test/testGeneMrnaCountsWeighted.py

   1 '''
   2 Created on Oct 20, 2010
   3
   4 @author: sau
   5 '''
   6 import unittest
   7 from erange import geneMrnaCountsWeighted
   8
   9
  10 class TestGeneMrnaCountsWeighted(unittest.TestCase):
  11
  12
  13     def setUp(self):
  14         pass
  15
  16
  17     def tearDown(self):
  18         pass
  19
  20
  21     #TODO: write test
  22     def testMain(self):
  23         pass
  24
  25
  26     #TODO: write test
  27     def testGeneMrnaCountsWeighted(self):
  28         pass
  29
  30
  31     def testDoNotProcessChromosome(self):
  32         chromosomeList = []
  33         self.assertTrue(geneMrnaCountsWeighted.doNotProcessChromosome("chr1", chromosomeList))
  34
  35         chromosomeList = ["chr1"]
  36         self.assertFalse(geneMrnaCountsWeighted.doNotProcessChromosome("chr1", chromosomeList))
  37
  38         chromosomeList = ["chr2"]
  39         self.assertTrue(geneMrnaCountsWeighted.doNotProcessChromosome("chr1", chromosomeList))
  40
  41
  42     #TODO: write test
  43     def testGetReadGIDs(self):
  44         pass
  45
  46
  47     def testGetGeneSymbolEmptyDicts(self):
  48         geneinfoDict = {}
  49         geneannotDict = {}
  50         genome = "hsapien"
  51         self.assertEquals("FARGene", geneMrnaCountsWeighted.getGeneSymbol("FARGene", genome, geneinfoDict, geneannotDict))
  52         self.assertEquals("LOCGene", geneMrnaCountsWeighted.getGeneSymbol("Gene", genome, geneinfoDict, geneannotDict))
  53
  54
  55     def testGetGeneSymbolFromInfoDict(self):
  56         geneinfoDict = {"Gene": [("GeneName", "AltGeneName")]}
  57         geneannotDict = {}
  58         self.assertEquals("GeneName", geneMrnaCountsWeighted.getGeneSymbol("Gene", "hsapien", geneinfoDict, geneannotDict))
  59         self.assertEquals("AltGeneName", geneMrnaCountsWeighted.getGeneSymbol("Gene", "celegans", geneinfoDict, geneannotDict))
  60
  61
  62     def testGetGeneSymbolFromAnnotDict(self):
  63         geneinfoDict = {}
  64         geneannotDict = {("hsapien", "Gene"): ["GeneName", "AltGeneName"]}
  65         self.assertEquals("GeneName", geneMrnaCountsWeighted.getGeneSymbol("Gene", "hsapien", geneinfoDict, geneannotDict))
  66         self.assertEquals("LOCGene", geneMrnaCountsWeighted.getGeneSymbol("Gene", "celegans", geneinfoDict, geneannotDict))
  67
  68
  69     #TODO: write test
  70     def testWriteCountsToFile(self):
  71         pass
  72
  73
  74     def testGetTagCount(self):
  75         self.assertEquals(0.0, geneMrnaCountsWeighted.getTagCount({}, "gene", {"gene": ""}, {}))
  76
  77         uniqueCountDict = {"gene": 1,
  78                            "related1": 1,
  79                            "related2": 1
  80         }
  81         gidReadDict = {"gene": ["read1"]}
  82         read2GidDict = {"read1": ["related1", "related2"]}
  83         self.assertEquals(0.5, geneMrnaCountsWeighted.getTagCount(uniqueCountDict, "gene", gidReadDict, read2GidDict))
  84         self.assertEquals(0.5, geneMrnaCountsWeighted.getTagCount({}, "gene", gidReadDict, read2GidDict))
  85
  86         uniqueCountDict["gene"] = 2
  87         self.assertEquals(1.0, geneMrnaCountsWeighted.getTagCount(uniqueCountDict, "gene", gidReadDict, read2GidDict))
  88
  89
  90 def suite():
  91     suite = unittest.TestSuite()
  92     suite.addTest(unittest.makeSuite(TestGeneMrnaCountsWeighted))
  93
  94     return suite
  95
  96
  97 if __name__ == "__main__":
  98     #import sys;sys.argv = ['', 'Test.testName']
  99     unittest.main()