Mercurial > repos > yufei-luo > s_mart
view commons/core/parsing/test/Test_PalsToAlign.py @ 18:94ab73e8a190
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author | m-zytnicki |
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date | Mon, 29 Apr 2013 03:20:15 -0400 |
parents | 769e306b7933 |
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import unittest from commons.core.utils.FileUtils import FileUtils import os from commons.core.parsing.PalsToAlign import PalsToAlign class Test_PalsToAlign(unittest.TestCase): def setUp(self): self._palsFileName = "input.gff" self._expAlignFileName = "file.align" self._obsAlignFileName = "output.align" def tearDown(self): os.remove(self._palsFileName) os.remove(self._expAlignFileName) os.remove(self._obsAlignFileName) def testRun(self): self._writePalsFile(self._palsFileName) self._writeExpAlignFile(self._expAlignFileName) iPalsToAlign = PalsToAlign(self._palsFileName,self._obsAlignFileName) iPalsToAlign.run() self.assertTrue(FileUtils.are2FilesIdentical(self._expAlignFileName, self._obsAlignFileName)) def _writePalsFile(self, fileName): f = open(fileName, "w") f.write("chunk01\tpals\thit\t32290\t32583\t252\t+\t.\tTarget chunk02 28975 29268; maxe 0.035\n") f.write("chunk01\tpals\thit\t28975\t29268\t252\t+\t.\tTarget chunk02 32290 32583; maxe 0.035\n") f.write("chunk01\tpals\thit\t65932\t66032\t68\t+\t.\tTarget chunk02 59293 59395; maxe 0.085\n") f.close() def _writeExpAlignFile(self, fileName): f = open(fileName, "w") f.write("chunk01\t28975\t29268\tchunk02\t32290\t32583\t0.0\t252\t96.5\n") f.write("chunk01\t32290\t32583\tchunk02\t28975\t29268\t0.0\t252\t96.5\n") f.write("chunk01\t65932\t66032\tchunk02\t59293\t59395\t0.0\t68\t91.5\n") f.close() if __name__ == "__main__": unittest.main()