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1 import os
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2 import re
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3 import shutil
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4 import sys
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5 import subprocess
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6 import zipfile
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7 import optparse
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8
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9 def main():
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10
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11 parser = optparse.OptionParser()
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12 parser.add_option('-s', action="store", dest='summary')
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13 parser.add_option('-e', action="store", dest='dataSetName')
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14 parser.add_option('-p', action="store", dest='new_file_path')
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15 parser.add_option('-c', action="store", dest='inputcdffull_name')
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16 parser.add_option('-f', action="store", dest='inputufl_name')
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17 parser.add_option('-g', action="store", dest='inputugp_name')
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18 parser.add_option('-a', action="store", dest='inputacs_name')
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19 parser.add_option('-d', action="store", dest='inputcdffull')
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20 parser.add_option('-v', action="store", dest='inputufl')
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21 parser.add_option('-w', action="store", dest='inputugp')
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22 parser.add_option('-b', action="store", dest='inputacs')
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23 parser.add_option('-t', action="store", dest='tumorcsv')
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24 parser.add_option('-y', action="store", dest='settingsType')
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25 parser.add_option('-o', action="store", dest='outputgraph')
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26 parser.add_option('-z', action="store", dest='zipfigures')
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27 parser.add_option('-k', action="store", dest='outputlog')
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28 parser.add_option('-l', action="store", dest='log')
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29 parser.add_option('-u', action="store", dest='user_id')
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30
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31 parser.add_option('-i', action="append", dest='inputFile', default=[])
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32 parser.add_option('-n', action='append', dest='inputFileName', default=[])
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33
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34 options, args = parser.parse_args()
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35
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36 dataSetName=options.dataSetName
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37 destinationPath=os.path.join(options.new_file_path, options.user_id, dataSetName)
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38
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39 mpagenomics_dir = os.path.join(options.new_file_path,"mpagenomics",options.user_id)
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40 data_dir = os.path.join(options.new_file_path, options.user_id)
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41
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42 try:
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43 os.makedirs(data_dir)
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44 except:
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45 shutil.rmtree(data_dir)
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46 os.makedirs(data_dir)
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47
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48 if (not os.path.isdir(mpagenomics_dir)):
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49 os.makedirs(mpagenomics_dir)
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50
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51 for inputFile, inputFileName in zip(options.inputFile,options.inputFileName):
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52 source = inputFile
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53 destination=os.path.join(data_dir,inputFileName)
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54 _copy(source,destination)
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55
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56
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57 cdffull_name=options.inputcdffull_name
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58 if (cdffull_name.count(",") != 0):
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59 chipType=cdffull_name.split(",",1)[0]
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60 tagExt=cdffull_name.split(",",1)[1]
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61 tag=tagExt.split(".",1)[0]
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62 else:
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63 chipType=cdffull_name.split(".",1)[0]
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64 tag=""
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65
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66 _copy(options.inputcdffull,os.path.join(data_dir, options.inputcdffull_name))
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67 _copy(options.inputugp,os.path.join(data_dir, options.inputugp_name))
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68 _copy(options.inputufl,os.path.join(data_dir, options.inputufl_name))
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69 _copy(options.inputacs,os.path.join(data_dir, options.inputacs_name))
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70
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71
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72 fig_dir = os.path.join("mpagenomics", options.user_id, "figures", dataSetName, "signal")
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73 abs_fig_dir = os.path.join(options.new_file_path, fig_dir)
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74
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75
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76 retcode = _preprocess(chipType, dataSetName, mpagenomics_dir, data_dir, options.new_file_path, options.tumorcsv, options.settingsType, options.outputgraph, options.outputlog, options.log, tag)
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77
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78 if (retcode == 0):
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79 if (os.path.isdir(abs_fig_dir)) and (options.outputgraph == "TRUE"):
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80
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81 new_files = os.listdir(abs_fig_dir)
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82 zipbuf = zipfile.ZipFile(os.path.join(abs_fig_dir, options.zipfigures), 'w', zipfile.ZIP_DEFLATED)
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83 for current_file in new_files:
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84 fn = os.path.join(abs_fig_dir, current_file)
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85 relfn = fn[len(abs_fig_dir) + len(os.sep):]
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86 zipbuf.write(fn, relfn)
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87
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88 f = open(options.summary, "w")
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89 # Create report
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90 try:
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91 for inputFileName in options.inputFileName:
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92 f.write("%s\t%s\t%s\n" %(inputFileName,dataSetName,chipType))
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93 finally:
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94 shutil.rmtree(data_dir)
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95 f.close()
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96
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97 sys.exit(retcode)
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98
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99 sys.exit(retcode)
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100
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101
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102 def _copy(source, destination):
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103 try:
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104 os.symlink(source, destination)
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105 except:
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106 shutil.copy(source, destination)
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107
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108 def _preprocess (chipType,dataset,mpagenomics_dir,data_dir,tmp_dir,tumor,settingType,outputgraph,outputlog,log,tag):
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109 script_dir=os.path.dirname(os.path.abspath(__file__))
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110
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111 if (outputlog=="TRUE"):
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112 errfile=open(log,'w')
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113 else:
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114 errfile=open(os.path.join(tmp_dir,"errfile.log"),'w')
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115
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116 retcode = subprocess.call(["Rscript", os.path.join(script_dir,"preprocess.R"), chipType, dataset, mpagenomics_dir, data_dir, tumor, settingType, outputgraph, tag], stdout = errfile, stderr = errfile)
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117 return(retcode)
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118
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119
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120 if __name__ == "__main__":
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121 main()
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