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I found myself in position where I need to render 6(or more) layers in different order. For example in 1,2,3,4,5,6 then 4,2,1,3,5,6 and so on. Some of the layers blend with the former or later one. It would be great If I could predetermine the order without actually doing it manually every time.

Basically move the layers up and down in the timeline panel and set their starting point.

Can I do that using some programming tools? If so, what do I need to learn? And in general, what properties of After Effects project can be edited without opening the application itself and edit project manually?

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To my knowledge there is no tool available for editing After Effects project files other than After Effects itself.

However you can script After Effect using Adobe's Extendscript language, so that it will work without user interaction, and even without showing the GUI. Extendscript is based on ECMAscript (basically it's Javascript) and allows you to do programatically anything you can do with the GUI app. It not only works in After Effects , but can be used to control most of the other Adobe CC apps.

The extendscript documentation for After Effects is here, and the docs for the more general Javascript tools including GUI elements available across the other Adobe applications is here.

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