def get_class_status(self, info_field):
"""Extract class status from nucleus.protos.Variant.info.
Args:
info_field: INFO field of nucleus.protos.Variant proto to extract
the classes status from. Must contain `info_field_name` field which is
set to one of self.classes_dict.keys().
Returns:
string. Class status. Has to be one of the keys of `classes_dict`.
Raises:
ValueError: if type is missing in info_field
ValueError: if type is not in self.classes_dict.keys()
"""
if self.info_field_name not in info_field.keys():
raise ValueError("Cannot create class labels: " +
"VCF file does not contain INFO/{} field".format(
self.info_field_name))
class_status = struct_utils.get_string_field(info_field,
self.info_field_name,
True)
if class_status not in self.classes_dict.keys():
raise ValueError("class_status status unknown: {}. "
"Known status: {}".format(
class_status, self.classes_dict.keys()))
return class_status
def test_get_string_field(self, value, is_single_field, expected):
key = 'field'
field_map = _set_protomap_from_dict({})
struct_utils.set_string_field(field_map, key, value)
actual = struct_utils.get_string_field(field_map, key, is_single_field)
self.assertEqual(actual, expected)