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.

  • 3
    Did you code script.py? Why not use os.walk to navigate the directory from within script.py?
    – iruvar
    Aug 14, 2014 at 20:23
  • There are over 4000 genomes, each containing 1 or more contigs. would have to use my command line 4000+ times just to get the files i need.
    – Jeff
    Aug 14, 2014 at 20:38
  • 1
    You use both folder and directory in your question. Is there a difference between those two things? If so, what is the difference? Also, please edit your question to include a portion of an example directory structure for us to look at.
    – dg99
    Aug 14, 2014 at 20:46
  • A tree representing the directory hierarchy would be nice. Aug 14, 2014 at 20:56
  • @Jeff does script.py takes file names or directories? Do .fna and .faa come in pairs?
    – Simply_Me
    Aug 14, 2014 at 21:48

1 Answer 1


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


Second script:

import sys

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


$ 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
  • No such file or directory: 'CP003033.faa', is there a way to specify the path?
    – Jeff
    Aug 14, 2014 at 21:46
  • @Jeff is that from your script.py?
    – Simply_Me
    Aug 14, 2014 at 21:47
  • @Jeff do you need to pass file names as well?
    – Simply_Me
    Aug 14, 2014 at 21:47
  • Yes I need to pass in 2 file names.
    – Jeff
    Aug 14, 2014 at 21:48
  • For example: python myscript.py -a .faa -b .fna
    – Jeff
    Aug 14, 2014 at 21:49

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