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