test/testGetSNPs.py

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