Python path-breaking script for use in R
Always throw things in main:

def main():
    # code

main()


It might seem pointless but it does help with preventing global pollution, which is good if you ever decide to add a function somewhere.

Using

x = sys.argv[1]


is acceptable for a trivial script, but it's not much harder to use docopt and implement a proper command-line parser:

"""
Name Of Program.

Usage: prog.py &lt;pathname&gt;
"""

import docopt

def main():
    args = docopt.docopt(__doc__)

    x = args["&lt;pathname&gt;"]


Trivial, but it gives you --help, error reporting and sane handling of bad input, nearly for free.

This can be simplified a little with pathlib:

parts = pathlib.PurePosixPath(args["&lt;pathname&gt;"]).parts

if len(parts) &gt;= 2 and parts[0] == "/":
    parts = ("/" + parts[1],) + parts[2:]


You can actually use just pathlib.Path but it may assume a Windows format on Windows machines.

Your quoting:

parts = ["'" + i + "'" for i in parts]


should be done with repr:

parts = map(repr, parts)


and the formatting should use .format:

res = "file.path({})".format(",\n    ".join(parts))


This gives

#!/usr/bin/env python3

"""
Name Of Program.

Usage: prog.py &lt;pathname&gt;
"""

import docopt
import pathlib

def main():
    args = docopt.docopt(__doc__)
    parts = pathlib.PurePosixPath(args["&lt;pathname&gt;"]).parts

    if len(parts) &gt;= 2 and parts[0] == "/":
        parts = ("/" + parts[1],) + parts[2:]

    args = ",\n    ".join(map(repr, parts))
    print("file.path({})".format(args))

main()


Technically PEP 8 says docopt should be separated from pathlib, the second being in the stdlib, but it looks nicer this way for now.