R/utils.R

In rintukutum/rpxmetadb: PRIDE metadb

#-------
# Get PRIDE ftp links
getPrideFTPlinks <- function(){
  url = 'ftp://ftp.pride.ebi.ac.uk/pride/data/archive/'

    cmd <- paste0("curl -s ",
                  url,
                  " | awk '{print $9}' > tmpfile"
    )
    system(cmd)
    dat <- readLines('tmpfile')
    unlink('tmpfile')
    # generate more urls
    urls <- paste(url,dat,'/',collpase='',sep='')
    ftpLinks <- list()
    k <- 1
    for(i in 1:length(urls)){

      cmd <- paste0("curl -s ",
                    urls[i],
                    " | awk '{print $9}' > tmpfile2"
      )
      system(cmd)
      dat <- readLines('tmpfile2')
      unlink('tmpfile2')
      urls2 <- paste(urls[i],dat,'/',collpase='',sep='')
      for(j in 1:length(urls2)){
        cat(paste0('i = ',i,'\t','j = ',j,'\n'))
        cmd <- paste0("curl -s ",
                      urls2[j],
                      " | awk '{print $9}' > tmpfile3"
        )
        system(cmd)
        prideIDs <- readLines('tmpfile3')
        unlink('tmpfile3')
        ftpLinks[[k]] <- paste(urls2[j],prideIDs,'/',collpase='',sep='')
        cat(paste(ftpLinks[[k]],'\n',collapse = '\n'))
        cat('\n')
        k <- k+1
      }
    }
    ftpLinks <- unlist(ftpLinks)
    #----
    # remove the test folder
    prideFTPlinks <- ftpLinks[-grep('test',ftpLinks)]
    #----
    # remove any unwanted folders
    prideFTPlinks <- prideFTPlinks[grep('P',prideFTPlinks)]
    return(prideFTPlinks)
}

prideFTPdf <- function(){
  data("prideFTPlinks")
  prideIDs <- sapply(prideFTPlinks,getPrideID)
  outDF <- data.frame(prideID=prideIDs,ftp=prideFTPlinks,stringsAsFactors = FALSE)
  rownames(outDF) <- 1:nrow(outDF)
  return(outDF)

}

getPrideID <- function(ftplink){
  parts <- strsplit(ftplink,split = '\\/')[[1]]
  prideID <- parts[length(parts)]
  return(prideID)
}
#------
# get meta information regarding process and raw
# data in PRIDE ftp
# additionally information about the size of the
# files (estimation of size)