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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 getopt
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5
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6 def main(argv):
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7
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8 symmetrize="False"
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9
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10 try:
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11 opts, args = getopt.getopt(argv,"hc:i:o:f:s:y:t:p:l:g:n:u:",["chrom=","input=","output=","new_file_path=","settings_type=","settings_tumor=","symmetrize=","outputlog=","log=","settings_signal=","settings_snp=","userid="])
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12 except getopt.GetoptError as err:
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13 print str(err)
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14 sys.exit(2)
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15 for opt, arg in opts:
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16 if opt == '-h':
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17 print 'extractCN.py'
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18 sys.exit()
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19 elif opt in ("-c", "--chrom"):
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20 chromosome = arg
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21 elif opt in ("-i", "--input"):
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22 input_file = arg
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23 elif opt in ("-o", "--output"):
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24 output_file = 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 ("-s", "--settings_type"):
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28 input_type = arg
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29 elif opt in ("-t", "--settings_tumor"):
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30 settings_tumor = arg
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31 elif opt in ("-y", "--symmetrize"):
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32 symmetrize = arg
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33 elif opt in ("-p", "--outputlog"):
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34 outputlog = arg
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35 elif opt in ("-l", "--log"):
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36 log = arg
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37 elif opt in ("-g", "--settings_signal"):
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38 signal = arg
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39 elif opt in ("-n", "--settings_snp"):
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40 snp = arg
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41 elif opt in ("-u", "--userid"):
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42 user_id = arg
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43
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44
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45
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46 #===========================================================================
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47 #chromosome=sys.argv[1]
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48 #input_file=sys.argv[2]
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49 # output_file=sys.argv[3]
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50 # tmp_dir=sys.argv[4]
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51 # input_type=sys.argv[5]
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52 # settings_tumor=sys.argv[6]
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53 # outputlog=sys.argv[7]
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54 # log=sys.argv[8]
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55 # signal=sys.argv[9]
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56 # snp=sys.argv[10]
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57 # user_id=sys.argv[11]
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58 #===========================================================================
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59 script_dir=os.path.dirname(os.path.abspath(__file__))
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60
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61 iFile=open(input_file,'r')
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62 dataSetLine=iFile.readline()
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63 dataset=dataSetLine.split("\t")[1]
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64 iFile.close()
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65
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66 if (outputlog=="TRUE"):
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67 errfile=open(log,'w')
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68 else:
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69 errfile=open(os.path.join(tmp_dir,"errfile.log"),'w')
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70
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71 retcode=subprocess.call(["Rscript", os.path.join(script_dir,"extractCN.R"), chromosome, dataset, output_file, tmp_dir, input_type, settings_tumor, signal,snp,user_id, symmetrize], stdout = errfile, stderr = errfile)
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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:]))
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