diff commons/core/parsing/test/Test_GffParser.py @ 6:769e306b7933

Change the repository level.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/parsing/test/Test_GffParser.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,62 @@
+import unittest
+from commons.core.parsing.GffParser import GffParser
+
+
+class Test_GffParser(unittest.TestCase):
+    
+
+    def test_Parser(self):
+        parser = GffParser("data/testGffParser1.gff3")
+
+        self.assertEqual(parser.getNbTranscripts(), 3)
+
+        cpt = 0
+        for transcript in parser.getIterator():
+            cpt += 1
+            if cpt == 1:
+                self.assertEqual(transcript.getChromosome(), "arm_X")
+                self.assertEqual(transcript.getName(), "test1")
+                self.assertEqual(transcript.getStart(), 1000)
+                self.assertEqual(transcript.getEnd(), 2000)
+                self.assertEqual(transcript.getDirection(), 1)
+                self.assertEqual(transcript.getNbExons(), 1)
+                self.assertEqual(transcript.getTagValue("field"), "value1")
+                exons = transcript.getExons()
+                self.assertEqual(exons[0].getChromosome(), "arm_X")
+                self.assertEqual(exons[0].getStart(), 1000)
+                self.assertEqual(exons[0].getEnd(), 2000)
+                self.assertEqual(exons[0].getDirection(), 1)
+                self.assertEqual(transcript.getSize(), 1001)
+            elif cpt == 2:
+                self.assertEqual(transcript.getChromosome(), "arm_X")
+                self.assertEqual(transcript.getName(), "test2")
+                self.assertEqual(transcript.getStart(), 10000)
+                self.assertEqual(transcript.getEnd(), 20000)
+                self.assertEqual(transcript.getDirection(), -1)
+                self.assertEqual(transcript.getNbExons(), 2)
+                self.assertEqual(transcript.getTagValue("field"), "value2")
+                exons = transcript.getExons()
+                self.assertEqual(exons[0].getChromosome(), "arm_X")
+                self.assertEqual(exons[0].getStart(), 10000)
+                self.assertEqual(exons[0].getEnd(), 10100)
+                self.assertEqual(exons[0].getDirection(), -1)
+                self.assertEqual(transcript.getSize(), 9602)
+            if cpt == 3:
+                self.assertEqual(transcript.getChromosome(), "arm_X")
+                self.assertEqual(transcript.getName(), "test1.1")
+                self.assertEqual(transcript.getStart(), 1000)
+                self.assertEqual(transcript.getEnd(), 2000)
+                self.assertEqual(transcript.getDirection(), 1)
+                self.assertEqual(transcript.getNbExons(), 1)
+                self.assertEqual(transcript.getTagValue("ID"), "test1.1-1")
+                exons = transcript.getExons()
+                self.assertEqual(exons[0].getChromosome(), "arm_X")
+                self.assertEqual(exons[0].getStart(), 1000)
+                self.assertEqual(exons[0].getEnd(), 2000)
+                self.assertEqual(exons[0].getDirection(), 1)
+                self.assertEqual(transcript.getSize(), 1001)
+
+
+if __name__ == '__main__':
+        unittest.main()
+