R/formatSequence.R

In dagLogo: dagLogo: a Bioconductor package for visualizing conserved amino acid sequence pattern in groups based on probability theory

#' Format already aligned peptide sequences.
#' 
#' Convert already aligned peptide sequences into an object of 
#' \code{\link{dagPeptides-class}}.
#' 
#' @param seq A vector of aligned peptide sequences of the same length
#' @param proteome An object of \code{\link{Proteome-class}}.
#' @param upstreamOffset An integer, the upstream offset relative to
#' the anchoring position.
#' @param downstreamOffset An integer, the downstream offset relative
#' to the anchoring position.
#'
#' @return An object of \code{\link{dagPeptides-class}} Class
#' @import methods
#' @export
#' @author Jianhong Ou, Haibo Liu
#' @examples
#' ## Suppose you already have the aligned peptides sequences at hands. Then you can use 
#' ## the formatSequence function to prepare an object of dagPeptides. Befor doing 
#' ## that, you need prepare a Proteome object by the prepareProteome function.
#' 
#' dat <- unlist(read.delim(system.file(
#'                                    "extdata", "grB.txt", package = "dagLogo"),
#'                          header = FALSE, as.is = TRUE))
#'                          
#' ## prepare an object of Proteome Class from a fasta file
#' proteome <- prepareProteome(fasta = system.file("extdata",
#'                                                 "HUMAN.fasta",
#'                                                 package = "dagLogo"), 
#'                             species = "Homo sapiens")
#'                             
#' ## prepare an object of dagPeptides Class from a Proteome object
#' seq <- formatSequence(seq = dat, proteome = proteome, upstreamOffset = 14,
#'                      downstreamOffset = 15)
#' 

formatSequence <-function(seq,
                          proteome,
                          upstreamOffset,
                          downstreamOffset) 
{
  if (missing(proteome) || class(proteome) != "Proteome") 
  {
    stop("proteome should be an object of Proteome Class. \n
         Try ?prepareProteome to get help.",
         call. = FALSE)
  }
  if (missing(seq)) 
  {
    stop("seq is a required parameter.", call. = FALSE)
  }
  if (!is.character(seq)) 
  {
    seq <- as.character(seq)
  }
  
  ## the number of characters in each seq should be the same
  width <- unique(unlist(lapply(seq, nchar)))
  
  if (length(width) > 1) 
  {
    stop("seq must be characters of the same length", call. = FALSE)
  }
  
  ## determine upstreamOffset and downstreamOffset
  if (missing(upstreamOffset) && missing(downstreamOffset)) 
  {
    upstreamOffset <- floor(width / 2)
    downstreamOffset <- width - upstreamOffset - 1
  } else
  {
    if (missing(downstreamOffset)) 
    {
      downstreamOffset <- width - upstreamOffset - 1
    } else
    {
      upstreamOffset <- width - downstreamOffset - 1
    }
  }
  
  ## check validity of upstreamOffset and downstreamOffset
  if (upstreamOffset < 0 || downstreamOffset < 0)
  {
    stop("upstreamOffset and downstreamOffset must be positive integers.", 
         call. = FALSE)
  }
  
  ## retrieve anchorAA and anchorPos
  ## This will not work for gapped alignments!
  center <- upstreamOffset + 1
  anchorAA <- unlist(lapply(seq, function(.ele)
    substr(.ele, center, center)))
  
  ## find the IDs and the starting positions of peptide sequences in Proteome 
  ## which match the sequences in seq
  m <- do.call(rbind, lapply(seq, function(.seq) {
    ## removing non-standard letter symbols, which makes subsequent pattern
    ## matching possible
    .seq <- gsub("[^ACDEFGHIKLMNPQRSTVWY]", "", .seq, perl = TRUE)
    ## a numeric vector: starting positions of the matches, -1 if no match
    .m <- regexpr(.seq, proteome@proteome$SEQUENCE) 
    ## index of sequence with true match
    .id <- which(.m != -1)
    ## index of first sequence with true match
    .id <- .id[1]
    ## starting position of the first match
    .pos <- .m[.id]
    ## return the index and starting position of the first match
    c(.id, .pos)
  }))
  
  ## starting positions of the first match in sequences in Proteome for each 
  ## aligned sequence from seq
  anchorPos <- m[, 2]
  
  ## IDs of sequences in Proteome, matching each aligned sequence in seq
  IDs <- proteome@proteome[m[, 1], "ID"]
  
  ## full sequences in Proteome, matching each aligned sequence in seq
  peptide <- proteome@proteome[m[, 1], "SEQUENCE"]
  dat <- data.frame(IDs = IDs,
                    anchorAA = anchorAA,
                    anchorPos = anchorPos,
                    peptide = peptide,
                    anchor = anchorAA)
  
  ## upstream and downstrean sequences and characters
  dat$upstream <- substr(seq, 1, upstreamOffset)
  dat$downstream <-
    substr(seq, upstreamOffset + 2, upstreamOffset + downstreamOffset + 1)
  seqchar.upstream <-
    do.call(rbind, lapply(dat$upstream, function(.seq) {
      .seq <- c(rep("NA", upstreamOffset),
                unlist(lapply(1:nchar(.seq), function(i)
                  substr(.seq, i, i))))
      .seq <- .seq[(length(.seq) - upstreamOffset + 1):length(.seq)]
      .seq
    }))
  seqchar.downstream <-
    do.call(rbind, lapply(dat$downstream, function(.seq) {
      .seq <-
        c(unlist(lapply(1:nchar(.seq), function(i)
          substr(.seq, i, i))),
          rep("NA", downstreamOffset))
      .seq <- .seq[1:downstreamOffset]
      .seq
    }))
  seqchar <-cbind(seqchar.upstream,
                  as.character(dat$anchorAA),
                  seqchar.downstream)
  new("dagPeptides",
      data = dat,
      peptides = seqchar,
      upstreamOffset = upstreamOffset,
      downstreamOffset = downstreamOffset,
      type = proteome@type)
}