Tried uploading code by repeatedly pressing the reset button everytime the LED flashed(since the previous program was Blink sample code). The Code was successfully uploaded by this process. By making one of the pins of the ATmega high at the beginning of code execution, inverting this signal and connecting it to the reset pin , it was ensured that ATmega 328 was reset everytime control was passed from the bootloader . This signal was given to a reset pin through a switch.Then was done using a relay due to the lack of a npn transistor or an inverter.
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