R/observed_wrapper.R

In motifcounter: R package for analysing TFBSs in DNA sequences

#' Length of sequences in a given fasta file
#'
#' The function returns a vector containing the lengths
#' of each sequence contained in a set of sequences. Sequences
#' containing 'N' or 'n' are skipped from the analysis and are
#' set to length zero.
#'
#' @param seqs A DNAStringSet or DNAString object
#' @return A vector containing the lengths of each individual sequences
#'
#' @examples
#'
#' # Load sequences
#' file = system.file("extdata", "seq.fasta", package = "motifcounter")
#' seqs = Biostrings::readDNAStringSet(file)
#'
#' # Retrieve sequence lengths
#' motifcounter:::lenSequences(seqs)
#'
lenSequences = function(seqs) {

    if (is(seqs, "DNAString")) {
        # wrap the sequence up as sequence set
        seqs = DNAStringSet(seqs)
    }
    
    stopifnot(is(seqs, "DNAStringSet"))

    lseq = vapply(seqs, function(seq) {
        return(.Call(motifcounter_slen, toString(seq)))
    }, FUN.VALUE = integer(1))

    return(as.vector(lseq))
}