diff --git a/src/pheval_exomiser/prepare/create_batch_commands.py b/src/pheval_exomiser/prepare/create_batch_commands.py index f662027..669c4a8 100644 --- a/src/pheval_exomiser/prepare/create_batch_commands.py +++ b/src/pheval_exomiser/prepare/create_batch_commands.py @@ -32,7 +32,7 @@ class ExomiserCommandLineArguments: output_formats: List[str] or None = None -def get_all_files_from_output_opt_directory(output_options_dir: Path) -> list[Path] or None: +def get_all_files_from_output_opt_directory(output_options_dir: Path) -> List[Path] or None: """Obtain all output options files if directory is specified - otherwise returns none.""" return None if output_options_dir is None else all_files(output_options_dir) @@ -46,11 +46,11 @@ def __init__( phenopacket_path: Path, phenopacket: Phenopacket or Family, variant_analysis: bool, - output_options_dir_files: list[Path] or None, + output_options_dir_files: List[Path] or None, output_options_file: Path or None, raw_results_dir: Path or None, analysis_yaml: Path or None, - output_formats: list[Path] or None, + output_formats: List[str] or None, ): self.environment = environment self.phenopacket_path = phenopacket_path @@ -148,8 +148,8 @@ def create_command_arguments( output_options_dir: Path or None = None, output_options_file: Path or None = None, analysis_yaml: Path or None = None, - output_formats: list[Path] or None = None, -) -> list[ExomiserCommandLineArguments]: + output_formats: List[str] or None = None, +) -> List[ExomiserCommandLineArguments]: """Return a list of Exomiser command line arguments for a directory of phenopackets.""" phenopacket_paths = files_with_suffix(phenopacket_dir, ".json") commands = [] @@ -281,7 +281,7 @@ class BatchFileWriter: def __init__( self, - command_arguments_list: list[ExomiserCommandLineArguments], + command_arguments_list: List[ExomiserCommandLineArguments], variant_analysis: bool, output_dir: Path, batch_prefix: str,