R/getSummaryFiles.R

In serratus-bio/tantalus: R Data Exploration for Serratus

#' getSummaryFiles
#' Downloads a specified list of summary files and parses them
#' into a Serratus S4 object
#'
#' Implicit system dependcies
#' - aws cli
#'
#' @param sras a string vector of the SRAs to download
#' @param s3_path a string s3 path to summary files
#' @param local_path local path into which to download the data
#' @keywords Tantalus, S4, Serratus, sra
#'
#' @return Serratus S4 class
#'
#' @examples
#' sras <- c("SRR9701190", "SRR9705127", "SRR975462", "SRR9843091", "SRR9843092")
#' serr <- getSummaryFiles(sras, 's3://lovelywater2/summary/', "summary_files")
#'
#' @export
#'
getSummaryFiles <- function(sras,
                            s3_path = 's3://lovelywater2/summary/',
                            local_path = 'summary_files'){

  summary_files <- paste(sras, "summary", sep=".")

  system(paste0( 'mkdir -p ', local_path))

  test <- sapply(summary_files, function(x){
    system_getSummary <- paste0("aws s3 cp ",
                                s3_path, x, " ",
                                local_path, "/")
    print(system_getSummary)
    system(system_getSummary)
  })

  sumWheres <- paste( local_path,
                      system( paste0("ls ", local_path, "*.summary"), intern = T ), sep="/")

  serratusObj <- readSerratus( sumWheres )

  return(serratusObj)

}