tRNA DAMBE check in R

gistfile1.txt

md <- read.csv(file.choose(), header=T) #This is not working, need to use FILE, IMPORT DATASET, FROM TEXT(BASE), then select csv, DESELECT "Strings as Factors", IMPORT

#removes leading and trailing numbers from sequences

for(i in 1:nrow(md)){
  md[i,] <- substr(md[i,], 3, nchar(md[i,])-2)
}


#Check for even length stem

trna_len_list <- c()

for(i in 1:nrow(md)){
  checkstem <- nchar(md[i,])-3 ## subtract 3 to account for anticodon
  trna_len_list[i] <- checkstem
  if(checkstem%%2 != 0){
    cat("tRNA", md[i,], "at row id", i, "has asymmetry\n\n")
  }
} 

#Get anticodon, then complement

anticodons <- c()
to_codon <- c()
codons <- c()


for(i in 1:nrow(md)){
  anticodons[i] <- substr(md[i,], (trna_len_list[i]/2)+1, (trna_len_list[i]/2)+3)
  to_codon[i] <-  strsplit(anticodons[i], "")
  for(j in 1:3){
    if(to_codon[[i]][j] == "G"){
      to_codon[[i]][j] <- sub("G", "C", to_codon[[i]][j])
    } else
    if(to_codon[[i]][j] == "C"){
      to_codon[[i]][j] <- sub("C", "G", to_codon[[i]][j])
    } else
    if(to_codon[[i]][j] == "A"){
      to_codon[[i]][j] <- sub("A", "U", to_codon[[i]][j])
    } else
    if(to_codon[[i]][j] == "U"){
      to_codon[[i]][j] <- sub("U", "A", to_codon[[i]][j])
    }
  }
  codons[i] <- paste(rev(to_codon[[i]]), collapse='')
}

for(i in 1:nrow(test)){
  print(codons[i] == test[i,])
}


#Check stem complimentarity 

#substr(md[1,], 0, (nchar(md[1,])/2)-1)
#substr(md[1,], (nchar(md[1,])/2)+5, nchar(md[,1]))

right_list <- c()
left_list <- c()
original_left <- c()
check_list <- c()

for(i in 1:nrow(md)){
  
  left <- strsplit(substr(md[i,], 0, (nchar(md[i,])/2)-3), "") 
  original_left[i] <- substr(md[i,], 0, (nchar(md[i,])/2)-3)
  right_list[i] <- substr(md[i,], (nchar(md[i,])/2)+5, nchar(md[i,]))
  
  for(j in 1:length(left[[1]])){
    if(left[[1]][j] == "G"){
      left[[1]][j] <- sub("G", "C", left[[1]][j])
    } else
      if(left[[1]][j] == "C"){
        left[[1]][j] <- sub("C", "G", left[[1]][j])
      } else
        if(left[[1]][j] == "A"){
          left[[1]][j] <- sub("A", "U", left[[1]][j])
        } else
          if(left[[1]][j] == "U"){
            left[[1]][j] <- sub("U", "A", left[[1]][j])
          }
  }
  
  left_list[i] <- paste(rev(left[[1]]), collapse="")
  check_list[i] <- left_list[i] == right_list[i]
  
}


output <- data.frame(tRNA=md[,1], ANTICODON=anticodons, LEFT.STEM=original_left, RIGHT.STEM=right_list, LEFT.COMPLEMENT=left_list, LC.RS.EQUIVALENCY=check_list)

output