Relationalizing Nexus files with Ruby and mx

Ok, so "relationalizing" isn't really a word, but I kind of like how it sounds. For the past couple of weeks I've been writing a Mesquite (i.e. Nexus) file parser in Ruby. It uses the same basic lexer/parser engine that reads Newick formatted trees that I mentioned in a previous post to create a Ruby Nexus file object, with all the good bits (well most of them, some blocks are not parsed yet, but that's just a matter of extending the parser) easily accessible from the object. With this Nexus file object it was relatively trivial to write a conversion to mx (see fig.), i.e. a fully relational format.

The Ruby file parsing code is currently a plugin/library in the mx source, it can be easily extracted for use in other projects. Look for the code in mx 0.2.1540 and onwards when it makes it to Sourceforge, or contact me directly if you're really keen to get your hands on it.