test/testMakeSiteTrack.py

   1 '''
   2 Created on Dec 2, 2010
   3
   4 @author: sau
   5 '''
   6 import unittest
   7 import os
   8 from erange import makesitetrack
   9
  10
  11 class TestMakeSiteTrack(unittest.TestCase):
  12
  13     testInputFile = "erangeTestSiteFile"
  14     testOutputFile = "erangeTestBedFile"
  15
  16
  17     def setUp(self):
  18         self.createCompactInputFile()
  19
  20
  21     def tearDown(self):
  22         try:
  23             os.remove(self.testInputFile)
  24         except OSError:
  25             print "site file does not exist"
  26
  27         try:
  28             os.remove(self.testOutputFile)
  29         except OSError:
  30             print "bed file does not exist"
  31
  32
  33     def createStandardInputFile(self):
  34         siteFile = open(self.testInputFile, "w")
  35         siteFile.write("#comment line\n")
  36         siteFile.write("name\tchr1\t100\t175\t11\t+\t-\n")
  37         siteFile.close()
  38
  39
  40     def createCompactInputFile(self):
  41         siteFile = open(self.testInputFile, "w")
  42         siteFile.write("#comment line\n")
  43         siteFile.write("chr1:100-175\t11\t+\t-\n")
  44         siteFile.close()
  45
  46
  47     def testMakeSiteTrack(self):
  48         self.createCompactInputFile()
  49         makesitetrack.makesitetrack(self.testInputFile, self.testOutputFile)
  50         bedfile = open(self.testOutputFile)
  51         header = 'track name="" visibility=4 itemRgb="On"\n'
  52         self.assertEquals(header, bedfile.readline())
  53         result = "chr1\t100\t176\t-1\t11\t+\t-\t-\t0,0,0\n"
  54         self.assertEquals(result, bedfile.readline())
  55
  56         makesitetrack.makesitetrack(self.testInputFile, self.testOutputFile, append=True, noHeader=True)
  57         bedfile = open(self.testOutputFile)
  58         header = bedfile.readline()
  59         firstEntry = bedfile.readline()
  60         self.assertEquals(firstEntry, bedfile.readline())
  61
  62
  63     def testNonCompactMakeSiteTrack(self):
  64         try:
  65             os.remove(self.testInputFile)
  66         except OSError:
  67             print "site file does not exist"
  68
  69         self.createStandardInputFile()
  70         makesitetrack.makesitetrack(self.testInputFile, self.testOutputFile, compact=False, color="255,255,255")
  71         bedfile = open(self.testOutputFile)
  72         bedfile.readline()
  73         result = "chr1\t100\t176\t-1\t1.0\t+\t-\t-\t255,255,255\n"
  74         self.assertEquals(result, bedfile.readline())
  75
  76
  77     def testMain(self):
  78         self.createCompactInputFile()
  79         argv = ["makesitetrack"]
  80         self.assertRaises(SystemExit, makesitetrack.main, argv)
  81         argv = ["makesitetrack", self.testInputFile, self.testOutputFile]
  82         makesitetrack.main(argv)
  83
  84
  85 def suite():
  86     suite = unittest.TestSuite()
  87     suite.addTest(unittest.makeSuite(TestMakeSiteTrack))
  88
  89     return suite
  90
  91
  92 if __name__ == "__main__":
  93     #import sys;sys.argv = ['', 'Test.testName']
  94     unittest.main()