Running Python script over multiple directories and multiple files

Here is my command line for python: python script.py -a .faa -n .fna I have a directory containing multiple directories. Out of these multiple directories, there could be 1 or more folders. In these 1 or more folders, I need to run my python script on the .faa and .fna files. How do I do this? Example tree:

Staph1 ----> [CO1, CO2] ----> [.fna, .faa] from CO1, [.fna, .faa] from CO2

Staph2 ----> [CO6] ----> [.fna, .faa] from CO6

My Python script will use the inputs .fna and .faa and output within the folder. Also the folder and directory are synonymous.