RRTscript.r

setwd("/Users/easss/Desktop/RRTbatch/")

library(ape)
library(pegas)
# list file in current directory, where the file is end with .phy
filelist <- list.files(path=".", pattern=".phy$")
# create a container to store output data
out_tab <- matrix(0, nrow=length(filelist), ncol=3)
colnames(out_tab) <- c("dna_seq", "Chi", "Pval")

i = 1
for ( f in filelist ) { 
    seq3 <- read.dna(f)
    out_tab[i,1] <- f
    out_tab[i,2] <- rr.test(x = seq3[2,], y = seq3[3, ], out = seq3[1, ])$Chi
    out_tab[i,3] <- rr.test(x = seq3[2,], y = seq3[3, ], out = seq3[1, ])$Pval
    i=i+1
}

# write output table
write.table(out_tab, file="out_tab.csv", sep=",", row.names=F)