--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/mappingToCoordinates.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,91 @@
+#! /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.
+#
+
+
+"""Convert files with some mapping format to coordinates format"""
+
+import os
+from optparse import OptionParser
+from commons.core.parsing.PslParser import PslParser
+from commons.core.parsing.AxtParser import AxtParser
+from commons.core.writer.Gff3Writer import Gff3Writer
+from commons.core.writer.MySqlTranscriptWriter import MySqlTranscriptWriter
+from SMART.Java.Python.structure.TranscriptListsComparator import TranscriptListsComparator
+from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
+from SMART.Java.Python.misc.Progress import Progress
+
+
+class MappingToCoordinates(object):
+    def __init__(self,verbosity=1, inputFileName=None, format = None, output=None,galaxy = False, title="S-MART"):
+        self.verbosity = verbosity
+        self.inputFileName = inputFileName
+        self.format = format
+        self.output = output
+        self.galaxy = galaxy
+        self.title = title
+    
+    def setAttributesFromCmdLine(self):
+        description = "Mapping To Coordinates v1.0.1: Convert a set of mappings (given by a mapping tool) to a set of transcripts. [Category: Conversion]"
+        parser = OptionParser(description = description)
+        parser.add_option("-i", "--input",     dest="inputFileName", action="store",                     type="string", help="input file [compulsory] [format: file in mapping format given by -f]")
+        parser.add_option("-f", "--format",    dest="format",        action="store",                     type="string", help="format of file [compulsory] [format: mapping file format]")
+        parser.add_option("-o", "--output",    dest="output",        action="store",      default=None,  type="string", help="output file [compulsory] [format: output file in GFF3 format]")
+        parser.add_option("-v", "--verbosity", dest="verbosity",     action="store",      default=1,     type="int",    help="trace level [format: int]")
+        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.verbosity = options.verbosity
+        self.inputFileName = options.inputFileName
+        self.format = options.format
+        self.output = options.output
+        self.galaxy = options.galaxy
+
+    def run(self):  
+        if self.verbosity > 0:
+            print "Reading input file..."
+        parser = TranscriptContainer(self.inputFileName, self.format, self.verbosity)
+        if self.verbosity > 0:
+            print "... done"
+        writer = Gff3Writer(self.output, self.verbosity, self.title)
+            
+        progress = Progress(parser.getNbTranscripts(), "Reading %s" % (self.inputFileName), self.verbosity)
+        for transcript in parser.getIterator():
+            writer.addTranscript(transcript)
+            progress.inc()
+        progress.done()
+        
+        if self.galaxy:
+            os.rename("%s.gff3" % (self.output), self.output) 
+            
+if __name__ == '__main__':
+    launcher = MappingToCoordinates()
+    launcher.setAttributesFromCmdLine()
+    launcher.run()