test/testMakeRdsFromBam.py

   1 '''
   2 Created on Jun 10, 2010
   3
   4 @author: sau
   5 '''
   6 import unittest
   7 from erange import MakeRdsFromBam
   8
   9
  10 class TestMakeRdsFromBam(unittest.TestCase):
  11
  12
  13     def testGetMismatches(self):
  14         querySequence = "GATTACA"
  15
  16         resultString = "A3T"
  17         self.assertEquals(resultString, MakeRdsFromBam.getMismatches("2A", querySequence, "+"))
  18         resultString = "T3A"
  19         self.assertEquals(resultString, MakeRdsFromBam.getMismatches("2A", querySequence, "-"))
  20         resultString = "T7A"
  21         self.assertEquals(resultString, MakeRdsFromBam.getMismatches("6T", querySequence, "+"))
  22
  23         resultString = "A3T,T7A"
  24         self.assertEquals(resultString, MakeRdsFromBam.getMismatches("2A3T0", querySequence, "+"))
  25
  26         resultString = ""
  27         self.assertEquals(resultString, MakeRdsFromBam.getMismatches("2^T", querySequence, "+"))
  28
  29         resultString = "T5A"
  30         self.assertEquals(resultString, MakeRdsFromBam.getMismatches("2^TT2T", querySequence, "+"))
  31         resultString = "A5T"
  32         self.assertEquals(resultString, MakeRdsFromBam.getMismatches("2^TT2T", querySequence, "-"))
  33
  34         resultString = "A3N"
  35         self.assertEquals(resultString, MakeRdsFromBam.getMismatches("2A", "", "+"))
  36         self.assertEquals(resultString, MakeRdsFromBam.getMismatches("2A"))
  37
  38         resultString = ""
  39         self.assertEquals(resultString, MakeRdsFromBam.getMismatches("badMismatchTagData", querySequence, "+"))
  40
  41
  42     #TODO: write test
  43     def testGetPairedReadNumberSuffix(self):
  44         pass
  45
  46
  47     #TODO: write test
  48     def testGetParser(self):
  49         pass
  50
  51
  52     #TODO: write test
  53     def testGetRDSEntry(self):
  54         pass
  55
  56
  57     #TODO: write test
  58     def testGetRDSSpliceEntry(self):
  59         pass
  60
  61
  62     def testGetReadSense(self):
  63         reverse = False
  64         self.assertEqual("+", MakeRdsFromBam.getReadSense(reverse))
  65         reverse = True
  66         self.assertEqual("-", MakeRdsFromBam.getReadSense(reverse))
  67
  68
  69     def testGetSpliceBounds(self):
  70         start, startR, stopL, stopR = MakeRdsFromBam.getSpliceBounds(0, 10, [(1,2), (3,6), (1,2)])
  71
  72         self.assertEqual(start, 0, "incorrect start position for 262")
  73         self.assertEqual(startR, 8, "incorrect right start position for 262")
  74         self.assertEqual(stopL, 2, "incorrect left stop position for 262")
  75         self.assertEqual(stopR, 10, "incorrect right stop position for 262")
  76
  77
  78     #TODO: write test
  79     def testIsPairedRead(self):
  80         pass
  81
  82
  83     def testIsSpliceEntry(self):
  84         self.assertTrue(MakeRdsFromBam.isSpliceEntry([(1,6), (3, 4), (1, 2)]))
  85         self.assertFalse(MakeRdsFromBam.isSpliceEntry([(1,6), (2, 4), (1, 2)]))
  86         self.assertFalse(MakeRdsFromBam.isSpliceEntry([]))
  87         self.assertFalse(MakeRdsFromBam.isSpliceEntry(""))
  88
  89
  90     #TODO: write test
  91     def testMain(self):
  92         pass
  93
  94
  95     #TODO: write test
  96     def testMakeRDSFromBAM(self):
  97         pass
  98
  99
 100 def suite():
 101     suite = unittest.TestSuite()
 102     suite.addTest(unittest.makeSuite(TestMakeRdsFromBam))
 103
 104     return suite
 105
 106
 107 if __name__ == "__main__":
 108     #import sys;sys.argv = ['', 'Test.testName']
 109     unittest.main()