diff TEiso/ClosestToStartSite_Wrapper.py @ 1:15d6811e6bf5 draft

Uploaded

--- a/TEiso/ClosestToStartSite_Wrapper.py	Fri Apr 29 09:11:18 2016 -0400
+++ b/TEiso/ClosestToStartSite_Wrapper.py	Tue May 24 08:59:28 2016 -0400
@@ -3,7 +3,6 @@
 
 import subprocess, tempfile, sys, os, glob, shutil, time
 from optparse import OptionParser
-from commons.core.utils.RepetOptionParser import RepetOptionParser
 
 
 class ClosestToStartSiteWrapper(object):
@@ -18,14 +17,16 @@
         
         
     def setAttributesFromCmdLine(self):
-        self._toolVersion = "1.0"
-        description = "ClosestToStartSite version %s" % self._toolVersion
-        epilog = "\n parses a bed file and create a bed file to create a report about positions of features A to features B. \n"
-        epilog += "example: ClosestToStartSite.py -i <inputFile> -o  <outputFile>\n"
-        parser = RepetOptionParser(description = description, epilog = epilog, version = self._toolVersion) 
-        parser.add_option("-i", "--inputFile",  dest = "inputFile",  action = "store", type = "string", help = "Input GTF File name(transcript.gtf of Cufflinks).",  default = "")
+        description = "ClosestToStartSite"
+        epilog = "\nParser a bed file and create a bed file to create a report about positions of features A to features B. \n"
+        epilog +="it can also add the class code of features A. \n"
+        epilog += "example: ClosestToStartSite.py -i <inputFile> -c <cuff_in.tmap> -o <outputFile>\n"
+        parser = OptionParser(description = description, version = "1.0")
+        parser.add_option("-i", "--inputFile",  dest = "inputFile",  action = "store", type = "string", help = "input bed file",  default = "")
+        parser.add_option("-c", "--cuffcom_tmap",  dest = "cuffcom_tmap",  action = "store", type = "string", help = "input gtf file",  default = "")
         parser.add_option("-o", "--outputFile", dest = "outputFile", action = "store", type = "string", help = "output Bed File name", default = "")
-        parser.add_option("-v", "--verbosity",  dest = "verbosity",  action = "store", type = "int",    help = "Verbosity [optional] [default: 3]",default = 3)
+        #parser.add_option("-t", "--outputFileclasscode", dest = "outputFile_classcode", action = "store", type = "string", help = "output Bed File name with class code.", default = "")
+        parser.add_option("-v", "--verbosity",  dest = "verbosity",  action = "store", type = "int",    help = "verbosity [optional] [default: 3]",default = 3)
         options = parser.parse_args()[0]
         self._setAttributesFromOptions(options)
 
@@ -36,6 +37,11 @@
         prg = "ClosestToStartSite.py"
         args = ""
         args += "-i %s" % self._options.inputFile
+	args += " "
+        args += "-o %s" % self._options.outputFile
+        if  self._options.cuffcom_tmap != "":
+            args += " "
+            args += "-c %s" % self._options.cuffcom_tmap
         cmd = "%s %s" %(prg, args)
         print cmd