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comparison commons/pyRepetUnit/hmmer/hmmOutput/tests/TestHmmpfamOutputProcessing.py @ 31:0ab839023fe4

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author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
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30:5677346472b5 31:0ab839023fe4
1 import os
2 import unittest
3 from commons.pyRepetUnit.hmmer.hmmOutput.HmmpfamOutputProcessing import HmmpfamOutputProcessing
4 from commons.core.utils.FileUtils import FileUtils
5
6 class TestHmmpfamOutputProcessing(unittest.TestCase):
7
8 def setUp(self):
9 self.fileUtils = FileUtils()
10 self.hmmpfamOutputProcess = HmmpfamOutputProcessing()
11 self._inputFile = "./datas/Outputhmmpfam"
12 self._inputFile2 = "./datas/test_hmmpfam_output"
13 self._outputFile = "./datas/dummyAlignFile.align"
14
15 def testReadHmmOutput(self):
16 file = open( self._inputFile )
17 pfamOutput = self.hmmpfamOutputProcess.readHmmOutput(file)
18 self.assertEqual(["7LES_DROME", "437", "522", "fn3", "1", "84", "8.8e-15", "48.3"], pfamOutput.get(0))
19 self.assertEqual(["7LES_DROME", "825", "914", "fn3", "1", "84", "2.2e-06", "13.4"], pfamOutput.get(1))
20 self.assertEqual(["7LES_DROME", "1292", "1389", "fn3", "1", "84", "1.2e-06", "15.9"], pfamOutput.get(2))
21 self.assertEqual(["7LES_DROME", "1799", "1891", "fn3", "1", "84", "2.3e-19", "63.5"], pfamOutput.get(3))
22 self.assertEqual(["7LES_DROME", "1899", "1978", "fn3", "1", "84", "1.5e-06", "15.2"], pfamOutput.get(4))
23 self.assertEqual(["7LES_DROME", "1993", "2107", "fn3", "1", "84", "4.3e-07", "20.3"], pfamOutput.get(5))
24 self.assertEqual(["7LES_DROME", "2209", "2483", "pkinase", "1", "294", "6e-95", "314.6"], pfamOutput.get(6))
25 self.assertEqual(["7LES_DROME", "2223", "2284", "rrm", "1", "77", "0.72", "-40.4"], pfamOutput.get(7))
26 file.close()
27
28 def test_readHmmOutput_empty_file(self):
29 file = open( "./datas/OutputhmmpfamEmpty", "w" )
30 file.close()
31 file = open( "./datas/OutputhmmpfamEmpty")
32 pfamOutput = self.hmmpfamOutputProcess.readHmmOutput(file)
33 file.close()
34 self.assertEqual(None, pfamOutput)
35 os.system("rm ./datas/OutputhmmpfamEmpty")
36
37 def testParseHmmpfamOutput2Align(self):
38 self.hmmpfamOutputProcess.readHmmOutputsAndWriteAlignFile(self._inputFile2, self._outputFile)
39 self.assertTrue(FileUtils.isRessourceExists(self._outputFile))
40 self.assertEqual(18, FileUtils.getNbLinesInSingleFile(self._outputFile))
41 os.system("rm " + self._outputFile)
42
43 def test_parseHmmpfamOutput2Align_empty_file(self):
44 file = open("./datas/dummy_hmmpfam_output", "w")
45 file.close()
46 self._inputFile = "./datas/dummy_hmmpfam_output"
47 self.hmmpfamOutputProcess.readHmmOutputsAndWriteAlignFile( self._inputFile, self._outputFile )
48 self.assertTrue(FileUtils.isEmpty(self._outputFile))
49 os.system("rm " + self._inputFile)
50 os.system("rm " + self._outputFile)
51
52 def test_parseHmmpfamOutput2Align_file_not_exists(self):
53 self._inputFile = "./datas/dummy_hmmpfam_output"
54 self.hmmpfamOutputProcess.readHmmOutputsAndWriteAlignFile(self._inputFile, self._outputFile )
55 self.assertFalse(FileUtils.isRessourceExists(self._outputFile))
56
57 if __name__ == "__main__":
58 unittest.main()