test/testMarkLinkers.py

   1 '''
   2 Created on Sep 15, 2010
   3
   4 @author: sau
   5 '''
   6 import unittest
   7 import os
   8 from erange.chiapet import markLinkers
   9
  10
  11 class TestMarkLinkers(unittest.TestCase):
  12     linkerFileName = "/Users/sau/Eclipse/erange/source/Erange/chiapet/linkers.fa"
  13     inFileName = "linkerTestIn.txt"
  14     outFileName = "linkerTestOut.txt"
  15
  16     def setUp(self):
  17         infile = open(self.inFileName, "w")
  18         infile.close()
  19
  20
  21     def tearDown(self):
  22         try:
  23             os.remove(self.inFileName)
  24         except OSError:
  25             pass
  26
  27         try:
  28             os.remove(self.outFileName)
  29         except OSError:
  30             pass
  31
  32
  33     def testMarkLinkers(self):
  34         markLinkers.markLinkers(self.linkerFileName, self.inFileName, self.outFileName)
  35         output = open(self.outFileName)
  36         for line in output:
  37             self.assertEquals("", line)
  38
  39         output.close()
  40         os.remove(self.outFileName)
  41
  42         infile = open(self.inFileName, "w")
  43         print >> infile, ""
  44         print >> infile, "@Linker1"
  45         print >> infile, "........................GTTGGATAAGATATCGCGG....."
  46         print >> infile, "@NoLinker"
  47         print >> infile, "GATTACA.GATTACA.GATTACA.GATTACA.GATTACA.GATTACA."
  48         print >> infile, "@Linker2"
  49         print >> infile, "........................GTTGGAATGTATATCGCGG....."
  50         print >> infile, "@Linker1Short"
  51         print >> infile, "..............GTTGGAATGTATATCGCGG..............."
  52         print >> infile, "@Linker2Short"
  53         print >> infile, "..............GTTGGAATGTATATCGCGG..............."
  54         infile.close()
  55
  56         markLinkers.markLinkers(self.linkerFileName, self.inFileName, self.outFileName)
  57         output = open(self.outFileName)
  58         self.assertEquals(">L1_Linker1\n", output.readline())
  59         self.assertEquals("....................\n", output.readline())
  60         self.assertEquals(">NA_NoLinker\n", output.readline())
  61         self.assertEquals("GATTACA.GATTACA.GATT\n", output.readline())
  62         self.assertEquals(">NA_NoLinker\n", output.readline())
  63         self.assertEquals("GATTACA.GATTACA.GATT\n", output.readline())
  64         self.assertEquals(">NA_Linker2\n", output.readline())
  65         self.assertEquals("....................\n", output.readline())
  66         self.assertEquals(">L2_Linker2\n", output.readline())
  67         self.assertEquals("....................\n", output.readline())
  68         self.assertEquals(">NA_Linker1Short\n", output.readline())
  69         self.assertEquals("..............GTTGGA\n", output.readline())
  70         self.assertEquals(">NA_Linker1Short\n", output.readline())
  71         self.assertEquals("..............GTTGGA\n", output.readline())
  72         self.assertEquals(">NA_Linker2Short\n", output.readline())
  73         self.assertEquals("..............GTTGGA\n", output.readline())
  74         self.assertEquals(">NA_Linker2Short\n", output.readline())
  75         self.assertEquals("..............GTTGGA\n", output.readline())
  76
  77         output.close()
  78         #TODO: Check that we really do want to output the same line
  79         #multiple times in the case where neither linker is detected.
  80         #See if downstream there is a real reason for doing it this way
  81         #or if it was handled as a bug introduced at this stage of the
  82         #analysis.
  83
  84
  85     def testGetLinkerInformation(self):
  86         linkerDict, linkerList = markLinkers.getLinkerInformation([])
  87         resultDict = {}
  88         resultList = []
  89         self.assertEquals(resultDict, linkerDict)
  90         self.assertEquals(resultList, linkerList)
  91
  92         linkerData = [">linker_b.1",
  93                       "GTTGGATAAGATATCGCGG",
  94                       ">linker_b.2",
  95                       "GTTGGAATGTATATCGCGG"
  96         ]
  97         linkerDict, linkerList = markLinkers.getLinkerInformation(linkerData)
  98         resultDict = {"linker_b.1": "GTTGGATAAG",
  99                       "linker_b.2": "GTTGGAATGT"
 100         }
 101         resultList = ["linker_b.1", "linker_b.2"]
 102         self.assertEquals(resultDict, linkerDict)
 103         self.assertEquals(resultList, linkerList)
 104
 105
 106     def testGetLinkerInformationFromFile(self):
 107         linkerDict, linkerList = markLinkers.getLinkerInformationFromFile("bad file name")
 108         resultDict = {}
 109         resultList = []
 110         self.assertEquals(resultDict, linkerDict)
 111         self.assertEquals(resultList, linkerList)
 112
 113         linkerDict, linkerList = markLinkers.getLinkerInformationFromFile(self.linkerFileName)
 114         resultDict = {"linker_b.1": "GTTGGATAAG",
 115                       "linker_b.2": "GTTGGAATGT"
 116         }
 117         resultList = ["linker_b.1", "linker_b.2"]
 118         self.assertEquals(resultDict, linkerDict)
 119         self.assertEquals(resultList, linkerList)
 120
 121
 122     def testMain(self):
 123         argv = ["markLinkers", self.linkerFileName, self.inFileName, self.outFileName]
 124         markLinkers.main(argv)
 125         output = open(self.outFileName)
 126         for line in output:
 127             self.assertEquals("", line)
 128
 129         output.close()
 130         os.remove(self.outFileName)
 131
 132
 133 def suite():
 134     suite = unittest.TestSuite()
 135     suite.addTest(unittest.makeSuite(TestMarkLinkers))
 136
 137     return suite
 138
 139
 140 if __name__ == "__main__":
 141     #import sys;sys.argv = ['', 'Test.testName']
 142     unittest.main()