def write_la4ice_done_script(self, output_dir):
"""
Write cmd to self.la4ice_done_script, the cmd creates
a sentinel file indicating all la4ice jobs compeleted.
The sentinel file that will be written is output/LA4ICE.DONE.
"""
cmd = "touch {out}".format(out=op.join(output_dir, "LA4ICE.DONE"))
write_cmd_to_script(cmd=cmd, script=self.la4ice_done_script)
def write_la4ice_done_script(self, output_dir):
"""
Write cmd to self.la4ice_done_script, the cmd creates
a sentinel file indicating all la4ice jobs compeleted.
The sentinel file that will be written is output/LA4ICE.DONE.
"""
cmd = "touch {out}".format(out=op.join(output_dir, "LA4ICE.DONE"))
write_cmd_to_script(cmd=cmd, script=self.la4ice_done_script)
def write_daligner_done_script(self, output_dir):
"""
Write cmd to self.daligner_done_script, the cmd creates
a sentinel file indicating all daligner jobs completed.
The sentinel file that will be written is output_dir/DALIGNER.DONE.
"""
cmd = "touch {out}".format(out=op.join(output_dir, "DALIGNER.DONE"))
write_cmd_to_script(cmd=cmd, script=self.daligner_done_script)
def write_daligner_done_script(self, output_dir):
"""
Write cmd to self.daligner_done_script, the cmd creates
a sentinel file indicating all daligner jobs completed.
The sentinel file that will be written is output_dir/DALIGNER.DONE.
"""
cmd = "touch {out}".format(out=op.join(output_dir, "DALIGNER.DONE"))
write_cmd_to_script(cmd=cmd, script=self.daligner_done_script)
def sanity_check_sge(sge_opts, scriptDir, testDirName="gcon_test_dir"):
"""Sanity check if sge can work."""
scriptDir = realpath(scriptDir)
testDir = op.join(scriptDir, testDirName)
if not op.exists(scriptDir):
os.makedirs(scriptDir)
if not op.exists(testDir):
os.makedirs(testDir)
testSh = op.join(scriptDir, 'test.sh')
consensusFa = op.join(testDir, "g_consensus.fasta")
testInFa = op.join(testDir, "gcon_in.fasta")
if op.exists(testInFa):
os.remove(testInFa)
shutil.copy(GCON_IN_FA, testInFa)
assert op.exists(testInFa)
cmd = " ".join([
gcon_py,
real_upath(testInFa),
"{testDir}/g_consensus".format(testDir=real_upath(testDir)), "c1"
])
write_cmd_to_script(cmd=cmd, script=testSh)
assert op.exists(testSh)
cmd = sge_opts.qsub_cmd(script=real_upath(testSh),
num_threads=1,
wait_before_exit=True)
logging.debug("Submitting cmd: " + cmd)
backticks(cmd)
if not filecmp.cmp(consensusFa, GCON_OUT_FA):
errMsg = "Trouble running qsub or output is not as " + \
"expected ({0} and {1} must agree). Abort!".format(
consensusFa, GCON_OUT_FA)
logging.error(errMsg)
return False
else:
shutil.rmtree(testDir)
logging.info("sge and gcon check passed.")
return True
def sanity_check_sge(sge_opts, scriptDir, testDirName="gcon_test_dir"):
"""Sanity check if sge can work."""
scriptDir = realpath(scriptDir)
testDir = op.join(scriptDir, testDirName)
if not op.exists(scriptDir):
os.makedirs(scriptDir)
if not op.exists(testDir):
os.makedirs(testDir)
testSh = op.join(scriptDir, 'test.sh')
consensusFa = op.join(testDir, "g_consensus.fasta")
testInFa = op.join(testDir, "gcon_in.fasta")
if op.exists(testInFa):
os.remove(testInFa)
shutil.copy(GCON_IN_FA, testInFa)
assert op.exists(testInFa)
cmd = " ".join([gcon_py, real_upath(testInFa),
"{testDir}/g_consensus".format(testDir=real_upath(testDir)),
"c1"])
write_cmd_to_script(cmd=cmd, script=testSh)
assert op.exists(testSh)
cmd = sge_opts.qsub_cmd(script=real_upath(testSh),
num_threads=1, wait_before_exit=True)
logging.debug("Submitting cmd: " + cmd)
backticks(cmd)
if not filecmp.cmp(consensusFa, GCON_OUT_FA):
errMsg = "Trouble running qsub or output is not as " + \
"expected ({0} and {1} must agree). Abort!".format(
consensusFa, GCON_OUT_FA)
logging.error(errMsg)
return False
else:
shutil.rmtree(testDir)
logging.info("sge and gcon check passed.")
return True