sort.py

import os
import csv

original_dir = 'first'
new_dir = 'other'
output_dir = 'output'

for (root, dirs, files) in os.walk(original_dir):
    for filename in files:
        relpath = os.path.join(root, filename)

        doc = {}
        with open(os.path.join(original_dir, relpath), 'r') as csvfile:
            for row in csv.DictReader(csvfile):
                doc[row[0]] = row[1]

        if os.path.exists(os.path.join(new_dir, relpath)):
            with open(os.path.join(new_dir, relpath), 'r') as csvfile:
                for row in csv.DictReader(csvfile):
                    doc[row[0]] = row[1]

        # Write
        output_path = os.path.join(output_dir, relpath)
        print "Would write to", output_path, do