R/GetProteomeFasta.R

In UniprotR: Retrieving Information of Proteins from Uniprot

#' Connect and DOWNLOAD Proteome info.
#'
#'The function is work to retrieve proteome information in FASTA format based on proteome id.
#'
#' @usage GetProteomeFasta(ProteomeID , directorypath = NULL)
#'
#' @param ProteomeID Proteome ID from UniProt
#'
#' @param directorypath path to save FASTA file containig results returened by the function.
#'
#' @note The function Download fasta format of proteome.
#'
#' @export
#'
#' @author Mohmed Soudy \email{Mohamed.soudy@57357.com} and Ali Mostafa \email{ali.mo.anwar@std.agr.cu.edu.eg}
GetProteomeFasta <- function(ProteomeID , directorypath = NULL)
{
  if(!has_internet())
  {
    message("Please connect to the internet as the package requires internect connection.")
    return()
  }
  baseUrl <- "https://rest.uniprot.org/uniprotkb/stream?format=fasta&query=proteome:"
  Request <- tryCatch(
    {
      GET(paste0(baseUrl , ProteomeID) , timeout(60))
    },error = function(cond)
    {
      message("Internet connection problem occurs and the function will return the original error")
      message(cond)
    }
  )
  if (length(Request) == 0)
  {
    message("Internet connection problem occurs")
    return()
  }
  if (Request$status_code == 200)
  {
    download.file(Request$url ,paste0(directorypath ,"/" , ProteomeID, ".fasta"))
  }
  else {
    HandleBadRequests(Request$status_code)
  }
}