--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/SMART/Java/Python/fold.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,95 @@
+#! /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 mapping file (many formats supported) and select some of them
+Mappings should be sorted by read names
+"""
+
+from optparse import OptionParser
+from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
+from SMART.Java.Python.toolLauncher.RnaFoldLauncher import RnaFoldLauncher
+from commons.core.writer.Gff3Writer import Gff3Writer
+
+
+class Fold(object):
+    """
+    Fold a series of transcripts
+    """
+
+    def __init__(self, verbosity = 0):
+        self.verbosity       = verbosity
+        self.rnaFoldLauncher = RnaFoldLauncher(verbosity)
+        self.gff3Writer      = None
+
+
+    def setInputFileName(self, fileName, format):
+        transcriptContainer = TranscriptContainer(fileName, format, options.verbosity)
+        self.rnaFoldLauncher.setTranscriptList(transcriptContainer)
+
+    
+    def setOutputFileName(self, fileName):
+        self.gff3Writer = Gff3Writer("%s.gff3" % (fileName), self.verbosity)
+
+
+    def setGenomeFileName(self, fileName):
+        self.rnaFoldLauncher.setGenomeFile(fileName)
+
+
+    def setExtensions(self, fivePrime, threePrime):
+        self.rnaFoldLauncher.setExtensions(fivePrime, threePrime)
+
+
+    def start(self):
+        self.gff3Writer.addTranscriptList(self.rnaFoldLauncher.getResults())
+
+
+
+if __name__ == "__main__":
+    
+    # parse command line
+    description = "Fold v1.0.1: Fold a list of transcript and give the energy. [Category: Personal]"
+
+    parser = OptionParser(description = description)
+    parser.add_option("-i", "--input",      dest="inputFileName",  action="store",            type="string", help="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 file [compulsory] [format: transcript file format]")
+    parser.add_option("-o", "--output",     dest="outputFileName", action="store",            type="string", help="output file [format: output file in GFF3 format]")
+    parser.add_option("-g", "--genome",     dest="genomeFileName", action="store",            type="string", help="genome file name [format: file in FASTA format]")
+    parser.add_option("-5", "--fivePrime",  dest="fivePrime",      action="store",            type="int",    help="extend towards the 5' end [format: int]")
+    parser.add_option("-3", "--threePrime", dest="threePrime",     action="store",            type="int",    help="extend towards the 3' end [format: int]")
+    parser.add_option("-v", "--verbosity",  dest="verbosity",      action="store", default=1, type="int",    help="trace level [format: int]")
+    (options, args) = parser.parse_args()
+
+    folder = Fold(options.verbosity)
+    folder.setInputFileName(options.inputFileName, options.format)
+    folder.setOutputFileName(options.outputFileName)
+    folder.setExtensions(options.fivePrime, options.threePrime)
+    folder.setGenomeFileName(options.genomeFileName)
+    folder.start()