[BioRuby] Bio::Assembly + Ace Parser

[Chase Miller]

Hi All

I finally got around to doing this and have written a simple Bio::Assembly
class with a streaming ace parser.   As part of this, I have
Bio::Assembly::Contig and Bio::Assembly::Read classes.  The general flow
goes like this - a Bio::Assembly object relates to a single ace file and is
made up of Bio::Assembly::Contig objects, which are in turn made up of
Bio::Assembly::Read objects.

It probably needs a bit more work (see TODO below), but I thought I'd go
ahead and get some feedback. Take a look and let me know what you think.

http://github.com/chmille4/bioruby


TODO:

   - Currently, the ace parser is integrated into bio/assembly.rb, but I'd
   like to extract this out to make it easier to support more file formats.
    Any ideas on a good (bioruby) way to do this?
   - Flesh out the features.  Any requests?
   - Add more tests (8 so far in test/unit/bio/test_assembly.rb)
   - Make sure that manipulating Bio::Assembly objects ( i.e deleting
   contigs ) does not the cause the ace unparser to create illegal ace files.
   - Add more documentation


Cheers!
Chase