test/testProcessVelvet.py

   1 '''
   2 Created on Sep 15, 2010
   3
   4 @author: sau
   5 '''
   6 import unittest
   7 import os
   8 from Erange.rnapath import processvelvet
   9
  10
  11 class TestProcessVelvet(unittest.TestCase):
  12     inFileName = "testProcessVelvetIn.txt"
  13     filterFileName = "testProcessVelvetFilter.txt"
  14     outFileName = "testProcessVelvetOut.txt"
  15
  16
  17     def setUp(self):
  18         infile = open(self.inFileName, "w")
  19         infile.close()
  20         filter = open(self.filterFileName, "w")
  21         filter.write("0\t1\t2\t3\t4\t5\t6\t7\t8\tNODE1-1_0\n")
  22         filter.close()
  23
  24
  25     def tearDown(self):
  26         try:
  27             os.remove(self.inFileName)
  28         except OSError:
  29             pass
  30
  31         try:
  32             os.remove(self.filterFileName)
  33         except OSError:
  34             pass
  35
  36         try:
  37             os.remove(self.outFileName)
  38         except OSError:
  39             pass
  40
  41
  42     def testProcessVelvet(self):
  43         processvelvet.processvelvet(self.inFileName, self.outFileName)
  44         outfile = open(self.outFileName)
  45         for line in outfile:
  46             self.assertEquals("", line)
  47
  48         os.remove(self.outFileName)
  49
  50         infile = open(self.inFileName, "w")
  51         print >> infile, ">NODE1-1_0"
  52         print >> infile, "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"
  53         infile.close()
  54
  55         processvelvet.processvelvet(self.inFileName, self.outFileName)
  56         outfile = open(self.outFileName)
  57         self.assertEquals(">chr0\n", outfile.readline())
  58         self.assertEquals("AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n", outfile.readline())
  59         self.assertEquals("", outfile.readline())
  60         outfile.close()
  61         os.remove(self.outFileName)
  62         processvelvet.processvelvet(self.inFileName, self.outFileName, filterFileName=self.filterFileName)
  63         outfile = open(self.outFileName)
  64         self.assertEquals("", outfile.readline())
  65         outfile.close()
  66         os.remove(self.outFileName)
  67
  68         infile = open(self.inFileName, "w")
  69         print >> infile, ">NODE1-1_1"
  70         print >> infile, "TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT"
  71         print >> infile, ">NODE1-1_0"
  72         print >> infile, "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"
  73         infile.close()
  74
  75         processvelvet.processvelvet(self.inFileName, self.outFileName)
  76         outfile = open(self.outFileName)
  77         self.assertEquals(">chr1\n", outfile.readline())
  78         self.assertEquals("TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\n", outfile.readline())
  79         self.assertEquals(">chr0\n", outfile.readline())
  80         self.assertEquals("AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n", outfile.readline())
  81         self.assertEquals("", outfile.readline())
  82         outfile.close()
  83         os.remove(self.outFileName)
  84         processvelvet.processvelvet(self.inFileName, self.outFileName, filterFileName=self.filterFileName)
  85         outfile = open(self.outFileName)
  86         self.assertEquals(">chr1\n", outfile.readline())
  87         self.assertEquals("TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\n", outfile.readline())
  88         self.assertEquals("", outfile.readline())
  89         outfile.close()
  90         os.remove(self.outFileName)
  91
  92         infile = open(self.inFileName, "w")
  93         print >> infile, ">NODE1-1_1"
  94         print >> infile, "TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT"
  95         print >> infile, ">NODE1-1_0"
  96         print >> infile, "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"
  97         print >> infile, ">NODE1-1_2"
  98         print >> infile, "GATTACA"
  99         infile.close()
 100
 101         processvelvet.processvelvet(self.inFileName, self.outFileName)
 102         outfile = open(self.outFileName)
 103         self.assertEquals(">chr1\n", outfile.readline())
 104         self.assertEquals("TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\n", outfile.readline())
 105         self.assertEquals(">chr0\n", outfile.readline())
 106         self.assertEquals("AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n", outfile.readline())
 107         self.assertEquals(">chr2\n", outfile.readline())
 108         self.assertEquals("GATTACA\n", outfile.readline())
 109         self.assertEquals("", outfile.readline())
 110         outfile.close()
 111         os.remove(self.outFileName)
 112         processvelvet.processvelvet(self.inFileName, self.outFileName, filterFileName=self.filterFileName)
 113         outfile = open(self.outFileName)
 114         self.assertEquals(">chr1\n", outfile.readline())
 115         self.assertEquals("TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\n", outfile.readline())
 116         self.assertEquals(">chr2\n", outfile.readline())
 117         self.assertEquals("GATTACA\n", outfile.readline())
 118         self.assertEquals("", outfile.readline())
 119         outfile.close()
 120         os.remove(self.outFileName)
 121         processvelvet.processvelvet(self.inFileName, self.outFileName, filterFileName=self.filterFileName, minSize=10)
 122         outfile = open(self.outFileName)
 123         self.assertEquals(">chr1\n", outfile.readline())
 124         self.assertEquals("TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\n", outfile.readline())
 125         self.assertEquals("", outfile.readline())
 126         outfile.close()
 127
 128
 129     def testGetFilterList(self):
 130         self.assertEquals([], processvelvet.getFilterList())
 131         self.assertEquals(["NODE1-1_0"], processvelvet.getFilterList(self.filterFileName))
 132         self.assertEquals([], processvelvet.getFilterList("whatfile?"))
 133
 134         filter = open(self.filterFileName, "a")
 135         filter.write("some fields without the key trigger string\n")
 136         filter.close()
 137         self.assertEquals(["NODE1-1_0"], processvelvet.getFilterList(self.filterFileName))
 138
 139         filter = open(self.filterFileName, "a")
 140         filter.write("0\t1\t2\t3\t4\t5\t6\t7\t8\tNODEAnything\n")
 141         filter.close()
 142         self.assertEquals(["NODE1-1_0", "NODEAnything"], processvelvet.getFilterList(self.filterFileName))
 143
 144         filter = open(self.filterFileName, "a")
 145         filter.write("0\tNODEWrongField\n")
 146         filter.close()
 147         self.assertEquals(["NODE1-1_0", "NODEAnything"], processvelvet.getFilterList(self.filterFileName))
 148
 149         filter = open(self.filterFileName, "a")
 150         filter.write("0\t1\t2\t3\t4\t5\t6\t7\t8\tNODEAnything\n")
 151         filter.close()
 152         self.assertEquals(["NODE1-1_0", "NODEAnything"], processvelvet.getFilterList(self.filterFileName))
 153
 154
 155     def testWriteNode(self):
 156         node = {"contigPrefix": "chr",
 157                 "completeID": "",
 158                 "currentSeq": ""
 159         }
 160
 161         counts = {"acceptedSize": 0,
 162                   "nSize": 0,
 163                   "contigsAccepted": 0,
 164                   "filteredSize": 0
 165         }
 166
 167         filterList = []
 168
 169         outfile = open(self.outFileName, "w")
 170         processvelvet.writeNode(outfile, node, filterList, counts, minSize=0, keepCoverage=False)
 171         outfile.close()
 172         results = open(self.outFileName)
 173         self.assertEquals("", results.readline())
 174         results.close()
 175         os.remove(self.outFileName)
 176
 177         node["completeID"] = "<5"
 178         node["currentSeq"] = "GATTACA\n"
 179         outfile = open(self.outFileName, "w")
 180         processvelvet.writeNode(outfile, node, filterList, counts, minSize=0, keepCoverage=False)
 181         self.assertEquals(counts["filteredSize"], 7)
 182         counts["filteredSize"] = 0
 183         outfile.close()
 184         results = open(self.outFileName)
 185         self.assertEquals("", results.readline())
 186         results.close()
 187         os.remove(self.outFileName)
 188
 189         node["completeID"] = "NODE1_1"
 190         node["currentSeq"] = "GATTACA\n"
 191         filterList = ["NODE1_1"]
 192         outfile = open(self.outFileName, "w")
 193         processvelvet.writeNode(outfile, node, filterList, counts, minSize=0, keepCoverage=False)
 194         self.assertEquals(counts["filteredSize"], 7)
 195         counts["filteredSize"] = 0
 196         outfile.close()
 197         results = open(self.outFileName)
 198         self.assertEquals("", results.readline())
 199         results.close()
 200         os.remove(self.outFileName)
 201
 202         node["completeID"] = "NODE1_1"
 203         node["currentSeq"] = "GATTACA\n"
 204         filterList = []
 205         outfile = open(self.outFileName, "w")
 206         processvelvet.writeNode(outfile, node, filterList, counts, minSize=0, keepCoverage=False)
 207         self.assertEquals(counts["acceptedSize"], 7)
 208         outfile.close()
 209         results = open(self.outFileName)
 210         self.assertEquals(">chr1\n", results.readline())
 211         self.assertEquals("GATTACA\n", results.readline())
 212         self.assertEquals("", results.readline())
 213         results.close()
 214         os.remove(self.outFileName)
 215
 216
 217     def testMain(self):
 218         argv = ["processVelvet", self.inFileName, self.outFileName]
 219         processvelvet.main(argv)
 220         outfile = open(self.outFileName)
 221         for line in outfile:
 222             self.assertEquals("", line)
 223
 224         os.remove(self.outFileName)
 225
 226
 227 def suite():
 228     suite = unittest.TestSuite()
 229     suite.addTest(unittest.makeSuite(TestProcessVelvet))
 230
 231     return suite
 232
 233
 234 if __name__ == "__main__":
 235     #import sys;sys.argv = ['', 'Test.testName']
 236     unittest.main()