Mercurial > repos > yufei-luo > s_mart
comparison commons/pyRepetUnit/hmmer/hmmOutput/tests/TestHmmscanOutputProcessing.py @ 18:94ab73e8a190
Uploaded
| author | m-zytnicki |
|---|---|
| date | Mon, 29 Apr 2013 03:20:15 -0400 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| 17:b0e8584489e6 | 18:94ab73e8a190 |
|---|---|
| 1 import os | |
| 2 import unittest | |
| 3 from commons.pyRepetUnit.hmmer.hmmOutput.HmmscanOutputProcessing import HmmscanOutputProcessing | |
| 4 from commons.core.utils.FileUtils import FileUtils | |
| 5 | |
| 6 class TestHmmscanOutputProcessing(unittest.TestCase): | |
| 7 | |
| 8 def setUp(self): | |
| 9 self.hmmscanOutputProcess = HmmscanOutputProcessing() | |
| 10 self._inputFile = "./datas/hmmscanOutputTab.txt" | |
| 11 self._inputFileScan2 = "./datas/hmmscanOutput" | |
| 12 self._outputFileScan2 = "./datas/hmmscanOutput.align" | |
| 13 self._outputFile = "./datas/dummyFile.align" | |
| 14 | |
| 15 def tearDown(self): | |
| 16 if os.path.exists(self._outputFile): | |
| 17 os.remove(self._outputFile) | |
| 18 | |
| 19 def testReadHmmerscanOutput(self): | |
| 20 file = open( self._inputFile ) | |
| 21 pfamOutput = self.hmmscanOutputProcess.readHmmOutput(file) | |
| 22 self.assertEqual(["Polinton-1_DY:classII:Polinton_4", "2742", "2766", "rve", "50", "78", "2.4e+03", "-3.3"], pfamOutput.get(0)) | |
| 23 self.assertEqual(["Polinton-1_DY:classII:Polinton_4", "2951", "3101", "rve", "4", "168", "6.7e-30", "103.4"], pfamOutput.get(1)) | |
| 24 self.assertEqual(["Polinton-1_DY:classII:Polinton_4", "3198", "3228", "Chromo", "4", "51", "8.5e-06", "24.7"], pfamOutput.get(2)) | |
| 25 self.assertEqual(["Polinton-1_DY:classII:Polinton_4", "2117", "2125", "GARS_A", "196", "204", "11", "2.5"], pfamOutput.get(3)) | |
| 26 file.close() | |
| 27 | |
| 28 def test_readHmmerscanOutput_empty_file(self): | |
| 29 file = open( "./datas/OutputhmmscanEmpty", "w" ) | |
| 30 file.close() | |
| 31 file = open( "./datas/OutputhmmscanEmpty") | |
| 32 pfamOutput = self.hmmscanOutputProcess.readHmmOutput(file) | |
| 33 file.close() | |
| 34 self.assertEqual(None, pfamOutput) | |
| 35 os.system("rm ./datas/OutputhmmscanEmpty") | |
| 36 | |
| 37 def testParseHmmscanOutput2Align(self): | |
| 38 self.hmmscanOutputProcess.readHmmOutputsAndWriteAlignFile(self._inputFileScan2, self._outputFile) | |
| 39 self.assertTrue(FileUtils.isRessourceExists(self._outputFile)) | |
| 40 self.assertTrue(FileUtils.are2FilesIdentical(self._outputFileScan2, self._outputFile)) | |
| 41 os.system("rm " + self._outputFile) | |
| 42 | |
| 43 def test_parseHmmscanOutput2Align_empty_file(self): | |
| 44 file = open("./datas/dummy_hmmpfam_output", "w") | |
| 45 file.close() | |
| 46 self._inputFile = "./datas/dummy_hmmpfam_output" | |
| 47 self.hmmscanOutputProcess.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_parseHmmscanOutput2Align_file_not_exists(self): | |
| 53 self._inputFile = "./datas/dummy_hmmpfam_output" | |
| 54 self.hmmscanOutputProcess.readHmmOutputsAndWriteAlignFile(self._inputFile, self._outputFile ) | |
| 55 self.assertFalse(FileUtils.isRessourceExists(self._outputFile)) | |
| 56 | |
| 57 if __name__ == "__main__": | |
| 58 unittest.main() |