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) != ""
def isSRAID(file):
return utils.translateToSRAURL(settings, file) != ""
