Mercurial > repos > yufei-luo > s_mart
comparison commons/pyRepetUnit/hmmer/hmmOutput/tests/TestHmmOutputProcessing.py @ 18:94ab73e8a190
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| author | m-zytnicki |
|---|---|
| date | Mon, 29 Apr 2013 03:20:15 -0400 |
| parents | |
| children |
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| 17:b0e8584489e6 | 18:94ab73e8a190 |
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| 1 import os | |
| 2 import unittest | |
| 3 from commons.pyRepetUnit.hmmer.hmmOutput.HmmOutput import HmmOutput | |
| 4 from commons.pyRepetUnit.hmmer.hmmOutput.HmmOutputProcessing import HmmOutputProcessing | |
| 5 from commons.pyRepetUnit.hmmer.hmmOutput.HmmpfamOutputProcessing import HmmpfamOutputProcessing | |
| 6 from commons.pyRepetUnit.hmmer.hmmOutput.HmmscanOutputProcessing import HmmscanOutputProcessing | |
| 7 from commons.core.utils.FileUtils import FileUtils | |
| 8 | |
| 9 class TestHmmOutputProcessing(unittest.TestCase): | |
| 10 | |
| 11 def setUp(self): | |
| 12 self.hmmOutput = HmmOutputProcessing() | |
| 13 self._inputFile = "./datas/test_hmmpfam_output" | |
| 14 self._outputFile = "./datas/dummyoutput.align" | |
| 15 self._inputFileScan2 = "./datas/hmmscanOutput" | |
| 16 self._outputFileScan2 = "./datas/hmmscanOutput.align" | |
| 17 | |
| 18 def test_writeHmmOutputToAlignFile(self): | |
| 19 output = open("./datas/output.align", "w") | |
| 20 output.write("SAR:satellite:satellite_5\t3\t9\tDUF751\t5\t11\t5.4\t5.4\t0\n") | |
| 21 output.write("SAR:satellite:satellite_5\t17\t23\tDUF751\t5\t11\t5.1\t5.5\t0\n") | |
| 22 output.write("SAR:satellite:satellite_5\t3\t21\tClenterotox\t173\t191\t0.66\t7.4\t0\n") | |
| 23 output.close() | |
| 24 pfamOutput = HmmOutput() | |
| 25 pfamOutput.append(["SAR:satellite:satellite_5", "3", "9", "DUF751", "5", "11", "5.4", "5.4"]) | |
| 26 pfamOutput.append(["SAR:satellite:satellite_5", "17", "23", "DUF751", "5", "11", "5.1", "5.5"]) | |
| 27 pfamOutput.append(["SAR:satellite:satellite_5", "3", "21", "Clenterotox", "173", "191", "0.66", "7.4"]) | |
| 28 fout = open("./datas/outputGen.align", "w") | |
| 29 self.hmmOutput.writeHmmOutputToAlignFile(pfamOutput, fout) | |
| 30 fout.close() | |
| 31 self.assertTrue(FileUtils.are2FilesIdentical("./datas/output.align", "./datas/outputGen.align")) | |
| 32 os.remove("./datas/output.align") | |
| 33 os.remove("./datas/outputGen.align") | |
| 34 | |
| 35 if __name__ == "__main__": | |
| 36 unittest.main() |