def _gen_annotation_name_key_pairs(self, annot_field):
# type: (str) -> (str, str)
annotation_names = annotation_parser.extract_annotation_names(
self._header_fields.infos[annot_field][_HeaderKeyConstants.DESC])
for name in annotation_names:
type_key = infer_headers_util.get_inferred_annotation_type_header_key(
annot_field, name)
yield name, type_key
def add_annotation_data(self, proc_var, annotation_field_name, data):
# type: (ProcessedVariant, str, List[str]) -> None
"""The main function for adding annotation data to `proc_var`.
This adds the data for annotation INFO field `annotation_field_name` based
on the format specified for it in the header. `data` items are split
among `proc_var._alternate_datas` based on the ALT matching logic.
The only assumption about `proc_var` is that its `_alternate_datas`
has been initialized with valid `AlternateBaseData` objects.
Args:
proc_var: The object to which the annotations are being added.
annotation_field_name: The name of the annotation field, e.g., ANN or CSQ.
data: The data part of the field separated on comma. A single element
of this list looks something like (taken from an Ensembl VEP run):
G|upstream_gene_variant|MODIFIER|PSMF1|ENSG00000125818|...
where the '|' character is the separator. The first element is a way
to identify the allele (one of the ALTs) that this annotation data
refers to. The rest of the elements are annotations corresponding to the
`annotation_field_name` format description in the header, e.g.,
Allele|Consequence|IMPACT|SYMBOL|Gene|...
"""
alt_list = [a.alternate_bases for a in proc_var._alternate_datas]
parser = annotation_parser.Parser(
proc_var.reference_bases, alt_list,
self._annotation_names_map[annotation_field_name],
self._use_allele_num, self._minimal_match)
for annotation_str in data:
try:
ind, annotation_map = parser.parse_and_match_alt(
annotation_str)
for name, value in annotation_map.items():
if name == annotation_parser.ANNOTATION_ALT:
continue
type_key = infer_headers_util.get_inferred_annotation_type_header_key(
annotation_field_name, name)
vcf_type = self._vcf_type_from_annotation_header(
annotation_field_name, type_key)
typed_value = VCF_TYPE_TO_PY[vcf_type](
value) if value else None
annotation_map[name] = typed_value
self._alt_match_counter.inc()
alt_datas = proc_var._alternate_datas[ind]
if annotation_field_name not in alt_datas._info:
alt_datas._info[annotation_field_name] = [annotation_map]
else:
alt_datas._info[annotation_field_name].append(
annotation_map)
alt_datas.annotation_field_names.add(annotation_field_name)
except annotation_parser.AnnotationParserException as e:
logging.warning(
'Parsing of annotation field %s failed at reference %s start %d: '
'%s', annotation_field_name, proc_var.reference_name,
proc_var.start, str(e))
if isinstance(e, annotation_parser.AnnotationAltNotFound):
self._alt_mismatch_counter.inc()
elif isinstance(e, annotation_parser.AlleleNumMissing):
self._allele_num_missing_counter.inc()
elif isinstance(e, annotation_parser.InvalidAlleleNumValue):
self._allele_num_incorrect_counter.inc()
elif isinstance(e,
annotation_parser.AmbiguousAnnotationAllele):
self._alt_minimal_ambiguous_counter.inc()