Running Python script over multiple directories and multiple files

I think this should help:

The script will use os.walk, as @1_CR suggested, and will call hello_world.py script with the path to both files when fna and faa files exist together (i.e. in same direcotry).

import glob, os

def scanfolder():
    for path, dirs, files in os.walk('/home/shadowe/test1/test1/'):
        flag_faa = 0
        flag_fna = 0
        for f in files:
            if f.endswith('.faa'):
                flag_faa  = 1
                faa_file_path = os.path.join(path,f)
            if f.endswith('.fna'):
                flag_fna = 1
                fna_file_path = os.path.join(path,f)
            if flag_faa == 1 and flag_fna == 1:
                print "Calling script"
                os.system("python hello_world.py" + " -a "+ faa_file_path + " -b " + fna_file_path)
                flag_faa  = 0
                flag_fna  = 0


scanfolder()

Second script:

import sys

print "Hello World"
print "This argument passing qualifies " + sys.argv[1] + " "  + sys.argv[2] + " " + sys.argv[3] + " " + sys.argv[4]

Output:

$ python test.py 
Calling script
Hello World
This argument passing qualifies -a /home/shadowe/test1/test1/test2/test3/two.faa -b     /home/shadowe/test1/test1/test2/test3/two.fna
Calling script
Hello World
This argument passing qualifies -a /home/shadowe/test1/test1/test6/test7/four.faa -b /home/shadowe/test1/test1/test6/test7/five.fna