test/testPeaksToRegion.py

   1 '''
   2 Created on Oct 4, 2010
   3
   4 @author: sau
   5 '''
   6 import unittest
   7 import os
   8 from erange import peakstoregion
   9
  10 inFileName = "testPeaksToRegionInFile.txt"
  11 outFileName = "testPeaksToRegionOutFile.txt"
  12
  13
  14 class TestPeaksToRegion(unittest.TestCase):
  15
  16
  17     def setUp(self):
  18         self.inFile = open(inFileName, "w")
  19         self.inFile.write("stuff\tpeak1\tchr1\t1000\t1.3\n")
  20         self.inFile.write("stuff\tpeak2\tchr1\t800\t9.7\n")
  21         self.inFile.write("stuff\tpeak3\tchr2\t1000\t3.0\n")
  22         self.inFile.close()
  23
  24
  25     def tearDown(self):
  26         try:
  27             os.remove(outFileName)
  28         except OSError:
  29             pass
  30
  31         try:
  32             os.remove(inFileName)
  33         except OSError:
  34             pass
  35
  36
  37     def testPeaksToRegion(self):
  38         peakstoregion.peakstoregion(inFileName, outFileName)
  39         output = open(outFileName)
  40         results = output.readlines()
  41         output.close()
  42         self.assertEquals(3, len(results))
  43         self.assertEquals("peak1\tchr1\t500\t1500\t1.3\n", results[0])
  44         self.assertEquals("peak2\tchr1\t300\t1300\t9.7\n", results[1])
  45         self.assertEquals("peak3\tchr2\t500\t1500\t3.0\n", results[2])
  46
  47
  48     def testMain(self):
  49         argv = ["peakstoregion", inFileName, outFileName]
  50         peakstoregion.main(argv)
  51         output = open(outFileName)
  52         results = output.readlines()
  53         output.close()
  54         self.assertEquals(3, len(results))
  55         self.assertEquals("peak1\tchr1\t500\t1500\t1.3\n", results[0])
  56         self.assertEquals("peak2\tchr1\t300\t1300\t9.7\n", results[1])
  57         self.assertEquals("peak3\tchr2\t500\t1500\t3.0\n", results[2])
  58
  59         argv = ["peakstoregion", inFileName, outFileName, 600, 2, 3, 1, -1]
  60         peakstoregion.main(argv)
  61         output = open(outFileName)
  62         results = output.readlines()
  63         output.close()
  64         self.assertEquals(3, len(results))
  65         self.assertEquals("peak1\tchr1\t400\t1600\t1.3\n", results[0])
  66         self.assertEquals("peak2\tchr1\t200\t1400\t9.7\n", results[1])
  67         self.assertEquals("peak3\tchr2\t400\t1600\t3.0\n", results[2])
  68
  69
  70 def suite():
  71     suite = unittest.TestSuite()
  72     suite.addTest(unittest.makeSuite(TestPeaksToRegion))
  73
  74     return suite
  75
  76
  77 if __name__ == "__main__":
  78     #import sys;sys.argv = ['', 'Test.testName']
  79     unittest.main()