autoflake can now do this with the --expand-star-imports option, provided

• There is only 1 wilcard import in the Python file
• There is no use of __all__ or del in the Python file

So you could do something like

autoflake --expand-star-imports --remove-all-unused-imports --in-place --exclude "__init__.py"  my-python-project/*.py

Ref. https://pypi.org/project/autoflake/