def handle(self, *args, **options): if settings.CUSTOM_ANNOTATOR_SETTINGS is not None: print("Load dbNSFP.. ") # note that you could use mall.get_custom_annotator() here too custom_annotator = CustomAnnotator(settings.CUSTOM_ANNOTATOR_SETTINGS) custom_annotator.load() get_reference().load() mall.get_annotator().load()
def handle(self, *args, **options): if settings.CUSTOM_ANNOTATOR_SETTINGS is not None: print("Load dbNSFP.. ") # note that you could use mall.get_custom_annotator() here too custom_annotator = CustomAnnotator( settings.CUSTOM_ANNOTATOR_SETTINGS) custom_annotator.load() get_reference().load() mall.get_annotator().load()
def get_custom_annotator(): global _custom_annotator # custom annotator can be None if _custom_annotator is None and settings.CUSTOM_ANNOTATOR_SETTINGS: _custom_annotator = CustomAnnotator(settings.CUSTOM_ANNOTATOR_SETTINGS) return _custom_annotator
} except Exception as e: print("\nWARNING: unable to parse predictors from vep fields: %s. %s" % (vep_fields, e)) return {} return annotations_dict if __name__ == '__main__': parser = argparse.ArgumentParser() parser.add_argument('command') parser.add_argument('--settings') parser.add_argument('--vcf_file_list') parser.add_argument('--custom_annotator_settings') args = parser.parse_args() annotator_settings = imp.load_source('annotator_settings', args.settings) custom_annotator = None if args.custom_annotator_settings: custom_annotator_settings = imp.load_source( 'custom_annotation_settings', args.custom_annotator_settings) custom_annotator = CustomAnnotator(custom_annotator_settings) annotator = VariantAnnotator(annotator_settings, custom_annotator=custom_annotator) if args.command == 'load': annotator.load() if args.command == 'add_vcf_files': vcf_file_paths = [l.strip() for l in open(args.vcf_file_list)] for vcf_path in vcf_file_paths: annotator.add_vcf_file_to_annotator(vcf_path)
def handle(self, *args, **options): _custom_annotator = CustomAnnotator(settings.CUSTOM_ANNOTATOR_SETTINGS) _custom_annotator.load()