def getFile(inFile, dest): base = os.path.basename(inFile) dest = dest.replace(".bz2", "").replace(".gz", "") doremove = False if isSRAID(inFile): inFile = utils.translateToSRAURL(settings, inFile) base = os.path.basename(inFile) os.system("curl -# -L %s -o %s"%(inFile, base)) os.system("%s/cpp%s%s-%s%ssra/bin/fastq-dump --split-3 -O %s %s"%(settings.METAMOS_UTILS, os.sep, settings.OSTYPE, settings.MACHINETYPE, os.sep, os.path.dirname(dest), base)) os.system("rm -rf %s"%(base)) return elif isRemote(inFile): base = "%s/download_%s"%(os.path.dirname(dest), base) os.system("curl -# -L %s -o %s"%(inFile, base)) doremove = True inFile = base if base.endswith("bz2"): os.system("bunzip2 -c %s > %s"%(inFile, dest)) elif base.endswith("gz"): os.system("gunzip -c %s > %s"%(inFile, dest)) else: os.system("cp %s %s"%(inFile, dest)) if doremove: os.system("rm -f %s"%(base))
def getFile(inFile, dest): base = os.path.basename(inFile) dest = dest.replace(".bz2", "").replace(".gz", "") doremove = False if isSRAID(inFile): inFile = utils.translateToSRAURL(settings, inFile) base = os.path.basename(inFile) os.system("curl -# -L %s -o %s" % (inFile, base)) os.system("%s%sfastq-dump --split-3 -O %s %s" % (settings.SRA, os.sep, os.path.dirname(dest), base)) os.system("rm -rf %s" % (base)) return elif isRemote(inFile): base = "%s/download_%s" % (os.path.dirname(dest), base) os.system("curl -# -L %s -o %s" % (inFile, base)) doremove = True inFile = base if base.endswith("bz2"): os.system("bunzip2 -c %s > %s" % (inFile, dest)) elif base.endswith("gz"): os.system("gunzip -c %s > %s" % (inFile, dest)) else: os.system("cp %s %s" % (inFile, dest)) if doremove: os.system("rm -f %s" % (base))
def checkFileExists(file): if isRemote(file): if isSRAID(file): file = utils.translateToSRAURL(settings, file) result = utils.getCommandOutput("curl -L -I %s && echo $?"%(file), False) if result == "": return False return True else: return os.path.exists(file)
def checkFileExists(file): if isRemote(file): if isSRAID(file): file = utils.translateToSRAURL(settings, file) result = utils.getCommandOutput("curl -L -I %s && echo $?" % (file), False) if result == "": return False return True else: return os.path.exists(file)
def isSRAID(file): return utils.translateToSRAURL(settings, file) != ""