for eachFile in glob(args.path + "/*/*.json"): <- this seems dangerous. Better way?
  # do something to the json file

  # output the modified data to its new home
  #outfile = os.path.join(args.output, os.path.dirname(eachFile), eachFile) <- doesn't work
  outfile = os.path.join(args.putout, os.path.dirname(eachFile)[1:], eachFile)

# Recurse and process files.
import os
import sys
from fnmatch import fnmatch
import shutil


def process(src_dir, dst_dir, pattern='*'):
    """Iterate through src_dir, processing all files that match pattern and
    store them, including their parent directories in dst_dir.
    """
    assert src_dir != dst_dir, 'Source and destination dir must differ.'
    for dirpath, dirnames, filenames in os.walk(src_dir):
        # Filter out files that match pattern only.
        filenames = filter(lambda fname: fnmatch(fname, pattern), filenames)

        if filenames:
            dir_ = os.path.join(dst_dir, dirpath)
            os.makedirs(dir_)
            for fname in filenames:
                in_fname = os.path.join(dirpath, fname)
                out_fname = os.path.join(dir_, fname)

                # At this point, the destination directory is created and you
                # have a valid input / output filename, so you'd call your
                # function to process these files.  I just copy them :D
                shutil.copyfile(in_fname, out_fname)

if __name__ == '__main__':
    process(sys.argv[1], sys.argv[2], '*.txt')