def test_region_partition_large_region(vcf_variants_loaders, temp_dirname):
fvars = vcf_variants_loaders("backends/partition")[0]
partition_desc = ParquetPartitionDescriptor(["1", "2"],
10000000,
root_dirname=temp_dirname)
parquet_writer = VariantsParquetWriter(fvars, partition_desc)
assert parquet_writer is not None
parquet_writer.write_dataset()
assert os.path.exists(os.path.join(temp_dirname, "region_bin=1_0"))
assert os.path.exists(os.path.join(temp_dirname, "region_bin=2_0"))
assert os.path.exists(
os.path.join(temp_dirname,
"region_bin=1_0/variants_region_bin_1_0.parquet"))
assert os.path.exists(
os.path.join(temp_dirname,
"region_bin=2_0/variants_region_bin_2_0.parquet"))
def test_region_partition_small_region(vcf_variants_loaders, temp_dirname):
fvars = vcf_variants_loaders("backends/partition")[0]
partition_desc = ParquetPartitionDescriptor(["1", "2"],
10,
root_dirname=temp_dirname)
parquet_writer = VariantsParquetWriter(fvars, partition_desc)
assert parquet_writer is not None
parquet_writer.write_dataset()
assert os.path.exists(os.path.join(temp_dirname, "region_bin=1_86558"))
assert os.path.exists(os.path.join(temp_dirname, "region_bin=1_86562"))
assert os.path.exists(os.path.join(temp_dirname, "region_bin=1_86566"))
assert os.path.exists(os.path.join(temp_dirname, "region_bin=1_86569"))
assert os.path.exists(os.path.join(temp_dirname, "region_bin=1_87810"))
assert os.path.exists(os.path.join(temp_dirname, "region_bin=1_90192"))
assert os.path.exists(os.path.join(temp_dirname, "region_bin=1_90595"))
assert os.path.exists(os.path.join(temp_dirname, "region_bin=1_122251"))
assert os.path.exists(os.path.join(temp_dirname, "region_bin=2_86558"))
assert os.path.exists(os.path.join(temp_dirname, "region_bin=2_86562"))
assert os.path.exists(os.path.join(temp_dirname, "region_bin=2_86566"))
assert os.path.exists(os.path.join(temp_dirname, "region_bin=2_86569"))
assert os.path.exists(os.path.join(temp_dirname, "region_bin=2_87810"))
assert os.path.exists(os.path.join(temp_dirname, "region_bin=2_90192"))
assert os.path.exists(os.path.join(temp_dirname, "region_bin=2_90595"))
assert os.path.exists(os.path.join(temp_dirname, "region_bin=2_122251"))
assert os.path.exists(
os.path.join(
temp_dirname,
"region_bin=1_90595/variants_region_bin_1_90595.parquet",
))
assert os.path.exists(
os.path.join(
temp_dirname,
"region_bin=2_122251/variants_region_bin_2_122251.parquet",
))
def test_region_family_frequency(vcf_variants_loaders, temp_dirname):
fvars = vcf_variants_loaders("backends/partition")[0]
temp_dirname = temp_dirname
partition_desc = ParquetPartitionDescriptor(
["1", "2"],
100000,
family_bin_size=100,
rare_boundary=30,
root_dirname=temp_dirname,
)
parquet_writer = VariantsParquetWriter(fvars, partition_desc)
assert parquet_writer is not None
parquet_writer.write_dataset()
assert os.path.exists(
os.path.join(
temp_dirname,
"region_bin=1_8",
"frequency_bin=2",
"family_bin=6",
))
assert os.path.exists(
os.path.join(
temp_dirname,
"region_bin=1_8",
"frequency_bin=2",
"family_bin=69",
))
assert os.path.exists(
os.path.join(
temp_dirname,
"region_bin=1_9",
"frequency_bin=2",
"family_bin=6",
))
assert os.path.exists(
os.path.join(
temp_dirname,
"region_bin=1_9",
"frequency_bin=2",
"family_bin=69",
))
assert os.path.exists(
os.path.join(
temp_dirname,
"region_bin=1_12",
"frequency_bin=3",
"family_bin=6",
))
assert os.path.exists(
os.path.join(
temp_dirname,
"region_bin=1_12",
"frequency_bin=3",
"family_bin=69",
))
assert os.path.exists(
os.path.join(
temp_dirname,
"region_bin=2_8",
"frequency_bin=2",
"family_bin=6",
))
assert os.path.exists(
os.path.join(
temp_dirname,
"region_bin=2_8",
"frequency_bin=2",
"family_bin=69",
))
assert os.path.exists(
os.path.join(
temp_dirname,
"region_bin=2_9",
"frequency_bin=2",
"family_bin=6",
))
assert os.path.exists(
os.path.join(
temp_dirname,
"region_bin=2_9",
"frequency_bin=2",
"family_bin=69",
))
assert os.path.exists(
os.path.join(
temp_dirname,
"region_bin=2_12",
"frequency_bin=3",
"family_bin=6",
))
assert os.path.exists(
os.path.join(
temp_dirname,
"region_bin=2_12",
"frequency_bin=3",
"family_bin=69",
))
assert os.path.exists(
os.path.join(
temp_dirname,
"region_bin=1_9",
"frequency_bin=2",
"family_bin=6",
"variants_region_bin_1_9_frequency_bin_2_family_bin_6.parquet",
))
assert os.path.exists(
os.path.join(
temp_dirname,
"region_bin=2_12",
"frequency_bin=3",
"family_bin=6",
"variants_region_bin_2_12_frequency_bin_3_family_bin_6.parquet",
))
def test_all(vcf_variants_loaders, temp_dirname):
fvars = vcf_variants_loaders("backends/partition")[0]
partition_desc = ParquetPartitionDescriptor(
["1", "2"],
100000,
family_bin_size=100,
coding_effect_types=[
"missense",
"nonsense",
"frame-shift",
"synonymous",
],
rare_boundary=30,
root_dirname=temp_dirname,
)
parquet_writer = VariantsParquetWriter(fvars, partition_desc)
assert parquet_writer is not None
parquet_writer.write_dataset()
assert os.path.exists(
os.path.join(
temp_dirname,
"region_bin=1_8",
"frequency_bin=2",
"coding_bin=1",
"family_bin=6",
))
assert os.path.exists(
os.path.join(
temp_dirname,
"region_bin=1_8",
"frequency_bin=2",
"coding_bin=1",
"family_bin=69",
))
assert os.path.exists(
os.path.join(
temp_dirname,
"region_bin=1_9",
"frequency_bin=2",
"coding_bin=1",
"family_bin=6",
))
assert os.path.exists(
os.path.join(
temp_dirname,
"region_bin=1_9",
"frequency_bin=2",
"coding_bin=1",
"family_bin=69",
))
assert os.path.exists(
os.path.join(
temp_dirname,
"region_bin=1_12",
"frequency_bin=3",
"coding_bin=1",
"family_bin=6",
))
assert os.path.exists(
os.path.join(
temp_dirname,
"region_bin=1_12",
"frequency_bin=3",
"coding_bin=1",
"family_bin=69",
))
assert os.path.exists(
os.path.join(
temp_dirname,
"region_bin=2_8",
"frequency_bin=2",
"coding_bin=0",
"family_bin=6",
))
assert os.path.exists(
os.path.join(
temp_dirname,
"region_bin=2_8",
"frequency_bin=2",
"coding_bin=0",
"family_bin=69",
))
assert os.path.exists(
os.path.join(
temp_dirname,
"region_bin=2_9",
"frequency_bin=2",
"coding_bin=0",
"family_bin=6",
))
assert os.path.exists(
os.path.join(
temp_dirname,
"region_bin=2_9",
"frequency_bin=2",
"coding_bin=0",
"family_bin=69",
))
assert os.path.exists(
os.path.join(
temp_dirname,
"region_bin=2_12",
"frequency_bin=3",
"coding_bin=0",
"family_bin=6",
))
assert os.path.exists(
os.path.join(
temp_dirname,
"region_bin=2_12",
"frequency_bin=3",
"coding_bin=0",
"family_bin=69",
))
assert os.path.exists(
os.path.join(
temp_dirname,
"region_bin=1_9",
"frequency_bin=2",
"coding_bin=1",
"family_bin=6",
"variants_region_bin_1_9_frequency_bin_2_coding_bin_1"
"_family_bin_6.parquet",
))
assert os.path.exists(
os.path.join(
temp_dirname,
"region_bin=2_12",
"frequency_bin=3",
"coding_bin=0",
"family_bin=6",
"variants_region_bin_2_12_frequency_bin_3_coding_bin_0"
"_family_bin_6.parquet",
))