--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/SMART/Java/Python/convertTranscriptFile.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,115 @@
+#! /usr/bin/env python
+#
+# Copyright INRA-URGI 2009-2010
+# 
+# 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.
+#
+"""
+Read a transcript file and convert it to another format
+"""
+
+import os, re
+from optparse import OptionParser
+from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
+from commons.core.writer.TranscriptWriter import TranscriptWriter
+from SMART.Java.Python.misc.Progress import Progress
+
+
+class ConvertTranscriptFile(object):
+    def __init__(self,inputFileName="", inputFormat ="", outputFileName="", outputFormat="", name="", sequenceFileName=None, strands=False, galaxy=False, feature=None, featurePart=None, verbosity=1):
+        self.inputFileName = inputFileName
+        self.inputFormat = inputFormat
+        self.outputFileName = outputFileName
+        self.outputFormat = outputFormat
+        self.name = name
+        self.sequenceFileName = sequenceFileName
+        self.strands = strands
+        self.galaxy = galaxy
+
+        self.feature=feature
+        self.featurePart=featurePart
+        
+        self.verbosity = verbosity
+         
+    def setAttributesFromCmdLine(self):
+        description = "Convert Transcript File v1.0.3: Convert a file from a format to another. [Category: Conversion]"
+        parser = OptionParser(description = description)
+        parser.add_option("-i", "--input",        dest="inputFileName",    action="store",                       type="string", help="input file [compulsory] [format: file in format given by -f]")
+        parser.add_option("-f", "--inputFormat",  dest="inputFormat",      action="store",                       type="string", help="format of the input file [compulsory] [format: transcript or mapping file format]")
+        parser.add_option("-o", "--output",       dest="outputFileName",   action="store",                       type="string", help="output file [compulsory] [format: output file in format given by -g]")
+        parser.add_option("-g", "--outputFormat", dest="outputFormat",     action="store",                       type="string", help="format of the output file [compulsory] [format: transcript file format]")
+        parser.add_option("-n", "--name",         dest="name",             action="store",      default="SMART", type="string", help="name for the transcripts [format: string] [default: SMART]")
+        parser.add_option("-s", "--sequences",    dest="sequenceFileName", action="store",      default=None,    type="string", help="give the corresponding Multi-Fasta file (useful for EMBL format) [format: string]")
+        parser.add_option("-t", "--strands",      dest="strands",          action="store_true", default=False,                  help="consider the 2 strands as different (only useful for writing WIG files) [format: bool] [default: False]")
+        parser.add_option("-v", "--verbosity",    dest="verbosity",        action="store",      default=1,       type="int",    help="trace level [format: int] [default: 1]")
+        parser.add_option("-G", "--galaxy",       dest="galaxy",           action="store_true", default=False,                  help="used for galaxy [format: bool] [default: False]")
+        (options, args) = parser.parse_args()
+        self._setAttributesFromOptions(options)
+
+    def _setAttributesFromOptions(self, options):
+        self.inputFileName = options.inputFileName
+        self.inputFormat = options.inputFormat
+        self.outputFileName = options.outputFileName
+        self.outputFormat = options.outputFormat
+        self.name = options.name  
+        self.sequenceFileName = options.sequenceFileName
+        self.strands = options.strands
+        self.galaxy =  options.galaxy
+        self.verbosity = options.verbosity
+
+    def run(self):
+        # create parser
+        parser = TranscriptContainer(self.inputFileName, self.inputFormat, self.verbosity)
+        # create writer
+        writer = TranscriptWriter(self.outputFileName, self.outputFormat, self.verbosity)
+        # connect parser and writer
+        writer.setContainer(parser)
+            
+        if self.name != None:
+            writer.setTitle(self.name)
+        if self.feature != None:
+            writer.setFeature(self.feature)
+        if self.featurePart != None:
+            writer.setFeaturePart(self.featurePart)
+        if self.sequenceFileName != None:
+            writer.addSequenceFile(self.sequenceFileName)
+            
+        nbItems = 0
+        if self.verbosity > 0:
+            nbItems = parser.getNbItems()
+            print "%i items found" % (nbItems)
+    
+        if self.strands:
+            writer.setStrands(True)
+        # convert
+        writer.write()
+        writer.close()
+
+if __name__ == "__main__":
+    iConvertTranscriptFile = ConvertTranscriptFile()
+    iConvertTranscriptFile.setAttributesFromCmdLine()
+    iConvertTranscriptFile.run()