aliscore <- function(x, path){
path <- "/Applications/Aliscore_v1.0"
rwd <- getwd()
setwd(path)
write.fas(x, "input.fas")
call <- "perl Aliscore.02.pl -i input.fas"
system(call)
id <- scan("input.fas_List-l_all.txt", what = "char",
quiet = TRUE)
id <- as.numeric(id)
nid <- length(id)
if (nid == 0)
cat("\nALISCORE did not remove any characters.") else {
x <- x[, -id]
cat("\nALISCORE removed", nid, "characters.")
}
setwd(rwd)
x
}
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