R/getSystemList.R

In ZjGaothu/OpenAnnotateR:

#' @title getSystemList
#' @import stringr
#' @import httr
#' @import RCurl
#' @description Get the corresponding tissue list
#' @param protocol : 1-DNase-seq(ENCODE),2-ATAC-seq(ENCODE),3-ATAC-seq(ATACdb)
#' @param species : genome version of human of mouse, 1-hg19,2-hg38,3-mm9,4-mm10
#' @export getSystemList
#' @examples getSystemList(1,11)

getSystemList <- function(protocol,species)
{
  protocolDict <- c('dseq','aseq','atbd')
  speciesDict <- c('1' ='hg19','2'='hg38','3'='mm09','4'='mm10')
  if(species == 2){species = 1}
  if(species == 4){species = 3}
  if(species == 3 & protocol == 3){
    print('The corresponding cell type was not found. Please reselect the parameters.')
    return(0)}
  url = sprintf('http://159.226.47.242:65533/openness/anno/info/stat/system_%s_%s.txt',speciesDict[as.character(species)],protocolDict[protocol])
  result <- getURL(url)
  result <- str_split(result,'\n',simplify = TRUE)
  for(i in 2: length(result) - 1){
    print(paste(c(as.character(i + 1) , " - " , substring(result[i],9,nchar(result[i]))),collapse = ''))
  }
}