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  • 3
    Did you code script.py? Why not use os.walk to navigate the directory from within script.py? Commented 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. Commented 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. Commented Aug 14, 2014 at 20:46
  • A tree representing the directory hierarchy would be nice. Commented Aug 14, 2014 at 20:56
  • @Jeff does script.py takes file names or directories? Do .fna and .faa come in pairs? Commented Aug 14, 2014 at 21:48