test/testmakebedfromrds.py

   1 '''
   2 Created on Jun 4, 2010
   3
   4 @author: sau
   5 '''
   6 import unittest
   7 from erange import makebedfromrds
   8
   9
  10 class TestMakeBedFromRds(unittest.TestCase):
  11
  12     def testGetSenseColor(self):
  13         senseColor = makebedfromrds.getSenseColor('+', .5)
  14         self.assertEqual(senseColor, makebedfromrds.MULTI_PLUS_COLOR, "incorrect color for low weight and plus sense color")
  15
  16         senseColor = makebedfromrds.getSenseColor('-', .5)
  17         self.assertEqual(senseColor, makebedfromrds.MULTI_MINUS_COLOR, "incorrect color for low weight and non-plus sense")
  18
  19         senseColor = makebedfromrds.getSenseColor('+', 5)
  20         self.assertEqual(senseColor, makebedfromrds.PLUS_COLOR, "incorrect color for high weight and plus sense")
  21
  22         senseColor = makebedfromrds.getSenseColor('-', 5)
  23         self.assertEqual(senseColor, makebedfromrds.MINUS_COLOR, "incorrect color for high weight and non-plus sense")
  24
  25
  26     def testGetMultiSenseColor(self):
  27         senseColor = makebedfromrds.getMultiSenseColor('+')
  28         self.assertEqual(senseColor, makebedfromrds.MULTI_PLUS_COLOR, "incorrect color for plus sense")
  29
  30         senseColor = makebedfromrds.getMultiSenseColor('-')
  31         self.assertEqual(senseColor, makebedfromrds.MULTI_MINUS_COLOR, "incorrect color for non-plus sense")
  32
  33
  34     def testGetSingleSenseColor(self):
  35         senseColor = makebedfromrds.getSingleSenseColor('+')
  36         self.assertEqual(senseColor, makebedfromrds.PLUS_COLOR, "incorrect color for plus sense")
  37
  38         senseColor = makebedfromrds.getSingleSenseColor('-')
  39         self.assertEqual(senseColor, makebedfromrds.MINUS_COLOR, "incorrect color for non-plus sense")
  40
  41
  42     def testGetReadSizes(self):
  43         numPieces = 3
  44         startList = [0, 1, 2]
  45         stopList = [3, 4, 5]
  46         readSizes = makebedfromrds.getReadSizes(numPieces, startList, stopList)
  47         self.assertEqual(readSizes, "3,3,3", "incorrect read size list")
  48
  49         readSizes = makebedfromrds.getReadSizes(1, startList, stopList)
  50         self.assertEquals(readSizes, "3", "incorrect read size list for numPieces=1")
  51
  52         self.assertRaises(IndexError, makebedfromrds.getReadSizes, numPieces, [], stopList)
  53         self.assertRaises(IndexError, makebedfromrds.getReadSizes, numPieces, startList, [])
  54         self.assertRaises(IndexError, makebedfromrds.getReadSizes, 4, startList, stopList)
  55
  56
  57     def testGetReadCoords(self):
  58         numPieces = 3
  59         startList = [0, 1, 2]
  60         readCoords = makebedfromrds.getReadCoords(numPieces, startList)
  61         self.assertEqual(readCoords, "0,1,2", "incorrect read coords list")
  62
  63         readCoords = makebedfromrds.getReadCoords(1, startList)
  64         self.assertEqual(readCoords, "0", "incorrect read coords list for numPieces=1")
  65
  66         self.assertRaises(IndexError, makebedfromrds.getReadCoords, numPieces, [])
  67         self.assertRaises(IndexError, makebedfromrds.getReadCoords, 4, startList)
  68
  69
  70     def testGetSpliceColor(self):
  71         lpart = 1
  72         rpart = 2
  73         leftweight = 0.0
  74         rightweight = 0.0
  75         aColor, bColor = makebedfromrds.getSpliceColor(lpart, rpart, leftweight, rightweight, hackType="1")
  76         self.assertEqual(aColor, makebedfromrds.SPLICE_COLOR, "incorrect first color for hacktype 1 splice")
  77         self.assertEqual(bColor, makebedfromrds.SPLICE_COLOR, "incorrect second color for hacktype 1 splice")
  78
  79         lpart = 0
  80         rpart = 0
  81         leftweight = 1.0
  82         rightweight = 0.0
  83         aColor, bColor = makebedfromrds.getSpliceColor(lpart, rpart, leftweight, rightweight, hackType="1")
  84         self.assertEqual(aColor, makebedfromrds.UNIQUE_COLOR, "incorrect first color for hacktype 1 left unique")
  85         self.assertEqual(bColor, makebedfromrds.UNIQUE_COLOR, "incorrect second color for hacktype 1 left unique")
  86
  87         lpart = 0
  88         rpart = 0
  89         leftweight = 0.0
  90         rightweight = 1.0
  91         aColor, bColor = makebedfromrds.getSpliceColor(lpart, rpart, leftweight, rightweight, hackType="1")
  92         self.assertEqual(aColor, makebedfromrds.UNIQUE_COLOR, "incorrect first color for hacktype 1 right unique")
  93         self.assertEqual(bColor, makebedfromrds.UNIQUE_COLOR, "incorrect second color for hacktype 1 right unique")
  94
  95         lpart = 0
  96         rpart = 0
  97         leftweight = 1.0
  98         rightweight = 1.0
  99         aColor, bColor = makebedfromrds.getSpliceColor(lpart, rpart, leftweight, rightweight, hackType="1")
 100         self.assertEqual(aColor, makebedfromrds.UNIQUE_COLOR, "incorrect first color for hacktype 1 left and right unique")
 101         self.assertEqual(bColor, makebedfromrds.UNIQUE_COLOR, "incorrect second color for hacktype 1 left and right unique")
 102
 103         lpart = 0
 104         rpart = 0
 105         leftweight = 0.0
 106         rightweight = 0.0
 107         aColor, bColor = makebedfromrds.getSpliceColor(lpart, rpart, leftweight, rightweight, hackType="1")
 108         self.assertEqual(aColor, makebedfromrds.MULTI_COLOR, "incorrect first color for hacktype 1 multi")
 109         self.assertEqual(bColor, makebedfromrds.MULTI_COLOR, "incorrect second color for hacktype 1 multi")
 110
 111         lpart = 1
 112         rpart = 1
 113         leftweight = 0.0
 114         rightweight = 0.0
 115         aColor, bColor = makebedfromrds.getSpliceColor(lpart, rpart, leftweight, rightweight, hackType="1")
 116         self.assertEqual(aColor, makebedfromrds.MULTI_COLOR, "incorrect first color for hacktype 1 lpart + rpart = 2")
 117         self.assertEqual(bColor, makebedfromrds.MULTI_COLOR, "incorrect second color for hacktype 1 lpart + rpart = 2")
 118
 119         lpart = 2
 120         rpart = 0
 121         leftweight = 0.0
 122         rightweight = 0.0
 123         aColor, bColor = makebedfromrds.getSpliceColor(lpart, rpart, leftweight, rightweight)
 124         self.assertEqual(aColor, makebedfromrds.SPLICE_COLOR, "incorrect first color for left splice")
 125         self.assertEqual(bColor, makebedfromrds.SPLICE_COLOR, "incorrect second color for left splice")
 126
 127         lpart = 0
 128         rpart = 0
 129         leftweight = 1.0
 130         rightweight = 0.0
 131         aColor, bColor = makebedfromrds.getSpliceColor(lpart, rpart, leftweight, rightweight)
 132         self.assertEqual(aColor, makebedfromrds.UNIQUE_COLOR, "incorrect first color for left unique")
 133         self.assertEqual(bColor, makebedfromrds.UNIQUE_COLOR, "incorrect second color for left unique")
 134
 135         lpart = 0
 136         rpart = 0
 137         leftweight = 0.0
 138         rightweight = 0.0
 139         aColor, bColor = makebedfromrds.getSpliceColor(lpart, rpart, leftweight, rightweight)
 140         self.assertEqual(aColor, makebedfromrds.MULTI_COLOR, "incorrect first color for multi splice")
 141         self.assertEqual(bColor, makebedfromrds.MULTI_COLOR, "incorrect second color for multi splice")
 142
 143         lpart = 1
 144         rpart = 0
 145         leftweight = 0.0
 146         rightweight = 0.0
 147         aColor, bColor = makebedfromrds.getSpliceColor(lpart, rpart, leftweight, rightweight)
 148         self.assertEqual(aColor, makebedfromrds.MULTI_COLOR, "incorrect first color for lpart = 1 multi splice")
 149         self.assertEqual(bColor, makebedfromrds.MULTI_COLOR, "incorrect second color for lpart = 1 multi splice")
 150
 151
 152     def testDoNotOutputChromosome(self):
 153         self.assertTrue(makebedfromrds.doNotOutputChromosome("chrM", True), "chrM is output when enforceChr=True")
 154         self.assertTrue(makebedfromrds.doNotOutputChromosome("chrM", False), "chrM is output when enforceChr=False")
 155         self.assertFalse(makebedfromrds.doNotOutputChromosome("chrAny", True), "chr is not output when enforceChr=True")
 156         self.assertFalse(makebedfromrds.doNotOutputChromosome("chrAny", False), "chr is not output when enforceChr=False")
 157         self.assertTrue(makebedfromrds.doNotOutputChromosome("Bad", True), "bad name chr is output when enforceChr=True")
 158         self.assertFalse(makebedfromrds.doNotOutputChromosome("Bad", False), "bad name chr is not output when enforceChr=True")
 159
 160
 161 def suite():
 162     suite = unittest.TestSuite()
 163     suite.addTest(unittest.makeSuite(TestMakeBedFromRds))
 164
 165     return suite
 166
 167
 168 if __name__ == "__main__":
 169     #import sys;sys.argv = ['', 'Test.testName']
 170     unittest.main()