test/testTranscripts.py

   1 '''
   2 Created on Oct 4, 2010
   3
   4 @author: sau
   5 '''
   6 import unittest
   7 import os
   8 from erange import transcripts
   9
  10 inFileName = "testTranscriptsInFile.txt"
  11 outFileName = "testTranscriptsOutFile.txt"
  12
  13
  14 class TestTranscripts(unittest.TestCase):
  15
  16
  17     def setUp(self):
  18         self.inFile = open(inFileName, "w")
  19         self.inFile.write("line1\t3.5\n")
  20         self.inFile.write("line2\t1.5\n")
  21         self.inFile.write("line3\tpadding\t3.5\n")
  22         self.inFile.close()
  23
  24
  25     def tearDown(self):
  26         try:
  27             os.remove(outFileName)
  28         except OSError:
  29             pass
  30
  31         try:
  32             os.remove(inFileName)
  33         except OSError:
  34             pass
  35
  36
  37     def testTranscripts(self):
  38         transcripts.transcripts(inFileName, outFileName)
  39         output = open(outFileName)
  40         results = output.readlines()
  41         output.close()
  42         self.assertEquals(3, len(results))
  43         self.assertEquals("line1\t700000.0\t2.3\n", results[0])
  44         self.assertEquals("line2\t300000.0\t1.0\n", results[1])
  45         self.assertEquals("line3\t700000.0\t2.3\n", results[2])
  46
  47     def testMain(self):
  48         argv = ["transcripts.py", inFileName, outFileName]
  49         transcripts.main(argv)
  50         output = open(outFileName)
  51         results = output.readlines()
  52         output.close()
  53         self.assertEquals(3, len(results))
  54         self.assertEquals("line1\t700000.0\t2.3\n", results[0])
  55         self.assertEquals("line2\t300000.0\t1.0\n", results[1])
  56         self.assertEquals("line3\t700000.0\t2.3\n", results[2])
  57
  58         argv = ["transcripts.py", inFileName, outFileName, "--transcriptome", "400000"]
  59         transcripts.main(argv)
  60         output = open(outFileName)
  61         results = output.readlines()
  62         output.close()
  63         self.assertEquals(3, len(results))
  64         self.assertEquals("line1\t1400000.0\t4.7\n", results[0])
  65         self.assertEquals("line2\t600000.0\t2.0\n", results[1])
  66         self.assertEquals("line3\t1400000.0\t4.7\n", results[2])
  67
  68         argv = ["transcripts.py", inFileName, outFileName, "--cells", "5e5"]
  69         transcripts.main(argv)
  70         output = open(outFileName)
  71         results = output.readlines()
  72         output.close()
  73         self.assertEquals(3, len(results))
  74         self.assertEquals("line1\t700000.0\t4.7\n", results[0])
  75         self.assertEquals("line2\t300000.0\t2.0\n", results[1])
  76         self.assertEquals("line3\t700000.0\t4.7\n", results[2])
  77
  78         argv = ["transcripts.py", inFileName, outFileName, "--efficiency", "0.15"]
  79         transcripts.main(argv)
  80         output = open(outFileName)
  81         results = output.readlines()
  82         output.close()
  83         self.assertEquals(3, len(results))
  84         self.assertEquals("line1\t700000.0\t4.7\n", results[0])
  85         self.assertEquals("line2\t300000.0\t2.0\n", results[1])
  86         self.assertEquals("line3\t700000.0\t4.7\n", results[2])
  87
  88
  89 def suite():
  90     suite = unittest.TestSuite()
  91     suite.addTest(unittest.makeSuite(TestTranscripts))
  92
  93     return suite
  94
  95
  96 if __name__ == "__main__":
  97     #import sys;sys.argv = ['', 'Test.testName']
  98     unittest.main()