The short answer is yes, it can be done in any programming language. Basic steps: Convert your HTML to XHTML (+ CSS). This can be done in your program or through an XSLT file. Copy your files (XHTML, CSS, any images and fonts) into a directory structure that follows the format. Zip the directory structure …
Pandoc supports conversion from Latex to e-Pub. The chances are high that it doesn’t handle your Latex documents completely, but it should help with the conversion process. Pandoc has converted Tex formulae to Mathml; I don’t know how good that conversion is since I haven’t used it.
The EPUB format brings together a bunch of different specifications / formats: one to say what the content of the book should look like (a subset of XHTML 1.1 + CSS) one to define a “manifest” that lists all of the files that make up that content (OPF, which is an XML file) one to …