def set_info(variant, field_name, value, vcf_object=None):
"""Sets a field of the info map of the `Variant` to the given value(s).
`variant.info` is analogous to the INFO field of a VCF record.
Args:
variant: Variant proto. The Variant to modify.
field_name: str. The name of the field to set.
value: A single value or list of values to update the Variant with. The type
of the value is determined by the `vcf_object` if one is given, otherwise
is looked up based on the reserved INFO fields in the VCF specification.
vcf_object: (Optional) nucleus.io.vcf.Vcf{Reader,Writer}. If not None, the
type of the field is inferred from the associated VcfReader or VcfWriter
based on its name. Otherwise, the type is inferred if it is a reserved
field.
"""
if vcf_object is None:
set_field_fn = vcf_constants.reserved_info_field_set_fn(field_name)
else:
set_field_fn = vcf_object.field_access_cache.info_field_set_fn(field_name)
set_field_fn(variant.info, field_name, value)
def test_invalid_reserved_info_field_set_fn(self, field):
with self.assertRaisesRegexp(ValueError,
'Unknown reserved INFO field:'):
vcf_constants.reserved_info_field_set_fn(field)
def test_reserved_info_field_set_fn(self, field, expected):
actual = vcf_constants.reserved_info_field_set_fn(field)
self.assertIs(actual, expected)
def test_invalid_reserved_info_field_set_fn(self, field):
with self.assertRaisesRegexp(ValueError, 'Unknown reserved INFO field:'):
vcf_constants.reserved_info_field_set_fn(field)
def test_reserved_info_field_set_fn(self, field, expected): actual = vcf_constants.reserved_info_field_set_fn(field) self.assertIs(actual, expected)