2 Created on Oct 20, 2010
7 from erange import geneMrnaCountsWeighted
10 class TestGeneMrnaCountsWeighted(unittest.TestCase):
27 def testGeneMrnaCountsWeighted(self):
31 def testDoNotProcessChromosome(self):
33 self.assertTrue(geneMrnaCountsWeighted.doNotProcessChromosome("chr1", chromosomeList))
35 chromosomeList = ["chr1"]
36 self.assertFalse(geneMrnaCountsWeighted.doNotProcessChromosome("chr1", chromosomeList))
38 chromosomeList = ["chr2"]
39 self.assertTrue(geneMrnaCountsWeighted.doNotProcessChromosome("chr1", chromosomeList))
43 def testGetReadGIDs(self):
47 def testGetGeneSymbolEmptyDicts(self):
51 self.assertEquals("FARGene", geneMrnaCountsWeighted.getGeneSymbol("FARGene", genome, geneinfoDict, geneannotDict))
52 self.assertEquals("LOCGene", geneMrnaCountsWeighted.getGeneSymbol("Gene", genome, geneinfoDict, geneannotDict))
55 def testGetGeneSymbolFromInfoDict(self):
56 geneinfoDict = {"Gene": [("GeneName", "AltGeneName")]}
58 self.assertEquals("GeneName", geneMrnaCountsWeighted.getGeneSymbol("Gene", "hsapien", geneinfoDict, geneannotDict))
59 self.assertEquals("AltGeneName", geneMrnaCountsWeighted.getGeneSymbol("Gene", "celegans", geneinfoDict, geneannotDict))
62 def testGetGeneSymbolFromAnnotDict(self):
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))
70 def testWriteCountsToFile(self):
74 def testGetTagCount(self):
75 self.assertEquals(0.0, geneMrnaCountsWeighted.getTagCount({}, "gene", {"gene": ""}, {}))
77 uniqueCountDict = {"gene": 1,
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))
86 uniqueCountDict["gene"] = 2
87 self.assertEquals(1.0, geneMrnaCountsWeighted.getTagCount(uniqueCountDict, "gene", gidReadDict, read2GidDict))
91 suite = unittest.TestSuite()
92 suite.addTest(unittest.makeSuite(TestGeneMrnaCountsWeighted))
97 if __name__ == "__main__":
98 #import sys;sys.argv = ['', 'Test.testName']