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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, subprocess, tempfile, shutil, tarfile, random
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5 from optparse import OptionParser
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6
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7 def stop_err(msg):
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8 sys.stderr.write('%s\n' % msg)
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9 sys.exit()
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10
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11 def toTar(tarFileName, outCountNames):
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12 dir = os.path.dirname(tarFileName)
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13 tfile = tarfile.open(tarFileName + ".tmp.tar", "w")
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14 currentPath = os.getcwd()
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15 os.chdir(dir)
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16 for file in outCountNames:
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17 relativeFileName = os.path.basename(file)
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18 tfile.add(relativeFileName)
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19 os.system("mv %s %s" % (tarFileName + ".tmp.tar", tarFileName))
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20 tfile.close()
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21 os.chdir(currentPath)
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22
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23
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24 def __main__():
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25 #Parse Command Line
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26 parser = optparse.OptionParser()
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27 parser.add_option("-i", "--input", dest="inputFile", help="input txt file, a list of overlapping results files.")
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28 parser.add_option("-o", "--output", dest="outputFile", help="Out txt file.")
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29 parser.add_option("-t", "--tar", dest="outputTar", default=None, help="output all count results in a tar file.")
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30 (options, args) = parser.parse_args()
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31
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32 #Parse the input txt file and read a list of transcripts files.
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33 file = open(options.inputFile, "r")
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34 lines = file.readlines()
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35 inputFileNames = []
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36 outCountNames = []
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37 outputName = options.outputFile
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38 resDirName = os.path.dirname(outputName) + '/'
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39
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40 #Write output txt file and define all output count file names
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41 out = open(outputName, "w")
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42 out.write("label\tfiles\tgroup\n")
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43 for line in lines:
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44 tab = line.split()
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45 inputFileNames.append(tab[1])
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46 outCountName = resDirName + tab[0] + "_outCount_%s.csv" % random.randrange(0, 10000)
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47 outCountNames.append(outCountName)
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48 out.write(tab[0] + '\t' + outCountName + '\t' + tab[0][5] + '\n')
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49 file.close()
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50 out.close()
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51
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52 #Construct the lines commands
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53 cmds = []
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54 for i in range(len(inputFileNames)):
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55 cmd = "perl %s/SMART/DiffExpAnal/countNumber.pl " % os.environ["REPET_PATH"]
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56 opts = "%s %s " % (inputFileNames[i], outCountNames[i])
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57 cmd += opts
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58 cmds.append(cmd)
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59
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60 tmp_files = []
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61 for i in range(len(cmds)):
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62 try:
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63 tmp_out = tempfile.NamedTemporaryFile().name
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64 tmp_files.append(tmp_out)
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65 tmp_stdout = open(tmp_out, 'wb')
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66 tmp_err = tempfile.NamedTemporaryFile().name
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67 tmp_files.append(tmp_err)
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68 tmp_stderr = open(tmp_err, 'wb')
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69 proc = subprocess.Popen(args=cmds[i], shell=True, cwd=".", stdout=tmp_stdout, stderr=tmp_stderr)
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70 returncode = proc.wait()
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71 tmp_stderr.close()
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72 #get stderr, allowing for case where it's very large
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73 tmp_stderr = open(tmp_err, 'rb')
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74 stderr = ''
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75 buffsize = 1048576
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76 try:
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77 while True:
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78 stderr += tmp_stderr.read(buffsize)
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79 if not stderr or len(stderr) % buffsize != 0:
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80 break
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81 except OverflowError:
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82 pass
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83 tmp_stdout.close()
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84 tmp_stderr.close()
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85 if returncode != 0:
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86 raise Exception, stderr
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87 except Exception, e:
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88 stop_err('Error in :\n' + str(e))
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89
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90 if options.outputTar != None:
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91 toTar(options.outputTar, outCountNames)
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92
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93 for tmp_file in tmp_files:
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94 os.remove(tmp_file)
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95
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96 if __name__=="__main__":__main__()
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