def test_DP_field(shared_datadir, tmpdir):
fields = [
"variants/CHROM",
"variants/POS",
"variants/ID",
"variants/REF",
"variants/ALT",
"calldata/GT",
"samples",
# extra
"calldata/DP",
"variants/DP",
]
types = {"calldata/DP": "i4"} # override default of i2
allel_vcfzarr_path = create_allel_vcfzarr(shared_datadir,
tmpdir,
fields=fields,
types=types)
allel_ds = sg.read_vcfzarr(allel_vcfzarr_path)
sg_vcfzarr_path = create_sg_vcfzarr(shared_datadir,
tmpdir,
fields=["INFO/DP", "FORMAT/DP"])
sg_ds = sg.load_dataset(str(sg_vcfzarr_path))
sg_ds = sg_ds.drop_vars(
"call_genotype_phased") # not included in scikit-allel
assert_identical(allel_ds, sg_ds)
def test_read_vcfzarr(shared_datadir, tmpdir):
vcfzarr_path = create_vcfzarr(shared_datadir,
tmpdir) # type: ignore[no-untyped-call]
ds = read_vcfzarr(vcfzarr_path)
assert ds.attrs["contigs"] == ["19", "20", "X"]
assert_array_equal(ds["variant_contig"], [0, 0, 1, 1, 1, 1, 1, 1, 2])
assert_array_equal(
ds["variant_position"],
[111, 112, 14370, 17330, 1110696, 1230237, 1234567, 1235237, 10],
)
assert_array_equal(
ds["variant_allele"],
[
["A", "C", "", ""],
["A", "G", "", ""],
["G", "A", "", ""],
["T", "A", "", ""],
["A", "G", "T", ""],
["T", "", "", ""],
["G", "GA", "GAC", ""],
["T", "", "", ""],
["AC", "A", "ATG", "C"],
],
)
assert_array_equal(
ds["variant_id"],
[
".", ".", "rs6054257", ".", "rs6040355", ".", "microsat1", ".",
"rsTest"
],
)
assert_array_equal(
ds["variant_id_mask"],
[True, True, False, True, False, True, False, True, False],
)
assert_array_equal(ds["sample_id"], ["NA00001", "NA00002", "NA00003"])
call_genotype = np.array(
[
[[0, 0], [0, 0], [0, 1]],
[[0, 0], [0, 0], [0, 1]],
[[0, 0], [1, 0], [1, 1]],
[[0, 0], [0, 1], [0, 0]],
[[1, 2], [2, 1], [2, 2]],
[[0, 0], [0, 0], [0, 0]],
[[0, 1], [0, 2], [-1, -1]],
[[0, 0], [0, 0], [-1, -1]],
[[0, -1], [0, 1], [0, 2]],
],
dtype="i1",
)
assert_array_equal(ds["call_genotype"], call_genotype)
assert_array_equal(ds["call_genotype_mask"], call_genotype < 0)
assert "call_genotype_phased" not in ds
def test_default_fields(shared_datadir, tmpdir):
allel_vcfzarr_path = create_allel_vcfzarr(shared_datadir, tmpdir)
allel_ds = sg.read_vcfzarr(allel_vcfzarr_path)
sg_vcfzarr_path = create_sg_vcfzarr(shared_datadir, tmpdir)
sg_ds = sg.load_dataset(str(sg_vcfzarr_path))
sg_ds = sg_ds.drop_vars(
"call_genotype_phased") # not included in scikit-allel
assert_identical(allel_ds, sg_ds)
def test_all_fields(shared_datadir, tmpdir, vcf_file, allel_exclude_fields,
sgkit_exclude_fields):
# change scikit-allel type defaults back to the VCF default
types = {
"calldata/DP": "i4",
"calldata/GQ": "i4",
"calldata/HQ": "i4",
"calldata/AD": "i4",
}
allel_vcfzarr_path = create_allel_vcfzarr(
shared_datadir,
tmpdir,
vcf_file=vcf_file,
fields=["*"],
exclude_fields=allel_exclude_fields,
types=types,
)
field_defs = {
"INFO/AF": {
"Number": "A"
},
"INFO/AC": {
"Number": "A"
},
"FORMAT/AD": {
"Number": "R"
},
"FORMAT/HQ": {
"dimension": "haplotypes"
},
"FORMAT/SB": {
"dimension": "strand_biases"
},
}
allel_ds = sg.read_vcfzarr(allel_vcfzarr_path, field_defs=field_defs)
sg_vcfzarr_path = create_sg_vcfzarr(
shared_datadir,
tmpdir,
vcf_file=vcf_file,
fields=["INFO/*", "FORMAT/*"],
exclude_fields=sgkit_exclude_fields,
field_defs=field_defs,
truncate_calls=True,
)
sg_ds = sg.load_dataset(str(sg_vcfzarr_path))
sg_ds = sg_ds.drop_vars(
"call_genotype_phased") # not included in scikit-allel
# scikit-allel only records contigs for which there are actual variants,
# whereas sgkit records contigs from the header
allel_ds_contigs = set(allel_ds.attrs["contigs"])
sg_ds_contigs = set(sg_ds.attrs["contigs"])
assert allel_ds_contigs <= sg_ds_contigs
del allel_ds.attrs["contigs"]
del sg_ds.attrs["contigs"]
if allel_ds_contigs < sg_ds_contigs:
# variant_contig variables are not comparable, so remove them before comparison
del allel_ds["variant_contig"]
del sg_ds["variant_contig"]
assert_identical(allel_ds, sg_ds)