chpasswd -R /path/to/build/tree <passwords.txt

root:swordfish
alibaba:opensesame

#!/usr/bin/python
import base64, crypt, os, re, sys
for line in sys.stdin.readlines():
    (username, password) = line.strip().split(":")
    salt = "$6$" + base64.b64encode(os.urandom(6))
    hashes[username] = crypt.crypt(password, salt)
old_shadow = open("etc/shadow")
new_shadow = open("etc/shadow.making", "w")
for line in old_shadow.readlines():
    (username, password, trail) = line.lstrip().split(":", 3)
    if hashes.has_key(username):
        line = username + ":" + hashes[username] + ":" + trail
    new_shadow.write(line)
old_shadow.close()
new_shadow.close()
os.rename("etc/shadow.making", "etc/shadow")