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1 import os
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2 import sys
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3 import subprocess
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4 import shutil
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5 import getopt
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6
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7
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8 def main(argv):
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9
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10 #default values
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11 cellularity="1"
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12 nbcall="3"
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13
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14 try:
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15 opts, args = getopt.getopt(argv,"h:i:f:p:o:l:og:g:m:st:u:",["input=","new_file_path=","outputlog=","output=","log=","outputgraph=", "graph=", "method=", "signalType=", "user_id=", "nbcall=", "cellularity="])
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16 except getopt.GetoptError as err:
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17 print str(err)
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18 sys.exit(2)
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19 for opt, arg in opts:
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20 if opt == '-h':
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21 print 'segmentation.py'
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22 sys.exit()
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23 elif opt in ("-i", "--input"):
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24 inputdata = arg
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25 elif opt in ("-f", "--new_file_path"):
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26 tmp_dir = arg
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27 elif opt in ("-p", "--outputlog"):
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28 outputlog = arg
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29 elif opt in ("-o", "--output"):
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30 output = arg
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31 elif opt in ("-l", "--log"):
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32 log = arg
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33 elif opt in ("-og", "--outputgraph"):
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34 plot = arg
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35 elif opt in ("-g", "--graph"):
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36 pdffigures = arg
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37 elif opt in ("-m", "--method"):
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38 method = arg
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39 elif opt in ("-st", "--signalType"):
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40 signalType = arg
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41 elif opt in ("-u", "--user_id"):
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42 userId = arg
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43 elif opt in ("-c", "--nbcall"):
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44 nbcall = arg
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45 elif opt in ("-e", "--cellularity"):
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46 cellularity = arg
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47
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48 #===========================================================================
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49 # inputdata=sys.argv[1]
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50 # tmp_dir=sys.argv[2]
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51 # nbcall=sys.argv[3]
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52 # cellularity=sys.argv[4]
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53 # outputlog=sys.argv[5]
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54 # output=sys.argv[6]
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55 # log=sys.argv[7]
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56 # plot=sys.argv[8]
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57 # pdffigures=sys.argv[9]
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58 # method=sys.argv[10]
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59 #===========================================================================
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60
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61 script_dir=os.path.dirname(os.path.abspath(__file__))
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62
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63 if (outputlog=="TRUE"):
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64 errfile=open(log,'w')
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65 else:
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66 errfile=open(os.path.join(tmp_dir,"errfile.log"),'w')
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67
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68 retcode=subprocess.call(["Rscript", os.path.join(script_dir,"segmentation.R"), inputdata, tmp_dir, nbcall, cellularity, output, method, userId, signalType], stdout = errfile, stderr = errfile)
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69
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70 if (plot=="TRUE"):
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71 shutil.copy(os.path.join(tmp_dir,"mpagenomics",userId,"Rplots.pdf"), pdffigures)
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72
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73 errfile.close()
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74
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75 sys.exit(retcode)
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76
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77 if __name__ == "__main__":
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78 main(main(sys.argv[1:])) |
