diff smart_toolShed/SMART/Java/Python/mySql/test/Test_MySqlTranscriptTable.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/SMART/Java/Python/mySql/test/Test_MySqlTranscriptTable.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,158 @@
+from commons.core.writer.MySqlTranscriptWriter import MySqlTranscriptWriter
+from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
+from SMART.Java.Python.structure.Transcript import Transcript
+from SMART.Java.Python.structure.Interval import Interval
+from SMART.Java.Python.mySql.MySqlConnection import MySqlConnection
+from SMART.Java.Python.mySql.MySqlTranscriptTable import MySqlTranscriptTable
+import unittest
+
+
+class Test_MySqlTranscriptTable(unittest.TestCase):
+  
+    def test_getRange(self):
+        transcript = Transcript()
+        transcript.setName("test1.1")
+        transcript.setChromosome("arm_X")
+        transcript.setStart(1000)
+        transcript.setEnd(4000)
+        transcript.setSize(2000)
+        transcript.setDirection("+")
+        
+        exon1 = Interval()
+        exon1.setName("test1.1")
+        exon1.setChromosome("arm_X")
+        exon1.setStart(1000)
+        exon1.setEnd(2000)
+        exon1.setSize(1000)
+        
+        exon2 = Interval()
+        exon2.setName("test1.1")
+        exon2.setChromosome("arm_X")
+        exon2.setStart(3000)
+        exon2.setEnd(4000)
+        exon2.setSize(1000)
+        
+        transcript.addExon(exon1)
+        transcript.addExon(exon2)
+        
+        connection = MySqlConnection()
+        writer = MySqlTranscriptWriter(connection, "testMySqlTranscriptTableGetRange")
+        writer.addTranscript(transcript)
+        writer.write()
+        
+        transcriptContainer = TranscriptContainer("testMySqlTranscriptTableGetRange", "sql")
+        transcriptContainer.mySqlConnection = connection
+        self.assertEqual(transcriptContainer.getNbTranscripts(), 1)
+        for transcript in transcriptContainer.getIterator():
+            self.assertEqual(transcript.getName(), "test1.1")
+            self.assertEqual(transcript.getChromosome(), "arm_X")
+            self.assertEqual(transcript.getStart(), 1000)
+            self.assertEqual(transcript.getEnd(), 4000)
+            self.assertEqual(transcript.getSize(), 2002)
+            self.assertEqual(transcript.getNbExons(), 2)
+            exons = transcript.getExons()
+            self.assertEqual(exons[0].getStart(), 1000)
+            self.assertEqual(exons[0].getEnd(), 2000)
+            self.assertEqual(exons[1].getStart(), 3000)
+            self.assertEqual(exons[1].getEnd(), 4000)
+    
+    
+    def test_setDefaultTagValue(self):
+        transcript1 = Transcript()
+        transcript1.setName("test1.1")
+        transcript1.setChromosome("arm_X")
+        transcript1.setStart(1000)
+        transcript1.setEnd(2000)
+        transcript1.setDirection("+")
+        
+        exon1 = Interval()
+        exon1.setName("test1.1")
+        exon1.setChromosome("arm_X")
+        exon1.setStart(1000)
+        exon1.setEnd(2000)
+        
+        transcript1.addExon(exon1)
+        
+        transcript2 = Transcript()
+        transcript2.setName("test2.1")
+        transcript2.setChromosome("arm_X")
+        transcript2.setStart(1000)
+        transcript2.setEnd(2000)
+        transcript2.setDirection("+")
+        transcript2.setTagValue("nbOccurrences", "2")
+        
+        exon2 = Interval()
+        exon2.setName("test2.1")
+        exon2.setChromosome("arm_X")
+        exon2.setStart(1000)
+        exon2.setEnd(2000)
+        
+        transcript2.addExon(exon2)
+        
+        transcript3 = Transcript()
+        transcript3.setName("test3.1")
+        transcript3.setChromosome("arm_X")
+        transcript3.setStart(1000)
+        transcript3.setEnd(2000)
+        transcript3.setDirection("+")
+        transcript3.setTagValue("occurrences", "2")
+        
+        exon3 = Interval()
+        exon3.setName("test3.1")
+        exon3.setChromosome("arm_X")
+        exon3.setStart(1000)
+        exon3.setEnd(2000)
+        
+        transcript3.addExon(exon3)
+        
+        connection = MySqlConnection()
+        table      = MySqlTranscriptTable(connection, "testMySqlTranscriptTableSetDefaultTagValue")
+        table.createTranscriptTable()
+        table.addTranscript(transcript1)
+        table.addTranscript(transcript2)
+        table.addTranscript(transcript3)
+        table.setDefaultTagValue("occurrence", "1")
+        
+        cpt = 0
+        for transcript in table.getIterator():
+            cpt += 1
+            self.assert_(cpt != 4)
+            if cpt == 1:
+                self.assertEqual(transcript.name, "test1.1")
+                self.assertEqual(transcript.getChromosome(), "arm_X")
+                self.assertEqual(transcript.getStart(), 1000)
+                self.assertEqual(transcript.getEnd(), 2000)
+                self.assertEqual(transcript.getSize(), 1001)
+                self.assertEqual(transcript.getNbExons(), 1)
+                exons = transcript.getExons()
+                self.assertEqual(exons[0].getStart(), 1000)
+                self.assertEqual(exons[0].getEnd(), 2000)
+                self.assertEqual(transcript.getTagValue("occurrence"), 1)
+            elif cpt == 2:
+                self.assertEqual(transcript.name, "test2.1")
+                self.assertEqual(transcript.getChromosome(), "arm_X")
+                self.assertEqual(transcript.getStart(), 1000)
+                self.assertEqual(transcript.getEnd(), 2000)
+                self.assertEqual(transcript.getSize(), 1001)
+                self.assertEqual(transcript.getNbExons(), 1)
+                exons = transcript.getExons()
+                self.assertEqual(exons[0].getStart(), 1000)
+                self.assertEqual(exons[0].getEnd(), 2000)
+                self.assertEqual(transcript.getTagValue("nbOccurrences"), 2)
+                self.assertEqual(transcript.getTagValue("occurrence"), 1)
+            elif cpt == 2:
+                self.assertEqual(transcript.name, "test3.1")
+                self.assertEqual(transcript.getChromosome(), "arm_X")
+                self.assertEqual(transcript.getStart(), 1000)
+                self.assertEqual(transcript.getEnd(), 2000)
+                self.assertEqual(transcript.getSize(), 1001)
+                self.assertEqual(transcript.getNbExons(), 1)
+                exons = transcript.getExons()
+                self.assertEqual(exons[0].getStart(), 1000)
+                self.assertEqual(exons[0].getEnd(), 2000)
+                self.assertEqual(transcript.getTagValue("occurrence"), 2)
+      
+        table.remove()
+
+if __name__ == '__main__':
+    unittest.main()