--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/SMART/Java/Python/CleanTranscriptFile.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,74 @@
+#! /usr/bin/env python
+#
+# Copyright INRA-URGI 2009-2011
+# 
+# This software is governed by the CeCILL license under French law and
+# abiding by the rules of distribution of free software. You can use,
+# modify and/ or redistribute the software under the terms of the CeCILL
+# license as circulated by CEA, CNRS and INRIA at the following URL
+# "http://www.cecill.info".
+# 
+# As a counterpart to the access to the source code and rights to copy,
+# modify and redistribute granted by the license, users are provided only
+# with a limited warranty and the software's author, the holder of the
+# economic rights, and the successive licensors have only limited
+# liability.
+# 
+# In this respect, the user's attention is drawn to the risks associated
+# with loading, using, modifying and/or developing or reproducing the
+# software by the user in light of its specific status of free software,
+# that may mean that it is complicated to manipulate, and that also
+# therefore means that it is reserved for developers and experienced
+# professionals having in-depth computer knowledge. Users are therefore
+# encouraged to load and test the software's suitability as regards their
+# requirements in conditions enabling the security of their systems and/or
+# data to be ensured and, more generally, to use and operate it in the
+# same conditions as regards security.
+# 
+# The fact that you are presently reading this means that you have had
+# knowledge of the CeCILL license and that you accept its terms.
+#
+from optparse import OptionParser
+from SMART.Java.Python.cleaning.CleanerChooser import CleanerChooser
+
+
+class CleanTranscriptFile(object):
+
+	def __init__(self, verbosity):
+		self.verbosity = verbosity
+		self.chooser   = CleanerChooser(self.verbosity)
+
+	def setInputFile(self, fileName, format):
+		self.chooser.findFormat(format)
+		self.cleaner = self.chooser.getCleaner()
+		self.cleaner.setInputFileName(fileName)
+
+	def setOutputFile(self, fileName):
+		self.cleaner.setOutputFileName(fileName)
+
+	def setAcceptedTypes(self, types):
+		if types != None:
+			self.cleaner.setAcceptedTypes(types)
+
+	def run(self):
+		self.cleaner.clean()
+
+
+if __name__ == "__main__":
+
+	description = "Clean Transcript File v1.0.1: Clean a transcript file so that it is useable for S-MART. [Category: Other]"
+
+	parser = OptionParser(description = description)
+	parser.add_option("-i", "--input",       dest="inputFileName",  action="store",                     type="string", help="query input file [compulsory] [format: file in transcript format given by -f]")
+	parser.add_option("-f", "--format",      dest="format",         action="store",                     type="string", help="format of previous file [compulsory] [format: transcript file format]")
+	parser.add_option("-t", "--types",       dest="acceptedTypes",  action="store",      default=None,  type="string", help="name of the types you want to keep in GFF/GTF (list separated by commas) [format: string] [default: None]")
+	parser.add_option("-o", "--output",      dest="outputFileName", action="store",                     type="string", help="output file [format: output file in GFF3 format]")
+	parser.add_option("-v", "--verbosity",   dest="verbosity",      action="store",      default=1,     type="int",    help="trace level [format: int]")
+	(options, args) = parser.parse_args()
+
+	ctf = CleanTranscriptFile(options.verbosity)
+	ctf.setInputFile(options.inputFileName, options.format)
+	ctf.setOutputFile(options.outputFileName)
+	ctf.setAcceptedTypes(None if options.acceptedTypes == None else options.acceptedTypes.split(","))
+	ctf.run()
+