download_fastq_from_SRA.R

destdir = "~/" #directory where fastq files will be stored
nmbr_of_cores = 20
SRAdb_path = '~/SRAmetadb.sqlite'
exp_ids=c("ERX620541")

require(SRAdb)
sqlfile <- SRAdb_path
if(!file.exists(SRAdb_path)) sqlfile <- getSRAdbFile()
sra_con <- dbConnect(SQLite(),sqlfile) #conection to SRA database

download = function(i, exp_ids=exp_ids, sra_con=sra_con, destdir=destdir){
  sra = getSRA(exp_ids[i], out_types=c('sra','study','experiment','sample','run'), sra_con, acc_only=FALSE)
  fas = getFASTQinfo( sra$run,  sra_con, srcType = "ftp" )
  filename <- basename(fas$ftp)
  download.file(fas$ftp, paste(destdir, filename, sep=""))
}


require(parallel)
mclapply(1:length(exp_ids), 
                  download,
                  exp_ids=exp_ids,
                  sra_con=sra_con,
                  destdir=destdir,
                  mc.cores=nmbr_of_cores)