view commons/tools/tests/Test_getCumulLengthFromTEannot.py @ 31:0ab839023fe4

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


class Test_getCumulLengthFromTEannot( unittest.TestCase ):
    
    def setUp( self ):
        self.fileUtils = FileUtils()
        self._getCumulLengthFromTEannot = None
        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 )
        
        
    def test_getAllSubjectsAsMapOfQueries( self ):
        inFileName = "dummyInFile_%s" % self._uniqId
        expFileName = "dummyExp_%s" % self._uniqId
        for f in [inFileName,expFileName]:
            if os.path.exists(f): os.remove(f)
        inFile = open( inFileName, "w" )
        inFile.write( "1\tchr1\t1501\t2500\tTE1\t1\t500\t0.0\t880\t95.7\n" )
        inFile.write( "2\tchr1\t3401\t4000\tTE3\t101\t700\t0.0\t950\t97.2\n" )
        inFile.close()
        inTable = "dummyPathTable_%s" % self._uniqId
        db = DbMySql(cfgFileName=self._configFileName)
        db.createTable(inTable, "path", inFileName)
        expFile = open( expFileName, "w" )
        expFile.write( "TE1\tchr1\t1501\t2500\n" )
        expFile.write( "TE3\tchr1\t3401\t4000\n" )
        expFile.close()
        self._getCumulLengthFromTEannot = getCumulLengthFromTEannot()
        self._getCumulLengthFromTEannot._tableName = inTable
        self._getCumulLengthFromTEannot._configFileName = self._configFileName
        self._getCumulLengthFromTEannot.setAdaptatorToTable()
        obsFileName = self._getCumulLengthFromTEannot.getAllSubjectsAsMapOfQueries()
        self.assertTrue( self.fileUtils.are2FilesIdentical( obsFileName, expFileName ) )
        for f in [inFileName,inTable+".map",expFileName]:
            if os.path.exists(f): os.remove(f)
        db.dropTable(inTable)
        db.close()
        
        
    def test_getCumulLength( self ):
        mergeFileName = "dummyInFile_%s" % self._uniqId
        mergeFile = open( mergeFileName, "w" )
        mergeFile.write( "TE1\tchr1\t1501\t2500\n" )
        mergeFile.write( "TE3\tchr1\t4000\t3401\n" )
        mergeFile.close()
        exp = 1000+600
        self._getCumulLengthFromTEannot = getCumulLengthFromTEannot()
        obs = self._getCumulLengthFromTEannot.getCumulLength( mergeFileName )
        self.assertEqual( obs, exp )
        os.remove( mergeFileName )

if __name__ == "__main__":
        unittest.main()