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
datapath = "."
outpath = './'
idList = []
idListFile = ''
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 ["-method", "--method"]:
g_params['method'], i = myfunc.my_getopt_int(sys.argv, i)
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 >> sys.stderr, ("Error! Wrong argument:%s" % sys.argv[i])
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)
cnt += 1
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):#{{{
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):
seqinfofile = "/data3/wk/MPTopo/pfamAna/pfam2-giid-refseqid-pfamid-description.txt"
seqidlistfile = "/data3/wk/MPTopo/pfamAna/pairwise/all/pfamfullseq.selTM_uniq.seqidlist"
seqInfoDict = {}
seqInfoDict = ReadSeqDefInfo(seqinfofile)
idList = myfunc.ReadIDList(seqidlistfile)
print "#gi_id | refseq_id | pfamid | sequence_description"
for idd in idList:
print "%s | %s | %s | %s" % ( idd,
seqInfoDict[idd]['refseqid'],seqInfoDict[idd]['pfamid'],
seqInfoDict[idd]['seqdef'])
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(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 SplitIDList(infile, nsplit, method, datapath, ext, outpath):#{{{
idList = myfunc.ReadIDList(infile)
rootname = os.path.basename(os.path.splitext(infile)[0])
numID = len(idList)
if numID <= 0:
print >> sys.stderr, "no ID in the idlist file %s"%(infile)
return 1
if method == 0:
nfile_per_split = int(ceil(numID / float(nsplit)))
i = 0
cntfile = 0
while i < numID:
outfile = outpath + os.sep + rootname + ".split_%d"%(cntfile)
fpout = myfunc.myopen(outfile, None, "w", True)
cntID_per_split = 0
for j in xrange(i, i + nfile_per_split):
if j < numID:
fpout.write("%s\n"%(idList[j]))
cntID_per_split += 1
myfunc.myclose(fpout)
print "split to %s \t %4d IDs"%(outfile, cntID_per_split)
cntfile += 1
i += nfile_per_split
elif method in [1,2]:
sumFileSize = 0.0
fsizeList = []
for idd in idList:
fname = datapath + os.sep + idd + ext
if os.path.exists(fname):
fsize = os.path.getsize(fname)
if fsize > 0:
if method == 1:
sumFileSize += float(fsize)
fsizeList.append((idd, float(fsize)))
elif method == 2:
sumFileSize += float(fsize)*float(fsize)
fsizeList.append((idd, float(fsize)*fsize))
sumfilesize_per_split = ceil(sumFileSize / float(nsplit))
fsizeList = sorted(fsizeList, key = lambda x:x[1], reverse=True)
print "sumfilesize_per_split = %g"% (sumfilesize_per_split)
i = 0
cntfile = 0
numID = len(fsizeList)
while i < numID:
outfile = outpath + os.sep + rootname + ".split_%d"%(cntfile)
fpout = myfunc.myopen(outfile, None, "w", True)
j = 0
cntID_per_split = 0
sumFileSize = 0.0
while sumFileSize <= sumfilesize_per_split:
idx = i+j
if i+j > numID -1:
break
idd = fsizeList[idx][0]
fsize = fsizeList[idx][1]
sumFileSize += fsize
fpout.write("%s\n"%(idd))
cntID_per_split += 1
j += 1
myfunc.myclose(fpout)
print "split to %s \t %4d IDs sumsize = %g"%(outfile, cntID_per_split, sumFileSize)
cntfile += 1
i += j
return 1
def main(g_params): #{{{
numArgv = len(sys.argv)
if numArgv < 2:
PrintHelp()
return 1
outFile = ""
idList = []
idListFile = ""
fastaFile = ""
i = 1
isNonOptionArg = False
while i < numArgv:
if isNonOptionArg == True:
idList.append(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 ["-l", "--l", "-list", "--list"]):
idListFile = sys.argv[i + 1]
i = i + 2
elif (sys.argv[i] in ["-f", "--f", "-fasta", "--fasta"]):
fastaFile = sys.argv[i + 1]
i = i + 2
elif (sys.argv[i] in ["-o", "--o", "-outfile", "--outfile"]):
outFile = sys.argv[i + 1]
i = i + 2
elif (sys.argv[i] in ["-mine", "--mine"]):
g_params['min_evalue'] = float(sys.argv[i + 1])
g_params['isEvalueSet'] = True
i = i + 2
elif (sys.argv[i] in ["-maxe", "--maxe"]):
g_params['max_evalue'] = float(sys.argv[i + 1])
g_params['isEvalueSet'] = True
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 fastaFile == "":
print("Fatal! fasta file not set. Exit.", file=sys.stderr)
return 1
elif not os.path.exists(fastaFile):
print("Fatal! fasta file %s does not exist. Exit." % (fastaFile),
file=sys.stderr)
return 1
if os.path.exists(idListFile):
idList += myfunc.ReadIDList(idListFile)
if len(idList) > 0:
isIDSet = True
else:
isIDSet = False
if not g_params['isEvalueSet'] and not isIDSet:
print("Error! no ID nor evalue threshold is set. Eixt",
file=sys.stderr)
return 1
idListSet = set(idList)
fpout = myfunc.myopen(filename=outFile,
default_fp=sys.stdout,
mode="w",
isRaise=False)
fpin = open(fastaFile, "r")
if not fpin:
print("Failed to open fastafile %s" % (fastaFile), file=sys.stderr)
return -1
unprocessedBuffer = ""
isEOFreached = False
BLOCK_SIZE = g_params['BLOCK_SIZE']
isEvalueSet = g_params['isEvalueSet']
min_evalue = g_params['min_evalue']
max_evalue = g_params['max_evalue']
while 1:
buff = fpin.read(BLOCK_SIZE)
if len(buff) < BLOCK_SIZE:
isEOFreached = True
buff = unprocessedBuffer + buff
recordList = []
unprocessedBuffer = myfunc.ReadFastaFromBuffer(buff, recordList,
isEOFreached)
if len(recordList) > 0:
for r in recordList:
if ((not isIDSet) or (r[0] in idListSet)):
if (not isEvalueSet or r[1].lower().find('evalue') < 0):
fpout.write(">%s\n" % r[1])
fpout.write("%s\n" % r[2])
else:
evalue = myfunc.GetEvalueFromAnnotation(r[1])
if (evalue == None or
(evalue >= min_evalue and evalue <= max_evalue)):
fpout.write(">%s\n" % r[1])
fpout.write("%s\n" % r[2])
if isEOFreached == True:
break
fpin.close()
myfunc.myclose(fpout)
def main(g_params):#{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
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 ["-nmax", "--nmax"]:
(g_params['nmax'], i) = myfunc.my_getopt_int(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 len(fileList) < 1:
print >> sys.stderr, "%s: no input file is set. exit"%(sys.argv[0])
fpout = myfunc.myopen(outfile, sys.stdout, "w", False)
pfamidset_all = set([])
pfamidset_output = set([])
nmax = g_params['nmax']
cnt_round = 0
while 1:
cnt_round += 1
famid2seqidDict = {}
for i in xrange(len(fileList)):
hdl = myfunc.ReadLineByBlock(fileList[i])
if hdl.failure:
continue
lines = hdl.readlines()
while lines != None:
for line in lines:
line = line.strip()
if not line or line[0] == "#":
continue
strs = line.split()
if len(strs) > 2:
seqid = strs[0]
pfamidlist = strs[2:]
for pfamid in pfamidlist:
if cnt_round == 1:
pfamidset_all.add(pfamid)
if pfamid in pfamidset_output:
continue
if not pfamid in famid2seqidDict:
if len(famid2seqidDict) < nmax:
famid2seqidDict[pfamid] = []
if pfamid in famid2seqidDict:
famid2seqidDict[pfamid].append(seqid)
else:
msg="broken item in file %s: line \"%s\""
print >> sys.stderr, msg%(fileList[i], line)
lines = hdl.readlines()
hdl.close()
for pfamid in famid2seqidDict:
pfamidset_output.add(pfamid)
seqidlist = famid2seqidDict[pfamid]
seqidlist = myfunc.uniquelist(seqidlist)
fpout.write("%s %d"%(pfamid, len(seqidlist)))
for seqid in seqidlist:
fpout.write(" %s"%(seqid))
fpout.write("\n")
if len(pfamidset_output) == len(pfamidset_all):
break
else:
print " %d / %d "%(len(pfamidset_output), len(pfamidset_all))
myfunc.myclose(fpout)
if outfile != "":
print "result output to %s"%(outfile)
return 0
def main(g_params): #{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
workdir = ""
fileListFile = ""
idListFile = ""
extList = []
maxfile_per_folder = 2000
method = 0
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 ["-idlist", "--idlist"]:
(idListFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-filelist", "--filelist"]:
(fileListFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-workdir", "--workdir"]:
(workdir, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-max", "--max"]:
(maxfile_per_folder, i) = myfunc.my_getopt_int(argv, i)
elif argv[i] in ["-method", "--method"]:
(method, i) = myfunc.my_getopt_int(argv, i)
elif argv[i] in ["-ext", "--ext"]:
(tmpstr, i) = myfunc.my_getopt_str(argv, i)
extList.append(tmpstr)
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 myfunc.checkfile(workdir) != 0:
return 1
if idListFile == "" and fileListFile == "":
print >> sys.stderr, "At least one of idListFile and fileListFile need to be set"
return 1
if idListFile != "":
if os.path.exists(idListFile):
idList = myfunc.ReadIDList(idListFile)
if len(idList) <= 0:
print >> sys.stderr, "No ID in idListFile %s" % (idListFile)
elif len(extList) <= 0:
print >> sys.stderr, "No extension set when idList is used."
else:
SplitToFolder_idlist(idList, workdir, extList,
maxfile_per_folder)
else:
print >> sys.stderr, "idListFile %s does not exist" % (idListFile)
if fileListFile != "":
if os.path.exists(fileListFile):
fileList = open(fileListFile, "r").read().split("\n")
fileList = filter(None, fileList)
if len(fileList) <= 0:
print >> sys.stderr, "No file in fileListFile %s" % (
fileListFile)
else:
SplitToFolder_filelist(fileList, workdir, maxfile_per_folder)
else:
print >> sys.stderr, "fileListFile %s does not exist" % (
fileListFile)
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 = ""
infile = ""
classfile = ""
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 ["-class", "--class"]:
(classfile, 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(classfile, "Class File") != 0:
return 1
if outpath == "":
outpath = os.path.dirname(infile)
if outpath == "":
outpath = "."
(id2ClassDict, classList) = ReadClassDict(classfile)
idList = myfunc.ReadIDList(infile)
rootname = os.path.basename(os.path.splitext(infile)[0])
ext = os.path.splitext(infile)[1]
fpoutList = {}
for i in range(len(classList)):
outfile = outpath + os.sep + rootname + ".%s" % classList[i] + ext
fpoutList[classList[i]] = open(outfile, "w")
for idd in idList:
try:
cls = id2ClassDict[idd]
except:
print >> sys.stderr, "id %s not in classDict" % idd
continue
fpoutList[cls].write("%s\n" % idd)
for i in range(len(classList)):
fpoutList[classList[i]].close()
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(argv)
if numArgv < 2:
PrintHelp()
return 1
outpath = "./"
outfile = ""
idListFile = ""
uniprotDBname = ""
idList = []
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 ["-outpath", "--outpath"]:
(outpath, 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 ["-uniprotdb", "--uniprotdb"]:
(uniprotDBname, 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 idListFile != "":
idList += myfunc.ReadIDList(idListFile)
if uniprotDBname == "":
print >> sys.stderr, "uniprotdb not set"
return 1
uniprotdbfile = "%s0.db" % uniprotDBname
if myfunc.checkfile(uniprotdbfile, "uniprotdbfile") != 0:
return 1
fpout = myfunc.myopen(outfile, sys.stdout, "w", False)
hdl = myfunc.MyDB(uniprotDBname)
if hdl.failure:
return 1
for seqid in idList:
data = hdl.GetRecord(seqid)
if data != None:
goinfo = GetGOInfoFromUniprotData(data)
WriteGOInfo(seqid, goinfo, fpout)
hdl.close()
myfunc.myclose(fpout)
def main():#{{{
argv = sys.argv
numArgv=len(sys.argv)
if numArgv < 2:
PrintHelp()
sys.exit()
max_numpair = 10*1000*1000
isQuiet = False
rand_seed = None
idList = []
idListFile = ""
outfile=""
method = 0
i = 1
isNonOptionArg=False
while i < numArgv:
if isNonOptionArg == True:
idList.append(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 sys.argv[i] in [ "-o" , "--o", "-outfile" , "--outfile"]:
outfile, i = myfunc.my_getopt_str(argv,i)
elif argv[i] in ["-m", "--m", "-method", "--method"]:
method, i = myfunc.my_getopt_int(argv,i)
elif sys.argv[i] in [ "-l" , "--l", "-listfile" , "--listfile"]:
idListFile, i = myfunc.my_getopt_str(argv,i)
elif sys.argv[i] in [ "-maxpair" , "--maxpair"]:
max_numpair, i = myfunc.my_getopt_int(argv,i)
elif sys.argv[i] in [ "-seed" , "--seed"]:
rand_seed, i = myfunc.my_getopt_int(argv,i)
elif sys.argv[i] == "-q":
isQuiet=True
i += 1
else:
print >> sys.stderr, "Error! Wrong argument:", sys.argv[i]
return 1
else:
idList.append(argv[i])
i += 1
if idListFile != "":
idList += myfunc.ReadIDList(idListFile)
numseqid = len(idList)
if numseqid <= 0:
print >> sys.stderr, "List file is empty."
return 1
elif numseqid < 2:
print >> sys.stderr, "Too few items. At least 2 are required."
return 1
fpout = myfunc.myopen(outfile, sys.stdout, "w", False)
if method == 0:
pairlist = myfunc.GenerateRandomPair(len(idList), max_numpair,
rand_seed)
elif method == 1:
pairlist = myfunc.GenerateRandomPair_no_repeat_use(len(idList),
max_numpair, rand_seed)
for pair in pairlist:
print >> fpout, "%s %s" %(idList[pair[0]], idList[pair[1]])
myfunc.myclose(fpout)
return 0
def main(g_params): #{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
outfile = ""
fileListFile = ""
fileList = []
pfamDefFile = "%s/data/pfam/pfam26.0/Pfam-A.clans.tsv" % (DATADIR3)
threshold_Fraction_Group_2 = 0.05
threshold_NumSeq_Group_2 = 2
tableinfoFile = ""
pdbtospFile = ""
sprotACListFile = ""
threshold_g12_seqidt = 20.0
topoalnFile = ""
aapath = ""
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 ["-l", "--l"]:
(fileListFile, 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 ["-topoaln", "--topoaln"]:
(topoalnFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-aapath", "--aapath"]:
(aapath, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-thncls2", "--thncls2"]:
(threshold_NumSeq_Group_2, i) = myfunc.my_getopt_int(argv, i)
elif argv[i] in ["-thfrac2", "--thfrac2"]:
(threshold_Fraction_Group_2,
i) = myfunc.my_getopt_float(argv, i)
elif argv[i] in ["-pfamdef", "--pfamdef"]:
(pfamDefFile, i) = myfunc.my_getopt_str(argv, i)
elif (argv[i] in ["-pdbtosp", "--pdbtosp"]):
pdbtospFile, i = myfunc.my_getopt_str(argv, i)
elif (argv[i] in ["-sprot", "--sprot"]):
sprotACListFile, 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 len(fileList) < 1:
print >> sys.stderr, "No input set. exit"
return 1
if myfunc.checkfile(topoalnFile, "topoalnFile") != 0:
return 1
if myfunc.checkfile(aapath, "aapath") != 0:
return 1
if outfile == "":
print >> sys.stderr, "outfile not set. Exit"
return 1
outpath = myfunc.my_dirname(outfile)
if not os.path.exists(outpath):
cmd = ["mkdir", "-p", outpath]
try:
subprocess.check_output(cmd)
except subprocess.CalledProcessError, e:
print e
return 1
cmd = ["mkdir", "-p", outpath]
try:
subprocess.check_output(cmd)
except subprocess.CalledProcessError, e:
print e
return 1
(pfamidDefDict, clanidDefDict) = lcmp.ReadPfamDefFile(pfamDefFile)
# Read in pdbtosp map
if pdbtospFile != "":
(pdb2uniprotMap, uniprot2pdbMap) = myfunc.ReadPDBTOSP(pdbtospFile)
else:
(pdb2uniprotMap, uniprot2pdbMap) = ({}, {})
# Read in swissprot ac list
if sprotACListFile != "":
swissprotAcSet = set(myfunc.ReadIDList(sprotACListFile))
else:
swissprotAcSet = set([])
fpout = myfunc.myopen(outfile, sys.stdout, "w", False)
if tableinfoFile != "":
pairalnStat = lcmp.ReadPairAlnTableInfo(tableinfoFile)
if pairalnStat != {}:
outfile_pair_g12 = outfile + ".pair_group1_2.txt"
fpout_pair = myfunc.myopen(outfile_pair_g12, sys.stdout, "w", False)
else:
fpout_pair = None
selectedPairList = [] # select pairs for draw pairwise topology alignment
# for each family, select the pair with highest sequence identity between
def main(g_params): #{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
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 ["-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 fileListFile != "":
fileList += myfunc.ReadIDList(fileListFile)
if len(fileList) < 1:
print >> sys.stderr, "%s: no input file is set. exit" % (sys.argv[0])
if not g_params['method'] in ["id", "seq"]:
print >> sys.stderr, "%s: bad method \"%s\"" % (sys.argv[0],
g_params['method'])
fpout = myfunc.myopen(outfile, sys.stdout, "w", False)
for i in xrange(len(fileList)):
status = IsUniqueSeq(fileList[i], g_params['method'],
g_params['isUseMD5'])
if status >= 0:
if status == 1:
yes_or_no = "yes"
else:
yes_or_no = "no"
print >> fpout, "%s\t%s" % (fileList[i], yes_or_no)
else:
print >> sys.stderr, "%s: Failed to read file %s" % (sys.argv[0],
fileList[i])
myfunc.myclose(fpout)
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
outfile = ""
datafile = "/data3/data/uniprot/uniprot_trembl.tableinfo"
idList = []
idListFile = ""
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 = argv[i + 1]
i += 2
elif argv[i] in ["-datafile", "--datafile"]:
datafile = argv[i + 1]
i += 2
elif argv[i] in ["-l", "--l", "-listfile", "--listfile"]:
idListFile = argv[i + 1]
i += 2
elif argv[i] in ["-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 os.path.exists(idListFile):
idList += myfunc.ReadIDList(idListFile)
if (len(idList)) < 1:
print >> sys.stderr, "id not set. Exit"
return 1
if not os.path.exists(datafile):
print >> sys.stderr, "datafile %s not set or not exists. Exit" % (
datafile)
return 1
uniprotInfoDict = ReadUniprotInfo(datafile)
fpout = myfunc.myopen(outfile, sys.stdout, "w", False)
UnirefSeqid2UniprotTableInfo(idList, uniprotInfoDict, fpout)
myfunc.myclose(fpout)
return 0
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
if fileListFile != "":
fileList += myfunc.ReadIDList(fileListFile)
if len(fileList) < 1:
print >> sys.stderr, "%s: no input file is set. exit" % (sys.argv[0])
if not g_params['method'] in ["id", "seq"]:
print >> sys.stderr, "%s: bad method \"%s\"" % (sys.argv[0],
g_params['method'])
for i in xrange(len(fileList)):
RemoveDupSeq(fileList[i], outpath, g_params['method'],
g_params['isUseMD5'])
#}}}
def main(g_params): #{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
SPE_PAIR_LIST = [(2, 1), (2, 4), (2, 6), (2, 8), (3, 6), (3, 7), (4, 6),
(4, 8), (4, 10), (5, 7), (5, 10), (6, 8), (6, 10),
(6, 12), (7, 14), (8, 10), (8, 12), (10, 12), (10, 13),
(11, 13), (12, 14)]
outfile = ""
infile = ""
pfamDefFile = "%s/data/pfam/pfam26.0/Pfam-A.clans.tsv" % (DATADIR3)
signalpFile = "%s/wk/MPTopo/pfamAna_refpro/pred_signalp/refpro20120604-celluar.selmaxlength-m1.nr100.signalp_list" % (
DATADIR3)
#seqid2clanidMapFile = "%s/wk/MPTopo/pfamAna_refpro/pfammap_from_uniprot/refpro20120604-celluar.selmaxlength-m1.nr100.filter.fragmented.seqid2clanid"%(DATADIR3)
#seqid2pfamidMapFile = "%s/wk/MPTopo/pfamAna_refpro/pfammap_from_uniprot/refpro20120604-celluar.selmaxlength-m1.nr100.filter.fragmented.seqid2pfamid"%(DATADIR3)
seqid2clanidMapFile = ""
seqid2pfamidMapFile = ""
tm_pfamidListFile = ""
tm_clanidListFile = ""
pfamid2seqidMapFile = ""
clanid2seqidMapFile = ""
dbname_predTM = ""
pairlistwithpfamidFile = ""
pfamtype = ""
pairListFile = ""
#classList_TableNumTMHeatMap = ["ALL", "RMSP"]
classList_TableNumTMHeatMap = ["ALL"]
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 ["-outpath", "--outpath"]:
(g_params['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 ["-pfamdef", "--pfamdef"]:
(pfamDefFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-signalp", "--signalp"]:
(signalpFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-mp", "--mp"]:
g_params[
'pairwise_comparison_method'], i = myfunc.my_getopt_int(
argv, i)
elif argv[i] in ["-mindiffpair", "--mindiffpair"]:
g_params['mindiffpair'], i = myfunc.my_getopt_int(argv, i)
elif argv[i] in ["-pfamtype", "--pfamtype"]:
pfamtype, i = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-clanidlist", "--clanidlist"]:
(tm_clanidListFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-pfamidlist", "--pfamidlist"]:
(tm_pfamidListFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-seqid2clanid", "--seqid2clanid"]:
(seqid2clanidMapFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-seqid2pfamid", "--seqid2pfamid"]:
(seqid2pfamidMapFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-pfamid2seqid", "--pfamid2seqid"]:
(pfamid2seqidMapFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-clanid2seqid", "--clanid2seqid"]:
(clanid2seqidMapFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-pairlistwithpfamid", "--pairlistwithpfamid"]:
(pairlistwithpfamidFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-predTMdbname", "--predTMdbname"]:
(dbname_predTM, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-pairlist", "--pairlist"]:
(pairListFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-winsize", "--winsize"]:
(g_params['winsize'], i) = myfunc.my_getopt_int(argv, i)
elif argv[i] in ["-outname", "--outname"]:
(g_params['outname'], i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-q", "--q"]:
g_params['isQuiet'] = True
i += 1
elif argv[i] in ["-prokar", "--prokar"]:
g_params['isOnlyAnaProkar'] = True
i += 1
elif argv[i] in ["-eukar", "--eukar"]:
g_params['isOnlyAnaEukar'] = True
i += 1
else:
print >> sys.stderr, "Error! Wrong argument:", argv[i]
return 1
else:
infile = argv[i]
i += 1
if myfunc.checkfile(
infile, "%s (line %d): infile" %
(__file__, inspect.currentframe().f_lineno)) != 0:
return 1
dirpath = myfunc.my_dirname(infile)
# try to obtain Pfam family tag
tag = ""
if pfamtype != "":
if pfamtype.upper().find("FAM") != -1:
tag = ".Family"
elif pfamtype.upper().find("DOM") != -1:
tag = ".Domain"
elif pfamtype.upper().find("REP") != -1:
tag = ".Repeat"
elif pfamtype.upper().find("MOT") != -1:
tag = ".Motif"
else:
tag = ""
else:
if infile.find(".Family.") != -1:
tag = ".Family"
elif infile.find(".Domain.") != -1:
tag = ".Domain"
elif infile.find(".Repeat.") != -1:
tag = ".Repeat"
elif infile.find(".Motif.") != -1:
tag = ".Motif"
else:
tag = ""
if seqid2clanidMapFile == "":
seqid2clanidMapFile = "%s/wk/MPTopo/pfamAna_refpro/pfammap_from_uniprot/Pfam-A-full.seqfrompfamfasta.percentTMpro_scampi.perTM75_nseq20.nr100.filter.fragmented.seqid2clanid" % (
DATADIR3)
if myfunc.checkfile(
seqid2clanidMapFile, "%s (line %d): seqid2clanidMapFile" %
(__file__, inspect.currentframe().f_lineno)):
return 1
if seqid2pfamidMapFile == "":
seqid2pfamidMapFile = "%s/wk/MPTopo/pfamAna_refpro/pfammap_from_uniprot/Pfam-A-full.seqfrompfamfasta.percentTMpro_scampi.perTM75_nseq20%s.nr100.filter.fragmented.seqid2pfamid" % (
DATADIR3, tag)
if myfunc.checkfile(
seqid2pfamidMapFile, "%s (line %d): seqid2pfamidMapFile" %
(__file__, inspect.currentframe().f_lineno)):
return 1
if pfamid2seqidMapFile == "":
pfamid2seqidMapFile = "%s/wk/MPTopo/pfamAna_refpro/pfammap_from_uniprot/Pfam-A-full.seqfrompfamfasta.percentTMpro_scampi.perTM75_nseq20.nr100.filter.fragmented.pfamid2seqid" % (
DATADIR3)
if myfunc.checkfile(
pfamid2seqidMapFile, "%s (line %d): pfamid2seqidMapFile" %
(__file__, inspect.currentframe().f_lineno)):
return 1
if clanid2seqidMapFile == "":
clanid2seqidMapFile = "%s/wk/MPTopo/pfamAna_refpro/pfammap_from_uniprot/Pfam-A-full.seqfrompfamfasta.percentTMpro_scampi.perTM75_nseq20%s.nr100.filter.fragmented.clanid2seqid" % (
DATADIR3, tag)
if myfunc.checkfile(
clanid2seqidMapFile, "%s (line %d): clanid2seqidMapFile" %
(__file__, inspect.currentframe().f_lineno)):
return 1
if tm_pfamidListFile == "":
tm_pfamidListFile = "%s/data/pfam/pfam26.0/Pfam-A-full.seqfrompfamfasta.percentTMpro_scampi.perTM75_nseq20%s.pfamidlist" % (
DATADIR3, tag)
if myfunc.checkfile(
tm_pfamidListFile, "%s (line %d): tm_pfamidListFile" %
(__file__, inspect.currentframe().f_lineno)):
return 1
if tm_clanidListFile == "":
tm_clanidListFile = "%s/data/pfam/pfam26.0/Pfam-A-full.seqfrompfamfasta.percentTMpro_scampi.perTM75_nseq20.clanidlist" % (
DATADIR3)
if myfunc.checkfile(
tm_clanidListFile, "%s (line %d): tm_clanidListFile" %
(__file__, inspect.currentframe().f_lineno)):
return 1
if dbname_predTM == "":
dbname_predTM = "%s/wk/MPTopo/pfamAna_refpro/pred_topcons_single_method4/refpro20120604-celluar.selmaxlength-m1.topcons-single_topcons_single.m1.agree-44.RMSP" % (
DATADIR3)
if myfunc.checkfile(
"%s0.db" % (dbname_predTM), "%s (line %d): dbname_predTM" %
(__file__, inspect.currentframe().f_lineno)):
return 1
if g_params['isOnlyAnaProkar']:
prokarseqidfile = "%s/data/uniprot/reference_proteome/refpro20120604-celluar.selmaxlength-m1.nr100.filter.fragmented.Prokaryota.seqidlist" % (
DATADIR3)
g_params['prokarSeqIDSet'] = set(myfunc.ReadIDList(prokarseqidfile))
if len(g_params['prokarSeqIDSet']) < 1:
return 1
if g_params['isOnlyAnaEukar']:
eukarseqidfile = "%s/data/uniprot/reference_proteome/refpro20120604-celluar.selmaxlength-m1.nr100.filter.fragmented.Eukaryota.seqidlist" % (
DATADIR3)
g_params['eukarSeqIDSet'] = set(myfunc.ReadIDList(eukarseqidfile))
if len(g_params['eukarSeqIDSet']) < 1:
return 1
if pairlistwithpfamidFile == "":
pairlistwithpfamidFile = "%s/../../Pfam-.maxpair100.pairlistwithpfamid" % (
dirpath)
if myfunc.checkfile(
pairlistwithpfamidFile, "%s (line %d): pairlistwithpfamidFile" %
(__file__, inspect.currentframe().f_lineno)):
return 1
pfamid_2_seqidpair_Dict = ReadPairListWithFamID(pairlistwithpfamidFile)
usedPfamIDSet = set(
pfamid_2_seqidpair_Dict.keys()) # pfamids used in pair selection
if pairListFile != "":
li = myfunc.ReadPairList(pairListFile)
SPE_PAIR_LIST = []
for tup in li:
SPE_PAIR_LIST.append((int(tup[0]), int(tup[1])))
(pfamidDefDict, clanidDefDict) = ReadPfamDefFile(pfamDefFile)
signalpDict = lcmp.ReadSignalPDict(signalpFile)
seqid2clanidDict = myfunc.ReadFam2SeqidMap(seqid2clanidMapFile)
seqid2pfamidDict = myfunc.ReadFam2SeqidMap(seqid2pfamidMapFile)
clanid2seqidDict = myfunc.ReadFam2SeqidMap(clanid2seqidMapFile)
pfamid2seqidDict = myfunc.ReadFam2SeqidMap(pfamid2seqidMapFile)
tm_pfamidList = myfunc.ReadIDList(tm_pfamidListFile)
tm_clanidList = myfunc.ReadIDList(tm_clanidListFile)
tm_pfamidSet = set(tm_pfamidList)
tm_clanidSet = set(tm_clanidList)
hdl_predTM = myfunc.MyDB(dbname_predTM)
if not hdl_predTM.failure:
idSet_TMpro = set(hdl_predTM.indexedIDList)
else:
idSet_TMpro = set([])
#classList_TableNumTMHeatMap = ["ALL", "RMSP", "RMDUP"]
#alignrangeList = ['FULL_ALIGNED', 'all', 'PART_ALIGNED']
alignrangeList = ['FULL_ALIGNED']
if g_params['outpath'] != "" and not os.path.exists(g_params['outpath']):
cmd = ["mkdir", "-p", g_params['outpath']]
try:
subprocess.check_call(cmd)
except subprocess.CalledProcessError, e:
print e
return 1
def main(g_params):#{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
outpath = ""
datapath = ""
pairListFile = ""
pairList = []
i = 1
isNonOptionArg=False
while i < numArgv:
if isNonOptionArg == True:
pairList.append(argv[i].split())
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 ["-datapath", "--datapath"]:
(datapath, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-l", "--l"] :
(pairListFile, 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:
pairList.append(argv[i].split())
i += 1
if pairListFile != "":
pairList += [x.split() for x in myfunc.ReadIDList(pairListFile,
delim="\n")]
numpair = len(pairListFile)
if numpair < 1:
print >> sys.stderr, "no pair set. exit"
return 1
if datapath == "":
print >> sys.stderr, "datapath not set"
return 1
elif not os.path.exists(datapath):
print >> sys.stderr, "datapath %s does not exist"%(datapath)
return 1
if outpath == "":
print >> sys.stderr, "outpath not set"
return 1
elif not os.path.exists(outpath):
cmd = ["mkdir", "-p", outpath]
subprocess.check_call(cmd)
WriteHTML(pairList, datapath, outpath)
def main(g_params): #{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
outpath = "./"
outfile = ""
real_topofile = ""
seqfile = ""
restrictIDListFile = ""
outfile_wrong_predtopo = ""
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 ["-owrong", "--owrong"]:
(outfile_wrong_predtopo, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-realtopo", "--realtopo"]:
(real_topofile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-seqfile", "--seqfile"]:
(seqfile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-mode", "--mode"]:
(g_params['mode'], i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-path_predtopo", "--path_predtopo"]:
(g_params['path_predtopo'], i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-basename", "--basename"]:
(g_params['basename'], i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-restrictidlist", "--restrictidlist"]:
(restrictIDListFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-q", "--q"]:
g_params['isQuiet'] = True
i += 1
elif argv[i] in ["-rmsp", "--rmsp"]:
g_params['isRMSP'] = 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:
print >> sys.stderr, "Error! Wrong argument:", argv[i]
return 1
i += 1
if myfunc.checkfile(g_params['path_predtopo'], "path_predtopo") != 0:
return 1
if g_params['basename'] == "":
print >> sys.stderr, "%s: basename not set. exit" % (argv[0])
return 1
if myfunc.checkfile(real_topofile, "real_topofile") != 0:
return 1
if restrictIDListFile != "":
g_params['restrictIDset'] = set(myfunc.ReadIDList(restrictIDListFile))
g_params['isRestrictIDList'] = True
if g_params['mode'] == "":
if g_params['path_predtopo'].find("topcons_single") >= 0:
g_params['mode'] = "tps"
elif g_params['path_predtopo'].find("topcons") >= 0:
g_params['mode'] = "tp"
else:
print >> sys.stderr, "mode not set, and can not be recognized from path_predtopo=%s" % (
path_predtopo)
return 1
if not g_params['mode'] in ["tp", "tps"]:
print >> sys.stderr, "Unrecognized mode = %s" % (g_params['mode'])
return 1
(real_idlist, real_annolist,
real_topolist) = myfunc.ReadFasta(real_topofile)
seqDict = {}
if seqfile != "" and os.path.exists(seqfile):
(seq_idlist, seq_annolist, seqlist) = myfunc.ReadFasta(seqfile)
for i in xrange(len(seq_idlist)):
seqDict[seq_idlist[i]] = seqlist[i]
if len(real_idlist) <= 0:
print >> sys.stderr, "Failed to read real_topofile %s" % (
real_topofile)
return 1
real_topodict = {}
for i in xrange(len(real_idlist)):
real_topodict[real_idlist[i]] = real_topolist[i]
fpout = myfunc.myopen(outfile, sys.stdout, "w", False)
fpout_wrong = myfunc.myopen(outfile_wrong_predtopo, None, "w", False)
idSet_single = set([])
idSet_multi = set([])
for seqid in real_topodict:
topo = real_topodict[seqid]
numTM = myfunc.CountTM(topo)
if numTM == 1:
idSet_single.add(seqid)
elif numTM > 1:
idSet_multi.add(seqid)
# print "len(real_topodict)", len(real_topodict)
# print "len(idSet_single)", len(idSet_single)
# print "len(idSet_multi)", len(idSet_multi)
#for TM_type in ["All_Alpha", "Single", "Multi"]:
for TM_type in ["All_Alpha"]:
if TM_type == "All_Alpha":
sub_real_topodict = real_topodict
else:
sub_real_topodict = {}
for seqid in real_topodict:
topo = real_topodict[seqid]
numTM = myfunc.CountTM(topo)
if TM_type == "Single" and numTM == 1:
sub_real_topodict[seqid] = topo
elif TM_type == "Multi" and numTM > 1:
sub_real_topodict[seqid] = topo
Benchmark(sub_real_topodict, idSet_single, idSet_multi, TM_type, fpout,
fpout_wrong, seqDict)
myfunc.myclose(fpout)
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
infile = ""
outfile = ""
keyIDListFile = ""
contentIDListFile = ""
isKeyIDSet = False
isContentIDSet = False
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 = argv[i+1]
i += 2
elif argv[i] in ["-idlist1", "--idlist1"] :
keyIDListFile = argv[i+1]
isKeyIDSet = True
i += 2
elif argv[i] in ["-idlist2", "--idlist2"] :
contentIDListFile = argv[i+1]
isContentIDSet = True
i += 2
elif argv[i] in ["-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 infile == "":
print >> sys.stderr, "infile not set. Exit"
return 1
elif not os.path.exists(infile):
print >> sys.stderr, "infile %s does not exist. Exit"%(infile)
return 1
keyIDSet = {}
contentIDSet = {}
if keyIDListFile != "":
keyIDSet = set(myfunc.ReadIDList(keyIDListFile))
if contentIDListFile != "":
contentIDSet = set(myfunc.ReadIDList(contentIDListFile))
fpout = myfunc.myopen(outfile, sys.stdout, "w", False)
# if idlist1 and idlist2 is empty, output nothing
if isKeyIDSet or isContentIDSet:
Filter_seqid2fam_map(infile, keyIDSet, contentIDSet, isKeyIDSet,
isContentIDSet, fpout)
else:
os.system("cat %s"%(infile))
myfunc.myclose(fpout)
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
infile = ""
progList = []
progListFile = ""
outpath = ""
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 ["-prog", "--prog"]:
tmpstr, i = myfunc.my_getopt_str(argv, i)
progList.append(tmpstr)
elif argv[i] in ["-gzip", "--gzip"]:
tmpstr, i = myfunc.my_getopt_str(argv, i)
if tmpstr.upper()[0] == "-":
print >> sys.stderr, "Bad argument, -gzip should be"\
" followed by yes or no"
return 1
elif tmpstr.upper()[0] == "Y":
g_params['isGzip'] = True
else:
g_params['isGzip'] = False
elif argv[i] in ["-num", "--num"]:
g_params['num_per_split'], i = myfunc.my_getopt_int(argv, i)
elif argv[i] in ["-proglist", "--proglist"]:
progListFile, 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 ["-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,"infile") != 0:
return 1
inputList = ReadInputList(infile) # [(filename, numseq)]
inputList = sorted(inputList, key=lambda x:x[1], reverse=False)
rtname_infile = os.path.basename(os.path.splitext(infile)[0])
# get progList
if len(progList) == 0 and progListFile == "":
progList = default_progList
else:
if progListFile != "":
tmp_list = myfunc.ReadIDList(progListFile)
if len(tmp_list) == 0:
print >> sys.stderr, "progListFile %s does not exist or empty"%(
progListFile)
return 1
else:
progList += tmp_list
if len(progList) == 0:
print >> sys.stderr, "progList is empty. exit"
return 1
if outpath != "" and not os.path.exists(outpath):
try:
subprocess.check_output(["mkdir", "-p", outpath])
except subprocess.CalledProcessError, e:
print e
return 1
