test/testAnalyzeGO.py

   1 '''
   2 Created on Aug 26, 2010
   3
   4 @author: sau
   5 '''
   6 import unittest
   7 import os
   8 from erange import analyzego
   9
  10
  11 class TestAnalyzeGO(unittest.TestCase):
  12     genome = "celegans"
  13     prefix = "testGO"
  14     inFileName = "testAnayzeGOInput.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("%s.gostat" % self.prefix)
  29         except OSError:
  30             pass
  31
  32         try:
  33             os.remove("%s.gozscore" % self.prefix)
  34         except OSError:
  35             pass
  36
  37         try:
  38             os.remove("%s.gosig" % self.prefix)
  39         except OSError:
  40             pass
  41
  42
  43     #TODO: write more tests
  44     def testAnalyzeGO(self):
  45         geneInfoList = []
  46         analyzego.analyzeGO(self.genome, geneInfoList, self.prefix)
  47         self.assertRaises(IOError, open, "%s.gostat" % self.prefix, "r")
  48         self.assertRaises(IOError, open, "%s.gozscore" % self.prefix, "r")
  49         self.assertRaises(IOError, open, "%s.gosig" % self.prefix, "r")
  50
  51         geneInfoList = ["worm\tgeneID"]
  52         analyzego.analyzeGO(self.genome, geneInfoList, self.prefix)
  53         statfile = open("%s.gostat" % self.prefix, "r")
  54         stats = statfile.readlines()
  55         print len(stats)
  56
  57         statfile.close()
  58         scorefile = open("%s.gozscore" % self.prefix, "r")
  59         scores = scorefile.readlines()
  60         print len(scores)
  61
  62         scorefile.close()
  63         sigfile = open("%s.gosig" % self.prefix, "r")
  64         sigs = sigfile.readlines()
  65         print len(sigs)
  66
  67         sigfile.close()
  68
  69
  70     def testMain(self):
  71         argv = ["analyzego", self.genome, self.inFileName, self.prefix]
  72         analyzego.main(argv)
  73
  74
  75 def suite():
  76     suite = unittest.TestSuite()
  77     suite.addTest(unittest.makeSuite(TestAnalyzeGO))
  78
  79     return suite
  80
  81
  82 if __name__ == "__main__":
  83     #import sys;sys.argv = ['', 'Test.testName']
  84     unittest.main()