1 """Unit Test for nussinov"""
   2 import unittest
   3 from nussinov import NussinovMatrix, Nussinov
   4 
   5 sample = 'GGGAAAUCC'
   6 
   7 class TestDataStructure(unittest.TestCase):
   8     def testStack(self):
   9         mystack = [1,2,3,4,5]
  10 	mystack.pop()
  11 	mystack.append('push')
  12 	self.assertEqual(mystack, [1,2,3,4,'push'])
  13 
  14 class TestNussinovMatrix(unittest.TestCase):
  15     def testInitialNussinovMatrix(self):
  16         matrix = NussinovMatrix(sample)
  17         initialMatrix = [[  0,'n','n','n','n','n','n','n','n'],
  18 	                 [  0,  0,'n','n','n','n','n','n','n'],
  19 		         ['n',  0,  0,'n','n','n','n','n','n'],
  20 		         ['n','n',  0,  0,'n','n','n','n','n'],
  21 		         ['n','n','n',  0,  0,'n','n','n','n'],
  22 		         ['n','n','n','n',  0,  0,'n','n','n'],
  23 		         ['n','n','n','n','n',  0,  0,'n','n'],
  24 		         ['n','n','n','n','n','n',  0,  0,'n'],
  25 		         ['n','n','n','n','n','n','n',  0,  0]]
  26 	self.assertEqual(matrix.getInitialMatrix(), initialMatrix)
  27     
  28     def testScorePair(self):
  29         matrix = NussinovMatrix(sample)
  30         self.assertEqual(matrix.score(1, 9), 1) 
  31 	
  32     def testScoreNonPair(self):
  33         matrix = NussinovMatrix(sample)
  34         self.assertEqual(matrix.score(1, 2), 0)
  35 	
  36     def testFinalNussinovMatrix(self):
  37         finalMatrix = [[  0,  0,  0,  0,  0,  0,  1,  2,  3],
  38 	               [  0,  0,  0,  0,  0,  0,  1,  2,  3],
  39 		       ['n',  0,  0,  0,  0,  0,  1,  2,  2],
  40 		       ['n','n',  0,  0,  0,  0,  1,  1,  1],
  41 		       ['n','n','n',  0,  0,  0,  1,  1,  1],
  42 		       ['n','n','n','n',  0,  0,  1,  1,  1],
  43 		       ['n','n','n','n','n',  0,  0,  0,  0],
  44 		       ['n','n','n','n','n','n',  0,  0,  0],
  45 		       ['n','n','n','n','n','n','n',  0,  0]]
  46 	matrix = NussinovMatrix(sample)
  47         self.assertEqual(matrix.getFinalMatrix(), finalMatrix)
  48     	
  49 class TestNussinovTraceback(unittest.TestCase):
  50     def testStackRecursion(self):
  51         matrix = [[  0,  0,  0,  0,  0,  0,  1,  2,  3],
  52 	          [  0,  0,  0,  0,  0,  0,  1,  2,  3],
  53 		  ['n',  0,  0,  0,  0,  0,  1,  2,  2],
  54 		  ['n','n',  0,  0,  0,  0,  1,  1,  1],
  55 		  ['n','n','n',  0,  0,  0,  1,  1,  1],
  56 		  ['n','n','n','n',  0,  0,  1,  1,  1],
  57 		  ['n','n','n','n','n',  0,  0,  0,  0],
  58 		  ['n','n','n','n','n','n',  0,  0,  0],
  59 		  ['n','n','n','n','n','n','n',  0,  0]]
  60         mystack = Nussinov(sample)
  61 	basepair = [(2,9),(3,8),(4,7)]
  62 	self.assertEqual(mystack.getBasePair(), basepair)
  63 
  64 if __name__=='__main__':
  65     unittest.main(argv=('','-v'))