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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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8
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23 parser.add_option("-p", "--output2", default=None, dest="output2",
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24 help="plot")
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25 parser.add_option("-m", "--myflag", default=None, dest="myflag",
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26 help="star genes")
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8
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27
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28 (options, args) = parser.parse_args()
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29
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30 try:
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31 open(options.input1, "r").close()
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32 except TypeError, e:
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33 stop_err("You need to supply the Gene Universe file:\n" + str(e))
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34 except IOError, e:
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35 stop_err("Can not open the Gene Universe file:\n" + str(e))
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36
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37
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38 ##########################################################
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39
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40 infile = open(options.input1,"r")
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41 inlist = []
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42 for line in infile:
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43 inlist.append(line.strip())
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44 infile.close()
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45 outfile = open(options.output1,"w")
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46 for l in inlist:
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47 outfile.write("* "+str(l)+"\n")
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48 outfile.write("--- TEST ---" + "\n")
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49 outfile.write(options.myflag + "\n")
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50 outfile.write("--- TEST ---" + "\n")
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51 outfile.close()
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52
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8
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53 ##########################################################
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54
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55 # Create temp direcotry
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56 tempdir = tempfile.mkdtemp()
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57 fixdir = options.myflag
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58
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59 # copy INPUT file to the temp directory
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60 # create R script => save in temp directory
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61 # generate new header
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62 new_script = open(tempdir+"/new_script.r","w")
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63 header = "setwd(\"%s\")" %tempdir
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64 new_script.write(header+"\n")
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65
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66 # add script body
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67 script = open(fixdir+"/r_plot.r","r")
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68 for line in script:
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69 new_script.write(line.strip()+"\n")
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70 new_script.close()
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71
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72 # run R script from temp directory
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73 s = "R CMD BATCH %s/new_script.r out.txt" %tempdir
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74 subprocess.call(s, shell=True)
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75
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76 os.system("mv %s/plot.pdf %s" %(tempdir,options.output2))
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77
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78 ##############################################
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79
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80 if __name__=="__main__":
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81 __main__()
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