--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/DiffExpAnal/countNumber_parallel_unSQL.py	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,91 @@
+#! /usr/bin/env python
+
+
+import optparse, os, sys, tarfile, random
+from optparse import OptionParser
+from commons.core.launcher.Launcher import Launcher
+from commons.core.sql.TableJobAdaptatorFactory import TableJobAdaptatorFactory
+
+def stop_err(msg):
+	sys.stderr.write('%s\n' % msg)
+	sys.exit()
+
+def toTar(tarFileName, outCountNames):
+	dir = os.path.dirname(tarFileName)
+	tfile = tarfile.open(tarFileName + ".tmp.tar", "w")
+	currentPath = os.getcwd()
+	os.chdir(dir)
+	for file in outCountNames:
+		relativeFileName = os.path.basename(file)
+		tfile.add(relativeFileName)
+	os.system("mv %s %s" % (tarFileName + ".tmp.tar", tarFileName))
+	tfile.close()
+	os.chdir(currentPath)
+
+def _map(iLauncher, cmd, cmdStart, cmdFinish ):
+	lCmds = []
+	lCmds.append(cmd)
+	lCmdStart = []
+	lCmdStart.append(cmdStart)
+	lCmdFinish = []
+	lCmdFinish.append(cmdFinish)
+	return(iLauncher.prepareCommands_withoutIndentation(lCmds, lCmdStart, lCmdFinish))
+
+def _createCountNumberCommand(iLauncher, inputFile, outputFile):
+		lArgs = []
+		lArgs.append("%s" % inputFile)
+		lArgs.append("%s" %  outputFile)
+		return iLauncher.getSystemCommand("perl %s/SMART/DiffExpAnal/countNumber.pl " %  os.environ["REPET_PATH"], lArgs)
+
+def __main__():
+	#Parse Command Line
+	parser = optparse.OptionParser()
+	parser.add_option("-i", "--input", dest="inputFile", help="input txt file, a list of overlapping results files.")
+	parser.add_option("-o", "--output", dest="outputFile", help="Out txt file.")
+	parser.add_option("-t", "--tar", dest="outputTar", default=None, help="output all count results in a tar file.")
+	(options, args) = parser.parse_args()
+
+	#Parse the input txt file and read a list of transcripts files.
+	file = open(options.inputFile, "r")
+	lines = file.readlines()
+	inputFileNames = []
+	outCountNames = []
+	outputName = options.outputFile
+	resDirName = os.path.dirname(outputName) + '/'
+
+	#Write output txt file and define all output count file names
+	out = open(outputName, "w")
+	out.write("label\tfiles\tgroup\n")
+	for line in lines:
+		tab = line.split()
+		inputFileNames.append(tab[1])
+		outCountName = resDirName + tab[0] + "_outCount_%s.csv" % random.randrange(0, 10000)
+		outCountNames.append(outCountName)
+		out.write(tab[0] + '\t' + outCountName + '\t' + tab[0][5] + '\n')
+	file.close()
+	out.close()
+	
+	#Launch on nodes
+	acronym = "countNumber"
+	jobdb = TableJobAdaptatorFactory.createJobInstance()
+	iLauncher = Launcher(jobdb, os.getcwd(), "", "", os.getcwd(), os.getcwd(), "jobs", "", acronym, acronym, False, True)
+	lCmdsTuples = []
+	for i in range(len(inputFileNames)):	#Construct the lines commands
+		inputFile = inputFileNames[i]
+		outputFile = outCountNames[i]
+		cmd2Launch = _createCountNumberCommand(iLauncher, inputFile, outputFile)
+		cmdStart = ""
+		cmdFinish = ""
+		lCmdsTuples.append(_map(iLauncher, cmd2Launch, cmdStart, cmdFinish))
+
+
+		
+	iLauncher.runLauncherForMultipleJobs(acronym, lCmdsTuples, True)
+
+
+	
+	if options.outputTar != None:
+		toTar(options.outputTar, outCountNames)
+
+
+if __name__=="__main__":__main__()