R/201-getProtUniProt.R

In nanxstats/Rcpi: Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery

#' Retrieve Protein Sequence in FASTA Format from the UniProt Database
#'
#' Retrieve Protein Sequence in FASTA Format from the UniProt Database
#'
#' This function retrieves protein sequences in FASTA format
#' from the UniProt database.
#'
#' @param id A character vector, as the protein ID.
#' @param parallel An integer, the parallel parameter, indicates how many
#'                 process the user would like to use for retrieving
#'                 the data (using RCurl), default is \code{5}.
#'                 For regular cases, we recommend a number less than \code{20}.
#'
#' @return A list, each component contains one of the protein sequences
#' in FASTA format.
#'
#' @seealso See \code{\link{getSeqFromUniProt}} for retrieving protein
#' represented by amino acid sequence from the UniProt database.
#' See \code{\link{readFASTA}} for reading FASTA format files.
#'
#' @export getFASTAFromUniProt
#'
#' @importFrom RCurl getURLAsynchronous
#'
#' @references
#' UniProt. \url{https://www.uniprot.org/}
#'
#' UniProt REST API Documentation. \url{https://www.uniprot.org/help/api}
#'
#' @examples
#' id = c('P00750', 'P00751', 'P00752')
#' \donttest{
#' getFASTAFromUniProt(id)}

getFASTAFromUniProt = function (id, parallel = 5) {

  # example id:  P00750
  # example url: https://rest.uniprot.org/uniprotkb/P00750.fasta

  fastaURL = paste0('https://rest.uniprot.org/uniprotkb/', id, '.fasta')

  fastaTxt = getURLAsynchronous(url = fastaURL, perform = parallel)

  return(fastaTxt)

}

#' Retrieve Protein Sequence from the UniProt Database
#'
#' Retrieve Protein Sequence from the UniProt Database
#'
#' This function retrieves protein represented by amino acid sequence
#' from the UniProt database.
#'
#' @param id A character vector, as the protein ID.
#' @param parallel An integer, the parallel parameter, indicates how many
#'                 process the user would like to use for retrieving
#'                 the data (using RCurl), default is \code{5}.
#'                 For regular cases, we recommend a number less than \code{20}.
#'
#' @return A list, each component contains one of the protein
#' represented by amino acid sequence(s).
#'
#' @seealso See \code{\link{getFASTAFromUniProt}} for retrieving protein
#' sequences in FASTA format from the UniProt database.
#'
#' @export getSeqFromUniProt
#'
#' @references
#' UniProt. \url{https://www.uniprot.org/}
#'
#' UniProt REST API Documentation. \url{https://www.uniprot.org/help/api}
#'
#' @examples
#' id = c('P00750', 'P00751', 'P00752')
#' \donttest{
#' getSeqFromUniProt(id)}

getSeqFromUniProt = function (id, parallel = 5) {

  # example id:  P00750
  # example url: https://rest.uniprot.org/uniprotkb/P00750.fasta

  fastaTxt = getFASTAFromUniProt(id, parallel)

  tmpfile = tempfile(pattern = paste0(id, '-'), fileext = 'fasta')
  for (i in 1:length(id)) write(fastaTxt[[i]], tmpfile[i])

  AASeq = lapply(tmpfile, readFASTA)

  unlink(tmpfile)

  return(AASeq)

}