alleleTools.argtypes module

Custom argument types for argparse validation. It validates file paths, output paths and specific file formats.

alleleTools.argtypes.check_dir_writable(directory: str) → None[source]

Check if a directory is writable and valid.

Parameters:: directory (str) – The directory path to check.
Raises:: argparse.ArgumentTypeError – If the directory does not exist, is not writable, or is not a directory.

alleleTools.argtypes.csv_file(in_string: str) → str[source]

Validate that a CSV file exists and has the correct extension.

Parameters:: in_string (str) – The CSV file path to validate.
Returns:: The validated CSV file path string.
Return type:: str
Raises:: argparse.ArgumentTypeError – If the file doesn’t exist, is not a file, or doesn’t have a .csv extension.

Example

>>> csv_file("/path/to/data.csv")
"/path/to/data.csv"

alleleTools.argtypes.file_path(in_string: str) → str[source]

Validate that a file exists and is actually a file (not a directory).

Parameters:: in_string (str) – The file path to validate.
Returns:: The validated file path string.
Return type:: str
Raises:: argparse.ArgumentTypeError – If the path doesn’t exist or is not a file.

Example

>>> file_path("/path/to/existing_file.txt")
"/path/to/existing_file.txt"

alleleTools.argtypes.output_path(in_string: str) → str[source]

Validate that the output directory exists and the file doesn’t already exist.

Parameters:: in_string (str) – The output file path to validate.
Returns:: The validated output path string.
Return type:: str
Raises:: argparse.ArgumentTypeError – If the parent directory doesn’t exist or if the file already exists.

Example

>>> output_path("/existing/dir/new_file.txt")
"/existing/dir/new_file.txt"

alleleTools.argtypes.path(in_string: str) → str[source]

Validate that a given path exists.

Example

>>> path("/existing/path")
"/existing/path"