def import_sequence_dataset(params: dict, dataset_name: str) -> RepertoireDataset:
base_result_path = params['result_path'] + "tmp_airr/"
unzipped_path = base_result_path + "tmp_unzipped/"
IReceptorImport._unzip_files(params['path'], unzipped_path, unzip_metadata=False)
airr_params = copy.deepcopy(params)
airr_params["path"] = unzipped_path
dataset = ImportHelper.import_dataset(AIRRImport, airr_params, dataset_name)
shutil.rmtree(unzipped_path)
return dataset
def import_repertoire_dataset(params: dict, dataset_name: str) -> RepertoireDataset:
base_result_path = params['result_path'] + "tmp_airr/"
metadata_file_path = base_result_path + "metadata.csv"
IReceptorImport._create_airr_repertoiredataset(params['path'], base_result_path, metadata_file_path)
airr_params = copy.deepcopy(params)
airr_params["path"] = base_result_path
airr_params["metadata_file"] = metadata_file_path
dataset = ImportHelper.import_dataset(AIRRImport, airr_params, dataset_name)
shutil.rmtree(base_result_path)
return dataset
def import_dataset(params: dict, dataset_name: str) -> Dataset:
return ImportHelper.import_dataset(AIRRImport, params, dataset_name)
def import_dataset(params: dict, dataset_name: str) -> Dataset:
return ImportHelper.import_dataset(TenxGenomicsImport, params,
dataset_name)
def import_dataset(params: dict, dataset_name: str) -> Dataset:
return ImportHelper.import_dataset(ImmunoSEQRearrangementImport, params, dataset_name)
def import_dataset(params: dict, dataset_name: str) -> Dataset:
return ImportHelper.import_dataset(ImmunoSEQSampleImport, params,
dataset_name)