diff mpagenomics_normalize-7dc6ce39fb89/segmentation.py @ 0:84b13b0e2b85

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mpagenomics_normalize-7dc6ce39fb89/segmentation.py	Thu May 07 08:22:36 2015 -0400
@@ -0,0 +1,78 @@
+import os
+import sys
+import subprocess
+import shutil
+import getopt
+
+
+def main(argv):
+
+    #default values 
+    cellularity="1"
+    nbcall="3"
+
+    try:
+        opts, args = getopt.getopt(argv,"h:i:f:p:o:l:og:g:m:st:u:",["input=","new_file_path=","outputlog=","output=","log=","outputgraph=", "graph=", "method=", "signalType=", "user_id=", "nbcall=", "cellularity="])
+    except getopt.GetoptError as err:
+        print str(err)
+        sys.exit(2)
+    for opt, arg in opts:
+        if opt == '-h':
+            print 'segmentation.py'
+            sys.exit()
+        elif opt in ("-i", "--input"):
+            inputdata = arg
+        elif opt in ("-f", "--new_file_path"):
+            tmp_dir = arg
+        elif opt in ("-p", "--outputlog"):
+            outputlog = arg
+        elif opt in ("-o", "--output"):
+            output = arg
+        elif opt in ("-l", "--log"):
+            log = arg
+        elif opt in ("-og", "--outputgraph"):
+            plot = arg
+        elif opt in ("-g", "--graph"):
+            pdffigures = arg
+        elif opt in ("-m", "--method"):
+            method = arg
+        elif opt in ("-st", "--signalType"):
+            signalType = arg
+        elif opt in ("-u", "--user_id"):
+            userId = arg
+        elif opt in ("-c", "--nbcall"):
+            nbcall = arg
+        elif opt in ("-e", "--cellularity"):
+            cellularity = arg
+
+    #===========================================================================
+    # inputdata=sys.argv[1]
+    # tmp_dir=sys.argv[2]
+    # nbcall=sys.argv[3]
+    # cellularity=sys.argv[4]
+    # outputlog=sys.argv[5] 
+    # output=sys.argv[6]
+    # log=sys.argv[7]
+    # plot=sys.argv[8]
+    # pdffigures=sys.argv[9]
+    # method=sys.argv[10]
+    #===========================================================================
+    
+    script_dir=os.path.dirname(os.path.abspath(__file__))
+        
+    if (outputlog=="TRUE"):
+        errfile=open(log,'w')
+    else:
+        errfile=open(os.path.join(tmp_dir,"errfile.log"),'w')
+    
+    retcode=subprocess.call(["Rscript", os.path.join(script_dir,"segmentation.R"), inputdata, tmp_dir, nbcall, cellularity, output, method, userId, signalType], stdout = errfile, stderr = errfile)
+    
+    if (plot=="TRUE"):
+        shutil.copy(os.path.join(tmp_dir,"mpagenomics",userId,"Rplots.pdf"), pdffigures)
+    
+    errfile.close()
+       
+    sys.exit(retcode)
+
+if __name__ == "__main__":
+    main(main(sys.argv[1:]))
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