view commons/tools/tests/Test_srptTableOverlap.py @ 18:94ab73e8a190

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import unittest
import os
import time
import pyRepet.sql.RepetDBMySQL
from commons.core.utils.FileUtils import FileUtils
from commons.tools import srptTableOverlap


class Test_srptTableOverlap( unittest.TestCase ):
    
    def setUp(self):
        self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S") , os.getpid() )
        self._db = pyRepet.sql.RepetDBMySQL.RepetDB( os.environ["REPET_USER"],
                                                     os.environ["REPET_HOST"],
                                                     os.environ["REPET_PW"],
                                                     os.environ["REPET_DB"] )
        
        
    def test_getOverlapAllPaths(self):
        qryFileName = "dummyQryFile_%s" % ( self._uniqId )
        qryF = open( qryFileName, "w" )
        qryF.write("1\tchr1\t1301\t2000\tTE2\t11\t17\t1e-20\t30\t90.2\n")
        qryF.close()
        qryTable = "dummyQryTable_%s" % ( self._uniqId )
        self._db.create_table( self._db, qryTable, qryFileName, "path" )
        sbjFileName = "dummySbjFile_%s" % ( self._uniqId )
        sbjF = open( sbjFileName, "w" )
        sbjF.write("1\tchr1\t1001\t1500\tTE1\t11\t17\t1e-20\t30\t90.2\n")   # 200-bp overlap: 1301-1500
        sbjF.write("2\tchr1\t1401\t1800\tTE2\t11\t17\t1e-20\t30\t90.2\n")   # 300-bp overlap: 1501-1800
        sbjF.write("3\tchr1\t2001\t2100\tTE2\t11\t17\t1e-20\t30\t90.2\n")
        sbjF.write("4\tchr2\t1301\t2000\tTE2\t11\t17\t1e-20\t30\t90.2\n")   # different query
        sbjF.close()
        sbjTable = "dummySbjTable_%s" % ( self._uniqId )
        self._db.create_table( self._db, sbjTable, sbjFileName, "path" )
        exp_sum_osize, exp_sum_non_osize, exp_sum_qsize = 500, 200, 700
        obs_sum_osize, obs_sum_non_osize, obs_sum_qsize = srptTableOverlap.getOverlapAllPaths( qryTable, "path", sbjTable, "path", self._db )
        self.assertEqual( obs_sum_osize, exp_sum_osize )
        self.assertEqual( obs_sum_non_osize, exp_sum_non_osize )
        self.assertEqual( obs_sum_qsize, exp_sum_qsize )
        os.remove( qryFileName )
        os.remove( sbjFileName )
        self._db.remove_if_exist( qryTable )
        self._db.remove_if_exist( sbjTable )
        
        
    def test_pathOverlapByPath(self):
        qryFileName = "dummyQryFile_%s" % ( self._uniqId )
        qryF = open( qryFileName, "w" )
        qryF.write("1\tchr1\t1301\t2000\tTE2\t1\t700\t1e-80\t850\t90.2\n")
        qryF.write("1\tchr1\t2301\t3000\tTE2\t801\t1500\t1e-90\t930\t90.2\n")
        qryF.close()
        qryTable = "dummyQryTable_%s" % ( self._uniqId )
        self._db.create_table( self._db, qryTable, qryFileName, "path" )
        sbjFileName = "dummySbjFile_%s" % ( self._uniqId )
        sbjF = open( sbjFileName, "w" )
        sbjF.write("1\tchr1\t1401\t1800\tTE2\t11\t17\t1e-20\t30\t90.2\n")
        sbjF.write("1\tchr1\t2101\t250000\tTE2\t11\t17\t1e-20\t30\t90.2\n")
        sbjF.write("2\tchr1\t3501\t4000\tTE3\t11\t17\t1e-20\t30\t90.2\n")
        sbjF.close()
        sbjTable = "dummySbjTable_%s" % ( self._uniqId )
        self._db.create_table( self._db, sbjTable, sbjFileName, "path" )
        expFileName = "dummyOutFileExp_%s" % ( self._uniqId )
        expF = open( expFileName, "w" )
        expF.write("1\tTE2\t1400\t1:TE2\t1\t248300\t1100\t0.785714\t0.004430\n")
        expF.close()
        obsFileName = "dummyOutFileObs_%s" % ( self._uniqId )
        obsF = open( obsFileName, "w" )
        srptTableOverlap.pathOverlapByPath( qryTable, "path", sbjTable, "path", self._db, obsF )
        obsF.close()
        self.assertTrue(  FileUtils.are2FilesIdentical( obsFileName, expFileName ) )
        for f in [ qryFileName, sbjFileName, expFileName, obsFileName ]:
            os.remove( f )
        self._db.remove_if_exist( qryTable )
        self._db.remove_if_exist( sbjTable )
        self._db.remove_if_exist( sbjTable+"_bin" )
        
        
if __name__ == "__main__":
        unittest.main()