diff TEiso/GFFToBed_Wrapper.py @ 16:836ce3d9d47a draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TEiso/GFFToBed_Wrapper.py	Thu Jul 21 07:42:47 2016 -0400
@@ -0,0 +1,81 @@
+#!/usr/bin/env python
+
+
+import subprocess, tempfile, sys, os, glob, shutil, time
+from optparse import OptionParser
+#from commons.core.utils.RepetOptionParser import RepetOptionParser
+
+
+class GFFToBedWrapper(object):
+
+    def __init__(self):
+        self._options = None
+        
+        
+    def stop_err(self, msg ):
+        sys.stderr.write( "%s\n" % msg )
+        sys.exit()
+        
+        
+    def setAttributesFromCmdLine(self):
+       ## self._toolVersion = "1.0"
+        description = "GFFToBed version"
+        epilog = "\n parses a GFF3 file and create a bed file. \n"
+        epilog += "example: GFFToBed.py -i <inputFile> -o  <outputFile>\n"
+        #parser = RepetOptionParser(description = description, epilog = epilog, version = self._toolVersion)
+        parser = OptionParser(description = description, version = "1.0") 
+        parser.add_option("-i", "--inputFile",  dest = "inputFile",  action = "store", type = "string", help = "Input GFF3 File name.",  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)
+        options = parser.parse_args()[0]
+        self._setAttributesFromOptions(options)
+
+    def _setAttributesFromOptions(self, options):
+        self._options = options
+
+    def run(self):
+	tmp = "%s_tmp" % ((os.path.splitext(self._options.outputFile)[0]))
+	prg = "GFFToBed.py"
+        args = ""
+        args += "-i %s" % self._options.inputFile
+        args += " "
+        args += "-o %s" % tmp
+        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 GFFToBed:\n' + str( e ) ) 
+
+	
+	try:
+	    cmdsort= "bedtools sort -i %s > %s" % (tmp, self._options.outputFile)
+	    os.system(cmdsort)
+        except Exception, e:
+            self.stop_err( 'Error in bedtools sort:\n' + str( e ) )
+
+
+
+if __name__ == "__main__":
+    iWrapper = GFFToBedWrapper()
+    iWrapper.setAttributesFromCmdLine()
+    iWrapper.run()