diff test_script_path.py @ 8:a303f3ffa153 draft default tip

Uploaded

--- a/test_script_path.py	Wed Aug 21 05:56:49 2013 -0400
+++ b/test_script_path.py	Wed Aug 21 07:05:54 2013 -0400
@@ -20,8 +20,11 @@
                       help="genes")
     parser.add_option("-o", "--output1", default=None, dest="output1", 
                       help="star genes")
+    parser.add_option("-p", "--output2", default=None, dest="output2", 
+                      help="plot")
     parser.add_option("-m", "--myflag", default=None, dest="myflag", 
                       help="star genes")
+    
     (options, args) = parser.parse_args()
 
     try:
@@ -47,6 +50,31 @@
     outfile.write("--- TEST ---" + "\n")
     outfile.close()
     
+    ##########################################################
+    
+    # Create temp direcotry
+    tempdir = tempfile.mkdtemp()
+    fixdir = options.myflag
+
+    # copy INPUT file to the temp directory
+    # create R script => save in temp directory
+    # generate new header 
+    new_script = open(tempdir+"/new_script.r","w")
+    header = "setwd(\"%s\")" %tempdir
+    new_script.write(header+"\n")
+    
+    # add script body
+    script = open(fixdir+"/r_plot.r","r")
+    for line in script:
+        new_script.write(line.strip()+"\n")
+    new_script.close()
+    
+    # run R script from temp directory
+    s = "R CMD BATCH %s/new_script.r out.txt" %tempdir
+    subprocess.call(s, shell=True)
+    
+    os.system("mv %s/plot.pdf %s" %(tempdir,options.output2))
+       
     ##############################################
     
 if __name__=="__main__":