--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/writer/test/Test_Gff3Writer.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,101 @@
+from commons.core.writer.Gff3Writer import Gff3Writer
+from SMART.Java.Python.structure.Transcript import Transcript
+from SMART.Java.Python.structure.Interval import Interval
+import unittest
+import os
+from SMART.Java.Python.misc import Utils
+
+class Test_Gff3Writer(unittest.TestCase):
+  
+    def test_writer(self):
+        obsFileName = "testGffWriter1.gff3"
+        writer = Gff3Writer(obsFileName)
+        
+        transcript = Transcript()
+        transcript.setName("test1.1")
+        transcript.setChromosome("arm_X")
+        transcript.setStart(1000)
+        transcript.setEnd(4000)
+        transcript.setDirection("+")
+        transcript.setTagValue("ID", "test1.1-1")
+        transcript.setTagValue("occurrence", 1)
+        transcript.setTagValue("nbOccurrences", 2)
+        
+        exon1 = Interval()
+        exon1.setChromosome("arm_X")
+        exon1.setStart(1000)
+        exon1.setEnd(2000)
+        exon1.setDirection("+")
+        
+        exon2 = Interval()
+        exon2.setChromosome("arm_X")
+        exon2.setStart(3000)
+        exon2.setEnd(4000)
+        exon2.setDirection("+")
+        
+        transcript.addExon(exon1)
+        transcript.addExon(exon2)
+        
+        writer.addTranscript(transcript)
+        writer.write()
+        writer.close()
+        
+        expFileName = "expFile.gff3"
+        f = open(expFileName, "w")
+        f.write("arm_X\tS-MART\ttranscript\t1000\t4000\t.\t+\t.\tnbOccurrences=2;ID=test1.1-1;occurrence=1;Name=test1.1\n")
+        f.write("arm_X\tS-MART\texon\t1000\t2000\t.\t+\t.\tID=test1.1-1-exon1;Name=test1.1-exon1;Parent=test1.1-1\n")
+        f.write("arm_X\tS-MART\texon\t3000\t4000\t.\t+\t.\tID=test1.1-1-exon2;Name=test1.1-exon2;Parent=test1.1-1\n")
+        f.close()
+        
+        self.assertTrue(Utils.diff(expFileName, obsFileName))
+        
+        os.remove(expFileName)
+        os.remove(obsFileName)
+        
+    def test_writerAltNames(self):
+        obsFileName = "testGffWriter1.gff3"
+        writer = Gff3Writer(obsFileName,title="ALTSOURCE", feature="Match", featurePart="Match-Part")
+        
+        transcript = Transcript()
+        transcript.setName("test1.1")
+        transcript.setChromosome("arm_X")
+        transcript.setStart(1000)
+        transcript.setEnd(4000)
+        transcript.setDirection("+")
+        transcript.setTagValue("ID", "test1.1-1")
+        transcript.setTagValue("occurrence", 1)
+        transcript.setTagValue("nbOccurrences", 2)
+        
+        exon1 = Interval()
+        exon1.setChromosome("arm_X")
+        exon1.setStart(1000)
+        exon1.setEnd(2000)
+        exon1.setDirection("+")
+        
+        exon2 = Interval()
+        exon2.setChromosome("arm_X")
+        exon2.setStart(3000)
+        exon2.setEnd(4000)
+        exon2.setDirection("+")
+        
+        transcript.addExon(exon1)
+        transcript.addExon(exon2)
+        
+        writer.addTranscript(transcript)
+        writer.write()
+        writer.close()
+        
+        expFileName = "expFile.gff3"
+        f = open(expFileName, "w")
+        f.write("arm_X\tALTSOURCE\tMatch\t1000\t4000\t.\t+\t.\tnbOccurrences=2;ID=test1.1-1;occurrence=1;Name=test1.1\n")
+        f.write("arm_X\tALTSOURCE\tMatch-Part\t1000\t2000\t.\t+\t.\tID=test1.1-1-Match-Part1;Name=test1.1-Match-Part1;Parent=test1.1-1\n")
+        f.write("arm_X\tALTSOURCE\tMatch-Part\t3000\t4000\t.\t+\t.\tID=test1.1-1-Match-Part2;Name=test1.1-Match-Part2;Parent=test1.1-1\n")
+        f.close()
+        
+        self.assertTrue(Utils.diff(expFileName, obsFileName))
+        
+        os.remove(expFileName)
+        os.remove(obsFileName)
+
+if __name__ == '__main__':
+    unittest.main()