weiju/cmonkey-python — pull request #8 by jashworth-isb (2012-03-30 23:24:24+00:00)
Title: meme suite 4.8.1, more useful logging, non-standard microbial runs

These changes include:

A meme suite 4.8.1 class (the command line arguments differ)
Warning if no sequences are loaded by organism class for any reason--this was happening to me when my E. coli ratios file had improper gene names, but the run continued anyway (should this be a hard error/stop?)
Config_params are logged at start of run
Option to preserve temp files (for debugging, default False)
Files for customizable microbial run (can set custom params and score functions--I'm using this for non-default E. coli runs) [or should I just keep these to myself instead?]
Attempt to resolve problem that project.conf is included in this pull request--since this file is user dependent, I've added project.conf.default and .gitignored project.conf. Please advise if there is a better solution...?

No test failures.