def test_caching_compression():
vcf_fn = 'fixture/sample.vcf.gz'
cache_fn = vcfnp.array._mk_cache_fn(vcf_fn, array_type='variants',
compress=True)
debug(cache_fn)
if os.path.exists(cache_fn):
os.remove(cache_fn)
a = variants(vcf_fn, cache=True, compress_cache=True, verbose=True)
a2 = np.load(cache_fn)['data']
assert_array_equal(a, a2)
cache_fn = vcfnp.array._mk_cache_fn(vcf_fn, array_type='calldata',
compress=True)
debug(cache_fn)
if os.path.exists(cache_fn):
os.remove(cache_fn)
a = calldata(vcf_fn, cache=True, compress_cache=True, verbose=True)
a2 = np.load(cache_fn)['data']
assert_array_equal(a, a2)
cache_fn = vcfnp.array._mk_cache_fn(vcf_fn, array_type='calldata_2d',
compress=True)
debug(cache_fn)
if os.path.exists(cache_fn):
os.remove(cache_fn)
a = calldata_2d(vcf_fn, cache=True, compress_cache=True, verbose=True)
a2 = np.load(cache_fn)['data']
assert_array_equal(a, a2)
def test_caching_cachedir():
vcf_fn = 'fixture/sample.vcf.gz'
cachedir = 'fixture/custom.vcfnp_cache/foo'
cache_fn = vcfnp.array._mk_cache_fn(vcf_fn, array_type='variants',
cachedir=cachedir)
debug(cache_fn)
if os.path.exists(cache_fn):
os.remove(cache_fn)
a = variants(vcf_fn, cache=True, verbose=True, cachedir=cachedir)
a2 = np.load(cache_fn)
assert_array_equal(a, a2)
cache_fn = vcfnp.array._mk_cache_fn(vcf_fn, array_type='calldata',
cachedir=cachedir)
debug(cache_fn)
if os.path.exists(cache_fn):
os.remove(cache_fn)
a = calldata(vcf_fn, cache=True, verbose=True, cachedir=cachedir)
a2 = np.load(cache_fn)
assert_array_equal(a, a2)
cache_fn = vcfnp.array._mk_cache_fn(vcf_fn, array_type='calldata_2d',
cachedir=cachedir)
debug(cache_fn)
if os.path.exists(cache_fn):
os.remove(cache_fn)
a = calldata_2d(vcf_fn, cache=True, verbose=True, cachedir=cachedir)
a2 = np.load(cache_fn)
assert_array_equal(a, a2)
def test_caching_cachedir():
vcf_fn = 'fixture/sample.vcf.gz'
cachedir = 'fixture/custom.vcfnp_cache/foo'
cache_fn = vcfnp.array._mk_cache_fn(vcf_fn,
array_type='variants',
cachedir=cachedir)
debug(cache_fn)
if os.path.exists(cache_fn):
os.remove(cache_fn)
a = variants(vcf_fn, cache=True, verbose=True, cachedir=cachedir)
a2 = np.load(cache_fn)
assert np.all(a == a2)
cache_fn = vcfnp.array._mk_cache_fn(vcf_fn,
array_type='calldata',
cachedir=cachedir)
debug(cache_fn)
if os.path.exists(cache_fn):
os.remove(cache_fn)
a = calldata(vcf_fn, cache=True, verbose=True, cachedir=cachedir)
a2 = np.load(cache_fn)
assert np.all(a == a2)
cache_fn = vcfnp.array._mk_cache_fn(vcf_fn,
array_type='calldata_2d',
cachedir=cachedir)
debug(cache_fn)
if os.path.exists(cache_fn):
os.remove(cache_fn)
a = calldata_2d(vcf_fn, cache=True, verbose=True, cachedir=cachedir)
a2 = np.load(cache_fn)
assert np.all(a == a2)
def test_caching():
vcf_fn = 'fixture/sample.vcf.gz'
cache_fn = vcfnp.array._mk_cache_fn(vcf_fn, array_type='variants')
debug(cache_fn)
if os.path.exists(cache_fn):
os.remove(cache_fn)
a = variants(vcf_fn, cache=True, verbose=True)
a2 = np.load(cache_fn)
assert np.all(a == a2)
cache_fn = vcfnp.array._mk_cache_fn(vcf_fn, array_type='calldata')
debug(cache_fn)
if os.path.exists(cache_fn):
os.remove(cache_fn)
a = calldata(vcf_fn, cache=True, verbose=True)
a2 = np.load(cache_fn)
assert np.all(a == a2)
cache_fn = vcfnp.array._mk_cache_fn(vcf_fn, array_type='calldata_2d')
debug(cache_fn)
if os.path.exists(cache_fn):
os.remove(cache_fn)
a = calldata_2d(vcf_fn, cache=True, verbose=True)
a2 = np.load(cache_fn)
assert np.all(a == a2)
def test_truncate():
# https://github.com/alimanfoo/vcfnp/issues/54
vcf_fn = 'fixture/test54.vcf.gz'
# truncate by default
v = variants(vcf_fn, region='chr1:10-100')
eq_(2, len(v))
c = calldata(vcf_fn, region='chr1:10-100')
eq_(2, len(c))
c2d = calldata_2d(vcf_fn, region='chr1:10-100')
eq_(2, len(c2d))
# don't truncate
v = variants(vcf_fn, region='chr1:10-100', truncate=False)
eq_(3, len(v))
c = calldata(vcf_fn, region='chr1:10-100', truncate=False)
eq_(3, len(c))
c2d = calldata_2d(vcf_fn, region='chr1:10-100', truncate=False)
eq_(3, len(c2d))
def test_truncate():
# https://github.com/alimanfoo/vcfnp/issues/54
vcf_fn = 'fixture/test54.vcf.gz'
# truncate by default
v = variants(vcf_fn, region='chr1:10-100')
eq_(2, len(v))
c = calldata(vcf_fn, region='chr1:10-100')
eq_(2, len(c))
c2d = calldata_2d(vcf_fn, region='chr1:10-100')
eq_(2, len(c2d))
# don't truncate
v = variants(vcf_fn, region='chr1:10-100', truncate=False)
eq_(3, len(v))
c = calldata(vcf_fn, region='chr1:10-100', truncate=False)
eq_(3, len(c))
c2d = calldata_2d(vcf_fn, region='chr1:10-100', truncate=False)
eq_(3, len(c2d))
def test_genotype_ac():
a = calldata_2d('fixture/test63.vcf',
fields=['GT', 'genotype', 'genotype_ac', 'ploidy'],
ploidy=3, arities=dict(genotype_ac=3))
debug(repr(a))
# check GT
expect = np.array([
[b'0/0', b'0/0/0', b'0'],
[b'1', b'0/1', b'0/1/2'],
[b'././.', b'.', b'./3'],
[b'././.', b'././.', b'././.'],
])
actual = a['GT']
assert_array_equal(expect, actual)
# check genotype
expect = np.array([
[(0, 0, -1), (0, 0, 0), (0, -1, -1)],
[(1, -1, -1), (0, 1, -1), (0, 1, 2)],
[(-1, -1, -1), (-1, -1, -1), (-1, 3, -1)],
[(-1, -1, -1), (-1, -1, -1), (-1, -1, -1)],
])
actual = a['genotype']
assert_array_equal(expect, actual)
# check ploidy
expect = np.array([
[2, 3, 1],
[1, 2, 3],
[3, 1, 2],
[-1, -1, -1],
])
actual = a['ploidy']
assert_array_equal(expect, actual)
# check genotype_ac
expect = np.array([
[(2, 0, 0), (3, 0, 0), (1, 0, 0)],
[(0, 1, 0), (1, 1, 0), (1, 1, 1)],
[(0, 0, 0), (0, 0, 0), (0, 0, 0)],
[(-1, -1, -1), (-1, -1, -1), (-1, -1, -1)],
])
actual = a['genotype_ac']
assert_array_equal(expect, actual)
