runCdhit <- function(file, out){
if (Sys.which('cd-hit')==''){
stop("cd-hit is not in your $PATH.")
}
if (missing(out)){
out <- rev(strsplit(file, '/')[[1]])[1]
out <- sub('[.]\\w+','.cdhit', out)
}
cdhit <- paste0('cd-hit -c 0.97 -s 0.9 -i ', file, ' -o ', out)
system(cdhit)
return(out)
}
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