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When using it as a lib you can pass a markdown string (https://github.com/get-alex/alex#markdownvalue-config) or raw text string (https://github.com/get-alex/alex#textvalue-config). This will return an object that should contain everything you need to perform a naive replacement.
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I’m not sure how much my suggestions answer your original question, but in the pursuit of proper grammatical structure when trying to rewrite speech, compromise [0] might be of use to you. I’ve only played around with it for a few hours at most, but from my limited experience it is a very effective (if verbose and/or a little bloated in it’s API) tool for language analysis. With some tomfoolery I’m confident you could combine it with the GP’s recommendation of alexjs to replace strings slightly-less-naively.
https://github.com/spencermountain/compromise
