def RunJob(infile, outpath, tmpdir, email, jobid, g_params): #{{{
blastdb = "/data3/data/blastdb/swissprot"
rootname = os.path.basename(os.path.splitext(infile)[0])
starttagfile = "%s/runjob.start" % (outpath)
runjob_errfile = "%s/runjob.err" % (outpath)
runjob_logfile = "%s/runjob.log" % (outpath)
finishtagfile = "%s/runjob.finish" % (outpath)
tmp_outfile = "%s/query.result" % (tmpdir)
resultpathname = jobid
outpath_result = "%s/%s" % (outpath, resultpathname)
outfile = "%s/query.result" % (outpath_result)
tarball = "%s.tar.gz" % (resultpathname)
tarball_fullpath = "%s.tar.gz" % (outpath_result)
isOK = True
try:
os.makedirs(outpath_result)
isOK = True
except OSError:
msg = "Failed to create folder %s" % (outpath_result)
myfunc.WriteFile(msg + "\n", runjob_errfile, "a")
isOK = False
if isOK:
g_params['runjob_log'].append("tmpdir = %s" % (tmpdir))
#cmd = [script_getseqlen, infile, "-o", tmp_outfile , "-printid"]
datetime = time.strftime("%Y-%m-%d %H:%M:%S")
rt_msg = myfunc.WriteFile(datetime, starttagfile)
if rt_msg:
g_params['runjob_err'].append(rt_msg)
cmd = [
blastall, "-i", infile, "-p", "blastp", "-o", tmp_outfile, "-d",
blastdb
]
g_params['runjob_log'].append(" ".join(cmd))
try:
myfunc.check_output(cmd)
except subprocess.CalledProcessError, e:
g_params['runjob_err'].append(str(e))
suqoutfilelist = glob.glob("%s/*.sh.*.out" % (tmpdir))
if len(suqoutfilelist) > 0:
suqoutfile = suqoutfilelist[0]
g_params['runjob_err'].append(myfunc.ReadFile(suqoutfile))
if os.path.exists(tmp_outfile):
cmd = ["cp", "-f", tmp_outfile, outfile]
try:
myfunc.check_output(cmd)
except subprocess.CalledProcessError, e:
g_params['runjob_err'].append(str(e))
def RunJob(infile, outpath, tmpdir, email, jobid, g_params):#{{{
blastdb = "/data3/data/blastdb/swissprot"
rootname = os.path.basename(os.path.splitext(infile)[0])
starttagfile = "%s/runjob.start"%(outpath)
runjob_errfile = "%s/runjob.err"%(outpath)
runjob_logfile = "%s/runjob.log"%(outpath)
finishtagfile = "%s/runjob.finish"%(outpath)
tmp_outfile = "%s/query.result" %(tmpdir)
resultpathname = jobid
outpath_result = "%s/%s"%(outpath, resultpathname)
outfile = "%s/query.result" %(outpath_result)
tarball = "%s.tar.gz"%(resultpathname)
tarball_fullpath = "%s.tar.gz"%(outpath_result)
isOK = True
try:
os.makedirs(outpath_result)
isOK = True
except OSError:
msg = "Failed to create folder %s"%(outpath_result)
myfunc.WriteFile(msg+"\n", runjob_errfile, "a")
isOK = False
if isOK:
g_params['runjob_log'].append("tmpdir = %s"%(tmpdir))
#cmd = [script_getseqlen, infile, "-o", tmp_outfile , "-printid"]
datetime = time.strftime("%Y-%m-%d %H:%M:%S")
rt_msg = myfunc.WriteFile(datetime, starttagfile)
if rt_msg:
g_params['runjob_err'].append(rt_msg)
cmd = [blastall, "-i", infile, "-p", "blastp","-o", tmp_outfile, "-d", blastdb ]
g_params['runjob_log'].append(" ".join(cmd))
try:
myfunc.check_output(cmd)
except subprocess.CalledProcessError, e:
g_params['runjob_err'].append(str(e))
suqoutfilelist = glob.glob("%s/*.sh.*.out"%(tmpdir))
if len(suqoutfilelist)>0:
suqoutfile = suqoutfilelist[0]
g_params['runjob_err'].append(myfunc.ReadFile(suqoutfile))
if os.path.exists(tmp_outfile):
cmd = ["cp","-f", tmp_outfile, outfile]
try:
myfunc.check_output(cmd)
except subprocess.CalledProcessError, e:
g_params['runjob_err'].append(str(e))
def main(g_params):#{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
outpath = ""
infile = ""
tmpdir = ""
email = ""
jobid = ""
i = 1
isNonOptionArg=False
while i < numArgv:
if isNonOptionArg == True:
infile = argv[i]
isNonOptionArg = False
i += 1
elif argv[i] == "--":
isNonOptionArg = True
i += 1
elif argv[i][0] == "-":
if argv[i] in ["-h", "--help"]:
PrintHelp()
return 1
elif argv[i] in ["-outpath", "--outpath"]:
(outpath, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-tmpdir", "--tmpdir"] :
(tmpdir, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-jobid", "--jobid"] :
(jobid, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-baseurl", "--baseurl"] :
(g_params['base_www_url'], i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-email", "--email"] :
(email, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-q", "--q"]:
g_params['isQuiet'] = True
i += 1
else:
print >> sys.stderr, "Error! Wrong argument:", argv[i]
return 1
else:
infile = argv[i]
i += 1
if jobid == "":
print >> sys.stderr, "%s: jobid not set. exit"%(sys.argv[0])
return 1
if myfunc.checkfile(infile, "infile"):
return 1
if outpath == "":
print >> sys.stderr, "outpath not set. exit"
return 1
elif not os.path.exists(outpath):
try:
myfunc.check_output(["mkdir", "-p", outpath])
except subprocess.CalledProcessError, e:
print >> sys.stderr, e
return 1
rt_msg = myfunc.WriteFile("\n".join(g_params['runjob_log']), runjob_logfile, "w")
if rt_msg:
g_params['runjob_err'].append(rt_msg)
datetime = time.strftime("%Y-%m-%d %H:%M:%S")
if os.path.exists(outfile):
rt_msg = myfunc.WriteFile(datetime, finishtagfile)
if rt_msg:
g_params['runjob_err'].append(rt_msg)
# make the tarball
pwd = os.getcwd()
os.chdir(outpath)
cmd = ["tar", "-czf", tarball, resultpathname]
try:
myfunc.check_output(cmd)
except subprocess.CalledProcessError, e:
g_params['runjob_err'].append(str(e))
os.chdir(pwd)
isSuccess = False
if (os.path.exists(finishtagfile) and os.path.exists(outfile) and
os.path.exists(tarball_fullpath)):
isSuccess = True
else:
isSuccess = False
failtagfile = "%s/runjob.failed"%(outpath)
datetime = time.strftime("%Y-%m-%d %H:%M:%S")
rt_msg = myfunc.WriteFile(datetime, failtagfile)
if rt_msg:
g_params['runjob_err'].append(rt_msg)
def main(g_params): #{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
outpath = ""
infile = ""
tmpdir = ""
email = ""
jobid = ""
i = 1
isNonOptionArg = False
while i < numArgv:
if isNonOptionArg == True:
infile = argv[i]
isNonOptionArg = False
i += 1
elif argv[i] == "--":
isNonOptionArg = True
i += 1
elif argv[i][0] == "-":
if argv[i] in ["-h", "--help"]:
PrintHelp()
return 1
elif argv[i] in ["-outpath", "--outpath"]:
(outpath, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-tmpdir", "--tmpdir"]:
(tmpdir, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-jobid", "--jobid"]:
(jobid, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-baseurl", "--baseurl"]:
(g_params['base_www_url'], i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-email", "--email"]:
(email, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-q", "--q"]:
g_params['isQuiet'] = True
i += 1
else:
print >> sys.stderr, "Error! Wrong argument:", argv[i]
return 1
else:
infile = argv[i]
i += 1
if jobid == "":
print >> sys.stderr, "%s: jobid not set. exit" % (sys.argv[0])
return 1
if myfunc.checkfile(infile, "infile"):
return 1
if outpath == "":
print >> sys.stderr, "outpath not set. exit"
return 1
elif not os.path.exists(outpath):
try:
myfunc.check_output(["mkdir", "-p", outpath])
except subprocess.CalledProcessError, e:
print >> sys.stderr, e
return 1
runjob_logfile, "w")
if rt_msg:
g_params['runjob_err'].append(rt_msg)
datetime = time.strftime("%Y-%m-%d %H:%M:%S")
if os.path.exists(outfile):
rt_msg = myfunc.WriteFile(datetime, finishtagfile)
if rt_msg:
g_params['runjob_err'].append(rt_msg)
# make the tarball
pwd = os.getcwd()
os.chdir(outpath)
cmd = ["tar", "-czf", tarball, resultpathname]
try:
myfunc.check_output(cmd)
except subprocess.CalledProcessError, e:
g_params['runjob_err'].append(str(e))
os.chdir(pwd)
isSuccess = False
if (os.path.exists(finishtagfile) and os.path.exists(outfile)
and os.path.exists(tarball_fullpath)):
isSuccess = True
else:
isSuccess = False
failtagfile = "%s/runjob.failed" % (outpath)
datetime = time.strftime("%Y-%m-%d %H:%M:%S")
rt_msg = myfunc.WriteFile(datetime, failtagfile)
if rt_msg:
g_params['runjob_err'].append(rt_msg)
