def checkValidArguments(argv):
arg_cnt = 0
for arg in argv:
if arg == "-o" or arg == "--tblout":
arg_cnt += 1
elif arg == "--domtblout" or arg == "--pfamtblout":
arg_cnt += 1
elif arg == "-cpu" and argv[argv.index("-cpu") + 1].isdigit():
arg_cnt += 2
elif arg[-1:] == "/" or arg[-2:] == "fa" or arg[-5:] == "fasta" or arg[-3:] == "fst":
arg_cnt += 1
if len(argv) != arg_cnt:
print "\nWrong option!, check your command!"
print hj_toolkit.makeCMD(argv)
exit(1)
def checkValidArgument(argv) :
if argv.has_key('-pt') == False or argv.has_key('-num') == False or argv.has_key('-r') == False :
print "\nCore values are missed, check your command!"
print hj_toolkit.makeCMD(sys.argv)
exit(1)
elif len(argv) == 4 and argv.has_key('-s') == False and argv.has_key('-o') == False :
print "\nUnknown options, check your command!"
print hj_toolkit.makeCMD(sys.argv)
exit(1)
elif len(argv) == 5 and (argv.has_key('-s') == False or argv.has_key('-o') == False) :
print "\nUnknown options, check your command!"
print hj_toolkit.makeCMD(sys.argv)
exit(1)
else :
fasta = self.fasta_stack.pop()
self.lock.release()
runMER(self.argv, fasta)
seedPostProcessing(self.argv, fasta)
runRepSeek(self.argv, fasta)
self.cnt += 1
# main part of program
if len(sys.argv) == 2 and sys.argv[1] == "-h" :
printUSAGE()
exit(0)
argv = hj_toolkit.parseArgument(sys.argv)
checkCoreValues(argv, hj_toolkit.makeCMD(sys.argv))
checkValidOpt(argv, hj_toolkit.makeCMD(sys.argv))
if argv.has_key('-r') :
sys.stdout = open(argv['-r'], "w")
if argv.has_key('-e') :
sys.stderr = open(argv['-e'], "a")
#prepare temp directories
dt = str(datetime.datetime.now())[:19].replace(' ','_').replace(':','')
seed_dir = 'LTR_' + dt + '/seed/'
tseed_dir = 'LTR_' + dt + '/tseed/'
tmp_dir = 'LTR_' + dt + '/tmp/'
os.mkdir('LTR_' + dt)
os.mkdir(seed_dir)
os.mkdir(tseed_dir)
prev = arg continue else : print >>sys.stderr, "\nWrong option! check your command" print >>sys.stderr, "Your command : " + cmd + "\n" exit(1) prev = arg if opts["-m"] and opts["-M"] : print >>sys.stderr, "\n-m and -M options are exclusive" print >>sys.stderr, "Your command : " + cmd + "\n" return opts # main part of program userCMD = hj_toolkit.makeCMD(sys.argv) if len(sys.argv) == 2 and sys.argv[1] == "-h" : printUSAGE() exit(0) elif len(sys.argv) < 3 : print >>sys.stderr, "\nplease input right format" print >>sts.stderr, "Your command : " + userCMD + "\n" opts = checkValidOpt(sys.argv[1:-2], userCMD) _file1 = open(sys.argv[-2], "r") _file2 = open(sys.argv[-1], "r") _data1 = _file1.readlines() _file1.close()
elif arg[-1:] == "/" or arg[-2:] == "fa" or arg[-5:] == "fasta" or arg[-3:] == "fst":
arg_cnt += 1
if len(argv) != arg_cnt:
print "\nWrong option!, check your command!"
print hj_toolkit.makeCMD(argv)
exit(1)
# main part of program
if len(sys.argv) == 2 and sys.argv[1] == "-h":
printUSAGE()
exit(1)
elif len(sys.argv) < 3:
print "\nToo short arguments!, please check your command!"
print hj_toolkit.makeCMD(sys.argv)
exit(1)
elif len(sys.argv) > 10:
print "\nToo long arguments!, please check your command!"
print hj_toolkit.makeCMD(sys.argv)
exit(1)
argv = sys.argv[1:]
checkValidArguments(argv)
hmm = ""
seq = ""
cpu = 0
rm_list = []
for arg in argv:
line = pt_file.readline()
while line != "" and line[0] != '>' :
seq += line[:-1]
line = pt_file.readline()
seq += makeRandomSeq(int(argv['-r']))
print pt_name[:-1]
writeString(seq)
#Main part of program
if len(sys.argv) != 1 and sys.argv[1] == '-h' :
printUSAGE()
exit(1)
elif len(sys.argv) < 4 :
print "Too short arguments! check your command!"
print "\n" + hj_toolkit.makeCMD(sys.argv)
exit(1)
elif len(sys.argv) > 6 :
print "Too long arguments! check your commad!"
print "\n" + hj_toolkit.makeCMD(sys.argv)
exit(1)
argv = hj_toolkit.parseArgument(sys.argv)
checkValidArgument(argv)
pt_file = open(argv['-pt'], "r")
if argv.has_key('-o') :
sys.stdout = open(argv['-o'], "w")
makeSequences(pt_file, argv)
