test/testGeneMrnaCounts.py

   1 '''
   2 Created on Aug 19, 2010
   3
   4 @author: sau
   5
   6 Located feature 728439 by:
   7     from Erange.commoncode import getFeaturesByChromDict
   8     genome = Genome(self.genomeName)
   9     featuresByChromDict = getFeaturesByChromDict(genome)
  10     print featuresByChromDict["1"][:3]
  11
  12 '''
  13 import unittest
  14 import os
  15 from erange import geneMrnaCounts
  16 from cistematic.core.geneinfo import geneinfoDB
  17 from cistematic.genomes import Genome
  18 from erange import ReadDataset
  19
  20
  21 class TestGeneMrnaCounts(unittest.TestCase):
  22     idb = geneinfoDB(cache=True)
  23     testDBName = "testRDS.rds"
  24     genomeName = "hsapiens"
  25     outfilename = "testGeneMrnaCounts.txt"
  26
  27     def setUp(self):
  28         self.rds = ReadDataset.ReadDataset(self.testDBName, initialize=True, datasetType="RNA", verbose=False)
  29
  30
  31     def tearDown(self):
  32         del(self.rds)
  33         os.remove(self.testDBName)
  34
  35
  36     def testGeneMrnaCounts(self):
  37         geneMrnaCounts.geneMrnaCounts(self.genomeName, self.testDBName, self.outfilename)
  38         outfile = open(self.outfilename, "r")
  39         for line in outfile:
  40             fields = line.split("\t")
  41             self.assertEquals("0\n", fields[2])
  42
  43         outfile.close()
  44         os.remove(self.outfilename)
  45
  46         rdsEntryList = [("testRead", "chr1", 18700, 18800, "+", 1.0, "", "")]
  47         self.rds.insertUniqs(rdsEntryList)
  48         geneMrnaCounts.geneMrnaCounts(self.genomeName, self.testDBName, self.outfilename)
  49         possibleCounts = ["0\n", "1\n"]
  50         outfile = open(self.outfilename, "r")
  51         for line in outfile:
  52             fields = line.split("\t")
  53             self.assertTrue(fields[2] in possibleCounts)
  54
  55         outfile.close()
  56         os.remove(self.outfilename)
  57
  58         geneMrnaCounts.geneMrnaCounts(self.genomeName, self.testDBName, self.outfilename,
  59                                       markGID=True, trackStrand=True)
  60
  61         possibleCounts = ["0\n", "1\n"]
  62         outfile = open(self.outfilename, "r")
  63         for line in outfile:
  64             fields = line.split("\t")
  65             self.assertTrue(fields[2] in possibleCounts)
  66
  67         outfile.close()
  68         os.remove(self.outfilename)
  69         reads = self.rds.getReadsDict(withFlag=True)
  70         self.assertEquals("728439", reads["1"][0]["flag"])
  71
  72         geneMrnaCounts.geneMrnaCounts(self.genomeName, self.testDBName, self.outfilename,
  73                                       countFeats=True, markGID=True, cachePages=150000)
  74
  75         possibleCounts = ["0\n", "1\n"]
  76         outfile = open(self.outfilename, "r")
  77         for line in outfile:
  78             fields = line.split("\t")
  79             self.assertTrue(fields[2] in possibleCounts)
  80
  81         outfile.close()
  82         os.remove(self.outfilename)
  83         reads = self.rds.getReadsDict(withFlag=True)
  84         self.assertEquals("728439", reads["1"][0]["flag"])
  85
  86
  87     def testCountFeatures(self):
  88         testDict = {}
  89         self.assertEquals(0, geneMrnaCounts.countFeatures(testDict))
  90
  91         testDict = {"chr1": []}
  92         self.assertEquals(0, geneMrnaCounts.countFeatures(testDict))
  93
  94         #TODO: This is likely not the result we want
  95         testDict = {"chr1": "not a list"}
  96         self.assertEquals(10, geneMrnaCounts.countFeatures(testDict))
  97
  98         testDict = {"chr1": 10}
  99         self.assertEquals(0, geneMrnaCounts.countFeatures(testDict))
 100
 101         testDict = {"chr1": 10,
 102                     "chr2": ["f1"]}
 103         self.assertEquals(1, geneMrnaCounts.countFeatures(testDict))
 104
 105         testDict = {"chr1": ["f1", "f2"]}
 106         self.assertEquals(2, geneMrnaCounts.countFeatures(testDict))
 107
 108         testDict = {"chr1": ["f1", "f2"],
 109                     "chr2": []}
 110         self.assertEquals(2, geneMrnaCounts.countFeatures(testDict))
 111
 112         testDict = {"chr1": ["f1", "f2"],
 113                     "chr2": ["f1"]}
 114         self.assertEquals(3, geneMrnaCounts.countFeatures(testDict))
 115
 116
 117     def testGetGeneSymbol(self):
 118         # Case: Null/None inputs
 119         gid = ""
 120         searchGID = False
 121         geneInfoDict = {}
 122         idb = None
 123         genomeName = ""
 124         geneAnnotDict = {}
 125         self.assertEquals("LOC", geneMrnaCounts.getGeneSymbol(gid, searchGID, geneInfoDict, idb, genomeName, geneAnnotDict))
 126
 127         # Case: symbol is in geneInfoDict
 128         gid = "1"
 129         searchGID = False
 130         geneInfoDict = {"1": [["gene1", "wrong name"], ["wrong name 2"]]}
 131         idb = None
 132         genomeName = "test"
 133         geneAnnotDict = {("test", "1"): ["wrong name 3"]}
 134         self.assertEquals("gene1", geneMrnaCounts.getGeneSymbol(gid, searchGID, geneInfoDict, idb, genomeName, geneAnnotDict))
 135
 136         # Case: symbol not in geneInfoDict, is in geneAnnotDict
 137         gid = "1"
 138         searchGID = False
 139         geneInfoDict = {"0": [["wrong name"], ["wrong name 2"]]}
 140         idb = None
 141         genomeName = "test"
 142         geneAnnotDict = {("test", "1"): ["gene1"]}
 143         self.assertEquals("gene1", geneMrnaCounts.getGeneSymbol(gid, searchGID, geneInfoDict, idb, genomeName, geneAnnotDict))
 144
 145         # Case: symbol not in geneInfoDict or geneAnnotDict - non-null/None inputs
 146         gid = "1"
 147         searchGID = False
 148         geneInfoDict = {"0": [["wrong name"], ["wrong name 2"]]}
 149         idb = None
 150         genomeName = "test"
 151         geneAnnotDict = {("test", "0"): ["wrong name 3"]}
 152         self.assertEquals("LOC1", geneMrnaCounts.getGeneSymbol(gid, searchGID, geneInfoDict, idb, genomeName, geneAnnotDict))
 153
 154         # Case: using search, gid not in idb
 155         gid = "almostCertainlyNotInTheIDB"
 156         searchGID = True
 157         geneInfoDict = {"0": [["wrong name"], ["wrong name 2"]]}
 158         idb = self.idb
 159         genomeName = "human"
 160         geneAnnotDict = {("human", "0"): ["wrong name 3"]}
 161         self.assertEquals("LOCalmostCertainlyNotInTheIDB", geneMrnaCounts.getGeneSymbol(gid, searchGID, geneInfoDict, idb, genomeName, geneAnnotDict))
 162
 163         # Case: using search
 164         # sql to get gid: select gID from gene_info where genome="human" and locustag !="-" and locustag != symbol limit 5;
 165         gid = "RP11-177A2.3"
 166         searchGID = True
 167         geneInfoDict = {"27": [["correct"], ["wrong name 2"]]}
 168         idb = self.idb
 169         genomeName = "human"
 170         geneAnnotDict = {("human", "0"): ["wrong name 3"]}
 171         self.assertEquals("correct", geneMrnaCounts.getGeneSymbol(gid, searchGID, geneInfoDict, idb, genomeName, geneAnnotDict))
 172
 173
 174     def testWriteOutputFile(self):
 175         genome = Genome(self.genomeName)
 176         gidList = ["RP11-177A2.3"]
 177         gidCount = {"RP11-177A2.3": 1}
 178         geneMrnaCounts.writeOutputFile(self.outfilename, genome, gidList, gidCount, searchGID=False)
 179
 180         outfile = open(self.outfilename, "r")
 181         line = outfile.readline()
 182         result = "RP11-177A2.3\tLOCRP11-177A2.3\t1\n"
 183         self.assertEquals(result, line)
 184         outfile.close()
 185         os.remove(self.outfilename)
 186
 187         genome = Genome("hsapiens")
 188         gidList = ["RP11-177A2.3"]
 189         gidCount = {"something else": 1}
 190         geneMrnaCounts.writeOutputFile(self.outfilename, genome, gidList, gidCount, searchGID=False)
 191
 192         outfile = open(self.outfilename, "r")
 193         line = outfile.readline()
 194         result = "RP11-177A2.3\tLOCRP11-177A2.3\t0\n"
 195         self.assertEquals(result, line)
 196         outfile.close()
 197         os.remove(self.outfilename)
 198
 199     def testMain(self):
 200         argv = ["geneMRNACounts", self.genomeName, self.testDBName, self.outfilename]
 201         geneMrnaCounts.main(argv)
 202         outfile = open(self.outfilename, "r")
 203         for line in outfile:
 204             fields = line.split("\t")
 205             self.assertEquals("0\n", fields[2])
 206
 207         outfile.close()
 208         os.remove(self.outfilename)
 209
 210
 211 def suite():
 212     suite = unittest.TestSuite()
 213     suite.addTest(unittest.makeSuite(TestGeneMrnaCounts))
 214
 215     return suite
 216
 217
 218 if __name__ == "__main__":
 219     #import sys;sys.argv = ['', 'Test.testName']
 220     unittest.main()