def __init__(self, config, genomes_db):
super(VariantAnnotatorBase, self).__init__(config, genomes_db)
if self.config.options.vcf:
self.variant_builder = VCFBuilder(self.config,
self.genomic_sequence)
else:
self.variant_builder = DAEBuilder(self.config,
self.genomic_sequence)
if not self.config.virtual_columns:
self.config = GPFConfigParser.modify_tuple(
self.config,
{
"virtual_columns": [
"CSHL_location",
"CSHL_chr",
"CSHL_position",
"CSHL_variant",
"VCF_chr",
"VCF_position",
"VCF_ref",
"VCF_alt",
]
},
)
def _build_annotator_for(self, score_name):
assert os.path.exists(
self.config.options.scores_directory
), self.config.options.scores_directory
score_filename = self._get_score_file(score_name)
options = GPFConfigParser.modify_tuple(
self.config.options, {"scores_file": score_filename}
)
columns = {score_name: getattr(self.config.columns, score_name)}
variant_config = AnnotationConfigParser.parse_section({
"options": options,
"columns": columns,
"annotator": "score_annotator.VariantScoreAnnotator",
"virtual_columns": [],
}
)
annotator = PositionScoreAnnotator(variant_config, self.genomes_db)
return annotator