test/testRNAPATH.py

   1 '''
   2 Created on Sep 10, 2010
   3
   4 @author: sau
   5 '''
   6 import unittest
   7 import os
   8 from erange.rnapath import RNAPATH
   9
  10 compDict = {"A": "T",
  11             "T": "A",
  12             "G": "C",
  13             "C": "G",
  14             "S": "S",
  15             "W": "W",
  16             "R": "Y",
  17             "Y": "R",
  18             "M": "K",
  19             "K": "M",
  20             "H": "D",
  21             "D": "H",
  22             "B": "V",
  23             "V": "B",
  24             "N": "N",
  25             "a": "t",
  26             "t": "a",
  27             "g": "c",
  28             "c": "g",
  29             "n": "n",
  30             "z": "z"
  31 }
  32
  33
  34 class TestRNAPATH(unittest.TestCase):
  35     incontigfilename = "contigIn.txt"
  36     distalPairsfile = "distalPair.txt"
  37     outpathfilename = "rnapathOut.txt"
  38     outcontigfilename = "contigOut.txt"
  39
  40     def setUp(self):
  41         inContigs = open(self.incontigfilename, "w")
  42         inContigs.close()
  43
  44         distal = open(self.distalPairsfile, "w")
  45         distal.close()
  46
  47
  48     def tearDown(self):
  49         try:
  50             os.remove(self.incontigfilename)
  51         except OSError:
  52             pass
  53
  54         try:
  55             os.remove(self.distalPairsfile)
  56         except OSError:
  57             pass
  58
  59         try:
  60             os.remove(self.outpathfilename)
  61         except OSError:
  62             pass
  63
  64         try:
  65             os.remove(self.outcontigfilename)
  66         except OSError:
  67             pass
  68
  69
  70     def testCompNT(self):
  71         for nt in compDict.keys():
  72             self.assertEquals(compDict[nt], RNAPATH.compNT(nt))
  73
  74         self.assertEquals("N", RNAPATH.compNT("5"))
  75         self.assertEquals("N", RNAPATH.compNT("anything"))
  76
  77
  78     def testComplement(self):
  79         self.assertEquals("", RNAPATH.complement(""))
  80         for nt in compDict.keys():
  81             self.assertEquals(compDict[nt], RNAPATH.complement(nt))
  82
  83         self.assertEquals("TGTAATC", RNAPATH.complement("GATTACA"))
  84         self.assertEquals("TGTAATC", RNAPATH.complement("GATTACA", 7))
  85         self.assertEquals("TGTAATC", RNAPATH.complement("GATTACA", -75632))
  86         self.assertEquals("TGTA", RNAPATH.complement("GATTACA", 4))
  87
  88         #TODO: do we want to return when length > seqlength?  This is
  89         # the current return and it seems very wrong we only N fill
  90         # after going more then seqlength in negative direction
  91         self.assertEquals("TGTAATCTG", RNAPATH.complement("GATTACA", 9))
  92         self.assertEquals("TGTAATCTGTAATCNNNNN", RNAPATH.complement("GATTACA", 19))
  93
  94     #TODO: write test
  95     def testRnaPath(self):
  96         RNAPATH.rnaPath(self.incontigfilename, self.distalPairsfile, self.outpathfilename, self.outcontigfilename)
  97         outfile = open(self.outpathfilename)
  98         self.assertTrue("#settings:" in outfile.readline())
  99         self.assertEquals("", outfile.readline())
 100         outfile.close()
 101         outcontig = open(self.outcontigfilename)
 102         self.assertEquals(0, len(outcontig.readlines()))
 103         outcontig.close()
 104
 105         #infile = open(self.incontigfilename, "w")
 106         #infile.write(">chr1 stuff\n")
 107         #infile.write("GATTACA\n")
 108         #infile.close()
 109         #RNAPATH.rnaPath(self.incontigfilename, self.distalPairsfile, self.outpathfilename, self.outcontigfilename)
 110         #outfile = open(self.outpathfilename)
 111         #self.assertTrue("#settings:" in outfile.readline())
 112         #self.assertEquals("", outfile.readline())
 113         #outfile.close()
 114
 115
 116     #TODO: write test
 117     def testGetPath(self):
 118         pass
 119
 120
 121     #TODO: write test
 122     def testTraverseGraph(self):
 123         leafList = []
 124         edgeMatrix = RNAPATH.EdgeMatrix(0)
 125         pathList, visitedDict = RNAPATH.traverseGraph(leafList, edgeMatrix)
 126         self.assertEquals([], pathList)
 127         self.assertEquals({}, visitedDict)
 128
 129         leafList = [1]
 130         edgeMatrix = RNAPATH.EdgeMatrix(3)
 131         edgeMatrix.edgeArray[2][1] = 3
 132         edgeMatrix.edgeArray[1][2] = 3
 133         pathList, visitedDict = RNAPATH.traverseGraph(leafList, edgeMatrix)
 134         self.assertEquals([ [1, 2] ], pathList)
 135         self.assertEquals({1: "", 2: ""}, visitedDict)
 136
 137         leafList = [1, 2]
 138         edgeMatrix = RNAPATH.EdgeMatrix(3)
 139         edgeMatrix.edgeArray[2][1] = 3
 140         edgeMatrix.edgeArray[1][2] = 3
 141         pathList, visitedDict = RNAPATH.traverseGraph(leafList, edgeMatrix)
 142         self.assertEquals([ [1, 2] ], pathList)
 143         self.assertEquals({1: "", 2: ""}, visitedDict)
 144
 145
 146     #TODO: write test
 147     def testGetContigsFromFile(self):
 148         contigNum, nameList, contigDict, origSize = RNAPATH.getContigsFromFile(self.incontigfilename)
 149         self.assertEquals(0, contigNum)
 150         self.assertEquals([], nameList)
 151         self.assertEquals({}, contigDict)
 152         self.assertEquals([], origSize)
 153
 154
 155     #TODO: check for boundary condition and special cases
 156     def testEdgeMatrix(self):
 157         edgeMatrix = RNAPATH.EdgeMatrix(0)
 158         result = "[]"
 159         self.assertEquals(result, str(edgeMatrix.edgeArray))
 160
 161         edgeMatrix = RNAPATH.EdgeMatrix(3)
 162         result = "[[0 0 0]\n [0 0 0]\n [0 0 0]]"
 163         self.assertEquals(result, str(edgeMatrix.edgeArray))
 164         self.assertEquals([], edgeMatrix.visitLink(0))
 165
 166         edgeMatrix.edgeArray[0][1] = 1
 167         self.assertEquals([], edgeMatrix.visitLink(0))
 168
 169         edgeMatrix.edgeArray[0][1] = 2
 170         result = [0]
 171         self.assertEquals(result, edgeMatrix.visitLink(0))
 172
 173         edgeMatrix.edgeArray[2][1] = 2
 174         result = []
 175         self.assertEquals(result, edgeMatrix.visitLink(0))
 176         edgeMatrix.edgeArray[2][1] = 2
 177         result = []
 178         self.assertEquals(result, edgeMatrix.visitLink(1))
 179         edgeMatrix.edgeArray[2][1] = 2
 180         result = [2]
 181         self.assertEquals(result, edgeMatrix.visitLink(2))
 182
 183         edgeMatrix.edgeArray[2][1] = 3
 184         edgeMatrix.edgeArray[1][2] = 3
 185         result = [1, 2]
 186         self.assertEquals(result, edgeMatrix.visitLink(1))
 187
 188
 189     def testMain(self):
 190         argv = ["RNAPATH", self.incontigfilename, self.distalPairsfile, self.outpathfilename, self.outcontigfilename]
 191         RNAPATH.main(argv)
 192         outfile = open(self.outpathfilename)
 193         self.assertTrue("#settings:" in outfile.readline())
 194         self.assertEquals("", outfile.readline())
 195         outfile.close()
 196         outcontig = open(self.outcontigfilename)
 197         self.assertEquals(0, len(outcontig.readlines()))
 198         outcontig.close()
 199
 200
 201 def suite():
 202     suite = unittest.TestSuite()
 203     suite.addTest(unittest.makeSuite(TestRNAPATH))
 204
 205     return suite
 206
 207
 208 if __name__ == "__main__":
 209     #import sys;sys.argv = ['', 'Test.testName']
 210     unittest.main()