new file
Initial commit of probabilistic annotation service. It is very much in a beta state.
Update readme.txt file
Automatic calcualtion of GPRs and other bugfixes
Merge ssh://git.kbase.us/probabilistic_annotation
Added readme.txt back in - merge blew it away
Added a prototype function to add reaction probabilities and other relevant info to the biochemistry object...
Remove parts of the code that are no longer useful (I left them as comments for now but most likely Ill just replace them wtih KBase calls later). Also.. tried to make the location of data files more fluid since we should not be assuming a specific location. Still needs some work.
Make directory an argument in ExtractorDriver and related functions
Added generic folders to the Impl and Probability calculation frontend. It should be OK for use for probabilistic annotations but I'm running it again just to be sure.
Fix a ton of completely moronic mistakes. Hopefully it works now.
Fallback to simplejson
Use same default folder as CDMI.py for now - this might need to be changed if we want it to work with earlier python versions becuase simplejson no longer supports pythons older than 2.5
Fix to allow running multiple instances without them colliding in filespace
Add git directions to git repo (so I can access it on other computers mostly)
... Im SO bad at perl. But at least it works now.
Minor improvements - update readme for the syntax to use on SEED machines and remove a spurious dependency on sqlite3 (which I later decided not to use)
I don't know why that didn't work but I reverted it.
Some organization and adding a script to add reaction probabilities and some other info to a biochemistry json object
Some small bugfixes and removing of debugging code