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1 from commons.core.utils.FileUtils import FileUtils
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2 import unittest
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3 import os
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4 import subprocess
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5 from commons.launcher.LaunchMatcher import LaunchMatcher
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6
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7 class Test_F_LaunchMatcher(unittest.TestCase):
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8
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9 def setUp(self):
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10 self._inFileName = "DmelChr4.align"
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11 self._fastaFileName = "DmelChr4.fa"
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12 inFilePath = "%s/Tools/%s" % (os.environ["REPET_DATA"], self._inFileName)
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13 inFastaPath = "%s/Tools/%s" % (os.environ["REPET_DATA"], self._fastaFileName)
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14 try:
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15 os.remove(self._inFileName)
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16 except:
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17 pass
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18 os.symlink(inFilePath, self._inFileName)
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19 os.symlink(inFastaPath, self._fastaFileName)
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20 self._iLaunchMatcher = LaunchMatcher(align=self._inFileName, queryFileName=self._fastaFileName, subjectFileName=self._fastaFileName, doJoin=True, evalue="1e-20", keepConflict=True)
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21 self._iLaunchMatcher.setVerbosity(2)
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22
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23 def tearDown(self):
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24 try:
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25 FileUtils.removeFilesByPattern("%s*" % self._inFileName)
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26 os.remove(self._fastaFileName)
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27 except:
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28 pass
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29
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30 def test_run_as_class_1_file(self):
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31 expPathFileName = "%s/Tools/DmelChr4.align.match.path" % os.environ["REPET_DATA"]
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32 expTabFileName = "%s/Tools/DmelChr4.align.match.tab" % os.environ["REPET_DATA"]
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33
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34 obsPathFileName = "%s.match.path" % self._inFileName
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35 obsTabFileName = "%s.match.tab" % self._inFileName
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36
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37 self._iLaunchMatcher.run()
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38
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39 self.assertTrue(FileUtils.are2FilesIdentical(expPathFileName, obsPathFileName))
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40 self.assertTrue(FileUtils.are2FilesIdentical(expTabFileName, obsTabFileName))
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41
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42 def test_run_as_script(self):
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43 expPathFileName = "%s/Tools/DmelChr4.align.match.path" % os.environ["REPET_DATA"]
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44 expTabFileName = "%s/Tools/DmelChr4.align.match.tab" % os.environ["REPET_DATA"]
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45
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46 cmd = "LaunchMatcher.py "
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47 cmd += "-a %s " % self._inFileName
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48 cmd += "-q %s " % self._fastaFileName
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49 cmd += "-s %s " % self._fastaFileName
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50 cmd += "-o DmelChr4.align "
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51 cmd += "-j "
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52 cmd += "-k "
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53 cmd += "-e 1e-20 "
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54 process = subprocess.Popen(cmd, shell = True)
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55 process.communicate()
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56 obsPathFileName = "%s.match.path" % self._inFileName
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57 obsTabFileName = "%s.match.tab" % self._inFileName
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58
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59 self.assertTrue(FileUtils.are2FilesIdentical(expPathFileName, obsPathFileName))
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60 self.assertTrue(FileUtils.are2FilesIdentical(expTabFileName, obsTabFileName))
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61
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62 if __name__ == "__main__":
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63 unittest.main() |
