I have a device which connects to its remote using rj45 port and 4 wire cable (a desk with adjustable height). I'm pretty sure it does not actually use an Ethernet protocol and uses sends some simple digital signals. I want to Raspberry Pi to be able to control the device, so I was wondering if it is possible to read and dump and then send signals using Ethernet port just like I can do with any other pins? Probably the actual question here is about a way to bypass Ethernet driver in Linux OS.
Reading signals on ethernet port directly with RaspberryPi
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This won't work. The Ethernet NIC on the RPi - just like any other NIC - can only receive Ethernet frames. Anything else needs to be connected over GPIO.
Edit: As NO-OP has reasonably pointed out, the signals may need to be made compatible with the GPIO pins - levels adjusted, maybe an opto-isolator here and there. Nothing expensive though usually. For controlling powered devices you likely need a driver or relais board - there are plenty around for the RPi.