diff TEiso/ClosestToStartSite_Wrapper.py @ 11:782306d67e39 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TEiso/ClosestToStartSite_Wrapper.py	Wed Jul 20 08:08:54 2016 -0400
@@ -0,0 +1,74 @@
+#!/usr/bin/env python
+
+
+import subprocess, tempfile, sys, os, glob, shutil, time
+from optparse import OptionParser
+
+
+class ClosestToStartSiteWrapper(object):
+
+    def __init__(self):
+        self._options = None
+        
+        
+    def stop_err(self, msg ):
+        sys.stderr.write( "%s\n" % msg )
+        sys.exit()
+        
+        
+    def setAttributesFromCmdLine(self):
+        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("-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)
+
+    def _setAttributesFromOptions(self, options):
+        self._options = options
+
+    def run(self):
+        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
+        
+        try:
+            tmp_err = tempfile.NamedTemporaryFile().name
+            tmp_stderr = open( tmp_err, 'wb' )
+            proc = subprocess.Popen( args=cmd, shell=True, cwd=".", stderr=tmp_stderr )
+            returncode = proc.wait()
+            tmp_stderr.close()
+            # get stderr, allowing for case where it's very large
+            tmp_stderr = open( tmp_err, 'rb' )
+            stderr = ''
+            buffsize = 1048576
+            try:
+                while True:
+                    stderr += tmp_stderr.read( buffsize )
+                    if not stderr or len( stderr ) % buffsize != 0:
+                        break
+            except OverflowError:
+                pass
+            tmp_stderr.close()
+            if stderr:
+                raise Exception, stderr
+        except Exception, e:
+            self.stop_err( 'Error in ClosestToStartSite:\n' + str( e ) ) 
+        
+if __name__ == "__main__":
+    iWrapper = ClosestToStartSiteWrapper()
+    iWrapper.setAttributesFromCmdLine()
+    iWrapper.run()