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()
def handle(self, *args, **options):
_custom_annotator = CustomAnnotator(settings.CUSTOM_ANNOTATOR_SETTINGS)
_custom_annotator.load()
