Hello I have a 1997 Honda civic ex coupe manual trans, my issue is that the power lock won't work and the passenger side window doesn't work either, the only one working is the driver side power window ,but locks and passenger window not working ,I check the fuses and all are good, what could be the problem?

The power source to the door or related wiring is broken open door a black rubber tube covers the wiring into door between hinges that may have come unplugged and the power source can be tested there.

Could be a few things. First is a bad window master switch, when they malfunction they can cause all sorts of non working issues on the windows in the car, also it is likely that the power window motor/assembly has gone bad, electric motors wear over time and if it is only one window this is the most likely cause. Remove the door panel and check for power and ground at the window motor while operating the switch, that will tell you if its a motor or switch issue. Door locks could have bad actuators or a bad switch but most likely a broken power or ground between the door and the body of the car. This area moves each time the door is opened or closed and this can cause wire shorts, especially in older cars. Hope this helps.

Check the switch output in the drivers side door for proper operation of the other doors, windows, and locks. It should control all the windows and locks, you should get the proper control output 12v, and reverse of polarity for up/ down on each window and lock. If not than you have a window lock function switch issue, it keeps passengers from playing with windows and the locks.
If that checks out than go to each door and check for the power and ground at the window motors and door lock servo's
Check for power and ground at each inoperable window motor, you should see the polarity reverse for the up / down operation of the window motor. if there is power than you need a new motor
If you don't get any response from testing for power and ground, you could have a bad switch, or broken wires between the car and the door, test the power supplied to the switch to eliminate possible broken wires. If power is being supplied to the switch than it would be a bad switch, and need replacement.
Expect to find polarity reversing from the lock switch, and if it does send the proper 12 volt signal and reverses polarity, for lock or unlock, than you would need a lock actuator / servo unit in the door.
If you find that you have broken wires between the car and the doors, isolate the old wires or remove them and run new wire through the weather seal / boot, it is much easier than trying to repair the existing wires, and will last for years.
All testing will require a volt /ohm meter, preferably a digital type meter. And I suggest using an automatic battery charger to keep the battery from being drained while diagnosis is being performed.

Most probable cause , ,,, when you open & close the door, the wires in the rubber boot (accordian like) harness in between the door hinges, get cut and will cause alot if issues, without burning a fuse !

Does the passenger window work from the passenger side? If so focus your efforts on the drivers side switches. Remove the drivers switch panel and see if the multi pin plug is secure, next check the cable where it goes through a rubber sleeve from the door post to the door. After main operations of the door sometimes the harness suffers a break. Because the power lock isn't working either I'd start at the drivers side.