Mercurial > repos > nanette > nanettetest3
comparison test_script_path.py @ 6:066c5504de31 draft
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author | nanette |
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date | Wed, 21 Aug 2013 04:51:37 -0400 |
parents | bfe8aba3fd1c |
children | b41fc3e15949 |
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5:94b0fd035fec | 6:066c5504de31 |
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1 """ | |
2 @summary: GO enrichment analysis (hotspots) | |
3 @author: nanette.coetzer@gmail.com | |
4 @version 5 | |
5 | |
6 """ | |
7 import optparse, sys | |
8 import subprocess | |
9 import tempfile | |
10 import os, re | |
11 | |
12 def stop_err( msg ): | |
13 sys.stderr.write( "%s\n" % msg ) | |
14 sys.exit() | |
15 | |
16 def __main__(): | |
17 #Parse Command Line | |
18 parser = optparse.OptionParser() | |
19 parser.add_option("-i", "--input1", default=None, dest="input1", | |
20 help="genes") | |
21 parser.add_option("-o", "--output1", default=None, dest="output1", | |
22 help="star genes") | |
23 parser.add_option("-m", "--myflag", default=None, dest="myflag", | |
24 help="star genes") | |
25 (options, args) = parser.parse_args() | |
26 | |
27 try: | |
28 open(options.input1, "r").close() | |
29 except TypeError, e: | |
30 stop_err("You need to supply the Gene Universe file:\n" + str(e)) | |
31 except IOError, e: | |
32 stop_err("Can not open the Gene Universe file:\n" + str(e)) | |
33 | |
34 | |
35 ########################################################## | |
36 | |
37 infile = open(options.input1,"r") | |
38 inlist = [] | |
39 for line in infile: | |
40 inlist.append(line.strip()) | |
41 infile.close() | |
42 outfile = open(options.output1,"w") | |
43 for l in inlist: | |
44 outfile.write("* "+str(l)+"\n") | |
45 outfile.write(options.myflag + "\n") | |
46 outfile.close() | |
47 | |
48 ############################################## | |
49 | |
50 if __name__=="__main__": | |
51 __main__() |