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1 import unittest
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2 import os
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3 import time
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4 from commons.core.sql.DbMySql import DbMySql
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5 from commons.tools.GetMultAlignAndPhylogenyPerTErefSeq import GetMultAlignAndPhylogenyPerTErefSeq
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6 from commons.core.utils.FileUtils import FileUtils
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7
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8
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9 class Test_GetMultAlignAndPhylogenyPerTErefSeq( unittest.TestCase ):
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10
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11 def setUp( self ):
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12 self.fileUtils = FileUtils()
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13 self._inputTEFile = "dummyTE"
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14 self._iGMAP = GetMultAlignAndPhylogenyPerTErefSeq()
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15 self._uniqId = "%s_%s" % ( time.strftime("%Y_%m_%d_%H_%M_%S") , os.getpid() )
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16 self._configFileName = "dummyConfig_%s" % self._uniqId
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17 configFile = open( self._configFileName, "w" )
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18 configFile.write("[repet_env]\n")
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19 configFile.write( "repet_host: %s\n" % ( os.environ["REPET_HOST"] ) )
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20 configFile.write( "repet_user: %s\n" % ( os.environ["REPET_USER"] ) )
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21 configFile.write( "repet_pw: %s\n" % ( os.environ["REPET_PW"] ) )
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22 configFile.write( "repet_db: %s\n" % ( os.environ["REPET_DB"] ) )
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23 configFile.write( "repet_port: %s\n" % ( os.environ["REPET_PORT"] ) )
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24 configFile.close()
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25
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26 def tearDown( self ):
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27 os.remove( self._configFileName )
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28 os.remove( self._inputTEFile )
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29
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30
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31 def test_getNamesOfTErefSeq_fromFile_ok(self):
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32 expTEList =["DHX-incomp-chim_Blc1_DmelChr4-L-B1-Map1_reversed",
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33 "DT-comp_DmelChr4-B-P0.0-Map3", "RLX-incomp_Blc3_DmelChr4-L-B3-Map1"]
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34 self._iGMAP._TErefseq = os.path.abspath(self._inputTEFile)
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35 self.writeInputTEFile()
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36 obsTEList = self._iGMAP.getNamesOfTErefSeq()
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37 self.assertEqual(obsTEList, expTEList)
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38
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39 def test_getNamesOfTErefSeq_from_empty_file(self):
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40 expTEList =[]
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41 self._iGMAP._TErefseq = os.path.abspath(self._inputTEFile)
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42 with open(self._inputTEFile,"w") as TEFile:
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43 TEFile.write("")
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44 obsTEList = self._iGMAP.getNamesOfTErefSeq()
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45 self.assertEqual(obsTEList, expTEList)
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46
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47 def writeInputTEFile(self):
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48 with open(self._inputTEFile,"w") as TEFile:
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49 TEFile.write("""DHX-incomp-chim_Blc1_DmelChr4-L-B1-Map1_reversed
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50 RLX-incomp_Blc3_DmelChr4-L-B3-Map1\t reverse
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51 DT-comp_DmelChr4-B-P0.0-Map3\t""")
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52
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53 if __name__ == "__main__":
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54 unittest.main() |
