--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/ncList/FindOverlaps_naif.py	Thu May 02 09:56:47 2013 -0400
@@ -0,0 +1,85 @@
+#! /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.
+#
+
+import os
+import struct
+from optparse import OptionParser
+from commons.core.parsing.GffParser import GffParser
+from commons.core.writer.Gff3Writer import Gff3Writer
+
+LONGSIZE = struct.calcsize('l')
+
+class FindOverlaps_naif(object):
+    
+    def __init__(self, inputRefGff3FileName, inputQueryGff3FileName):
+        self._inputRefGff3FileName = inputRefGff3FileName
+        self._inputQueryGff3FileName = inputQueryGff3FileName
+                
+    def close(self):
+        self._iGff3Writer.close()
+    
+    def setGff3FileName(self, fileName):
+        self._inputRefGff3FileName = fileName
+        
+    def setQueryGff3FileName(self, fileName):
+        self._inputQueryGff3FileName = fileName
+    
+    def setOutputGff3FileName(self, outputGff3FileName):
+        if outputGff3FileName != '':
+            self._outputGff3FileName = outputGff3FileName
+        self._iGff3Writer = Gff3Writer(self._outputGff3FileName)
+                
+    def run(self):
+        queryParser = GffParser(self._inputQueryGff3FileName, 0)
+        for queryTranscript in queryParser.getIterator():
+            ids       = []
+            refParser = GffParser(self._inputRefGff3FileName, 0)
+            for refTranscript in refParser.getIterator():
+                if queryTranscript.overlapWith(refTranscript):
+                    ids.append(refTranscript.getTagValue('ID'))
+            if ids:
+                queryTranscript.setTagValue("nbOverlaps", len(ids))
+                queryTranscript.setTagValue("overlapsWith", "--".join(ids))
+                self._iGff3Writer.addTranscript(queryTranscript)
+    
+if __name__ == "__main__":
+    description = "FindOverlapsWithSeveralInterval: Finds overlaps with several query intervals."
+
+    parser = OptionParser(description = description)
+    parser.add_option("-i", "--inputRef", dest="inputRefGff3FileName", action="store", type="string", help="Reference input file [compulsory] [format: file in gff3 format]")
+    parser.add_option("-j", "--inputQuery", dest="inputQueryGff3FileName", action="store", type="string", help="Query input file [compulsory] [format: file in gff3 format]")
+    parser.add_option("-o", "--output", dest="outputGff3FileName", action="store", type="string", help="output file [compulsory] [format: output file in gff3 format]")
+    (options, args) = parser.parse_args()
+    
+    iFON = FindOverlaps_naif(options.inputRefGff3FileName, options.inputQueryGff3FileName)
+    iFON.setOutputGff3FileName(options.outputGff3FileName)
+    iFON.run()
+    iFON.close()