def main(g_params): #{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
outpath = ""
fileListFile = ""
fileList = []
i = 1
isNonOptionArg = False
while i < numArgv:
if isNonOptionArg == True:
fileList.append(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 ["-m", "--m"]:
(g_params['method'], i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-md5", "--md5"]:
(tmpstr, i) = myfunc.my_getopt_str(argv, i)
if tmpstr.lower() == "yes":
g_params['isUseMD5'] = True
elif tmpstr.lower() == "no":
g_params['isUseMD5'] = False
else:
print >> sys.stderr, "Bad syntax. option -md5 must be followed by yes or no"
return 1
elif argv[i] in ["-l", "--l"]:
(fileListFile, 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:
fileList.append(argv[i])
i += 1
if outpath != "" and not os.path.exists(outpath):
cmd = ["mkdir", "-p", outpath]
try:
subprocess.check_call(cmd)
except subprocess.CalledProcessError, e:
print e
raise
def main(g_params): #{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
outfile = ""
infile = ""
gramfile = ""
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 ["-o", "--o", "-outfile"]:
(outfile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-gram", "--gram"]:
(gramfile, 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 myfunc.checkfile(infile) != 0:
return 1
if myfunc.checkfile(gramfile) != 0:
return 1
grampairlist = myfunc.ReadPairList(gramfile)
gramMapDict = {}
for tup in grampairlist:
gramMapDict[tup[0]] = tup[1]
gi2taxidpairlist = myfunc.ReadPairList(infile)
fpout = myfunc.myopen(outfile, sys.stdout, "w", False)
for tup in gi2taxidpairlist:
try:
fpout.write("%s\t%s\t%s\n" % (tup[0], tup[1], gramMapDict[tup[1]]))
except KeyError:
fpout.write("%s\t%s\t%s\n" % (tup[0], tup[1], "NA"))
myfunc.myclose(fpout)
def main(g_params):#{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
outpath = "./"
outfile = ""
fileListFile = ""
fileList = []
i = 1
isNonOptionArg=False
while i < numArgv:
if isNonOptionArg == True:
fileList.append(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 ["-o", "--o", "-outfile"]:
(outfile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-outpath", "--outpath"]:
(outpath, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-l", "--l"] :
(fileListFile, 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:
fileList.append(argv[i])
i += 1
# if infile == "":
# print >> sys.stderr, "infile not set"
# print >> sys.stderr, usage_short
# return 1
# elif not os.path.exists(infile):
# print >> sys.stderr, "infile %s does not exist"%(infile)
# return 1
if fileListFile != "":
fileList += myfunc.ReadIDList(fileListFile)
print "outfile = %s"%(outfile)
print "Number of ID =", len(fileList)
print "They are:"
for i in xrange(len(fileList)):
print "%d --> %s" %(i, fileList[i])
def main(g_params): #{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
outpath = ""
fileListFile = ""
fileList = []
i = 1
isNonOptionArg = False
while i < numArgv:
if isNonOptionArg == True:
fileList.append(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 ["-e", "--e"]:
(g_params['evalue_threshold'],
i) = myfunc.my_getopt_float(argv, i)
elif argv[i] in ["-l", "--l"]:
(fileListFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-q", "--q"]:
g_params['isQuiet'] = True
i += 1
elif argv[i] in ["-overwrite", "--overwrite", "-force", "--force"]:
g_params['isOverwrite'] = True
i += 1
else:
print >> sys.stderr, "Error! Wrong argument:", argv[i]
return 1
else:
fileList.append(argv[i])
i += 1
if fileListFile != "":
fileList += myfunc.ReadIDList(fileListFile)
if len(fileList) < 1:
print >> sys.stderr, "%s: no input file is set. exit" % (sys.argv[0])
return 1
if outpath != "" and not os.path.exists():
cmd = ["mkdir", "-p", outpath]
subprocess.check_output(cmd)
for i in xrange(len(fileList)):
Build_seqid2pfamid(fileList[i], outpath)
def main(g_params):#{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
outpath = ""
fileListFile = ""
fileList = []
i = 1
isNonOptionArg=False
while i < numArgv:
if isNonOptionArg == True:
fileList.append(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 ["-m", "--m"]:
(g_params['method'], i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-md5", "--md5"]:
(tmpstr, i) = myfunc.my_getopt_str(argv, i)
if tmpstr.lower() == "yes":
g_params['isUseMD5'] = True
elif tmpstr.lower() == "no":
g_params['isUseMD5'] = False
else:
print >> sys.stderr, "Bad syntax. option -md5 must be followed by yes or no"
return 1
elif argv[i] in ["-l", "--l"] :
(fileListFile, 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:
fileList.append(argv[i])
i += 1
if outpath != "" and not os.path.exists(outpath):
cmd = ["mkdir","-p",outpath]
try:
subprocess.check_call(cmd)
except subprocess.CalledProcessError, e:
print e
raise
def main(g_params): #{{{
# Check argv
numArgv = len(sys.argv)
if numArgv < 2:
PrintHelp()
return 1
outfile = ""
fileList = []
fileListFile = ""
i = 1
isNonOptionArg = False
while i < numArgv:
if isNonOptionArg == True:
fileList.append(sys.argv[i])
isNonOptionArg = False
i += 1
elif sys.argv[i] == "--":
isNonOptionArg = True
i += 1
elif sys.argv[i][0] == "-":
if sys.argv[i] in ["-h", "--help"]:
PrintHelp()
return 1
elif sys.argv[i] in ["-l", "--l"]:
fileListFile, i = myfunc.my_getopt_str(sys.argv, i)
elif sys.argv[i] in ["-o", "--o", "-outfile"]:
outfile, i = myfunc.my_getopt_str(sys.argv, i)
elif sys.argv[i] in ["-evalue", "--evalue"]:
g_params['evalue_th'], i = myfunc.my_getopt_float(sys.argv, i)
elif sys.argv[i] in ["-seqidt", "--seqidt"]:
g_params['seqidt_th'], i = myfunc.my_getopt_float(sys.argv, i)
elif sys.argv[i] in ["-round", "--round"]:
g_params['iteration'] = myfunc.my_getopt_int(sys.argv, i)
else:
print >> sys.stderr, ("Error! Wrong argument: '%s'" %
sys.argv[i])
return 1
else:
fileList.append(sys.argv[i])
i += 1
if fileListFile != "":
fileList += myfunc.ReadIDList(fileListFile, delim="\n")
if len(fileList) < 1:
print >> sys.stderr, "No input set. exit"
return 1
fpout = myfunc.myopen(outfile, sys.stdout, "w", False)
for infile in fileList:
BlastM9toPairlist(infile, fpout)
myfunc.myclose(fpout)
def main(g_params): #{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
outfile = ""
idListFile = ""
idList = []
i = 1
isNonOptionArg = False
while i < numArgv:
if isNonOptionArg == True:
idList.append(argv[i])
i += 1
isNonOptionArg = False
elif argv[i] == "--":
isNonOptionArg = True
i += 1
elif argv[i][0] == "-":
if argv[i] in ["-h", "--help"]:
PrintHelp()
return 1
elif argv[i] in ["-o", "--o", "-outfile"]:
(outfile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-l", "--l", "-list"]:
(idListFile, i) = myfunc.my_getopt_str(argv, i)
else:
print >> sys.stderr, "Error! Wrong argument:", argv[i]
return 1
else:
idList.append(argv[i])
i += 1
if idListFile != "":
idList += myfunc.ReadIDList(idListFile)
numID = len(idList)
if numID < 1:
print >> sys.stderr, "No ID set. exit"
return 1
params = {}
params['from'] = 'P_GI'
params['to'] = 'ID' # to uniprot id
params['format'] = 'tab'
params['query'] = " ".join(idList)
fpout = myfunc.myopen(outfile, sys.stdout, "w", False)
GIID2UniprotID(params, fpout)
myfunc.myclose(fpout)
def main(g_params):
# Check argv
numArgv = len(sys.argv)
if numArgv < 2:
PrintHelp()
return 1
outFile = ""
inFile = ""
begin = 0
end = 999999999
method = 2
i = 1
isNonOptionArg = False
while i < numArgv:
if isNonOptionArg == True:
isNonOptionArg = False
i = i + 1
elif sys.argv[i] == "--":
isNonOptionArg = True
i = i + 1
elif sys.argv[i][0] == "-":
if sys.argv[i] in ["-h", "--help"]:
PrintHelp()
return 1
elif sys.argv[i] in ["-i", "--i", "--infile"]:
inFile, i = myfunc.my_getopt_str(sys.argv, i)
elif sys.argv[i] in ["-b", "--b", "--begin"]:
begin, i = myfunc.my_getopt_int(sys.argv, i)
elif sys.argv[i] in ["-e", "--e", "--end"]:
end, i = myfunc.my_getopt_int(sys.argv, i)
elif sys.argv[i] in ["-o", "--o", "--outfile"]:
outFile, i = myfunc.my_getopt_str(sys.argv, i)
else:
print >> sys.stderr, ("Error! Wrong argument:%s" % sys.argv[i])
return 1
else:
inFile = sys.argv[i]
i += 1
if myfunc.checkfile(inFile, "Input file") != 0:
return 1
fpout = myfunc.myopen(outFile, sys.stdout, "w", False)
if method == 1:
CatFasta(inFile, begin, end, fpout)
else:
CatFasta2(inFile, begin, end, fpout)
myfunc.myclose(fpout)
return 0
def main(g_params):#{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
outpath = "./"
outfile = ""
fileListFile = ""
fileList = []
pfamDefFile = "%s/data/pfam/pfam26.0/Pfam-A.clans.tsv"%(DATADIR3)
i = 1
isNonOptionArg=False
while i < numArgv:
if isNonOptionArg == True:
fileList.append(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 ["-o", "--o", "-outfile"]:
(outfile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-outpath", "--outpath"]:
(outpath, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-l", "--l"] :
(fileListFile, 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:
fileList.append(argv[i])
i += 1
if fileListFile != "":
fileList += myfunc.ReadIDList(fileListFile)
(pfamidDefDict, clanidDefDict) = ReadPfamDefFile(pfamDefFile)
fpout = myfunc.myopen(outfile, sys.stdout, "w", False)
for i in xrange(len(fileList)):
CountUniquePairInvertedInfo(fileList[i], pfamidDefDict, fpout)
myfunc.myclose(fpout)
def main(g_params): #{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
outpath = ""
pfamid2seqidFile = ""
topodb = ""
seqdb = ""
i = 1
isNonOptionArg = False
while i < numArgv:
if isNonOptionArg == True:
print >> sys.stderr, "Error! Wrong argument:", argv[i]
return 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 ["-pfamid2seqid", "--pfamid2seqid"]:
(pfamid2seqidFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-seqdb", "--seqdb"]:
(seqdb, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-topodb", "--topodb"]:
(topodb, 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:
print >> sys.stderr, "Error! Wrong argument:", argv[i]
return 1
if outpath == "":
print >> sys.stderr, "Error! outpath not set. Exit"
print usage_short
return 1
elif not os.path.exists(outpath):
try:
subprocess.check_output(["mkdir", "-p", outpath])
except subprocess.CalledProcessError, e:
print e
return 1
def main():#{{{
numArgv=len(sys.argv)
if numArgv < 2:
PrintHelp()
return 1
argv = sys.argv
topofile = ""
sigpepfile = ""
outfile = ""
isQuiet = False
isDeleteSeqWithSignalPeptide = False
i = 1
isNonOptionArg=False
while i < numArgv:
if isNonOptionArg == True:
isNonOptionArg = False
i += 1
elif sys.argv[i] == "--":
isNonOptionArg=True
i += 1
elif sys.argv[i][0] == "-":
if sys.argv[i] in [ "-h", "--help"]:
PrintHelp()
return 1
elif argv[i] in [ '-o', '--o', "-outfile", "--outfile"]:
outfile, i = myfunc.my_getopt_str(argv, i)
elif argv[i] in ['-topo', '--topo']:
topofile, i = myfunc.my_getopt_str(argv, i)
elif argv[i] in ['-sig', '--sig']:
sigpepfile, i = myfunc.my_getopt_str(argv, i)
elif argv[i] == "-q":
isQuiet=True; i += 1
elif argv[i] in ["-deleteseq", "--deleteseq"]:
isDeleteSeqWithSignalPeptide=True; i += 1
else:
print >> sys.stderr, "Error! Wrong argument:", argv[i]
return 1
else:
print >> sys.stderr, "Error! Wrong argument:", argv[i]
return 1
if myfunc.checkfile(topofile, 'topofile') != 0:
return 1
if myfunc.checkfile(sigpepfile, 'sigpepfile') != 0:
return 1
sigpepDict = lcmp.ReadSignalPDict(sigpepfile)
FilterSignalPeptide(topofile, sigpepDict, outfile, isDeleteSeqWithSignalPeptide)
return 0
def main(g_params): #{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
outpath = ""
outfile = ""
fileListFile = ""
fileList = []
i = 1
isNonOptionArg = False
while i < numArgv:
if isNonOptionArg == True:
fileList.append(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 ["-o", "--o", "-outfile"]:
(outfile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-outpath", "--outpath"]:
(outpath, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-l", "--l"]:
(fileListFile, 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:
fileList.append(argv[i])
i += 1
if fileListFile != "":
fileList += myfunc.ReadIDList(fileListFile)
if outpath != "" and not os.path.exists(outpath):
os.system("mkdir -p %s" % (outpath))
for i in xrange(len(fileList)):
ExcludeConsensus(fileList[i], outpath)
def main(): #{{{
numArgv = len(sys.argv)
if numArgv < 2:
PrintHelp()
return 1
outFile = ""
inFile = ""
N = 999999999
rand_seed = None
i = 1
isNonOptionArg = False
while i < numArgv:
if isNonOptionArg == True:
isNonOptionArg = False
i = i + 1
elif sys.argv[i] == "--":
isNonOptionArg = True
i = i + 1
elif sys.argv[i][0] == "-":
if sys.argv[i] in ["-h", "--help"]:
PrintHelp()
return 1
elif sys.argv[i] in ["-i", "--infile"]:
inFile, i = myfunc.my_getopt_str(sys.argv, i)
elif sys.argv[i] in ["-n", "--n"]:
N, i = myfunc.my_getopt_int(sys.argv, i)
elif sys.argv[i] in ["-seed", "--seed"]:
rand_seed, i = myfunc.my_getopt_int(sys.argv, i)
elif sys.argv[i] in ["-o", "--outfile"]:
outFile, i = myfunc.my_getopt_str(sys.argv, i)
elif sys.argv[i] in ["-bs", "--block-size", "-block-size"]:
BLOCK_SIZE, i = myfunc.my_getopt_int(sys.argv, i)
if BLOCK_SIZE < 0:
print("Error! BLOCK_SIZE should >0", file=sys.stderr)
return 1
else:
print(("Error! Wrong argument:%s" % sys.argv[i]),
file=sys.stderr)
return 1
else:
inFile = sys.argv[i]
i += 1
if myfunc.checkfile(inFile, "Input file") != 0:
return 1
fpout = myfunc.myopen(outFile, sys.stdout, "w", False)
RandFasta(inFile, N, rand_seed, fpout)
myfunc.myclose(fpout)
def main():#{{{
numArgv=len(sys.argv)
if numArgv < 2:
PrintHelp()
return 1
outFile=""
inFile=""
N=999999999
rand_seed=None
i = 1
isNonOptionArg=False
while i < numArgv:
if isNonOptionArg == True:
isNonOptionArg=False
i = i + 1
elif sys.argv[i] == "--":
isNonOptionArg=True
i = i + 1
elif sys.argv[i][0] == "-":
if sys.argv[i] in [ "-h", "--help"]:
PrintHelp()
return 1
elif sys.argv[i] in ["-i", "--infile"]:
inFile, i = myfunc.my_getopt_str(sys.argv, i)
elif sys.argv[i] in [ "-n" , "--n"]:
N,i = myfunc.my_getopt_int(sys.argv, i)
elif sys.argv[i] in [ "-seed" , "--seed"]:
rand_seed, i = myfunc.my_getopt_int(sys.argv, i)
elif sys.argv[i] in [ "-o" , "--outfile"]:
outFile,i = myfunc.my_getopt_str(sys.argv, i)
elif sys.argv[i] in [ "-bs" , "--block-size" , "-block-size"]:
BLOCK_SIZE, i = myfunc.my_getopt_int(sys.argv, i)
if BLOCK_SIZE < 0:
print >> sys.stderr,"Error! BLOCK_SIZE should >0"
return 1
else:
print >> sys.stderr,("Error! Wrong argument:%s" % sys.argv[i])
return 1
else:
inFile = sys.argv[i]
i+=1
if myfunc.checkfile(inFile, "Input file") != 0:
return 1
fpout = myfunc.myopen(outFile, sys.stdout, "w", False)
RandFasta(inFile, N, rand_seed, fpout)
myfunc.myclose(fpout)
def main(g_params): #{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
resultdir = ""
outfile = ""
i = 1
isNonOptionArg = False
while i < numArgv:
if isNonOptionArg == True:
print >> sys.stderr, "Error! Wrong argument:", argv[i]
return 1
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 ["-o", "--o", "-outfile"]:
(outfile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-resultdir", "--resultdir"]:
(resultdir, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-l", "--l"]:
(fileListFile, 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:
print >> sys.stderr, "Error! Wrong argument:", argv[i]
return 1
if resultdir == "":
print >> sys.stderr, "%s: resultdir not set. exit" % (sys.argv[0])
return 1
elif not os.path.exists(resultdir):
print >> sys.stderr, "%s: resultdir %s does not exist. exit" % (
sys.argv[0], resultdir)
return 1
CalculateQueue(resultdir, outfile)
def main(g_params):#{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
outfile = ""
infile = ""
mapfile = ""
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 ["-o", "--o", "-outfile"]:
(outfile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-map", "--map", "-mapfile"]:
(mapfile, 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 myfunc.checkfile(infile) != 0:
return 1
if myfunc.checkfile(mapfile) != 0:
return 1
clanid2pfamidDict = myfunc.ReadFam2SeqidMap(mapfile)
pfamPercentTMDict = ReadPercentTM(infile)
fpout = myfunc.myopen(outfile, sys.stdout, "w", False)
GetPercentTMOfClan(pfamPercentTMDict, clanid2pfamidDict, fpout)
myfunc.myclose(fpout)
def main(g_params): # {{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
resultdir = ""
outfile = ""
i = 1
isNonOptionArg = False
while i < numArgv:
if isNonOptionArg == True:
print >>sys.stderr, "Error! Wrong argument:", argv[i]
return 1
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 ["-o", "--o", "-outfile"]:
(outfile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-resultdir", "--resultdir"]:
(resultdir, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-l", "--l"]:
(fileListFile, 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:
print >>sys.stderr, "Error! Wrong argument:", argv[i]
return 1
if resultdir == "":
print >>sys.stderr, "%s: resultdir not set. exit" % (sys.argv[0])
return 1
elif not os.path.exists(resultdir):
print >>sys.stderr, "%s: resultdir %s does not exist. exit" % (sys.argv[0], resultdir)
return 1
CalculateQueue(resultdir, outfile)
def main(): #{{{
numArgv = len(sys.argv)
if numArgv < 2:
PrintHelp()
return 1
argv = sys.argv
outfile = ""
infile = ""
output_format = "mfa"
i = 1
isNonOptionArg = False
while i < numArgv:
if isNonOptionArg == True:
infile = sys.argv[i]
isNonOptionArg = False
i = i + 1
elif sys.argv[i] == "--":
isNonOptionArg = True
i = i + 1
elif sys.argv[i][0] == "-":
if sys.argv[i] in ["-h", "--help"]:
PrintHelp()
return 1
elif sys.argv[i] in ["-o", "--o"]:
outfile, i = myfunc.my_getopt_str(argv, i)
elif sys.argv[i] in ["-of", "--of"]:
output_format, i = myfunc.my_getopt_str(argv, i)
else:
print >> sys.stderr, ("Error! Wrong argument:%s" % argv[i])
return 1
else:
infile = argv[i]
i += 1
if myfunc.checkfile(infile, "MSA file") != 0:
return 1
fpout = myfunc.myopen(outfile, sys.stdout, "w", False)
# detect the format of mpa files, the old format
MPA2MSA(infile, output_format, fpout)
myfunc.myclose(fpout)
def main(g_params): #{{{#{{{
# Check argv
numArgv = len(sys.argv)
if numArgv < 2:
PrintHelp()
return 1
outfile = ""
infile = ""
BLOCK_SIZE = 100000
isPrintID = False
isJustPrintSum = False
i = 1
isNonOptionArg = False
while i < numArgv:
if isNonOptionArg == True:
isNonOptionArg = False
infile = sys.argv[i]
i = i + 1
elif sys.argv[i] == "--":
isNonOptionArg = True
i = i + 1
elif sys.argv[i][0] == "-":
if sys.argv[i] in ["-h", "--help"]:
PrintHelp()
return 0
elif sys.argv[i] in ["-i", "--i", "-printid", "--printid"]:
isPrintID = True
i += 1
elif sys.argv[i] in ["-just-print-sum", "--just-print-sum"]:
isJustPrintSum = True
i += 1
elif sys.argv[i] in ["-o", "--o", "-outfile", "--outfile"]:
outfile, i = myfunc.my_getopt_str(sys.argv, i)
elif sys.argv[i] in ["-bs", "--bs", "-block-size", "--block-size"]:
BLOCK_SIZE, i = myfunc.my_getopt_int(sys.argv, i)
if BLOCK_SIZE < 0:
print("Error! BLOCK_SIZE should >0", file=sys.stderr)
return 1
else:
print(("Error! Wrong argument:%s" % sys.argv[i]),
file=sys.stderr)
return 1
else:
infile = sys.argv[i]
i += 1
if myfunc.checkfile(infile) != 0:
return 1
fpout = myfunc.myopen(outfile, sys.stdout, "w", False)
status = Getseqlen(infile, isPrintID, isJustPrintSum, BLOCK_SIZE, fpout)
myfunc.myclose(fpout)
return status
def main(g_params):#{{{#{{{
# Check argv
numArgv=len(sys.argv)
if numArgv < 2:
PrintHelp()
return 1
outfile = ""
infile = ""
BLOCK_SIZE = 100000
isPrintID = False
isJustPrintSum = False
i = 1
isNonOptionArg=False
while i < numArgv:
if isNonOptionArg == True:
isNonOptionArg=False
infile = sys.argv[i]
i = i + 1
elif sys.argv[i] == "--":
isNonOptionArg=True
i = i + 1
elif sys.argv[i][0] == "-":
if sys.argv[i] in ["-h", "--help"]:
PrintHelp()
return 0
elif sys.argv[i] in ["-i", "--i", "-printid", "--printid"]:
isPrintID = True
i += 1
elif sys.argv[i] in ["-just-print-sum", "--just-print-sum"]:
isJustPrintSum = True
i += 1
elif sys.argv[i] in [ "-o", "--o", "-outfile", "--outfile"]:
outfile, i = myfunc.my_getopt_str(sys.argv, i)
elif sys.argv[i] in [ "-bs", "--bs", "-block-size", "--block-size"]:
BLOCK_SIZE, i = myfunc.my_getopt_int(sys.argv, i)
if BLOCK_SIZE < 0:
print >> sys.stderr,"Error! BLOCK_SIZE should >0"
return 1
else:
print >> sys.stderr,("Error! Wrong argument:%s" % sys.argv[i])
return 1
else:
infile=sys.argv[i]
i += 1
if myfunc.checkfile(infile) != 0:
return 1
fpout = myfunc.myopen(outfile, sys.stdout, "w", False)
status = Getseqlen(infile, isPrintID, isJustPrintSum, BLOCK_SIZE, fpout)
myfunc.myclose(fpout)
return status
def main(g_params):
# Check argv
numArgv=len(sys.argv)
if numArgv < 2:
PrintHelp()
return 1
outFile = ""
inFile = ""
begin = 0
end = 999999999
method = 2
i = 1
isNonOptionArg=False
while i < numArgv:
if isNonOptionArg == True:
isNonOptionArg=False
i = i + 1
elif sys.argv[i] == "--":
isNonOptionArg=True
i = i + 1
elif sys.argv[i][0] == "-":
if sys.argv[i] in ["-h", "--help"]:
PrintHelp()
return 1
elif sys.argv[i] in ["-i", "--i", "--infile"]:
inFile, i = myfunc.my_getopt_str(sys.argv, i)
elif sys.argv[i] in ["-b", "--b", "--begin"]:
begin, i = myfunc.my_getopt_int(sys.argv, i)
elif sys.argv[i] in ["-e", "--e", "--end"]:
end, i = myfunc.my_getopt_int(sys.argv, i)
elif sys.argv[i] in ["-o" , "--o","--outfile"]:
outFile, i = my_getopt_str(sys.argv,i )
else:
print >> sys.stderr,("Error! Wrong argument:%s" % sys.argv[i])
return 1
else:
inFile=sys.argv[i]
i+=1
if myfunc.checkfile(inFile, "Input file") != 0:
return 1
fpout = myfunc.myopen(outFile, sys.stdout, "w", False)
if method == 1:
CatFasta(inFile,begin, end, fpout)
else:
CatFasta2(inFile,begin, end, fpout)
myfunc.myclose(fpout)
return 0
def main(g_params): #{{{
argv = sys.argv
outpath = ''
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
fileList = []
method = 0
i = 1
isNonOptionArg = False
while i < numArgv:
if isNonOptionArg == True:
isNonOptionArg = False
fileList.append(argv[i])
i = i + 1
elif argv[i] == "--":
isNonOptionArg = True
i = i + 1
elif argv[i][0] == "-":
if argv[i] == "-h" or argv[i] == "--help":
PrintHelp()
sys.exit(0)
elif argv[i] in ["-outpath", "--outpath"]:
(outpath, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-m", "--m"]:
(method, i) = myfunc.my_getopt_int(argv, i)
else:
print >> sys.stderr, ("Error! Wrong argument:%s" % argv[i])
return 1
else:
fileList.append(argv[i])
i += 1
if len(fileList) < 1:
print >> sys.stderr, "No input set"
return 1
cnt = 0
for treefile in fileList:
print "================== ", cnt, treefile, " ===================="
if method == 0:
Itol_Tree_m0(treefile, outpath, method)
elif method == 1:
Itol_Tree_m1(treefile, outpath, method)
cnt += 1
def main(g_params): #{{{
argv = sys.argv
datapath = ''
ext = ""
outpath = ''
fileList = []
fileListFile = ''
i = 1
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return ()
isNonOptionArg = False
while i < numArgv:
if isNonOptionArg == True:
isNonOptionArg = False
fileList.append(argv[i])
i = i + 1
elif argv[i] == "--":
isNonOptionArg = True
i = i + 1
elif argv[i][0] == "-":
if argv[i] == "-h" or argv[i] == "--help":
PrintHelp()
return (0)
elif argv[i] == "-outpath" or argv[i] == "--outpath":
(outpath, i) = myfunc.my_getopt_str(argv, i)
else:
print(("Error! Wrong argument:%s" % argv[i]), file=sys.stderr)
return (1)
else:
fileList.append(argv[i])
i += 1
if fileListFile != "":
fileList += myfunc.ReadIDList(fileListFile)
if len(fileList) <= 0:
print("No input set. Exit", file=sys.stderr)
return (1)
else:
cnt = 0
for treefile in fileList:
print("================== ", cnt, treefile,
" ====================")
GetTreeListOrder(treefile, outpath)
cnt += 1
def main(g_params): #{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
outpath = ""
infile = ""
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 ["-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 myfunc.checkfile(infile) != 0:
return 1
if outpath == "":
print >> sys.stderr, "outpath not set"
elif not os.path.exists(outpath):
os.system("mkdir -p %s" % (outpath))
SplitPfamFasta(infile, outpath)
def main(g_params):#{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
outfile = ""
infile = ""
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 ["-o", "--o", "-outfile"]:
(outfile, 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 myfunc.checkfile(infile) != 0:
return 1
fpout = myfunc.myopen(outfile, sys.stdout, "w", False)
goancDict =
myfunc.myclose(fpout)
def main(): #{{{
numArgv = len(sys.argv)
if numArgv < 2:
PrintHelp()
return 1
argv = sys.argv
outfile = ""
infile = ""
i = 1
isNonOptionArg = False
while i < numArgv:
if isNonOptionArg == True:
infile = sys.argv[i]
isNonOptionArg = False
i = i + 1
elif sys.argv[i] == "--":
isNonOptionArg = True
i = i + 1
elif sys.argv[i][0] == "-":
if sys.argv[i] in ["-h", "--help"]:
PrintHelp()
return 1
elif sys.argv[i] in ["-o", "--o"]:
outfile, i = myfunc.my_getopt_str(argv, i)
else:
print >> sys.stderr, ("Error! Wrong argument:%s" % argv[i])
return 1
else:
infile = argv[i]
i += 1
if myfunc.checkfile(infile) != 0:
return 1
return ReWriteFasta(infile, outfile)
def main(g_params): #{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
outfile = ""
outfile_with_famid = ""
outfile_with_pdb = ""
outfile_fam2seqmap = ""
idListFile = ""
mapfile = "%s%s%s" % (
DATADIR3, os.sep,
"wk/MPTopo/pfamAna_refpro/pfammap_from_uniprot/refpro20120604-celluar.selmaxlength-m1.nr100.filter.fragmented.clanid2seqid"
)
restrictIDListFile = ""
idList = []
maxseq_for_fam = 200
maxpair_for_fam = 300
method = 0
rand_seed = None
pdbtospFile = ""
isOnlyPDB = False
i = 1
isNonOptionArg = False
while i < numArgv:
if isNonOptionArg == True:
idList.append(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 ["-o", "--o", "-outfile", "--outfile"]:
outfile, i = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-outwithfamid", "--outwithfamid"]:
outfile_with_famid, i = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-outfam2seqmap", "--outfam2seqmap"]:
outfile_fam2seqmap, i = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-outwithpdb", "--outwithpdb"]:
outfile_with_pdb, i = myfunc.my_getopt_str(argv, i)
elif argv[i] in [
"-tmprolist", "--tmprolist", "-restrictlist",
"--restrictlist"
]:
restrictIDListFile, i = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-mapfile", "--mapfile"]:
mapfile, i = myfunc.my_getopt_str(argv, i)
elif (argv[i] in ["-pdbtosp", "--pdbtosp"]):
pdbtospFile, i = myfunc.my_getopt_str(argv, i)
elif sys.argv[i] in ["-seed", "--seed"]:
rand_seed, i = myfunc.my_getopt_int(argv, i)
elif argv[i] in ["-l", "--l"]:
idListFile, i = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-maxseq", "--maxseq"]:
maxseq_for_fam, i = myfunc.my_getopt_int(argv, i)
elif argv[i] in ["-maxpair", "--maxpair"]:
maxpair_for_fam, i = myfunc.my_getopt_int(argv, i)
elif argv[i] in ["-m", "--m", "-method", "--method"]:
method, i = myfunc.my_getopt_int(argv, i)
elif argv[i] in ["-q"]:
g_params['isQuiet'] = True
i += 1
elif argv[i] in ["-onlypdb", "--onlypdb"]:
g_params['isOnlyPDB'] = True
i += 1
else:
print >> sys.stderr, "Error! Wrong argument:", argv[i]
return 1
else:
idList.append(argv[i])
i += 1
if os.path.exists(idListFile):
idList += myfunc.ReadIDList(idListFile)
if len(idList) < 1:
print >> sys.stderr, "no ID set. exit"
return 1
if myfunc.checkfile(mapfile, "idMapFile") != 0:
return 1
idMapDict = myfunc.ReadFam2SeqidMap(mapfile)
# Read in pdbtosp map
if pdbtospFile != "":
(pdb2uniprotMap, uniprot2pdbMap) =\
myfunc.ReadPDBTOSP(pdbtospFile)
g_params['uniprotidlist_with_pdb'] = set(uniprot2pdbMap.keys())
g_params['uniprot2pdbMap'] = uniprot2pdbMap
if g_params['isOnlyPDB'] == True:
if pdbtospFile == "":
print >> sys.stderr, "onlypdb is true but pdbtospFile is not set. exit."
return 1
elif g_params['uniprotidlist_with_pdb'] == set([]):
print >> sys.stderr, "onlypdb is true but uniprotidlist_with_pdb is empty. exit."
return 1
restrictIDSet = set([])
if restrictIDListFile != "":
restrictIDSet = set(myfunc.ReadIDList(restrictIDListFile))
fpout = myfunc.myopen(outfile, sys.stdout, "w", False)
fpout_withfamid = myfunc.myopen(outfile_with_famid, None, "w", False)
fpout_withpdb = myfunc.myopen(outfile_with_pdb, None, "w", False)
fpout_fam2seqmap = myfunc.myopen(outfile_fam2seqmap, None, "w", False)
if method == 0:
GeneratePairWithinFam_m_0(idList, idMapDict, restrictIDSet,
maxseq_for_fam, rand_seed, fpout,
fpout_withfamid)
elif method == 1:
GeneratePairWithinFam_m_1(idList, idMapDict, restrictIDSet,
maxpair_for_fam, rand_seed, fpout,
fpout_withfamid, fpout_fam2seqmap)
elif method == 2: #all to all
GeneratePairWithinFam_m_2(idList, idMapDict, restrictIDSet, fpout,
fpout_withfamid, fpout_withpdb)
myfunc.myclose(fpout)
myfunc.myclose(fpout_withfamid)
myfunc.myclose(fpout_withpdb)
myfunc.myclose(fpout_fam2seqmap)
return 0
def main(g_params): #{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
outfile = ""
idListFile = ""
euk = ""
gram_pos = ""
gram_neg = ""
i = 1
isNonOptionArg = False
while i < numArgv:
if isNonOptionArg == True:
idListFile = 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 ["-o", "--o", "-outfile"]:
(outfile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-euk", "--euk"]:
(euk, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-gram+", "--gram+"]:
(gram_pos, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-gram-", "--gram-"]:
(gram_neg, 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:
idListFile = argv[i]
i += 1
if myfunc.checkfile(idListFile, "idListFile") != 0:
return 1
if myfunc.checkfile(euk, "euk") != 0:
return 1
if myfunc.checkfile(gram_pos, "gram_pos") != 0:
return 1
if myfunc.checkfile(gram_neg, "gram_neg") != 0:
return 1
idList = myfunc.ReadIDList(idListFile)
set_euk_idlist = set(myfunc.ReadIDList(euk))
set_gram_pos_idlist = set(myfunc.ReadIDList(gram_pos))
set_gram_neg_idlist = set(myfunc.ReadIDList(gram_neg))
fpout = myfunc.myopen(outfile, sys.stdout, "w", False)
NCBI_TaxID = ""
for i in xrange(len(idList)):
seqid = idList[i]
cls = ""
if seqid in set_euk_idlist:
cls = "euk"
elif seqid in set_gram_pos_idlist:
cls = "gram+"
elif seqid in set_gram_neg_idlist:
cls = "gram-"
else:
cls = "NA"
print >> fpout, "%s\t%s\t%s" % (seqid, NCBI_TaxID, cls)
myfunc.myclose(fpout)
def main(g_params):#{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
outpath = ""
modelfile = ""
seqfile = ""
tmpdir = ""
email = ""
jobid = ""
isKeepFiles = "no"
isRepack = "yes"
targetlength = None
i = 1
isNonOptionArg=False
while i < numArgv:
if isNonOptionArg == True:
modelfile = 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 ["-fasta", "--fasta"] :
(seqfile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-k", "--k"] :
(isKeepFiles, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-r", "--r"] :
(isRepack, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-t", "--t"] :
(targetlength, i) = myfunc.my_getopt_int(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
elif argv[i] in ["-force", "--force"]:
g_params['isForceRun'] = True
i += 1
else:
print >> sys.stderr, "Error! Wrong argument:", argv[i]
return 1
else:
modelfile = argv[i]
i += 1
if jobid == "":
print >> sys.stderr, "%s: jobid not set. exit"%(sys.argv[0])
return 1
if myfunc.checkfile(modelfile, "modelfile") != 0:
return 1
if outpath == "":
print >> sys.stderr, "outpath not set. exit"
return 1
elif not os.path.exists(outpath):
try:
subprocess.check_output(["mkdir", "-p", outpath])
except subprocess.CalledProcessError, e:
print >> sys.stderr, e
return 1
def main(g_params): #{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
outfile = ""
msafile = ""
topofile = ""
topodb = ""
isIgnoreBadseq = True
method_match = 1
i = 1
isNonOptionArg = False
while i < numArgv:
if isNonOptionArg == True:
print("Error! Wrong argument:", argv[i], file=sys.stderr)
return 1
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 ["-o", "--o", "-outfile"]:
(outfile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-msa", "--msa"]:
(msafile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-topo", "--topo"]:
(topofile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-m", "--m"]:
(method_match, i) = myfunc.my_getopt_int(argv, i)
if method_match not in [0, 1]:
print("method_match %d not in [0,1]" % method_match,
file=sys.stderr)
return 1
elif argv[i] in ["-topodb", "--topodb"]:
(topodb, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in [
"-ig", "--ig", "-ignore-badseq", "--ignore-badseq"
]:
(tmpss, i) = myfunc.my_getopt_str(argv, i)
if tmpss[0].lower() == "y":
isIgnoreBadseq = True
else:
isIgnoreBadseq = False
elif argv[i] in ["-q", "--q"]:
g_params['isQuiet'] = True
i += 1
else:
print("Error! Wrong argument:", argv[i], file=sys.stderr)
return 1
else:
print("Error! Wrong argument:", argv[i], file=sys.stderr)
return 1
if myfunc.checkfile(msafile) != 0:
return 1
if topodb != "":
if not os.path.exists(topodb + '0.db'):
print("topodb %s does not exist" % (topodb), file=sys.stderr)
return 1
else:
return MatchMSATopo_using_topodb(msafile, topodb, isIgnoreBadseq,
method_match, outfile)
elif topofile != "":
if not os.path.exists(topofile):
print("topofile %s does not exist" % (topofile), file=sys.stderr)
return 1
else:
return MatchMSATopo_using_topofile(msafile, topofile,
isIgnoreBadseq, method_match,
outfile)
else:
print("neither topofile nor topodb is set. exit", file=sys.stderr)
return 1
return 0
def main(g_params): #{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
rmsg = ""
outpath = ""
jobid = ""
datapath = ""
numseq = -1
numseq_this_user = -1
email = ""
host_ip = ""
base_www_url = ""
i = 1
isNonOptionArg = False
while i < numArgv:
if isNonOptionArg == True:
print >> g_params['fperr'], "Error! Wrong argument:", argv[i]
return 1
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 ["-email", "--email"]:
(email, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-host", "--host"]:
(host_ip, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-nseq", "--nseq"]:
(numseq, i) = myfunc.my_getopt_int(argv, i)
elif argv[i] in ["-nseq-this-user", "--nseq-this-user"]:
(numseq_this_user, i) = myfunc.my_getopt_int(argv, i)
elif argv[i] in ["-baseurl", "--baseurl"]:
(base_www_url, 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 ["-datapath", "--datapath"]:
(datapath, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-force", "--force"]:
g_params['isForceRun'] = True
i += 1
elif argv[i] in ["-q", "--q"]:
g_params['isQuiet'] = True
i += 1
else:
print >> g_params['fperr'], "Error! Wrong argument:", argv[i]
return 1
else:
print >> g_params['fperr'], "Error! Wrong argument:", argv[i]
return 1
if outpath == "":
print >> g_params['fperr'], "outpath not set. exit"
return 1
elif not os.path.exists(outpath):
cmd = ["mkdir", "-p", outpath]
try:
rmsg = subprocess.check_output(cmd, stderr=subprocess.STDOUT)
except subprocess.CalledProcessError, e:
print e
print rmsg
return 1
def main(g_params): #{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
outfile = ""
datapath = ""
idListFile = ""
idList = []
ext = ""
i = 1
isNonOptionArg = False
while i < numArgv:
if isNonOptionArg == True:
idList.append(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 ["-o", "--o", "-outfile"]:
(outfile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-ext", "--ext"]:
(ext, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-datapath", "--datapath"]:
(datapath, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-l", "--l"]:
(idListFile, 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:
idList.append(argv[i])
i += 1
if ext == "":
print >> sys.stderr, "file extension not set. exit"
return 1
if datapath == "":
print >> sys.stderr, "datapath not set. exit"
return 1
elif not os.path.exists(datapath):
print >> sys.stderr, "datapath %s does not exist. exit" % (datapath)
return 1
if idListFile != "":
idList += myfunc.ReadIDList(idListFile)
if len(idList) < 1:
print >> sys.stderr, "No input set. exit"
return 1
fpout = sys.stdout
if outfile != "":
fpout = myfunc.myopen(outfile, sys.stdout, "w", False)
id2pathmapfile = "%s%s%s" % (datapath, os.sep, "id2pathmap.txt")
id2pathMapDict = myfunc.ReadIDPathMapDict(id2pathmapfile)
for idd in idList:
filename = ID2File(idd, datapath, id2pathMapDict, ext)
if filename != "":
print >> fpout, filename
if outfile != "":
myfunc.myclose(fpout)
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
elif argv[i] in ["-force", "--force"]:
g_params['isForceRun'] = 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
g_params['jobid'] = jobid
# create a lock file in the resultpath when run_job.py is running for this
# job, so that daemon will not run on this folder
lockname = "runjob.lock"
lock_file = "%s/%s/%s"%(path_result, jobid, lockname)
g_params['lockfile'] = lock_file
fp = open(lock_file, 'w')
try:
fcntl.lockf(fp, fcntl.LOCK_EX | fcntl.LOCK_NB)
except IOError:
print >> sys.stderr, "Another instance of %s is running"%(progname)
return 1
if myfunc.checkfile(infile, "infile") != 0:
return 1
if outpath == "":
print >> sys.stderr, "outpath not set. exit"
return 1
elif not os.path.exists(outpath):
cmd = ["mkdir", "-p", outpath]
(t_isCmdSuccess, t_runtime) = webcom.RunCmd(cmd, gen_logfile, gen_errfile)
if not t_isCmdSuccess:
return 1
if tmpdir == "":
print >> sys.stderr, "tmpdir not set. exit"
return 1
elif not os.path.exists(tmpdir):
cmd = ["mkdir", "-p", tmpdir]
(t_isCmdSuccess, t_runtime) = webcom.RunCmd(cmd, gen_logfile, gen_errfile)
if not t_isCmdSuccess:
return 1
numseq = myfunc.CountFastaSeq(infile)
g_params['debugfile'] = "%s/debug.log"%(outpath)
return RunJob(infile, outpath, tmpdir, email, jobid, g_params)
def main(g_params): #{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
outpath = "./"
listfile = ""
hhprofilepathList = []
hhalignpathList = []
nonPosArgList = []
i = 1
isNonOptionArg = False
while i < numArgv:
if isNonOptionArg == True:
nonPosArgList.append(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 [
"-hhprofile", "--hhprofile", "-hhprofile1", "--hhprofile1"
]:
(ss, i) = myfunc.my_getopt_str(argv, i)
hhprofilepathList.append(ss)
elif argv[i] in ["-hhalign", "--hhalign"]:
(ss, i) = myfunc.my_getopt_str(argv, i)
hhalignpathList.append(ss)
elif argv[i] in ["-l", "--l"]:
(listfile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-hhopt", "--hhopt"]:
g_params['hhalignopt'] = argv[i + 1]
i += 2
elif argv[i] in ["-q", "--q"]:
g_params['isQuiet'] = True
i += 1
elif argv[i] in ["-outpng", "--outpng"]:
g_params['isOutputPNG'] = True
i += 1
elif argv[i] in ["-outhfa", "--outhfa"]:
g_params['isOutputHFA'] = True
i += 1
elif argv[i] in ["-overwrite", "-forcewrite", "--forcewrite"]:
g_params['isForceOverWrite'] = True
i += 1
else:
print >> sys.stderr, "Error! Wrong argument:", argv[i]
return 1
else:
nonPosArgList.append(argv[i])
i += 1
if len(hhprofilepathList) < 1:
print >> sys.stderr, "hhprofilepath not set. exit"
return 1
pairlist = []
if len(nonPosArgList) == 2:
pairlist.append((nonPosArgList[0], nonPosArgList[1]))
elif len(nonPosArgList) > 0:
msg = "Wrong number of non positional argument (%d)"
print >> sys.stderr, msg % (len(nonPosArgList))
return 1
if listfile != "":
pairlist += myfunc.ReadPairList(listfile)
numpair = len(pairlist)
if numpair <= 0:
print >> sys.stderr, "input pair is 0, exit"
return 1
if not os.path.exists(outpath):
try:
os.makedirs(outpath)
except OSError:
pass
if not os.path.exists(outpath):
print >> sys.stderr, "failed to created outpath %s" % (outpath)
return 1
# read in hhprofile dict
hhprofilepathMapDictList = []
for hhprofilepath in hhprofilepathList:
hhprofilemapfile = hhprofilepath + os.sep + "id2pathmap.txt"
if not os.path.exists(hhprofilemapfile):
print >> sys.stderr, "hhprofilemapfile not exist. exit"
hhprofilepathMapDictList.append({})
else:
hhprofilepathMapDictList.append(
ReadSeqPathMapDict(hhprofilemapfile))
#print
#print hhprofilemapfile
#print ReadSeqPathMapDict(hhprofilemapfile)
# read in index dictionary for hhalign result file
hhalignpathMapDictList = []
if len(hhalignpathList) > 0:
g_params['isUsePreBuildHHalignResult'] = True
for hhalignpath in hhalignpathList:
hhalignmapfile = hhalignpath + os.sep + "id2pathmap.txt"
if not os.path.exists(hhalignmapfile):
print >> sys.stderr, "hhalignmapfile not exist. exit"
hhalignpathMapDictList.append({})
else:
hhalignpathMapDictList.append(
ReadSeqPathMapDict(hhalignmapfile))
RunHHAlignPairwise(pairlist, hhprofilepathList, hhprofilepathMapDictList,
hhalignpathList, hhalignpathMapDictList, outpath)
return 0
def main(g_params): #{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
outfile = ""
infile = ""
gramPositiveFile = ""
gramNegativeFile = ""
eukFile = ""
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 ["-o", "--o", "-outfile"]:
(outfile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-gram+", "--gram+"]:
(gramPositiveFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-gram-", "--gram-"]:
(gramNegativeFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-euk", "--euk"]:
(eukFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-q", "--q"]:
g_params['isQuiet'] = True
i += 1
elif argv[i] in ["-debug", "--debug"]:
g_params['isDEBUG'] = True
i += 1
else:
print >> sys.stderr, "Error! Wrong argument:", argv[i]
return 1
else:
infile = argv[i]
i += 1
if myfunc.checkfile(infile, "taxidwithtaxoFile") != 0:
return 1
if myfunc.checkfile(gramPositiveFile, "gramPositiveFile") != 0:
return 1
if myfunc.checkfile(gramNegativeFile, "gramNegativeFile") != 0:
return 1
if myfunc.checkfile(eukFile, "eukFile") != 0:
return 1
gramPositiveDict = ReadSignalPFile(gramPositiveFile)
gramNegativeDict = ReadSignalPFile(gramNegativeFile)
eukDict = ReadSignalPFile(eukFile)
fpout = myfunc.myopen(outfile, sys.stdout, "w", False)
hdl = myfunc.ReadLineByBlock(infile)
if hdl.failure:
return 1
lines = hdl.readlines()
while lines != None:
for line in lines:
strs = line.split("\t")
if len(strs) == 3:
seqid = strs[0].strip()
taxo = strs[2].strip()
info = ""
try:
if taxo == "Gram+" or taxo == "gram+":
info = gramPositiveDict[seqid]
elif taxo == "Gram-" or taxo == "gram-":
info = gramNegativeDict[seqid]
elif taxo == "Euk" or taxo == "euk":
info = eukDict[seqid]
if g_params['isDEBUG']:
print >> sys.stderr, "%s: %s" % (seqid, taxo)
except KeyError:
info = ""
if info != "":
fpout.write("%s\n" % info)
lines = hdl.readlines()
hdl.close()
myfunc.myclose(fpout)
def main(g_params):#{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
outpath = "./"
tableinfoFile = ""
hhprofilepathList = []
hhsearchpathList = []
dupfile = ""
topofile = ""
# /data3/wk/MPTopo/pfamAna_refpro/pred_topcons_single_method4/refpro20120604-celluar.selmaxlength-m1.topcons-single_topcons_single.m1.agree-44.topo
i = 1
isNonOptionArg=False
while i < numArgv:
if isNonOptionArg == True:
tableinfoFile = 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 ["-hhprofile", "--hhprofile", "-hhprofile1", "--hhprofile1"] :
(ss, i) = myfunc.my_getopt_str(argv, i)
hhprofilepathList.append(ss)
elif argv[i] in ["-hhsearch", "--hhsearch"] :
(ss, i) = myfunc.my_getopt_str(argv, i)
hhsearchpathList.append(ss)
elif argv[i] in ["-dupfile", "--dupfile"] :
(dupfile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-topofile", "--topofile"] :
(topofile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-l", "--l"] :
(tableinfoFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-q", "--q"]:
g_params['isQuiet'] = True; i += 1
elif argv[i] in ["-overwrite", "-forcewrite", "--forcewrite"]:
g_params['isForceOverWrite'] = True; i += 1
else:
print >> sys.stderr, "Error! Wrong argument:", argv[i]
return 1
else:
tableinfoFile = argv[i]
i += 1
if tableinfoFile == "":
print >> sys.stderr, "tableinfoFile not set. exit"
return 1
if len(hhprofilepathList) < 1:
print >> sys.stderr, "hhprofilepath not set. exit"
return 1
if not os.path.exists(outpath):
os.makedirs(outpath)
if not os.path.exists(outpath):
print >> sys.stderr, "failed to created outpath %s"%(outpath)
return 1
topoDict = {}
if topofile != "":
(idList, topoList) = myfunc.ReadFasta_without_annotation(topofile)
for i in xrange(len(idList)):
topoDict[idList[i]] = topoList[i]
if dupfile != "" and topoDict == {}:
print >> sys.stderr, "Error! topoDict is empty when dupfile"\
"is set. Exit"
return 1
# read in hhprofile dict
hhprofilepathMapDictList = []
for hhprofilepath in hhprofilepathList:
hhprofilemapfile = hhprofilepath + os.sep + "id2pathmap.txt"
if not os.path.exists(hhprofilemapfile):
print >> sys.stderr, "hhprofilemapfile not exist. exit"
hhprofilepathMapDictList.append({})
else:
hhprofilepathMapDictList.append(ReadSeqPathMapDict(hhprofilemapfile))
#print
#print hhprofilemapfile
#print ReadSeqPathMapDict(hhprofilemapfile)
# read in index dictionary for hhsearch result file
hhsearchpathMapDictList = []
if len(hhsearchpathList) > 0:
g_params['isUsePreBuildHHSearchResult'] = True
for hhsearchpath in hhsearchpathList:
hhsearchmapfile = hhsearchpath + os.sep + "id2pathmap.txt"
if not os.path.exists(hhsearchmapfile):
print >> sys.stderr, "hhsearchmapfile not exist. exit"
hhsearchpathMapDictList.append({})
else:
hhsearchpathMapDictList.append(ReadSeqPathMapDict(hhsearchmapfile))
RunHHSearchPairwise(tableinfoFile,
hhprofilepathList, hhprofilepathMapDictList,
hhsearchpathList, hhsearchpathMapDictList, topoDict,
outpath, dupfile)
return 0
def main(g_params):#{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
datapath = "."
outpath = './'
idList = []
idListFile = ''
treefile = ""
fastafile = ""
i = 1;
isNonOptionArg=False
while i < numArgv:
if isNonOptionArg == True:
isNonOptionArg=False;
idList.append(sys.argv[i])
i = i + 1;
elif sys.argv[i] == "--":
isNonOptionArg=True;
i = i + 1;
elif sys.argv[i][0] == "-":
if sys.argv[i] in [ "-h", "--help"]:
PrintHelp();
return 1
elif sys.argv[i] in [ "-datapath", "--datapath"]:
datapath = sys.argv[i+1]
i += 2;
elif argv[i] in [ "-m", "--m", "-method", "--method"]:
g_params['method'], i = myfunc.my_getopt_str(sys.argv, i)
elif sys.argv[i] in [ "-treefile", "--treefile"]:
treefile = sys.argv[i+1]
i += 2;
elif sys.argv[i] in [ "-fastafile", "--fastafile"]:
fastafile = sys.argv[i+1]
i += 2;
elif sys.argv[i] in [ "-l", "--l"]:
idListFile = sys.argv[i+1]
i = i + 2;
elif sys.argv[i] in ["-outpath", "--outpath"]:
outpath = sys.argv[i+1];
i = i + 2;
else:
print(("Error! Wrong argument:%s" % sys.argv[i]), file=sys.stderr);
return 1
else:
idList.append(sys.argv[i]);
i+=1;
if idListFile != "":
idList += myfunc.ReadIDList(idListFile)
if len(idList) > 0:
os.system("mkdir -p %s"%outpath)
cnt = 0
for pfamid in idList:
print("================== ", cnt , pfamid, " ====================")
if g_params['method'] == "0":
Itol_Tree_m0(pfamid, datapath, outpath)
elif g_params['method'] == "1":
Itol_Tree_m1(pfamid, datapath, outpath)
elif g_params['method'] == "sd1":
Itol_Tree_m_sd1(pfamid, datapath, outpath)
elif g_params['method'] == "sd2":
Itol_Tree_m_sd2(pfamid, datapath, outpath)
elif g_params['method'] == "sd3":
Itol_Tree_m_sd3(pfamid, datapath, outpath)
cnt += 1
if treefile != "":
if g_params['method'] == "linear":
Itol_Tree_linear(treefile, fastafile, outpath)
def main(g_params): #{{{
argv = sys.argv
numArgv = len(sys.argv)
if numArgv < 2:
PrintHelp()
return 1
infile = ""
outpath = "./"
isQuiet = False
tableinfoFile = ""
cmpclassList = []
restrictIDListFile = ""
signalpFile = ""
dupFile = ""
outfile = ""
i = 1
isNonOptionArg = False
while i < numArgv:
if isNonOptionArg == True:
infile = sys.argv[i]
isNonOptionArg = False
i += 1
elif sys.argv[i] == "--":
isNonOptionArg = True
i += 1
elif sys.argv[i][0] == "-":
if sys.argv[i] in ["-h", "--help"]:
PrintHelp()
sys.exit()
elif argv[i] in ["-o", "--o"]:
(outfile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-cmpclass", "--cmpclass"]:
(tmpstr, i) = myfunc.my_getopt_str(argv, i)
cmpclassList.append(tmpstr)
elif argv[i] in ["-signalp", "--signalp"]:
(signalpFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-restrictidlist", "--restrictidlist"]:
(restrictIDListFile, i) = myfunc.my_getopt_str(argv, i)
g_params['isRestrictIDListSet'] = True
elif argv[i] in ["-dup", "--dup", "-dupfile", "--dupfile"]:
(dupFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-rmsp", "--rmsp"]:
g_params['isRemoveSignalP'] = True
i += 1
elif argv[i] in ["-rmdup", "--rmdup"]:
g_params['isRemoveDup'] = True
i += 1
elif argv[i] in ["-seq2fammap", "--seq2fammap"]:
(seq2famMapfile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-seqidttype", "--seqidttype"]:
g_params['seqidttype'], i = myfunc.my_getopt_int(argv, i)
elif argv[i] in ["-tableinfo", "--tableinfo"]:
tableinfoFile, i = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-min-seqidt", "--min-seqidt"]:
g_params['minSeqIDT'], i = myfunc.my_getopt_float(argv, i)
elif argv[i] in ["-max-seqidt", "--max-seqidt"]:
g_params['maxSeqIDT'], i = myfunc.my_getopt_float(argv, i)
elif argv[i] in ["-evodist", "--evodist"]:
g_params['isEvodist'] = True
i += 1
elif argv[i] in ["-alignrange", "--alignrange"]:
g_params['alignrange'], i = myfunc.my_getopt_str(argv, i)
if not g_params['alignrange'] in ['all', 'full', 'part']:
print >> sys.stderr, "alignrange must be one of [all, full, part]"
return 1
else:
if g_params['alignrange'] == 'full':
g_params['alignrange'] = 'FULL_ALIGNED'
elif g_params['alignrange'] == 'part':
g_params['alignrange'] = 'PART_ALIGNED'
elif argv[i] in ["-debug", "--debug"]:
if argv[i + 1][0].lower() == 'y':
g_params['isDEBUG'] = True
else:
g_params['isDEBUG'] = False
i += 2
elif argv[i] in [
"-debug-unmapped-position", "--debug-unmapped-position"
]:
DEBUG_UNMAPPED_TM_POSITION = 1
i += 2
elif sys.argv[i] == "-q":
isQuiet = True
i += 1
else:
print >> sys.stderr, "Error! Wrong argument:", sys.argv[i]
return -1
else:
infile = sys.argv[i]
i += 1
if infile == "":
print >> sys.stderr, "infile not set. Exit."
return -1
elif not os.path.exists(infile):
print >> sys.stderr, "infile %s does not exists. Exit." % infile
try:
fpin = open(infile, "rb")
except IOError:
print >> sys.stderr, "Failed to open input file %s" % (infile)
return -1
pairalnStat = {}
if g_params['seqidttype'] != 0:
if tableinfoFile == "" or not os.path.exists(tableinfoFile):
print >> sys.stderr, "tableinfoFile must be set when seqidttype is set to 1 or 2"
print >> sys.stderr, "but seqidttype = %d is set. Exit." % g_params[
'seqidttype']
return -1
pairalnStat = lcmp.ReadPairAlnTableInfo(tableinfoFile)
rootname = os.path.basename(os.path.splitext(infile)[0])
binpath = os.path.dirname(sys.argv[0])
signalpDict = {}
if signalpFile != "":
signalpDict = lcmp.ReadSignalPDict(signalpFile)
if signalpDict != {}:
g_params['isSignalPSet'] = True
dupPairList = []
if dupFile != "":
dupPairList = lcmp.ReadDupPairList(dupFile)
if len(dupPairList) > 0:
g_params['isDupSet'] = True
dupPairSet = set(dupPairList)
restrictIDSet = set([])
if restrictIDListFile != "":
restrictIDSet = set(myfunc.ReadIDList(restrictIDListFile))
rltyDict = {}
fpout = myfunc.myopen(outfile, sys.stdout, "w", False)
unprocessedBuffer = ""
cntTotalReadInRecord = 0
cntTotalOutputRecord = 0
isEOFreached = False
while 1:
buff = fpin.read(BLOCK_SIZE)
if buff == "":
isEOFreached = True
buff = unprocessedBuffer + buff
pairCmpRecordList = []
unprocessedBuffer = lcmp.ReadPairCmpResultFromBuffer(
buff, pairCmpRecordList)
AddTableInfo(pairCmpRecordList, pairalnStat)
AddSignalPInfo(pairCmpRecordList, signalpDict)
AddDupInfo(pairCmpRecordList, dupPairSet)
cntTotalReadInRecord += len(pairCmpRecordList)
pairCmpRecordList = FilterPairCmpResult(pairCmpRecordList,
cmpclassList, rltyDict,
restrictIDSet)
if len(pairCmpRecordList) > 0:
lcmp.WritePairCmpRecord(pairCmpRecordList, cntTotalOutputRecord,
fpout)
cntTotalOutputRecord += len(pairCmpRecordList)
if isEOFreached == True:
break
fpin.close()
print "cntTotalReadInRecord =", cntTotalReadInRecord
print "cntTotalOutputRecord =", cntTotalOutputRecord
myfunc.myclose(fpout)
return 0
def main(g_params):#{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
rmsg = ""
outpath = ""
jobid = ""
datapath = ""
numseq = -1
numseq_this_user = -1
email = ""
host_ip = ""
base_www_url = ""
i = 1
isNonOptionArg=False
while i < numArgv:
if isNonOptionArg == True:
print >> g_params['fperr'], "Error! Wrong argument:", argv[i]
return 1
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 ["-email", "--email"]:
(email, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-host", "--host"]:
(host_ip, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-nseq", "--nseq"]:
(numseq, i) = myfunc.my_getopt_int(argv, i)
elif argv[i] in ["-nseq-this-user", "--nseq-this-user"]:
(numseq_this_user, i) = myfunc.my_getopt_int(argv, i)
elif argv[i] in ["-baseurl", "--baseurl"]:
(base_www_url, 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 ["-datapath", "--datapath"] :
(datapath, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-force", "--force"]:
g_params['isForceRun'] = True
i += 1
elif argv[i] in ["-runlocal", "--runlocal"]:
g_params['isRunLocal'] = True
i += 1
elif argv[i] in ["-q", "--q"]:
g_params['isQuiet'] = True
i += 1
else:
print >> g_params['fperr'], "Error! Wrong argument:", argv[i]
return 1
else:
print >> g_params['fperr'], "Error! Wrong argument:", argv[i]
return 1
if outpath == "":
print >> g_params['fperr'], "outpath not set. exit"
return 1
elif not os.path.exists(outpath):
cmd = ["mkdir", "-p", outpath]
try:
rmsg = subprocess.check_output(cmd, stderr=subprocess.STDOUT)
except subprocess.CalledProcessError, e:
print e
print rmsg
return 1
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
