library(msarc)
args <- commandArgs(T)
if (length(args) == 2) {
  in.fn <- args[1]
  out.fn <- args[2]
  control.fn <- NULL
} else {
  in.fn <- args[1]
  control.fn <- args[2]
  out.fn <- args[3]
}
msa <- msarc.loadMS(in.fn)
if (!is.null(control.fn)) {
  control <- msarc.loadMS(control.fn)
  msa <- msarc.subtract(msa,control)
}
msa <- msarc.findGOterms(msa)
msarc.saveTerms(msa,file=out.fn)
imageFN <- sprintf("%s.RData",out.fn)
save(msa,file=imageFN)
