def test_load_expand():
expand = ['gt_types', 'gt_ref_depths', 'gt_alt_depths']
v = VCFDB(vcf, db, ped, expand=expand)
eng = sql.create_engine(get_dburl(db))
metadata = sql.MetaData(bind=eng)
metadata.reflect()
for e in expand:
yield check_expanded_length, metadata, e
yield check_expanded_columns, metadata, e
def test_load_expand():
expand = ['gt_types', 'gt_ref_depths', 'gt_alt_depths']
v = VCFDB(vcf, db, ped, expand=expand)
eng = sql.create_engine(get_dburl(db))
metadata = sql.MetaData(bind=eng)
metadata.reflect()
for e in expand:
yield check_expanded_length, metadata, e
yield check_expanded_columns, metadata, e
def test_load():
v = VCFDB(vcf, db, ped)
eng = sql.create_engine(get_dburl(db))
metadata = sql.MetaData(bind=eng)
metadata.reflect()
res, = next(iter(eng.execute("select count(*) from variants")))
assert res == n_variants, res
assert "variants" in metadata.tables
assert "variant_impacts" in metadata.tables
assert "samples" in metadata.tables
assert "vcf_header" in metadata.tables
yield check_header, metadata
yield check_samples, metadata
yield check_variants, metadata
yield check_aaf, metadata
def test_extra_impacts():
db = "tests/xx-impacts.db"
impacts_extras = ["MQ", "QD", "HRun", "M-CAP_pred"]
v = VCFDB(vcf, db, ped, impacts_extras=impacts_extras)
eng = sql.create_engine(get_dburl(db))
metadata = sql.MetaData(bind=eng)
metadata.reflect()
yield check_header, metadata
yield check_samples, metadata
yield check_variants, metadata
yield check_aaf, metadata
yield check_cap, metadata
vi = metadata.tables["variant_impacts"]
ixs = list(map(clean, impacts_extras))
# check that all of the impacts_extras are in the variant_impacts table.
cs = {c.name: c for c in vi.columns}
for c in ixs:
assert c in cs
