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view commons/core/parsing/test/Test_pilerTAToGrouperMap.py @ 6:769e306b7933
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author | yufei-luo |
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date | Fri, 18 Jan 2013 04:54:14 -0500 |
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import unittest import os from commons.core.parsing.PilerTAToGrouperMap import PilerTAToGrouperMap from commons.core.utils.FileUtils import FileUtils class Test_pilerTAToGrouperMap(unittest.TestCase): def setUp(self): self._inputGffFileName = "input.gff" self._inputPYRFileName = "input_pyr.gff" self._inputMOTIFFileName = "input_motif.gff" self._obsOutFileName = "output.info" self._obsGrouperFileName = "input_motif.gff.grp" self._obsGrpMapFileName = "input_motif.gff.grp.map" self._expOutFileName = "exp_output.info" self._expGrouperFileName = "exp_motif.gff.grp" self._expGrpMapFileName = "exp_motif.gff.grp.map" def tearDown(self): os.remove(self._inputGffFileName) os.remove(self._inputPYRFileName) os.remove(self._inputMOTIFFileName) os.remove(self._obsOutFileName) os.remove(self._obsGrouperFileName) os.remove(self._obsGrpMapFileName) os.remove(self._expOutFileName) os.remove(self._expGrouperFileName) os.remove(self._expGrpMapFileName) def testRun(self): self._writePilerTAFilePYR(self._inputPYRFileName) self._writePilerTAFileMOTIF(self._inputMOTIFFileName) self._writePilerTAGff(self._inputGffFileName) self._writeExpOutputFile(self._expOutFileName) self._writeExpGrouperFile(self._expGrouperFileName) self._writeExpGrouperMapFile(self._expGrpMapFileName) iPilerTAToGrouperMap = PilerTAToGrouperMap(self._inputGffFileName, self._inputPYRFileName,self._inputMOTIFFileName, self._obsOutFileName) iPilerTAToGrouperMap.run() self.assertTrue(FileUtils.are2FilesIdentical(self._expOutFileName, self._obsOutFileName)) self.assertTrue(FileUtils.are2FilesIdentical(self._expGrouperFileName, self._obsGrouperFileName)) self.assertTrue(FileUtils.are2FilesIdentical(self._expGrpMapFileName, self._obsGrpMapFileName)) def _writePilerTAGff(self, fileName): f = open(fileName, "w") f.write("chunk21\tpiler\thit\t155146\t156020\t0\t+\t.\tTarget chunk21 150519 151392 ; Pile 510 ; Pyramid 0\n") f.write("chunk21\tpiler\thit\t154790\t156023\t0\t+\t.\tTarget chunk21 150519 151751 ; Pile 510 ; Pyramid 0\n") f.write("chunk21\tpiler\thit\t154078\t156023\t0\t+\t.\tTarget chunk21 150519 152463 ; Pile 510 ; Pyramid 0\n") f.write("chunk21\tpiler\thit\t154256\t156023\t0\t+\t.\tTarget chunk21 150519 152285 ; Pile 510 ; Pyramid 0\n") f.write("chunk21\tpiler\thit\t154434\t156023\t0\t+\t.\tTarget chunk21 150519 152107 ; Pile 510 ; Pyramid 0\n") f.close() def _writePilerTAFilePYR(self, fileName): f = open(fileName, "w") f.write("chunk21\tpiler\tpyramid\t150519\t156023\t0\t.\t.\tPyramidIndex 0\n") f.write("chunk21\tpiler\tpyramid\t150519\t156023\t0\t.\t.\tPyramidIndex 1\n") f.write("chunk21\tpiler\tpyramid\t165574\t174424\t0\t.\t.\tPyramidIndex 2\n") f.write("chunk21\tpiler\tpyramid\t166301\t174424\t0\t.\t.\tPyramidIndex 3\n") f.write("chunk21\tpiler\tpyramid\t168967\t174424\t0\t.\t.\tPyramidIndex 4\n") f.write("chunk21\tpiler\tpyramid\t170215\t174424\t0\t.\t.\tPyramidIndex 5\n") f.close() def _writePilerTAFileMOTIF(self, fileName): f = open(fileName, "w") f.write("chunk21\tpiler\ttandemmotif\t155843\t156020\t0\t.\t.\tTarget chunk21 151215 151392 ; Pyramid 0\n") f.write("chunk21\tpiler\ttandemmotif\t151215\t151392\t0\t.\t.\tTarget chunk21 155843 156020 ; Pyramid 0\n") f.write("chunk21\tpiler\ttandemmotif\t151574\t151751\t0\t.\t.\tTarget chunk21 155843 156020 ; Pyramid 0\n") f.write("chunk21\tpiler\ttandemmotif\t152286\t152463\t0\t.\t.\tTarget chunk21 155843 156020 ; Pyramid 0\n") f.write("chunk21\tpiler\ttandemmotif\t152108\t152285\t0\t.\t.\tTarget chunk21 155843 156020 ; Pyramid 0\n") f.close() def _writeExpOutputFile(self, fileName): f = open(fileName, "w") f.write("Pile 510\tPyramid 0\n") f.write("\tPyramid 1\n") f.write("\tPyramid 2\n") f.write("\tPyramid 3\n") f.write("\tPyramid 4\n") f.write("\tPyramid 5\n") f.close() def _writeExpGrouperFile(self, fileName): f = open(fileName, "w") f.write("MbS1Gr0Cl510\tchunk21\tpiler\ttandemmotif\t155843\t156020\t0\t.\t.\tTarget chunk21 151215 151392 \tPile 510\tPyramid 0\n") f.write("MbS2Gr0Cl510\tchunk21\tpiler\ttandemmotif\t151215\t151392\t0\t.\t.\tTarget chunk21 155843 156020 \tPile 510\tPyramid 0\n") f.write("MbS3Gr0Cl510\tchunk21\tpiler\ttandemmotif\t151574\t151751\t0\t.\t.\tTarget chunk21 155843 156020 \tPile 510\tPyramid 0\n") f.write("MbS4Gr0Cl510\tchunk21\tpiler\ttandemmotif\t152286\t152463\t0\t.\t.\tTarget chunk21 155843 156020 \tPile 510\tPyramid 0\n") f.write("MbS5Gr0Cl510\tchunk21\tpiler\ttandemmotif\t152108\t152285\t0\t.\t.\tTarget chunk21 155843 156020 \tPile 510\tPyramid 0\n") f.close() def _writeExpGrouperMapFile(self, fileName): f = open(fileName, "w") f.write("MbS1Gr0Cl510\tchunk21\t155843\t156020\n") f.write("MbS2Gr0Cl510\tchunk21\t151215\t151392\n") f.write("MbS3Gr0Cl510\tchunk21\t151574\t151751\n") f.write("MbS4Gr0Cl510\tchunk21\t152286\t152463\n") f.write("MbS5Gr0Cl510\tchunk21\t152108\t152285\n") f.close() if __name__ == "__main__": unittest.main()