comparison test_script_path.py @ 6:066c5504de31 draft

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author nanette
date Wed, 21 Aug 2013 04:51:37 -0400
parents bfe8aba3fd1c
children b41fc3e15949
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5:94b0fd035fec 6:066c5504de31
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__()