Yet another DNA manipulation package, except this one does exactly what I want
DNAssembly is a framework that lets you do your cloning as you would in the wet lab, but on your computer. In place of colorless liquids in test tubes, DNAssembly will take your plasmid files in your favorite format (Genbank, Snapgene) and run them through an assembly protocol to produce fully annotated cloning products. All input sequences are verified to avoid common cloning pitfalls.
DNAssembly is initially implemented to perform Modular Golden Gate Cloning as described in "A Highly Characterized Yeast Toolkit for Modular, Multipart Assembly" (Lee et al. 2013).