test/testGetSNPs.py

   1 '''
   2 Created on Jun 4, 2010
   3
   4 @author: sau
   5 '''
   6 import os, unittest
   7 from Erange.commoncode import readDataset
   8 from Erange import getSNPs
   9
  10
  11 class TestGetSNPs(unittest.TestCase):
  12
  13     def setUp(self):
  14         self.rdsDNA = readDataset("testDNARDSForUnitTests.rds", True, "DNA", verbose=True)
  15
  16         uniqueInsertList = [("uniqueID1", "chr1", 10, 20, "+", 1.0, "", ""),
  17                             ("uniqueID2", "chr1", 100, 200, "+", 1.0, "", ""),
  18                             ("uniqueID3", "chr1", 1000, 2000, "+", 1.0, "", "G10A")]
  19
  20         multiInsertList = [("multiID1", "chr2", 1010, 1020, "+", 0.5, "", ""),
  21                            ("multiID1", "chr2", 1010, 1020, "+", 0.5, "", ""),
  22                            ("multiID2", "chr2", 10100, 10200, "+", 0.25, "", ""),
  23                            ("multiID2", "chr2", 10100, 10200, "+", 0.25, "", ""),
  24                            ("multiID2", "chr2", 10100, 10200, "+", 0.25, "", ""),
  25                            ("multiID2", "chr2", 10100, 10200, "+", 0.25, "", "")]
  26
  27         self.rdsDNA.insertUniqs(uniqueInsertList)
  28         self.rdsDNA.insertMulti(multiInsertList)
  29
  30
  31     def tearDown(self):
  32         os.remove("./testDNARDSForUnitTests.rds")
  33         self.rdsDNA = None
  34
  35
  36     def testGetMatchDict(self):
  37         uniqueTestDict = getSNPs.getMatchDict(self.rdsDNA, "chr1", withSplices=False)
  38
  39         self.assertEqual(uniqueTestDict[10][0], 20, "incorrect result for unique chr position 10")
  40         self.assertEqual(uniqueTestDict[100][0], 200, "incorrect result for unique chr position 100")
  41         self.assertEqual(uniqueTestDict[1000][0], 2000, "incorrect result for unique chr position 1000")
  42
  43         self.assertRaises(KeyError, getSNPs.getMatchDict, self.rdsDNA, "chr2", withSplices=False)
  44
  45
  46     def testGetMismatchDict(self):
  47         mismatchDict = getSNPs.getMismatchDict(self.rdsDNA, "chr1")
  48         result = {1009: {"totalBaseDict": {"A-G": 1},
  49                          "uniqueReadCount": 1,
  50                          "uniqBaseDict": {"A-G": 1},
  51                          "back": "1000:A-G", "totalCount": 1
  52                          }
  53         }
  54         self.assertEquals(result, mismatchDict)
  55
  56
  57     #TODO: write unit test
  58     def testGetSNPs(self):
  59         pass
  60
  61
  62     #TODO: write unit test
  63     def testWriteSNPsToFile(self):
  64         pass
  65
  66
  67     def testDoNotProcessChromosome(self):
  68         self.assertFalse(getSNPs.doNotProcessChromosome(True, "chr1"))
  69         self.assertFalse(getSNPs.doNotProcessChromosome(False, "chr1"))
  70         self.assertFalse(getSNPs.doNotProcessChromosome(False, "badName"))
  71         self.assertTrue(getSNPs.doNotProcessChromosome(True, "badName"))
  72         self.assertTrue(getSNPs.doNotProcessChromosome(True, ""))
  73
  74
  75 def suite():
  76     suite = unittest.TestSuite()
  77     suite.addTest(unittest.makeSuite(TestGetSNPs))
  78
  79     return suite
  80
  81
  82 if __name__ == "__main__":
  83     #import sys;sys.argv = ['', 'Test.testName']
  84     unittest.main()