diff commons/core/parsing/test/Test_MapParser.py @ 31:0ab839023fe4

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/parsing/test/Test_MapParser.py	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,53 @@
+import unittest
+import os
+from commons.core.parsing.MapParser import MapParser
+
+class Test_MapParser(unittest.TestCase):
+
+    
+    def setUp(self):
+        self.inputMapFileName = "testMapParser.map"
+        self._writeInputMapFile()
+        
+    def tearDown(self):
+        if os.path.exists(self.inputMapFileName):
+            os.remove(self.inputMapFileName)
+    
+    def test_Parser(self):
+        parser = MapParser(self.inputMapFileName)
+        
+        cpt = 0
+        for transcript in parser.getIterator():
+            cpt += 1
+            if cpt == 1:
+                self.assertEqual(transcript.getChromosome(), "dmel_chr4")
+                self.assertEqual(transcript.getName(), "aagatgcgtaacggccatac_17")
+                self.assertEqual(transcript.getStart(), 4380)
+                self.assertEqual(transcript.getEnd(), 4400)
+                self.assertEqual(transcript.getDirection(), 1)
+                self.assertEqual(transcript.getSize(), 21)
+            elif cpt == 10:
+                self.assertEqual(transcript.getChromosome(), "dmel_chr4")
+                self.assertEqual(transcript.getName(), "aacggccatacattggtttg_12")
+                self.assertEqual(transcript.getStart(), 4389)
+                self.assertEqual(transcript.getEnd(), 4409)
+                self.assertEqual(transcript.getDirection(), 1)
+                self.assertEqual(transcript.getSize(), 21)
+                
+                
+    def _writeInputMapFile(self):
+        inputFile = open(self.inputMapFileName,'w')
+        inputFile.write("aagatgcgtaacggccatac_17\tdmel_chr4\t4380\t4400\n")
+        inputFile.write("agatgcgtaacggccataca_16\tdmel_chr4\t4381\t4401\n")
+        inputFile.write("gatgcgtaacggccatacat_16\tdmel_chr4\t4382\t4402\n")
+        inputFile.write("atgcgtaacggccatacatt_15\tdmel_chr4\t4383\t4403\n")
+        inputFile.write("tgcgtaacggccatacattg_15\tdmel_chr4\t4384\t4404\n")
+        inputFile.write("gcgtaacggccatacattgg_15\tdmel_chr4\t4385\t4405\n")
+        inputFile.write("cgtaacggccatacattggt_14\tdmel_chr4\t4386\t4406\n")
+        inputFile.write("gtaacggccatacattggtt_14\tdmel_chr4\t4387\t4407\n")
+        inputFile.write("taacggccatacattggttt_14\tdmel_chr4\t4388\t4408\n")
+        inputFile.write("aacggccatacattggtttg_12\tdmel_chr4\t4389\t4409\n")
+        inputFile.close()
+
+if __name__ == '__main__':
+        unittest.main()
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