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1 """
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2 @summary: GO enrichment analysis (hotspots)
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3 @author: nanette.coetzer@gmail.com
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4 @version 5
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5
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6 """
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7 import optparse, sys
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8 import subprocess
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9 import tempfile
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10 import os, re
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11
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12 def stop_err( msg ):
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13 sys.stderr.write( "%s\n" % msg )
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14 sys.exit()
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15
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16 def __main__():
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17 #Parse Command Line
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18 parser = optparse.OptionParser()
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19 parser.add_option("-i", "--input1", default=None, dest="input1",
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20 help="genes")
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21 parser.add_option("-o", "--output1", default=None, dest="output1",
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22 help="star genes")
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23 parser.add_option("-m", "--myflag", default=None, dest="myflag",
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24 help="star genes")
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25 (options, args) = parser.parse_args()
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26
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27 try:
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28 open(options.input1, "r").close()
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29 except TypeError, e:
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30 stop_err("You need to supply the Gene Universe file:\n" + str(e))
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31 except IOError, e:
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32 stop_err("Can not open the Gene Universe file:\n" + str(e))
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33
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34
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35 ##########################################################
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36
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37 infile = open(options.input1,"r")
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38 inlist = []
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39 for line in infile:
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40 inlist.append(line.strip())
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41 infile.close()
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42 outfile = open(options.output1,"w")
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43 for l in inlist:
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44 outfile.write("* "+str(l)+"\n")
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45 outfile.write("--- TEST ---" + "\n")
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46 outfile.write(options.myflag + "\n")
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7
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47 outfile.write("--- TEST ---" + "\n")
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48 outfile.close()
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49
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50 ##############################################
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51
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52 if __name__=="__main__":
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53 __main__()
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