--- a/SMART/Java/Python/structure/Transcript.py	Mon Apr 22 11:11:10 2013 -0400
+++ b/SMART/Java/Python/structure/Transcript.py	Mon Apr 29 03:20:15 2013 -0400
@@ -347,6 +347,31 @@
 		newTranscript.exons = theseExons
 		return newTranscript
 			
+
+	def getIntersection(self, transcript):
+		"""
+		Get the intersection between this transcript and another one
+		@param transcript: object to be compared to
+		@type  transcript: class L{Transcript<Transcript>}
+		@return:           an other transcript
+		"""
+		if self.getChromosome() != transcript.getChromosome() or self.getDirection() != transcript.getDirection():
+			return None
+		newTranscript = Transcript()
+		newTranscript.setDirection(self.getDirection())
+		newTranscript.setChromosome(self.getChromosome())
+		newTranscript.setName("%s_intersect_%s" % (self.getName(), transcript.getName()))
+		newExons = []
+		for thisExon in self.getExons():
+			for thatExon in transcript.getExons():
+				newExon = thisExon.getIntersection(thatExon)
+				if newExon != None:
+					newExons.append(newExon)
+		if not newExons:
+			return None
+		newTranscript.exons = newExons
+		return newTranscript
+			
 	
 	def getSqlVariables(cls):
 		"""