I Own A 99 Civic Ex,

One Morning I Woke Up To My Battery Dead, A Little Confused A Charged It And It Was Fine,
Got Into The Car, And The Dome Light Wouldn't Go Off (It Was In The Door Position), So
I Turned It To The Off Position, And All's Well. The I Put My Key In The Ignition And Its Beeping At
Me Like I Have My Door Open, I Put The Car In Accessory, And It Beeps The Same, Until I Put The Car
Into Run, Then It Stops. Also When I Have My Lights On And My Cars Off It Will Beep At Me Like Again My
Doors Open, But Its Definately Closed....So I'm Not Quite Sure Where To Begin To Look...

 

check the button on the door frames, im not sure if they are n/o or n/c but check to see that there is a change in continuity when you push it, then i would check the wiring, maby a wire broke or the insulation rubed off, and is shorting on the frame

 

Get an amp meter, hook it up to the battery. Take the key out. See what the meter says. If the meter shows a current draw, pull fuses one by one until the draw goes away. Once you find the fuse that causes the current draw to go away, look at the circuit that the fuse is a part of and check to make sure nothing is malfunctioning.