diff SMART/Java/Python/test/Test_F_getExons.py @ 18:94ab73e8a190

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/test/Test_F_getExons.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,145 @@
+import unittest
+import os
+from SMART.Java.Python.getExons import GetExons
+from commons.core.parsing.GffParser import GffParser
+
+class Test_F_GetExons(unittest.TestCase):
+
+    def setUp(self):
+        self._inputFileName = "inputFileTest.bed"
+        self._writeInputFile()
+        self._outputFileName = "output.gff3"
+        
+    def tearDown(self):
+        os.remove(self._inputFileName)
+        os.remove(self._outputFileName)
+
+    def test_run_simple(self):
+        ge = GetExons(0)
+        ge.setInputFile(self._inputFileName, "bed")
+        ge.setOutputFile(self._outputFileName)
+        ge.run()
+        parser = GffParser(self._outputFileName, 0)
+        self.assertEqual(parser.getNbTranscripts(), 5)
+        for cpt, transcript in enumerate(parser.getIterator()):
+            self.assertEqual(transcript.getChromosome(), "arm_X")
+            self.assertEqual(transcript.getDirection(), 1)
+            self.assertEqual(transcript.getNbExons(), 1)
+            if cpt == 0:
+                self.assertEqual(transcript.getStart(), 10000001)
+                self.assertEqual(transcript.getEnd(),   10000100)
+            elif cpt == 1:
+                self.assertEqual(transcript.getStart(), 10000201)
+                self.assertEqual(transcript.getEnd(),   10000300)
+            elif cpt == 2:
+                self.assertEqual(transcript.getStart(), 10000401)
+                self.assertEqual(transcript.getEnd(),   10000500)
+            elif cpt == 3:
+                self.assertEqual(transcript.getStart(), 10000601)
+                self.assertEqual(transcript.getEnd(),   10000700)
+            elif cpt == 4:
+                self.assertEqual(transcript.getStart(), 10000801)
+                self.assertEqual(transcript.getEnd(),   10000900)
+
+    def test_run_firstExon(self):
+        ge = GetExons(0)
+        ge.setInputFile(self._inputFileName, "bed")
+        ge.setOutputFile(self._outputFileName)
+        ge.setSelection("1")
+        ge.run()
+        parser = GffParser(self._outputFileName, 0)
+        self.assertEqual(parser.getNbTranscripts(), 1)
+        for cpt, transcript in enumerate(parser.getIterator()):
+            self.assertEqual(transcript.getChromosome(), "arm_X")
+            self.assertEqual(transcript.getDirection(), 1)
+            self.assertEqual(transcript.getNbExons(), 1)
+            self.assertEqual(transcript.getStart(), 10000001)
+            self.assertEqual(transcript.getEnd(),   10000100)
+
+    def test_run_lastExon(self):
+        ge = GetExons(0)
+        ge.setInputFile(self._inputFileName, "bed")
+        ge.setOutputFile(self._outputFileName)
+        ge.setSelection("-1")
+        ge.run()
+        parser = GffParser(self._outputFileName, 0)
+        self.assertEqual(parser.getNbTranscripts(), 1)
+        for cpt, transcript in enumerate(parser.getIterator()):
+            self.assertEqual(transcript.getChromosome(), "arm_X")
+            self.assertEqual(transcript.getDirection(), 1)
+            self.assertEqual(transcript.getNbExons(), 1)
+            self.assertEqual(transcript.getStart(), 10000801)
+            self.assertEqual(transcript.getEnd(),   10000900)
+
+    def test_run_first_lastExon(self):
+        ge = GetExons(0)
+        ge.setInputFile(self._inputFileName, "bed")
+        ge.setOutputFile(self._outputFileName)
+        ge.setSelection("1,-1")
+        ge.run()
+        parser = GffParser(self._outputFileName, 0)
+        self.assertEqual(parser.getNbTranscripts(), 2)
+        for cpt, transcript in enumerate(parser.getIterator()):
+            self.assertEqual(transcript.getChromosome(), "arm_X")
+            self.assertEqual(transcript.getDirection(), 1)
+            self.assertEqual(transcript.getNbExons(), 1)
+            if cpt == 0:
+                self.assertEqual(transcript.getStart(), 10000001)
+                self.assertEqual(transcript.getEnd(),   10000100)
+            elif cpt == 1:
+                self.assertEqual(transcript.getStart(), 10000801)
+                self.assertEqual(transcript.getEnd(),   10000900)
+
+    def test_run_interval(self):
+        ge = GetExons(0)
+        ge.setInputFile(self._inputFileName, "bed")
+        ge.setOutputFile(self._outputFileName)
+        ge.setSelection("2..3")
+        ge.run()
+        parser = GffParser(self._outputFileName, 0)
+        self.assertEqual(parser.getNbTranscripts(), 2)
+        for cpt, transcript in enumerate(parser.getIterator()):
+            self.assertEqual(transcript.getChromosome(), "arm_X")
+            self.assertEqual(transcript.getDirection(), 1)
+            self.assertEqual(transcript.getNbExons(), 1)
+            if cpt == 0:
+                self.assertEqual(transcript.getStart(), 10000201)
+                self.assertEqual(transcript.getEnd(),   10000300)
+            elif cpt == 1:
+                self.assertEqual(transcript.getStart(), 10000401)
+                self.assertEqual(transcript.getEnd(),   10000500)
+
+    def test_run_interval_element(self):
+        ge = GetExons(0)
+        ge.setInputFile(self._inputFileName, "bed")
+        ge.setOutputFile(self._outputFileName)
+        ge.setSelection("2..3,-1")
+        ge.run()
+        parser = GffParser(self._outputFileName, 0)
+        self.assertEqual(parser.getNbTranscripts(), 3)
+        for cpt, transcript in enumerate(parser.getIterator()):
+            self.assertEqual(transcript.getChromosome(), "arm_X")
+            self.assertEqual(transcript.getDirection(), 1)
+            self.assertEqual(transcript.getNbExons(), 1)
+            if cpt == 0:
+                self.assertEqual(transcript.getStart(), 10000201)
+                self.assertEqual(transcript.getEnd(),   10000300)
+            elif cpt == 1:
+                self.assertEqual(transcript.getStart(), 10000401)
+                self.assertEqual(transcript.getEnd(),   10000500)
+            elif cpt == 2:
+                self.assertEqual(transcript.getStart(), 10000801)
+                self.assertEqual(transcript.getEnd(),   10000900)
+
+
+
+    def _writeInputFile(self):
+        f = open(self._inputFileName, "w")
+        f.write("arm_X\t10000001\t10000900\ttest1.1\t100\t+\t10000100\t10000200\t0\t5\t100,100,100,100,100,\t0,200,400,600,800,\n")
+        f.close()
+        
+                
+
+if __name__ == "__main__":
+    unittest.main()
+