R/GetProteomeInfo.R

In UniprotR: Retrieving Information of Proteins from Uniprot

#' Connect and DOWNLOAD Proteome info.
#'
#'The function is work to retrieve proteome information based on proteome id.
#'
#' @usage GetProteomeInfo(ProteomeID , directorypath = NULL)
#'
#' @param ProteomeID Proteome ID from UniProt
#'
#' @param directorypath path to save CSV file containig results returened by the function.
#'
#' @note The function Download csv Info of proteome.
#'
#' @export
#'
#' @author Mohmed Soudy \email{Mohamed.soudy@57357.com} and Ali Mostafa \email{ali.mo.anwar@std.agr.cu.edu.eg}
GetProteomeInfo <- 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=tsv&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)
    }
  )
  ProteinInfoParsed <- data.frame()
  if (length(Request) == 0)
  {
    message("Internet connection problem occurs")
    return()
  }
  if (Request$status_code == 200)
    {
    # parse the information in DataFrame
    ProteinDataTable <- tryCatch(read.table(Request$url, header = TRUE, sep = '\t'), error=function(e) NULL)
    if (!is.null(ProteinDataTable))
    {
      ProteinInfoParsed <- as.data.frame(ProteinDataTable)
    }
    
  }
  else {
    HandleBadRequests(Request$status_code)
  }
  if(!is.null(directorypath))
    {
    write.csv(ProteinInfoParsed , paste0(directorypath ,"/" , "Proteome Info.csv"))
    }
return(ProteinInfoParsed)
}