test/testGetFasta.py

   1 '''
   2 Created on Aug 27, 2010
   3
   4 @author: sau
   5 '''
   6 import unittest
   7 import os
   8 from erange import getfasta
   9 #from erange import ReadDataset
  10 from erange import ReadDataset
  11
  12 testDBName = "testRDS.rds"
  13
  14
  15 class TestGetFasta(unittest.TestCase):
  16
  17
  18     def setUp(self):
  19         self.regionDict = {}
  20         self.minHitThresh = -1
  21         self.maxsize = 3000
  22         self.outfilename = "testFileForTestGetFasta.fa"
  23
  24
  25     def tearDown(self):
  26         try:
  27             os.remove(self.outfilename)
  28         except OSError:
  29             print "fasta file does not exist"
  30
  31         try:
  32             os.remove(testDBName)
  33         except OSError:
  34             print "RDS file does not exist"
  35
  36
  37     def testGetDefaultRegion(self):
  38         self.assertEquals({}, getfasta.getDefaultRegion(self.regionDict, self.maxsize))
  39
  40         regionDict = {"1": [],
  41                       "2": []
  42         }
  43         result = {"2": [],
  44                   "1": []
  45         }
  46         self.assertEquals(result, getfasta.getDefaultRegion(regionDict, self.maxsize))
  47
  48         regionDict = {"1": [(10, 20, 10)],
  49                       "2": []
  50         }
  51         result = {"2": [],
  52                   "1": [{"start": 10, "length": 10, "topPos": [-1]}]
  53         }
  54         self.assertEquals(result, getfasta.getDefaultRegion(regionDict, self.maxsize))
  55
  56         regionDict = {"1": [(10, 20, 10)],
  57                       "2": [(11, 21, 11)]
  58         }
  59         result = {"2": [{"start": 11, "length": 11, "topPos": [-1]}],
  60                   "1": [{"start": 10, "length": 10, "topPos": [-1]}]
  61         }
  62         self.assertEquals(result, getfasta.getDefaultRegion(regionDict, self.maxsize))
  63
  64         regionDict = {"1": [(10, 20, 10), (100, 4000, 3900)],
  65                       "2": [(11, 21, 11)]
  66         }
  67         result = {"2": [{"start": 11, "length": 11, "topPos": [-1]}],
  68                   "1": [{"start": 10, "length": 10, "topPos": [-1]}]
  69         }
  70         self.assertEquals(result, getfasta.getDefaultRegion(regionDict, self.maxsize))
  71
  72         regionDict = {"1": [(10, 20, 10), (100, 4000, 3900), (50, 60, 10)],
  73                       "2": [(11, 21, 11)]
  74         }
  75         result = {"2": [{"start": 11, "length": 11, "topPos": [-1]}],
  76                   "1": [{"start": 10, "length": 10, "topPos": [-1]},
  77                         {"start": 50, "length": 10, "topPos": [-1]}]
  78         }
  79         self.assertEquals(result, getfasta.getDefaultRegion(regionDict, self.maxsize))
  80
  81
  82     def testGetRegionUsingPeaks(self):
  83         self.assertEquals({}, getfasta.getRegionUsingPeaks(self.regionDict, self.minHitThresh, self.maxsize))
  84
  85         regionDict = {"1": [],
  86                       "2": []
  87         }
  88         result = {"2": [],
  89                   "1": []
  90         }
  91         self.assertEquals(result, getfasta.getRegionUsingPeaks(regionDict, self.minHitThresh, self.maxsize))
  92
  93         regionDict = {"1": [(10, 20, 10, 15, 1)],
  94                       "2": []
  95         }
  96         result = {"2": [],
  97                   "1": [{"start": 10, "length": 10, "topPos": [5]}]
  98         }
  99         self.assertEquals(result, getfasta.getRegionUsingPeaks(regionDict, self.minHitThresh, self.maxsize))
 100
 101         result = {"2": [],
 102                   "1": []
 103         }
 104         self.assertEquals(result, getfasta.getRegionUsingPeaks(regionDict, 3, self.maxsize))
 105
 106         regionDict = {"1": [(10, 20, 10, 15, 1)],
 107                       "2": [(11, 21, 11, 18, 1)]
 108         }
 109         result = {"2": [{"start": 11, "length": 11, "topPos": [7]}],
 110                   "1": [{"start": 10, "length": 10, "topPos": [5]}]
 111         }
 112         self.assertEquals(result, getfasta.getRegionUsingPeaks(regionDict, self.minHitThresh, self.maxsize))
 113
 114         regionDict = {"1": [(10, 20, 10, 15, 1), (100, 4000, 3900, 111, 1)],
 115                       "2": [(11, 21, 11, 18, 1)]
 116         }
 117         result = {"2": [{"start": 11, "length": 11, "topPos": [7]}],
 118                   "1": [{"start": 10, "length": 10, "topPos": [5]}]
 119         }
 120         self.assertEquals(result, getfasta.getRegionUsingPeaks(regionDict, self.minHitThresh, self.maxsize))
 121
 122         regionDict = {"1": [(10, 20, 10, 15, 1), (100, 4000, 3900, 111, 1), (50, 60, 10, 59, 1)],
 123                       "2": [(11, 21, 11, 18, 1)]
 124         }
 125         result = {"2": [{"start": 11, "length": 11, "topPos": [7]}],
 126                   "1": [{"start": 10, "length": 10, "topPos": [5]},
 127                         {"start": 50, "length": 10, "topPos": [9]}]
 128         }
 129         self.assertEquals(result, getfasta.getRegionUsingPeaks(regionDict, self.minHitThresh, self.maxsize))
 130
 131
 132     #TODO: write test.  This seems to not make sense.  We are always returning a "topPos" of range(rlen).
 133     # need to check to see if the issue might be with commoncode.findPeak as there is a lot of questionable
 134     # logic in that one
 135     def testGetRegionUsingRDS(self):
 136         rds = ReadDataset.ReadDataset(testDBName, initialize=True, datasetType="DNA", verbose=False)
 137         rds.insertMetadata([("readsize", "100")])
 138         rdsEntryList = [("testRead", "chr1", 10, 100, "+", 1.0, "", "")]
 139         rds.insertUniqs(rdsEntryList)
 140         self.assertEquals({}, getfasta.getRegionUsingRDS(self.regionDict, rds, self.minHitThresh, self.maxsize))
 141
 142         regionDict = {"1": [],
 143                       "2": []
 144         }
 145         result = {"2": [],
 146                   "1": []
 147         }
 148         self.assertEquals(result, getfasta.getRegionUsingRDS(regionDict, rds, self.minHitThresh, self.maxsize))
 149
 150         # Ack with a capital ACK.
 151         regionDict = {"1": [(1, 600, 5)],
 152                       "2": []
 153         }
 154         result = {"1": [{"start": 1, "length": 5, "topPos": [0, 1, 2, 3, 4]}],
 155                   "2": []
 156         }
 157         self.assertEquals(result, getfasta.getRegionUsingRDS(regionDict, rds, self.minHitThresh, self.maxsize))
 158
 159         del(rds)
 160
 161
 162     def testWriteFastaFile(self):
 163         ncregions = {}
 164         getfasta.writeFastaFile(ncregions, "hsapiens", self.outfilename)
 165         for line in open(self.outfilename):
 166             self.assertEquals("", line)
 167
 168         ncregions = {"1": [],
 169                      "2": []
 170         }
 171         getfasta.writeFastaFile(ncregions, "hsapiens", self.outfilename)
 172         for line in open(self.outfilename):
 173             self.assertEquals("", line)
 174
 175         ncregions = {"1": [{"start": 12000, "length": 50, "topPos": [6]}],
 176                      "2": []
 177         }
 178         getfasta.writeFastaFile(ncregions, "hsapiens", self.outfilename)
 179         fastaFile = open(self.outfilename)
 180         self.assertEquals(">chr1:11956-12057\n", fastaFile.readline())
 181         self.assertEquals("tcatagtcccctggccccattaatggattctgggatagacatgaggaccaagccaggTGGGATGAGTGAGTGTGGCTTCTGGAGGAAGTGGGGACACAGGA\n", fastaFile.readline())
 182         self.assertEquals("", fastaFile.readline())
 183
 184         ncregions = {"1": [{"start": 12000, "length": 50, "topPos": [6]}],
 185                      "2": [{"start": 18000, "length": 50, "topPos": [30]}]
 186         }
 187         getfasta.writeFastaFile(ncregions, "hsapiens", self.outfilename)
 188         fastaFile = open(self.outfilename)
 189         self.assertEquals(">chr1:11956-12057\n", fastaFile.readline())
 190         self.assertEquals("tcatagtcccctggccccattaatggattctgggatagacatgaggaccaagccaggTGGGATGAGTGAGTGTGGCTTCTGGAGGAAGTGGGGACACAGGA\n", fastaFile.readline())
 191         self.assertEquals(">chr2:17980-18081\n", fastaFile.readline())
 192         self.assertEquals("ATCATTTCAAGGATGCTTTGAGGGTAAAAAGAATGATCAATTGTGAAGCAGTGAATTGTGCTGCCAGGCACAATTCATTGGGTAATAGAAAGCTTCATTTA\n", fastaFile.readline())
 193         self.assertEquals("", fastaFile.readline())
 194
 195         ncregions = {"1": [{"start": 12000, "length": 50, "topPos": [6, 20]}],
 196                      "2": [{"start": 18000, "length": 50, "topPos": [30]}]
 197         }
 198         getfasta.writeFastaFile(ncregions, "hsapiens", self.outfilename)
 199         fastaFile = open(self.outfilename)
 200         self.assertEquals(">chr1:11956-12057\n", fastaFile.readline())
 201         self.assertEquals("tcatagtcccctggccccattaatggattctgggatagacatgaggaccaagccaggTGGGATGAGTGAGTGTGGCTTCTGGAGGAAGTGGGGACACAGGA\n", fastaFile.readline())
 202         self.assertEquals(">chr2:17980-18081\n", fastaFile.readline())
 203         self.assertEquals("ATCATTTCAAGGATGCTTTGAGGGTAAAAAGAATGATCAATTGTGAAGCAGTGAATTGTGCTGCCAGGCACAATTCATTGGGTAATAGAAAGCTTCATTTA\n", fastaFile.readline())
 204         self.assertEquals("", fastaFile.readline())
 205
 206         ncregions = {"1": [{"start": 12000, "length": 50, "topPos": [6]},
 207                            {"start": 15000, "length": 50, "topPos": [2]}
 208                           ],
 209                      "2": [{"start": 18000, "length": 50, "topPos": [30]}]
 210         }
 211         getfasta.writeFastaFile(ncregions, "hsapiens", self.outfilename)
 212         fastaFile = open(self.outfilename)
 213         self.assertEquals(">chr1:11956-12057\n", fastaFile.readline())
 214         self.assertEquals("tcatagtcccctggccccattaatggattctgggatagacatgaggaccaagccaggTGGGATGAGTGAGTGTGGCTTCTGGAGGAAGTGGGGACACAGGA\n", fastaFile.readline())
 215         self.assertEquals(">chr1:14952-15053\n", fastaFile.readline())
 216         self.assertEquals("AGTGAATGAGGGAAAGGGCAGGGCCCGGGACTGGGGAATCTGTAGGGTCAATGGAGGAGTTCAGAGAAGGTGCAACATTTCTGACCCCCTACAAGGTGCTT\n", fastaFile.readline())
 217         self.assertEquals(">chr2:17980-18081\n", fastaFile.readline())
 218         self.assertEquals("ATCATTTCAAGGATGCTTTGAGGGTAAAAAGAATGATCAATTGTGAAGCAGTGAATTGTGCTGCCAGGCACAATTCATTGGGTAATAGAAAGCTTCATTTA\n", fastaFile.readline())
 219         self.assertEquals("", fastaFile.readline())
 220
 221
 222 def suite():
 223     suite = unittest.TestSuite()
 224     suite.addTest(unittest.makeSuite(TestGetFasta))
 225
 226     return suite
 227
 228
 229 if __name__ == "__main__":
 230     #import sys;sys.argv = ['', 'Test.testName']
 231     unittest.main()