todo.txt

Paper todo:
1) Finalize phylogenetic tree plots  
    I talked to Dave about this.  He thinks that the plots that I have are than they aren't properly bootstrapped.  I'm not sure about what is the best way to bootstrap these trees.  
	One person ISMB suggested that I need an outgroup.  Do you think this is a good idea?
	Another person at ISMB recommended that I use GraPhlAn https://bitbucket.org/nsegata/graphlan/wiki/Home.  It looks like a neat package, but I'll need to evaluate if it is feasible to get results within the next few days
2) Finalize violinplots
3) Generate validation results
   Species comparison between BAGEL and our tool
   Annotation comparision concerning context genes discovered by our tool
4) Draw all operons related to Streptococcus Pyogenes sag operon
5) Draw all operons related to Thermotoga martima (maybe)
6) Draw barplots of operons and their function distributions

Todo:
1) Consider getting rid of protein sequences after the first step of the pipeline
   Only use DNA sequences
   Pros: No six-frame translation BS
         Take advantage of nhmmer speedup
2) Seriously cleanup code
   e.g. genbank.py and genome.py
3) Double check to see if all unittests are working
   Consider installing nosetests
4) Consider making package portable