All right, so I am positive my Arduino circuit is correct and the code for it. I know this because when I use the serial monitor built into the Arduino IDE and send 'H' an LED lights up, when I send 'L' that LED turns off.
Now I made a Python program
import serial
ser = serial.Serial("COM4",9600)
ser.write("H")
When I run the code the LED blinks on for a second then goes back off. However when I do each of these lines separately in the shell it works just like it is supposed to.
Any ideas?
When you open the serial port, this causes the Arduino to reset. Since the Arduino takes some time to bootup, all the input goes to the bitbucket (or probably to the bootloader which does god knows what with it). If you insert a sleep, you wait for the Arduino to come up so your serial code. This is why it works interactively; you were waiting the 1.5 seconds needed for the software to come up.
I confirmed that opening the serial port resets my Arduino Uno; I flashed a program which will blink the LED from the setup() routine -- calling open("/dev/ttyACM0") was sufficient to trigger the reset. This is IMHO a confusing and undocumented wrinkle in the serial support.
I had the same problem and it works if I add a delay of about 2 seconds from opening the serial connection to writing on it, 1 second was not enough.
Just to make it a bit more clear I'll modify the code so everyone can see what needs to be added!
import serial
import time
ser = serial.Serial("COM4",9600)
time.sleep(3)
ser.write("H")
Adding in a sleep statment helps to let the serial open up without any problems!
The USB port and the Uno serial bus exposed on pins 1 and 0 share the same RX/TX lines. I suggest getting a USB to TTL adapter like the one here so that you can communicate to the Arduino without using the USB port. The Arduino IDE has its own method for disengaging from the USB driver such that a virtual serial port can be created. Have your Ardunio use SoftwareSerial instead.
Here is an example I found on the internet where somebody had clashing bus issues.
