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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
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6 def main():
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7
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8 input_file=sys.argv[1]
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9 tmp_dir=sys.argv[4]
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10 script_dir=os.path.dirname(os.path.abspath(__file__))
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11 plot=sys.argv[11]
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12 pdffigures=sys.argv[13]
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13 outputlog=sys.argv[14]
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14 log=sys.argv[15]
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15 user=sys.argv[16]
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16 package=sys.argv[17]
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17
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18 iFile=open(input_file,'r')
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19 dataSetLine=iFile.readline()
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20 dataset=dataSetLine.split("\t")[1]
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21 iFile.close()
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22
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23 if (outputlog=="TRUE"):
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24 errfile=open(log,'w')
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25 else:
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26 errfile=open(os.path.join(tmp_dir,"errfile.log"),'w')
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27
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28 retcode=subprocess.call(["Rscript", os.path.join(script_dir,"selection.R"), dataset, sys.argv[2], sys.argv[3], sys.argv[4], sys.argv[5], sys.argv[6], sys.argv[7], sys.argv[8], sys.argv[9], sys.argv[10], sys.argv[11], sys.argv[12],sys.argv[16],package], stdout = errfile, stderr = errfile)
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29
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30 if (plot=="TRUE"):
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31 shutil.copy(os.path.join(tmp_dir,"mpagenomics",user,"Rplots.pdf"), pdffigures)
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32
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33 errfile.close()
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34
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35 sys.exit(retcode)
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36
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37 if __name__ == "__main__":
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38 main()
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