test/testMakeSNPTrack.py

   1 '''
   2 Created on Aug 25, 2010
   3
   4 @author: sau
   5 '''
   6 import unittest
   7 from erange import makeSNPtrack
   8
   9
  10 class TestMakeSNPTrack(unittest.TestCase):
  11
  12     baseColor = {"A": "200, 0, 255",
  13                  "T": "200, 0, 255",
  14                  "C": "200, 0, 255",
  15                  "G": "200, 0, 255"
  16     }
  17
  18     specialColors = {"A-G": "255, 0, 0",
  19                      "T-C": "0, 0, 255"
  20     }
  21
  22
  23     def setUp(self):
  24         pass
  25
  26
  27     def tearDown(self):
  28         pass
  29
  30
  31     def testGetHeader(self):
  32         track = "test track"
  33         header = "track name=%s description=%s visibility=2 itemRgb=\"On\"\n" % (track, track)
  34         self.assertEquals(header, makeSNPtrack.getHeader(track))
  35
  36
  37     def testDoNotProcessLine(self):
  38         self.assertTrue(makeSNPtrack.doNotProcessLine("#anything"))
  39         self.assertFalse(makeSNPtrack.doNotProcessLine("line to process"))
  40
  41
  42     def testGetBedOutputLine(self):
  43         chromosome = "chr1"
  44         readStart = 10
  45         readStop = 11
  46         readName = "A"
  47         score = "0"
  48         sense = "+"
  49         color = self.baseColor[readName]
  50         snpPropertiesList = ["0", "1", chromosome, 11, "4", "5", "6", readName]
  51         outline = "%s\t%d\t%d\t%s\t%s\t%s\t-\t-\t\t%s\n" % (chromosome, readStart, readStop, readName, score, sense, color)
  52         self.assertEquals(outline, makeSNPtrack.getBedOutputLine(snpPropertiesList))
  53
  54         snpPropertiesList = ["0", "1", chromosome, 11, "4", "5", "6"]
  55         self.assertRaises(IndexError, makeSNPtrack.getBedOutputLine, snpPropertiesList)
  56
  57         snpPropertiesList = []
  58         self.assertRaises(IndexError, makeSNPtrack.getBedOutputLine, snpPropertiesList)
  59
  60         snpPropertiesList = ["0", "1", chromosome, "some string", "4", "5", "6", readName]
  61         self.assertRaises(ValueError, makeSNPtrack.getBedOutputLine, snpPropertiesList)
  62
  63
  64     def testGetSNPColor(self):
  65         for base in self.baseColor.keys():
  66             self.assertEquals(self.baseColor[base], makeSNPtrack.getSNPColor(base))
  67
  68         for base in self.specialColors.keys():
  69             self.assertEquals(self.specialColors[base], makeSNPtrack.getSNPColor(base))
  70
  71         defaultColor = "200, 0, 255"
  72         self.assertEquals(defaultColor, makeSNPtrack.getSNPColor(""))
  73         self.assertEquals(defaultColor, makeSNPtrack.getSNPColor("V"))
  74
  75
  76 def suite():
  77     suite = unittest.TestSuite()
  78     suite.addTest(unittest.makeSuite(TestMakeSNPTrack))
  79
  80     return suite
  81
  82
  83 if __name__ == "__main__":
  84     #import sys;sys.argv = ['', 'Test.testName']
  85     unittest.main()