R/translate.R

In seqinr: Biological Sequences Retrieval and Analysis

translate <- function(seq, frame = 0, sens = "F", numcode = 1, NAstring = "X",
                      ambiguous = FALSE)
{
    
    if(any(seq%in%LETTERS)){
        seq <- tolower(seq)
    }
    #
    # Take the reverse complementary strand when required:
    #
    
    if(sens == "R") seq <- comp(rev(seq), ambiguous = ambiguous)
    
    #
    # Transform the sequence in its numerical encoding equivalent
    # with textbook order, that is t = 0, c = 1, a = 2, g = 3
    #
    
    seqn <- s2n(seq, levels = s2c("tcag"))
    
    #
    # Compute the length of the sequence when its length in codons
    # is an integer:
    #
    
    l <- 3*((length(seq) - frame) %/% 3)
    
    #
    # Compute the indices for the first codon positions:
    #
    
    c1 <- seq(from = frame + 1, to = frame + l, by = 3)
    
    #
    # Compute the indices of codons in the translation table:
    #
    
    tra <-  16*seqn[c1] + 4*seqn[c1 + 1] + seqn[c1 + 2] + 1
    
    #
    # Get the translation table:
    #
    
    code <- s2c(SEQINR.UTIL$CODES.NCBI$CODES[numcode])
    
    #
    # Translate the sequence:
    #
    
    result <- code[tra]
    
    #
    # Replace missing values by the string for missing amino-acids:
    #
    
    result[is.na(result)] <- NAstring
    
    #
    # More work is required if ambiguous bases are handled:
    #
    
    if(ambiguous){
        toCheck <- which(result == NAstring)
        for( i in toCheck ){
            codon <- seq[c1[i]:(c1[i]+2)]
            allcodons <- as.vector(outer(as.vector(outer(amb(codon[1]), amb(codon[2]), paste, sep = "")), amb(codon[3]), paste, sep = ""))
            allaminoacids <- sapply(allcodons, function(x) translate(s2c(x), numcode = numcode, ambiguous = FALSE))
            if( all(allaminoacids == allaminoacids[1])) result[i] <- allaminoacids[1]
        }
    }
    
    return( result )
}