comparison commons/tools/tests/Test_GetMultAlignAndPhylogenyPerTErefSeq.py @ 31:0ab839023fe4

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31:0ab839023fe4

import unittest
import os
import time
from commons.core.sql.DbMySql import DbMySql
from commons.tools.GetMultAlignAndPhylogenyPerTErefSeq import GetMultAlignAndPhylogenyPerTErefSeq
from commons.core.utils.FileUtils import FileUtils


class Test_GetMultAlignAndPhylogenyPerTErefSeq( unittest.TestCase ):
    
    def setUp( self ):
        self.fileUtils = FileUtils()
        self._inputTEFile = "dummyTE"
        self._iGMAP = GetMultAlignAndPhylogenyPerTErefSeq()
        self._uniqId = "%s_%s" % ( time.strftime("%Y_%m_%d_%H_%M_%S") , os.getpid() )
        self._configFileName = "dummyConfig_%s" % self._uniqId
        configFile = open( self._configFileName, "w" )
        configFile.write("[repet_env]\n")
        configFile.write( "repet_host: %s\n" % ( os.environ["REPET_HOST"] ) )
        configFile.write( "repet_user: %s\n" % ( os.environ["REPET_USER"] ) )
        configFile.write( "repet_pw: %s\n" % ( os.environ["REPET_PW"] ) )
        configFile.write( "repet_db: %s\n" % ( os.environ["REPET_DB"] ) )
        configFile.write( "repet_port: %s\n" % ( os.environ["REPET_PORT"] ) )
        configFile.close()
        
    def tearDown( self ):
        os.remove( self._configFileName )
        os.remove( self._inputTEFile )
    
        
    def test_getNamesOfTErefSeq_fromFile_ok(self):
        expTEList =["DHX-incomp-chim_Blc1_DmelChr4-L-B1-Map1_reversed",
                    "DT-comp_DmelChr4-B-P0.0-Map3", "RLX-incomp_Blc3_DmelChr4-L-B3-Map1"]
        self._iGMAP._TErefseq = os.path.abspath(self._inputTEFile)
        self.writeInputTEFile()
        obsTEList = self._iGMAP.getNamesOfTErefSeq()
        self.assertEqual(obsTEList, expTEList)
    
    def test_getNamesOfTErefSeq_from_empty_file(self):
        expTEList =[]
        self._iGMAP._TErefseq = os.path.abspath(self._inputTEFile)
        with open(self._inputTEFile,"w") as TEFile:
            TEFile.write("")
        obsTEList = self._iGMAP.getNamesOfTErefSeq()
        self.assertEqual(obsTEList, expTEList)
        
    def writeInputTEFile(self):
        with open(self._inputTEFile,"w") as TEFile:
            TEFile.write("""DHX-incomp-chim_Blc1_DmelChr4-L-B1-Map1_reversed
RLX-incomp_Blc3_DmelChr4-L-B3-Map1\t reverse
DT-comp_DmelChr4-B-P0.0-Map3\t""")
            
if __name__ == "__main__":
        unittest.main()