working version of mp2 with up to pipeline stage 13 working
ran to end of pipeline
merged kishoris changes for generating seed2ncbi, orf annotation text files
removed pyc files
fixed edge cases when not running with refseq
realized that the names file was wrong - also fixed meagan output. what's metacyc_orf_table.txt?
Addressed issue #1 about not creating the formatted folder on-the-fly.
changes for kishoris return
Added the utilities folder
Added the utilities folder
changes to accomodate the seed
fixed the memory problem in parse blast
steps log always writes a new file
added sample name  in the message log
Fixed the parser problem in parse blast
runs samples in sorted order
the real deal