--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/parsing/test/Test_CoordsParser.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,105 @@
+import unittest
+from commons.core.parsing.CoordsParser import CoordsParser
+from SMART.Java.Python.mappingToCoordinates import MappingToCoordinates
+
+
+class Test_CoordsParser(unittest.TestCase):
+    
+
+    def test_Parser(self):
+        parser = CoordsParser("data/testCoordsParser.coords")
+        
+        cpt = 0
+        for mapping in parser.getIterator():
+            transcript = mapping.getTranscript()
+            cpt += 1
+            if cpt == 1:
+                self.assertEqual(transcript.getChromosome(), "scaffold_1")
+                self.assertEqual(transcript.getName(), "gi|240254421:1-30427671")
+                self.assertEqual(transcript.getStart(), 1)
+                self.assertEqual(transcript.getEnd(), 6251)
+                self.assertEqual(transcript.getDirection(), -1)
+                self.assertEqual(transcript.getNbExons(), 1)
+                self.assertEqual(transcript.getTagValue("identity"), 89.030000000000001)
+                exons = transcript.getExons()
+                self.assertEqual(exons[0].getChromosome(), "scaffold_1")
+                self.assertEqual(exons[0].getStart(), 1)
+                self.assertEqual(exons[0].getEnd(), 6251)
+                self.assertEqual(exons[0].getDirection(), -1)
+                self.assertEqual(transcript.getSize(), 6251)
+            elif cpt == 2:
+                self.assertEqual(transcript.getChromosome(), "scaffold_1")
+                self.assertEqual(transcript.getName(), "gi|240254421:1-30427671")
+                self.assertEqual(transcript.getStart(), 9127)
+                self.assertEqual(transcript.getEnd(), 11947)
+                self.assertEqual(transcript.getDirection(), -1)
+                self.assertEqual(transcript.getNbExons(), 1)
+                self.assertEqual(transcript.getTagValue("identity"), 90.450000000000003)
+                exons = transcript.getExons()
+                self.assertEqual(exons[0].getChromosome(), "scaffold_1")
+                self.assertEqual(exons[0].getStart(), 9127)
+                self.assertEqual(exons[0].getEnd(), 11947)
+                self.assertEqual(exons[0].getDirection(), -1)
+                self.assertEqual(transcript.getSize(), 2821)
+            if cpt == 3:
+                self.assertEqual(transcript.getChromosome(), "scaffold_1")
+                self.assertEqual(transcript.getName(), "gi|240254421:1-30427671")
+                self.assertEqual(transcript.getStart(), 12201)
+                self.assertEqual(transcript.getEnd(), 12953)
+                self.assertEqual(transcript.getDirection(), -1)
+                self.assertEqual(transcript.getNbExons(), 1)
+                exons = transcript.getExons()
+                self.assertEqual(exons[0].getChromosome(), "scaffold_1")
+                self.assertEqual(exons[0].getStart(), 12201)
+                self.assertEqual(exons[0].getEnd(), 12953)
+                self.assertEqual(exons[0].getDirection(), -1)
+                self.assertEqual(transcript.getSize(), 753)
+            
+    def test_Parser_showcoord(self):
+        parser = CoordsParser("data/testCoordsParser_showcoord.coords")
+        expTranscriptCount = 1
+        obsTranscriptCount = 0
+        
+        for mapping in parser.getIterator():
+            transcript = mapping.getTranscript()
+            obsTranscriptCount += 1
+            self.assertEqual(transcript.getChromosome(), "mivi_sl_A1_scaffold00001")
+            self.assertEqual(transcript.getName(), "mivi_sl_A2_scaffold00003")
+            self.assertEqual(transcript.getStart(), 296)
+            self.assertEqual(transcript.getEnd(), 2292)
+            self.assertEqual(transcript.getDirection(), 1)
+            self.assertEqual(transcript.getTagValue("identity"), 98.30)
+            self.assertEqual(transcript.getTagValue("target_pident"), 98.30)                
+            self.assertEqual(transcript.getTagValue("target_pcover"), 3.32)
+            self.assertEqual(transcript.getTagValue("target_length"), 60273)                
+            self.assertEqual(transcript.getTagValue("Target"), "mivi_sl_A2_scaffold00003 1 2001")
+            self.assertEqual(transcript.getSize(), 1997)
+                
+        self.assertEquals(expTranscriptCount, obsTranscriptCount)
+                            
+    def test_Parser_showcoord_promer(self):
+        parser = CoordsParser("data/testCoordsParser_showcoord_promer.coords")
+        expTranscriptCount = 1
+        obsTranscriptCount = 0
+        
+        for mapping in parser.getIterator():
+            transcript = mapping.getTranscript()
+            obsTranscriptCount += 1
+            self.assertEqual(transcript.getChromosome(), "mivi_sl_A1_scaffold00001")
+            self.assertEqual(transcript.getName(), "mivi_sl_A2_scaffold00003")
+            self.assertEqual(transcript.getStart(), 291)
+            self.assertEqual(transcript.getEnd(), 1229)
+            self.assertEqual(transcript.getDirection(), -1)
+            self.assertEqual(transcript.getTagValue("identity"), 94.25)
+            self.assertEqual(transcript.getTagValue("target_pident"), 94.25)                
+            self.assertEqual(transcript.getTagValue("target_pcover"), 1.56)
+            self.assertEqual(transcript.getTagValue("target_length"), 60273)                
+            self.assertEqual(transcript.getTagValue("Target"), "mivi_sl_A2_scaffold00003 939 1")
+            self.assertEqual(transcript.getSize(), 939)
+                
+        self.assertEquals(expTranscriptCount, obsTranscriptCount)
+        
+ 
+if __name__ == '__main__':
+        unittest.main()
+