',
'HG00280', 'HG00280', 'HG00280', 'HG00280']),
'pos_start': pd.Series(
[12141, 12141, 12546, 12546, 13354, 13354, 13375, 13396,
13414, 13452, 13520, 13545, 17319, 17480], dtype=np.int32),
'pos_end': pd.Series(
[12277, 12277, 12771, 12771, 13374, 13389, 13395, 13413,
13451, 13519, 13544, 13689, 17479, 17486], dtype=np.int32)})
# Region partitions
dask_df = test_ds.read_dask(attrs=['sample_name', 'pos_start', 'pos_end'],
region_partitions=10)
df = dask_df.compute()
_check_dfs(expected_df, df)
# Sample partitions (we have to sort to check the result)
dask_df = test_ds.read_dask(attrs=['sample_name', 'pos_start', 'pos_end'],
sample_partitions=2)
df = dask_df.compute().sort_values('sample_name').reset_index(drop=True)
_check_dfs(expected_df.sort_values('sample_name').reset_index(drop=True),
df)
# Both
dask_df = test_ds.read_dask(attrs=['sample_name', 'pos_start', 'pos_end'],
region_partitions=10, sample_partitions=2)
df = dask_df.compute().sort_values('sample_name').reset_index(drop=True)
_check_dfs(expected_df.sort_values('sample_name').reset_index(drop=True),
df)
# No partitioning
dask_df = test_ds.read_dask(attrs=['sample_name', 'pos_start', 'pos_end'])
df = dask_df.compute()
_check_dfs(expected_df, df)
# Subset of partitions (limit_partitions)
dask_df = test_ds.read_dask(attrs=['sample_name', 'pos_start', 'pos_end'],
region_partitions=10, sample_partitions=2,
limit_partitions=2)
assert dask_df.npartitions == 2
def test_map_incomplete():
# Using undocumented "0 MB" budget to test incomplete reads.
uri = os.path.join(TESTS_INPUT_DIR, 'arrays/v3/ingested_2samples')
cfg = tiledbvcf.ReadConfig(memory_budget_mb=0)
test_ds = tiledbvcf.Dataset(uri, mode='r', cfg=cfg)
expected_df = pd.DataFrame(
{'sample_name': pd.Series(['HG00280', 'HG01762']),
'pos_start': pd.Series([12141, 12141], dtype=np.int32),
'pos_end': pd.Series([12277, 12277], dtype=np.int32)})
# Region partitions
dask_df = test_ds.map_dask(lambda df: df[df.pos_start * 2 < 25000],
attrs=['sample_name', 'pos_start', 'pos_end'],
region_partitions=10)
df = dask_df.compute()
_check_dfs(expected_df, df)
def test_incomplete_read_generator():
# Using undocumented "0 MB" budget to test incomplete reads.
uri = os.path.join(TESTS_INPUT_DIR, 'arrays/v3/ingested_2samples')
cfg = tiledbvcf.ReadConfig(memory_budget_mb=0)
test_ds = tiledbvcf.Dataset(uri, mode='r', cfg=cfg)
overall_df = None
for df in test_ds.read_iter(attrs=['pos_end'], regions=['1:12700-13400']):
if overall_df is None:
overall_df = df
else:
overall_df = overall_df.append(df, ignore_index=True)
assert len(overall_df) == 6
_check_dfs(
pd.DataFrame.from_dict({
'pos_end':
np.array([12771, 12771, 13374, 13389, 13395, 13413],
dtype=np.int32)
}), overall_df)
def test_map_incomplete():
# Using undocumented "0 MB" budget to test incomplete reads.
uri = os.path.join(TESTS_INPUT_DIR, "arrays/v3/ingested_2samples")
cfg = tiledbvcf.ReadConfig(memory_budget_mb=0)
test_ds = tiledbvcf.Dataset(uri, mode="r", cfg=cfg)
expected_df = pd.DataFrame({
"sample_name":
pd.Series(["HG00280", "HG01762"]),
"pos_start":
pd.Series([12141, 12141], dtype=np.int32),
"pos_end":
pd.Series([12277, 12277], dtype=np.int32),
})
# Region partitions
dask_df = test_ds.map_dask( # pylint:disable=no-member
lambda df: df[df.pos_start * 2 < 25000],
attrs=["sample_name", "pos_start", "pos_end"],
region_partitions=10,
) # pylint:disable=no-member
df = dask_df.compute()
_check_dfs(expected_df, df)
def test_read_null_attrs(tmp_path):
uri = os.path.join(tmp_path, "dataset")
ds = tiledbvcf.Dataset(uri, mode="w")
samples = [
os.path.join(TESTS_INPUT_DIR, s) for s in ["small3.bcf", "small.bcf"]
]
ds.create_dataset()
ds.ingest_samples(samples)
ds = tiledbvcf.Dataset(uri, mode="r")
df = ds.read(
attrs=[
"sample_name",
"pos_start",
"pos_end",
"info_BaseQRankSum",
"info_DP",
"fmt_DP",
"fmt_MIN_DP",
],
regions=["1:12700-13400", "1:69500-69800"],
)
expected_df = pd.DataFrame({
"sample_name":
pd.Series([
"HG00280",
"HG00280",
"HG00280",
"HG00280",
"HG01762",
"HG01762",
"HG00280",
"HG00280",
"HG00280",
"HG00280",
"HG00280",
"HG00280",
]),
"pos_start":
pd.Series(
[
12546,
13354,
13375,
13396,
12546,
13354,
69371,
69511,
69512,
69761,
69762,
69771,
],
dtype=np.int32,
),
"pos_end":
pd.Series(
[
12771,
13374,
13395,
13413,
12771,
13389,
69510,
69511,
69760,
69761,
69770,
69834,
],
dtype=np.int32,
),
"info_BaseQRankSum":
pd.Series([
None,
None,
None,
None,
None,
None,
None,
np.array([-0.787], dtype=np.float32),
None,
np.array([1.97], dtype=np.float32),
None,
None,
]),
"info_DP":
pd.Series([
None,
None,
None,
None,
None,
None,
None,
np.array([89], dtype=np.int32),
None,
np.array([24], dtype=np.int32),
None,
None,
]),
"fmt_DP":
pd.Series([0, 15, 6, 2, 0, 64, 180, 88, 97, 24, 23, 21],
dtype=np.int32),
"fmt_MIN_DP":
pd.Series([0, 14, 3, 1, 0, 30, 20, None, 24, None, 23, 19]),
}).sort_values(ignore_index=True, by=["sample_name", "pos_start"])
_check_dfs(
expected_df,
df.sort_values(ignore_index=True, by=["sample_name", "pos_start"]))
def test_ds_attrs():
return tiledbvcf.Dataset(
os.path.join(TESTS_INPUT_DIR, "arrays/v3/ingested_2samples_GT_DP_PL"))
