Copy of RTL text puts characters in wrong order


I am trying to convert a pdf document in Persian to html. I have done this before in Notepad++ that has a toggle between rtl and ltr text. But if I copy the text from the document into Atom it puts the charac.
ters in the reverse order.
So if I type a word like like word it comes out looking like drow.
Is there some setting that can rectify this?