def test_take(self):
a = np.rec.array(variant_table_data, dtype=variant_table_dtype)
vt = VariantTable(a)
# take variants not in original order
indices = [2, 0]
t = vt.take(indices)
eq(2, t.n_variants)
expect = a.take(indices)
aeq(expect, t)
def filter_phasing(
genotypes_un: allel.GenotypeArray,
variants_un: allel.VariantTable,
window_size: int = 100) -> (allel.GenotypeArray, allel.VariantTable):
""" Filters 'genotypes_un' and 'variants_un' whether there are phasing genotypes.
Parameters:
genotypes_un (allel.GenotypeArray): GenotypeArray object.
variants_un (allel.VariantTable): VariantTable object.
window_size (int): Number of previous heterozygous sites to include when phasing each parent.
Returns:
Tuple (allel.GenotypeArray, allel.VariantTable):
- allel.GenotypeArray: GenotypeArray object
- allel.VariantTable: VariantTable object
"""
# Phasing by transmission
genotypes_phased = allel.phase_by_transmission(genotypes_un,
window_size=window_size)
# locate variants where all genotype calls were phased
np_array_loc_phased_all = np.all(genotypes_phased.is_phased, axis=1)
count_loc_phased_all = np.count_nonzero(np_array_loc_phased_all)
if count_loc_phased_all == 0:
# At least 1 variant could not be phased
logger.warning("Could not find enough phased calls. Using all calls")
return genotypes_phased[:], variants_un
logger.debug("Found {num_phased} phased variant calls".format(
num_phased=count_loc_phased_all))
genotypes_phased_all = genotypes_phased[np_array_loc_phased_all]
variants_un_phased_all = variants_un.compress(np_array_loc_phased_all)
return genotypes_phased_all, variants_un_phased_all
def test_get_item_types(self):
vt = VariantTable(variant_table_data, dtype=variant_table_dtype)
# row slice
s = vt[1:]
assert isinstance(s, VariantTable)
# row index
s = vt[0]
assert isinstance(s, np.record)
assert not isinstance(s, VariantTable)
# col access
s = vt['CHROM']
assert isinstance(s, np.ndarray)
assert not isinstance(s, VariantTable)
s = vt[['CHROM', 'POS']]
assert isinstance(s, VariantTable)
def test_constructor(self):
# missing data arg
with pytest.raises(TypeError):
# noinspection PyArgumentList
VariantTable()
def setup_instance(self, data, index=None, **kwargs):
return VariantTable(data, index=index, **kwargs)
def variants_filter(variants: allel.VariantTable,
filter_expression: str) -> np.ndarray:
variant_selection = variants.eval(filter_expression)
return variant_selection