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urx is a python library to control a robot from 'Universal robot'. It has currently been used with several versions of UR5.
Both the 'secondary port' interface and the real-time/matlab interface of the UR controller are used. 
urx can optionally use the python-math3d https://launchpad.net/pymath3d library to receive and send transformation matrices to the robot

Example use:

import urx

rob = urx.robot("192.168.0.100")
rob.set_tcp((0, 0, 0.1, 0, 0, 0))
rob.set_payload(2, (0, 0, 0.1))
rob.movej((1, 2, 3, 4, 5, 6), a, v) 
rob.movel((x, y, z, rx, ry, rz), a, v)
print "Current tool pose is: ",  rob.getl()
rob.movel((0.1, 0, 0, 0, 0, 0), a, v, relative=true)# move relative to current pose
rob.translate((0.1, 0, 0), a, v) #move tool and keep orientation
rob.orient((0.1, 0, 0), a, v) #orient tool and keep tool tip position
rob.stopj(a)

robot.movel(x, y, z, rx, ry, rz), wait=False)
while True :
    sleep(0.1) #sleep first since the information may be outdated
    if robot.is_program_running():
        break

robot.movel(x, y, z, rx, ry, rz), wait=False)
while.robot.getForce() < 50:
    sleep(0.01)
    if not robot.is_program_running():
        break
robot.stopl()

try:
    robot.movel((0,0,0.1,0,0,0), relative=True)
except RobotError, ex:
    print "Robot could not execute move (emergency stop for example), do something", ex

Using matrices:

robot = Robot("192.168.1.1")
robot.set_tcp((0,0,0.23,0,0,0)
calib = mathd3d.Transform() 
calib.orient.rotate_zb(pi/4) #just an example
robot.add_csys("mycsys", calib) #set robot corrdinate system
robot.set_default_csys("mycsys")
trans = robot.get_transform() # get current transformation matrix (tool to base)
trans.orient.rotate_yt(pi/2)
robot.apply_transform(trans)
trans.pos += math3d.Vector(0,0,0.3)
robot.apply_transform(trans)


#or only work with orientation part
o = robot.get_orientation()
o.rotate_yb(pi)
robot.orient(o)