Mercurial > repos > nanette > nanettetest3
comparison test_script_path.py @ 8:a303f3ffa153 draft default tip
Uploaded
| author | nanette |
|---|---|
| date | Wed, 21 Aug 2013 07:05:54 -0400 |
| parents | b41fc3e15949 |
| children |
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| 7:b41fc3e15949 | 8:a303f3ffa153 |
|---|---|
| 18 parser = optparse.OptionParser() | 18 parser = optparse.OptionParser() |
| 19 parser.add_option("-i", "--input1", default=None, dest="input1", | 19 parser.add_option("-i", "--input1", default=None, dest="input1", |
| 20 help="genes") | 20 help="genes") |
| 21 parser.add_option("-o", "--output1", default=None, dest="output1", | 21 parser.add_option("-o", "--output1", default=None, dest="output1", |
| 22 help="star genes") | 22 help="star genes") |
| 23 parser.add_option("-p", "--output2", default=None, dest="output2", | |
| 24 help="plot") | |
| 23 parser.add_option("-m", "--myflag", default=None, dest="myflag", | 25 parser.add_option("-m", "--myflag", default=None, dest="myflag", |
| 24 help="star genes") | 26 help="star genes") |
| 27 | |
| 25 (options, args) = parser.parse_args() | 28 (options, args) = parser.parse_args() |
| 26 | 29 |
| 27 try: | 30 try: |
| 28 open(options.input1, "r").close() | 31 open(options.input1, "r").close() |
| 29 except TypeError, e: | 32 except TypeError, e: |
| 45 outfile.write("--- TEST ---" + "\n") | 48 outfile.write("--- TEST ---" + "\n") |
| 46 outfile.write(options.myflag + "\n") | 49 outfile.write(options.myflag + "\n") |
| 47 outfile.write("--- TEST ---" + "\n") | 50 outfile.write("--- TEST ---" + "\n") |
| 48 outfile.close() | 51 outfile.close() |
| 49 | 52 |
| 53 ########################################################## | |
| 54 | |
| 55 # Create temp direcotry | |
| 56 tempdir = tempfile.mkdtemp() | |
| 57 fixdir = options.myflag | |
| 58 | |
| 59 # copy INPUT file to the temp directory | |
| 60 # create R script => save in temp directory | |
| 61 # generate new header | |
| 62 new_script = open(tempdir+"/new_script.r","w") | |
| 63 header = "setwd(\"%s\")" %tempdir | |
| 64 new_script.write(header+"\n") | |
| 65 | |
| 66 # add script body | |
| 67 script = open(fixdir+"/r_plot.r","r") | |
| 68 for line in script: | |
| 69 new_script.write(line.strip()+"\n") | |
| 70 new_script.close() | |
| 71 | |
| 72 # run R script from temp directory | |
| 73 s = "R CMD BATCH %s/new_script.r out.txt" %tempdir | |
| 74 subprocess.call(s, shell=True) | |
| 75 | |
| 76 os.system("mv %s/plot.pdf %s" %(tempdir,options.output2)) | |
| 77 | |
| 50 ############################################## | 78 ############################################## |
| 51 | 79 |
| 52 if __name__=="__main__": | 80 if __name__=="__main__": |
| 53 __main__() | 81 __main__() |