import serial
import threading
from queue import Queue

class SerialPort(object):
    def ___init__(self, timeout=None):
        self.ser = serial.Serial(baud=_, stopbits=_, ... timeout=timeout)
        self.out_q = Queue()
        self.in_q = Queue()
        self.THREAD = None

    def setup(self, com):
        self.ser.port = com
        self.ser.open()

    def run(self):
        self.THREAD = threading.Thread(target=self.listen, args=(self.out_q, self.in_q,))
        self.THREAD.start()

    def listen(self, in_q, out_q):
        while True:
            if not in_q.empty():
                # This code is never reached, even though it should be
                message = in_q.get()
                if message == 'DIE':
                    break
                else:
                    self.ser.write(message)

    def send_command(self, command):
        self.in_q.put(command)


class GUI(object):
    def __init__(self):
        self.POWER = False
        self.server_port = SerialPort(timeout=0.1)
        self.client_port = SerialPort(timeout=0.1)
        #etc etc Tkinter stuff and things

    def on_power_button_click(self):
        # Tkinter Button already made, know the button works as expected
        self.POWER = not self.POWER
        if self.POWER:
            self.server_port.setup('COM5')
            self.client_port.setup('COM6')
            self.server_port.run()
            self.client_port.run()
        else:
            self.server_port.send_command('DIE')
            self.client_port.send_command('DIE')
            time.sleep(0.3)
            self.server_port.ser.close()
            self.client_port.ser.close()

my_example_problem = GUI()
# Creates threads and 'turns on' the application
my_example_problem.on_power_button_click()
# Should Turn off the application but doesn't
my_example_problem.on_power_button_click()