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1 #! /usr/bin/env python
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2
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3
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4 import optparse, os, sys, tarfile, random
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5 from optparse import OptionParser
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6 from commons.core.launcher.Launcher import Launcher
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7 from commons.core.sql.TableJobAdaptatorFactory import TableJobAdaptatorFactory
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8
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9 def stop_err(msg):
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10 sys.stderr.write('%s\n' % msg)
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11 sys.exit()
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12
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13 def toTar(tarFileName, outCountNames):
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14 dir = os.path.dirname(tarFileName)
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15 tfile = tarfile.open(tarFileName + ".tmp.tar", "w")
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16 currentPath = os.getcwd()
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17 os.chdir(dir)
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18 for file in outCountNames:
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19 relativeFileName = os.path.basename(file)
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20 tfile.add(relativeFileName)
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21 os.system("mv %s %s" % (tarFileName + ".tmp.tar", tarFileName))
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22 tfile.close()
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23 os.chdir(currentPath)
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24
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25 def _map(iLauncher, cmd, cmdStart, cmdFinish ):
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26 lCmds = []
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27 lCmds.append(cmd)
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28 lCmdStart = []
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29 lCmdStart.append(cmdStart)
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30 lCmdFinish = []
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31 lCmdFinish.append(cmdFinish)
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32 return(iLauncher.prepareCommands_withoutIndentation(lCmds, lCmdStart, lCmdFinish))
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33
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34 def _createCountNumberCommand(iLauncher, inputFile, outputFile):
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35 lArgs = []
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36 lArgs.append("%s" % inputFile)
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37 lArgs.append("%s" % outputFile)
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38 return iLauncher.getSystemCommand("perl %s/SMART/DiffExpAnal/countNumber.pl " % os.environ["REPET_PATH"], lArgs)
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39
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40 def __main__():
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41 #Parse Command Line
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42 parser = optparse.OptionParser()
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43 parser.add_option("-i", "--input", dest="inputFile", help="input txt file, a list of overlapping results files.")
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44 parser.add_option("-o", "--output", dest="outputFile", help="Out txt file.")
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45 parser.add_option("-t", "--tar", dest="outputTar", default=None, help="output all count results in a tar file.")
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46 (options, args) = parser.parse_args()
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47
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48 #Parse the input txt file and read a list of transcripts files.
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49 file = open(options.inputFile, "r")
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50 lines = file.readlines()
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51 inputFileNames = []
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52 outCountNames = []
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53 outputName = options.outputFile
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54 resDirName = os.path.dirname(outputName) + '/'
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55
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56 #Write output txt file and define all output count file names
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57 out = open(outputName, "w")
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58 out.write("label\tfiles\tgroup\n")
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59 for line in lines:
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60 tab = line.split()
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61 inputFileNames.append(tab[1])
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62 outCountName = resDirName + tab[0] + "_outCount_%s.csv" % random.randrange(0, 10000)
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63 outCountNames.append(outCountName)
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64 out.write(tab[0] + '\t' + outCountName + '\t' + tab[0][5] + '\n')
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65 file.close()
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66 out.close()
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67
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68 #Launch on nodes
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69 acronym = "countNumber"
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70 jobdb = TableJobAdaptatorFactory.createJobInstance()
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71 iLauncher = Launcher(jobdb, os.getcwd(), "", "", os.getcwd(), os.getcwd(), "jobs", "", acronym, acronym, False, True)
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72 lCmdsTuples = []
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73 for i in range(len(inputFileNames)): #Construct the lines commands
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74 inputFile = inputFileNames[i]
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75 outputFile = outCountNames[i]
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76 cmd2Launch = _createCountNumberCommand(iLauncher, inputFile, outputFile)
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77 cmdStart = ""
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78 cmdFinish = ""
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79 lCmdsTuples.append(_map(iLauncher, cmd2Launch, cmdStart, cmdFinish))
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80
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81
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82
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83 iLauncher.runLauncherForMultipleJobs(acronym, lCmdsTuples, True)
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84
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85
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86
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87 if options.outputTar != None:
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88 toTar(options.outputTar, outCountNames)
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89
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90
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91 if __name__=="__main__":__main__()
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