Python: Failing to open a file using os.system()

You can avoid (potential) problems with quoting, escaping, and so on, with subprocess:

import subprocess

subprocess.call(['pdftk', '1.pdf', '2.pdf', 'cat', 'output', 'result.pdf'])

It's just as easy to use as os.system, and even easier if you are building the argument list dynamically.

You need to set the current working directory of the process. If the .pdf files are located at /some/path/to/pdf/files/:

>>> os.getcwd()
'/home/vz0'
>>> os.chdir('/some/path/to/pdf/files/')