Mercurial > repos > nanette > nanettetest3
diff test_script_path.py @ 0:bfe8aba3fd1c draft
Uploaded
author | nanette |
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date | Wed, 21 Aug 2013 04:24:49 -0400 |
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children | b41fc3e15949 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test_script_path.py Wed Aug 21 04:24:49 2013 -0400 @@ -0,0 +1,51 @@ +""" +@summary: GO enrichment analysis (hotspots) +@author: nanette.coetzer@gmail.com +@version 5 + +""" +import optparse, sys +import subprocess +import tempfile +import os, re + +def stop_err( msg ): + sys.stderr.write( "%s\n" % msg ) + sys.exit() + +def __main__(): + #Parse Command Line + parser = optparse.OptionParser() + parser.add_option("-i", "--input1", default=None, dest="input1", + help="genes") + parser.add_option("-o", "--output1", default=None, dest="output1", + help="star genes") + parser.add_option("-m", "--myflag", default=None, dest="myflag", + help="star genes") + (options, args) = parser.parse_args() + + try: + open(options.input1, "r").close() + except TypeError, e: + stop_err("You need to supply the Gene Universe file:\n" + str(e)) + except IOError, e: + stop_err("Can not open the Gene Universe file:\n" + str(e)) + + + ########################################################## + + infile = open(options.input1,"r") + inlist = [] + for line in infile: + inlist.append(line.strip()) + infile.close() + outfile = open(options.output1,"w") + for l in inlist: + outfile.write("* "+str(l)+"\n") + outfile.write(options.myflag + "\n") + outfile.close() + + ############################################## + +if __name__=="__main__": + __main__()