Even if you need to deal with binary files, most likely they will be of some standard format, e.g. an image, a zip-file, an excel file, etc. For most of the standard formats there are specialized libraries that can read and write them. So you will have high-level abstraction and you won't need to deal with the binary files directly.
Nevertheless it might be useful to take a quick look how binary files can be handled in Perl.
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