R/get_GSE_links.R

In jmzeng1314/humanid: gene id annotation

#' Get the links for GSE studyID
#'
#'
#' @param studyID A standard study ID
#' @param destdir where to store the files download according to current GSE studyID
#' @return write some files
#' @export
#' @keywords get_GSE_links
#' @examples
#' #' get_GSE_links();get_GSE_links(studyID='GSE1009',down=T);get_GSE_links('GSE42872')
#'
#'

get_GSE_links <- function(studyID = "GSE1009", down = F, destdir = "./") {
    ## studyID destdir ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1009/matrix/GSE1009_series_matrix.txt.gz
    ## ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1009/suppl/GSE1009_RAW.tar
    ## http://www.ncbi.nlm.nih.gov/geo/browse/?view=samples&mode=csv&series=1009
    supp_link = paste0("ftp://ftp.ncbi.nlm.nih.gov/geo/series/", substr(studyID, 1, nchar(studyID) - 3), "nnn/", 
        studyID, "/suppl/", studyID, "_RAW.tar")
    meta_link = paste0("http://www.ncbi.nlm.nih.gov/geo/browse/?view=samples&mode=csv&series=", substr(studyID, 
        4, nchar(studyID)))
    matrix_link = paste0("ftp://ftp.ncbi.nlm.nih.gov/geo/series/", substr(studyID, 1, nchar(studyID) - 3), "nnn/", 
        studyID, "/matrix/", studyID, "_series_matrix.txt.gz")
    print(paste0("The URL for raw data is : ", supp_link))
    print(paste0("The URL for metadata is : ", meta_link))
    print(paste0("The URL for matrix   is : ", matrix_link))
    
    if (down) {
        if (.Platform$OS.type == "windows") {
            print("Wait a few months,we do not solve the problem about downloading files in windows!!!")
        } else if (.Platform$OS.type == "unix") {
            
            if (!file.exists(file.path(destdir, studyID))) {
                dir.create((file.path(destdir, studyID)))
            }
            # download.file(meta_link,destfile = './tmp.csv')
            a = read.csv(meta_link)
            write.csv(a, file.path(destdir, paste0(studyID, ".meta.txt")))
            download.file(supp_link, destfile = file.path(destdir, studyID, paste0(studyID, "_RAW.tar")), method = "auto")
            download.file(matrix_link, destfile = file.path(destdir, paste0(studyID, "_series_matrix.txt.gz")), 
                method = "auto")
            # system('tar xvf *.tar')
            setwd(file.path(destdir, studyID))
            for (i in list.files(pattern = "*tar")) {
                untar(i, exdir = destdir)
            }
            all_cel_files = list.files(destdir, pattern = "^GSM")
            old_dir <- getwd()
            setwd(destdir)
            for (i in all_cel_files) {
                if (grepl("[-_]", i) && (grepl(".CEL.gz", i) || grepl(".cel.gz", i))) {
                  new = paste(sub("[-_].*", "", i), ".CEL.gz", sep = "")
                  file.rename(i, new)
                  print(paste0(i, "\t to \t", new, "\n"))
                }
            }
            setwd(old_dir)
            # system('mv *.CEL.gz ../')
            
        }
        
        
    }
}

# get_GSE_links(studyID='GSE1009',down=T)