test/testGetSNPGeneInfo.py

   1 '''
   2 Created on Aug 26, 2010
   3
   4 @author: sau
   5 '''
   6 import unittest
   7 from erange import getSNPGeneInfo
   8
   9
  10 class TestGetSNPGeneInfo(unittest.TestCase):
  11
  12
  13     def setUp(self):
  14         self.geneDict = {}
  15         self.snpDict = {}
  16         self.rpkmDict = {}
  17         self.withSense = False
  18
  19
  20     def tearDown(self):
  21         pass
  22
  23
  24     def testDoNotProcessLine(self):
  25         self.assertTrue(getSNPGeneInfo.doNotProcessLine("#anything"))
  26         self.assertFalse(getSNPGeneInfo.doNotProcessLine("line to process"))
  27
  28
  29     def testGetSNPGeneInfoList(self):
  30         geneInfoList = getSNPGeneInfo.getSNPGeneInfoList(self.geneDict, self.snpDict, self.rpkmDict, self.withSense)
  31         self.assertEquals([], geneInfoList)
  32
  33         badGeneDict = {"badEntry": "foo"}
  34         self.assertRaises(ValueError, getSNPGeneInfo.getSNPGeneInfoList, badGeneDict, self.snpDict, self.rpkmDict, self.withSense)
  35
  36         self.geneDict[("gene1", "ID1")] = {"position": [("1", 1)], "sense": "+"}
  37         self.assertRaises(KeyError, getSNPGeneInfo.getSNPGeneInfoList, self.geneDict, self.snpDict, self.rpkmDict, self.withSense)
  38
  39         self.snpDict[("1", 1)] = "chr1\tpos 1\n"
  40         result = [{"symbol": "gene1",
  41                    "rpkm": "N\\A",
  42                    "geneID": "ID1",
  43                    "snpDescription": "chr1\tpos 1" }
  44         ]
  45         self.assertEquals(result, getSNPGeneInfo.getSNPGeneInfoList(self.geneDict, self.snpDict, self.rpkmDict, self.withSense))
  46
  47         self.rpkmDict["ID1"] = 300
  48         result = [{"symbol": "gene1",
  49                    "rpkm": "300",
  50                    "geneID": "ID1",
  51                    "snpDescription": "chr1\tpos 1" }
  52         ]
  53         self.assertEquals(result, getSNPGeneInfo.getSNPGeneInfoList(self.geneDict, self.snpDict, self.rpkmDict, self.withSense))
  54
  55         self.geneDict[("gene1", "ID1")] = {"position": [("1", 1), ("1", 1)], "sense": "+"}
  56         self.assertEquals(result, getSNPGeneInfo.getSNPGeneInfoList(self.geneDict, self.snpDict, self.rpkmDict, self.withSense))
  57
  58         result = [{"symbol": "gene1",
  59                    "sense": "+",
  60                    "rpkm": "300",
  61                    "geneID": "ID1",
  62                    "snpDescription": "chr1\tpos 1" }
  63         ]
  64         self.assertEquals(result, getSNPGeneInfo.getSNPGeneInfoList(self.geneDict, self.snpDict, self.rpkmDict, True))
  65
  66         self.geneDict[("gene1", "ID1")] = {"position": [("1", 1), ("1", 10)], "sense": "+"}
  67         self.snpDict[("1", 10)] = "chr1\tpos 10\n"
  68         result = [{"symbol": "gene1",
  69                    "rpkm": "300",
  70                    "geneID": "ID1",
  71                    "snpDescription": "chr1\tpos 10" },
  72                   {"symbol": "gene1",
  73                    "rpkm": "300",
  74                    "geneID": "ID1",
  75                    "snpDescription": "chr1\tpos 1" }
  76         ]
  77         self.assertEquals(result, getSNPGeneInfo.getSNPGeneInfoList(self.geneDict, self.snpDict, self.rpkmDict, self.withSense))
  78
  79
  80     #TODO: write test
  81     def testGetSNPGeneInfo(self):
  82         pass
  83
  84
  85     def testGetSNPGeneOutputList(self):
  86         geneOutputList = getSNPGeneInfo.getSNPGeneOutputList(self.geneDict, self.snpDict, self.rpkmDict, self.withSense)
  87         self.assertEquals([], geneOutputList)
  88
  89         badGeneDict = {"badEntry": "foo"}
  90         self.assertRaises(ValueError, getSNPGeneInfo.getSNPGeneOutputList, badGeneDict, self.snpDict, self.rpkmDict, self.withSense)
  91
  92         self.geneDict[("gene1", "ID1")] = {"position": [("1", 1)], "sense": "+"}
  93         self.assertRaises(KeyError, getSNPGeneInfo.getSNPGeneOutputList, self.geneDict, self.snpDict, self.rpkmDict, self.withSense)
  94
  95         self.snpDict[("1", 1)] = "chr1\tpos 1\n"
  96         result = ["chr1\tpos 1\tgene1\tID1\tN\\A"]
  97         self.assertEquals(result, getSNPGeneInfo.getSNPGeneOutputList(self.geneDict, self.snpDict, self.rpkmDict, self.withSense))
  98
  99         self.rpkmDict["ID1"] = 300
 100         result = ["chr1\tpos 1\tgene1\tID1\t300"]
 101         self.assertEquals(result, getSNPGeneInfo.getSNPGeneOutputList(self.geneDict, self.snpDict, self.rpkmDict, self.withSense))
 102
 103         self.geneDict[("gene1", "ID1")] = {"position": [("1", 1), ("1", 1)], "sense": "+"}
 104         self.assertEquals(result, getSNPGeneInfo.getSNPGeneOutputList(self.geneDict, self.snpDict, self.rpkmDict, self.withSense))
 105
 106         result = ["chr1\tpos 1\tgene1\tID1\t300\t+"]
 107         self.assertEquals(result, getSNPGeneInfo.getSNPGeneOutputList(self.geneDict, self.snpDict, self.rpkmDict, True))
 108
 109         self.geneDict[("gene1", "ID1")] = {"position": [("1", 1), ("1", 10)], "sense": "+"}
 110         self.snpDict[("1", 10)] = "chr1\tpos 10\n"
 111         result = ["chr1\tpos 10\tgene1\tID1\t300",
 112                   "chr1\tpos 1\tgene1\tID1\t300"
 113         ]
 114         self.assertEquals(result, getSNPGeneInfo.getSNPGeneOutputList(self.geneDict, self.snpDict, self.rpkmDict, self.withSense))
 115
 116
 117     #TODO: write test
 118     def testWriteSNPGeneInfo(self):
 119         pass
 120
 121
 122 def suite():
 123     suite = unittest.TestSuite()
 124     suite.addTest(unittest.makeSuite(TestGetSNPGeneInfo))
 125
 126     return suite
 127
 128
 129 if __name__ == "__main__":
 130     #import sys;sys.argv = ['', 'Test.testName']
 131     unittest.main()