R/misc-05-getUniProt.R

In protr: Generating Various Numerical Representation Schemes for Protein Sequences

#' Retrieve Protein Sequences from UniProt by Protein ID
#'
#' This function retrieves protein sequences from uniprot.org by protein ID(s).
#'
#' @param id A character vector, as the protein ID(s).
#'
#' @return A list, each component contains one protein sequence.
#'
#' @author Nan Xiao <\url{https://nanx.me}>
#'
#' @seealso See \code{\link{readFASTA}} for reading FASTA format files.
#'
#' @export getUniProt
#'
#' @examples
#' \dontrun{
#' # Network latency may slow down this example
#' # Only test this when your connection is fast enough
#' ids <- c("P00750", "P00751", "P00752")
#' getUniProt(ids)
#' }
getUniProt <- function(id) {
  id <- as.character(id)
  n <- length(id)
  proteins <- vector("list", n)

  # API format:
  # https://www.uniprot.org/uniprot/P00750.fasta

  for (i in 1:n) {
    proteins[[i]] <-
      readFASTA(paste(
        "https://www.uniprot.org/uniprot/", id[i], ".fasta",
        sep = ""
      ))[[1]]
  }

  proteins
}