[BioRuby] Bio::Assembly + Ace Parser
chmille4 at gmail.com
Tue Sep 7 23:01:09 EDT 2010
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
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.
- 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
More information about the BioRuby