view smart_toolShed/commons/core/coord/test/Test_MapUtils.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

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import unittest
import os
import sys
from commons.core.coord.MapUtils import MapUtils
from commons.core.coord.Map import Map
from commons.core.coord.Set import Set
from commons.core.utils.FileUtils import FileUtils


class Test_MapUtils( unittest.TestCase ):
    
    def test_getMapListSortedByIncreasingMinThenMax( self ):
        iMap1 = Map("name1", "chr1", 1, 350)
        iMap2 = Map("name2", "chr1", 1, 100)
        iMap3 = Map("name3", "chr1", 50, 350)
        iMap4 = Map("name4", "chr1", 5, 450)
        lMaps = [ iMap1, iMap2, iMap3, iMap4 ]
        
        expLMaps = [ iMap2, iMap1, iMap4, iMap3 ]
        
        obsLMaps = MapUtils.getMapListSortedByIncreasingMinThenMax( lMaps )
        
        self.assertEquals( expLMaps, obsLMaps )
        
        
    def test_getMapListSortedByIncreasingMinThenMax_ordered( self ):
        iMap1 = Map("name1", "chr1", 1, 100)
        iMap2 = Map("name2", "chr1", 1, 350)
        
        lMaps = [ iMap1, iMap2 ]
        expLMaps = [ iMap1, iMap2 ]
        
        obsLMaps = MapUtils.getMapListSortedByIncreasingMinThenMax( lMaps )
        
        self.assertEquals( expLMaps, obsLMaps )
        
        
    def test_getMapListSortedByIncreasingMinThenMax_unordered( self ):
        iMap1 = Map("name1", "chr1", 1, 350)
        iMap2 = Map("name2", "chr1", 1, 100)
        
        lMaps = [ iMap1, iMap2 ]
        expLMaps = [ iMap2, iMap1 ]
        
        obsLMaps = MapUtils.getMapListSortedByIncreasingMinThenMax( lMaps )
        
        self.assertEquals( expLMaps, obsLMaps )
        
        
    def test_getMapListSortedByIncreasingMinThenMax_nonOverlapping( self ):
        iMap1 = Map("name1", "chr1", 1, 350)
        iMap2 = Map("name2", "chr1", 400, 600)
        
        lMaps = [ iMap2, iMap1 ]
        expLMaps = [ iMap1, iMap2 ]
        
        obsLMaps = MapUtils.getMapListSortedByIncreasingMinThenMax( lMaps )
        
        self.assertEquals( expLMaps, obsLMaps )
        
        
    def test_getMapListSortedByIncreasingMinThenMax_sameMinThreeMaps( self ):
        iMap1 = Map("name1", "chr1", 350, 1)
        iMap2 = Map("name2", "chr1", 400, 1)
        iMap3 = Map("name3", "chr1", 500, 1)
        
        lMaps = [ iMap2, iMap1, iMap3 ]
        expLMaps = [ iMap1, iMap2, iMap3 ]
        
        obsLMaps = MapUtils.getMapListSortedByIncreasingMinThenMax( lMaps )
        
        self.assertEquals( expLMaps, obsLMaps )
        
        
    def test_getMapListSortedByIncreasingMinThenMax_included( self ):
        iMap1 = Map("name1", "chr1", 350, 1)
        iMap2 = Map("name2", "chr1", 300, 10)
        
        lMaps = [ iMap2, iMap1 ]
        expLMaps = [ iMap1, iMap2]
        
        obsLMaps = MapUtils.getMapListSortedByIncreasingMinThenMax( lMaps )
        
        self.assertEquals( expLMaps, obsLMaps )
        
        
    def test_getMapListSortedByIncreasingMinThenMax_equal( self ):
        iMap1 = Map("name1", "chr1", 350, 1)
        iMap2 = Map("name2", "chr1", 350, 1)
        
        lMaps = [ iMap2, iMap1 ]
        expLMaps = [ iMap2, iMap1 ]
        notExpLMaps = [ iMap1, iMap2 ]
        
        obsLMaps = MapUtils.getMapListSortedByIncreasingMinThenMax( lMaps )
        
        self.assertEquals( expLMaps, obsLMaps )
        self.assertNotEquals( notExpLMaps, obsLMaps )
        
        
    def test_getMapListSortedByIncreasingNameThenSeqnameThenMinThenMax( self ):
        iMap1 = Map("name1", "chr1", 1, 350)
        iMap2 = Map("name4", "chr2", 5, 450)
        iMap3 = Map("name4", "chr1", 10, 450)
        iMap4 = Map("name4", "chr1", 10, 500)
        iMap5 = Map("name4", "chr1", 5, 450)
        iMap6 = Map("name3", "chr1", 50, 350)
        iMap7 = Map("name2", "chr1", 1, 100)

        lMaps = [ iMap1, iMap2, iMap3, iMap4, iMap5, iMap6, iMap7 ]
        
        expLMaps = [ iMap1, iMap7, iMap6, iMap5, iMap3, iMap4, iMap2 ]
        
        obsLMaps = MapUtils.getMapListSortedByIncreasingNameThenSeqnameThenMinThenMax( lMaps )
        
        self.assertEquals( expLMaps, obsLMaps )
        
        
    def test_getMapListSortedByIncreasingNameThenSeqnameThenMinThenMax_ordered( self ):
        iMap1 = Map("name1", "chr1", 1, 100)
        iMap2 = Map("name1", "chr2", 1, 350)
        
        lMaps = [ iMap1, iMap2 ]
        expLMaps = [ iMap1, iMap2 ]
        
        obsLMaps = MapUtils.getMapListSortedByIncreasingNameThenSeqnameThenMinThenMax( lMaps )
        
        self.assertEquals( expLMaps, obsLMaps )
        
        
    def test_getMapListSortedByIncreasingNameThenSeqnameThenMinThenMax_unordered( self ):
        iMap1 = Map("name1", "chr2", 1, 350)
        iMap2 = Map("name1", "chr1", 1, 100)
        
        lMaps = [ iMap1, iMap2 ]
        expLMaps = [ iMap2, iMap1 ]
        
        obsLMaps = MapUtils.getMapListSortedByIncreasingNameThenSeqnameThenMinThenMax( lMaps )
        
        self.assertEquals( expLMaps, obsLMaps )
        
        
    def test_getMapListSortedByIncreasingNameThenSeqnameThenMinThenMax_nonOverlapping( self ):
        iMap1 = Map("name1", "chr1", 1, 350)
        iMap2 = Map("name2", "chr1", 400, 600)
        
        lMaps = [ iMap2, iMap1 ]
        expLMaps = [ iMap1, iMap2 ]
        
        obsLMaps = MapUtils.getMapListSortedByIncreasingNameThenSeqnameThenMinThenMax( lMaps )
        
        self.assertEquals( expLMaps, obsLMaps )
        
        
    def test_getMapListSortedByIncreasingNameThenSeqnameThenMinThenMax_sameMinThreeMaps( self ):
        iMap1 = Map("name2", "chr1", 150, 10)
        iMap2 = Map("name2", "chr1", 1, 100)
        iMap3 = Map("name2", "chr1", 100, 1)
        
        lMaps = [ iMap1, iMap2, iMap3 ]
        expLMaps = [ iMap2, iMap3, iMap1 ]
        
        obsLMaps = MapUtils.getMapListSortedByIncreasingNameThenSeqnameThenMinThenMax( lMaps )
        
        self.assertEquals( expLMaps, obsLMaps )
        

    def test_getDictPerNameFromMapFile( self ):
        iMap1 = Map( "chunk1", "chromosome1", 1, 100 )
        iMap2 = Map( "chunk2", "chromosome1", 91, 190 )
        iMap3 = Map( "chunk3", "chromosome2", 1, 100 )
        iMap4 = Map( "chunk1", "chromosome1", 1, 100 )  # redundant with iMap1
        
        mapFile = "dummyFile.map"
        mapFileHandler = open( mapFile, "w" )
        for iMap in [ iMap1, iMap2, iMap3, iMap4 ]:
            iMap.write( mapFileHandler )
        mapFileHandler.close()
        
        dExp = { "chunk1": iMap1, "chunk2": iMap2, "chunk3": iMap3 }
        
        dObs = MapUtils.getDictPerNameFromMapFile( mapFile )
        
        self.assertEquals( dExp, dObs )
        
        os.remove( mapFile )
        
        
    def test_mapList2SetList(self):
        map1 = Map( "name1", "desc1", 1, 120 )
        map2 = Map( "name2", "desc2", 1, 20 )
        lMap = [ map1, map2 ]
        set1 = Set( 1, "name1", "desc1", 1, 120 )
        set2 = Set( 2, "name2", "desc2", 1, 20 )
        explMapSet = [ set1, set2 ]
        obslMapSet = MapUtils.mapList2SetList( lMap )
        
        self.assertEquals( explMapSet, obslMapSet )
        
        
    def test_mergeCoordsInFile( self ):
        if sys.modules.has_key( "commons.core.checker.CheckerUtils" ):
            inFile = "dummyInFile"
            inFileHandler = open( inFile, "w" )
            inFileHandler.write( "TE1\tchr1\t1501\t2500\n" )
            inFileHandler.write( "TE3\tchr1\t4000\t3401\n" )
            inFileHandler.write( "TE3\tchr1\t3800\t3601\n" )
            inFileHandler.close()
            expFile = "dummyExpFile"
            expFileHandler = open( expFile, "w" )
            expFileHandler.write( "TE1\tchr1\t1501\t2500\n" )
            expFileHandler.write( "TE3\tchr1\t4000\t3401\n" )
            expFileHandler.close()
            obsFile = "dummyObsFile"
            MapUtils.mergeCoordsInFile( inFile, obsFile )
            self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
            for f in [ inFile, expFile, obsFile ]:
                os.remove( f )
                
                
    def test_getDictPerSeqNameFromMapFile( self ):
        inFile = "dummyInFile"
        inFileHandler = open( inFile, "w" )
        inFileHandler.write( "TE1\tchr1\t1\t10\n" )
        inFileHandler.write( "TE2\tchr1\t60\t41\n" )
        inFileHandler.write( "TE3\tchr2\t5\t36\n" )
        inFileHandler.close()
        dExp = { "chr1": [ Map( "TE1", "chr1", 1, 10 ), Map( "TE2", "chr1", 60, 41 ) ],
                "chr2": [ Map( "TE3", "chr2", 5, 36 ) ] }
        dObs = MapUtils.getDictPerSeqNameFromMapFile( inFile )
        self.assertEqual( dExp, dObs )
        os.remove( inFile )

    def test_convertMapFileIntoSetFile(self):
        mapInputFile = "dummyExpFile"
        mapFileHandler = open( mapInputFile, "w" )
        mapFileHandler.write( "seq31\tchr1\t151\t250\n" )
        mapFileHandler.write( "seq27\tchr2\t301\t500\n" )
        mapFileHandler.write( "seq40\tchr2\t600\t700\n" )
        mapFileHandler.write( "seq2\tchr3\t301\t500\n" )
        mapFileHandler.close()

        expSetFile = "dummyexpSetFile"
        expSetFileHandler = open( expSetFile, "w" )
        expSetFileHandler.write( "1\tseq31\tchr1\t151\t250\n" )
        expSetFileHandler.write( "2\tseq27\tchr2\t301\t500\n" )
        expSetFileHandler.write( "3\tseq40\tchr2\t600\t700\n" )
        expSetFileHandler.write( "4\tseq2\tchr3\t301\t500\n" )
        expSetFileHandler.close()
        
        obsFile = "dummyObsFile"
        
        MapUtils.convertMapFileIntoSetFile( mapInputFile, obsFile )
        
        self.assertTrue( FileUtils.are2FilesIdentical( expSetFile, obsFile ) )
        
        for f in [ expSetFile, mapInputFile, obsFile ]:
            os.remove( f )

    def test_convertMapFileIntoSetFile_one_line(self):
        mapInputFile = "dummyExpFile"
        mapFileHandler = open( mapInputFile, "w" )
        mapFileHandler.write( "seq31\tchr1\t151\t250\n" )
        mapFileHandler.close()

        expSetFile = "dummyexpSetFile"
        expSetFileHandler = open( expSetFile, "w" )
        expSetFileHandler.write( "1\tseq31\tchr1\t151\t250\n" )
        expSetFileHandler.close()
        
        obsFile = "dummyObsFile"
        
        MapUtils.convertMapFileIntoSetFile( mapInputFile, obsFile )
        
        self.assertTrue( FileUtils.are2FilesIdentical( expSetFile, obsFile ) )
        
        for f in [ expSetFile, mapInputFile, obsFile ]:
            os.remove( f )

    def test_convertMapFileIntoSetFile_empty_file(self):
        mapInputFile = "dummyFile.map"
        mapFileHandler = open( mapInputFile, "w" )
        mapFileHandler.close()
        
        expFile = "dummyExpFile.map.set"
        expFileHandler = open( expFile, "w" )
        expFileHandler.close()
        
        obsFile = "dummyFile.map.set"
        
        MapUtils.convertMapFileIntoSetFile( mapInputFile )
        
        self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
        
        for f in [ expFile, mapInputFile, obsFile ]:
            os.remove( f )
            
    def test_writeListInFile_empty_list(self):
        lMaps = [ ]
        expFileName = "expFileName"
        fileHandle = open(expFileName, "w")
        fileHandle.close()
 
        obsFileName = "obsFileName"
        fileHandle = open(obsFileName, "w")
        MapUtils.writeListInFile(lMaps, obsFileName, "w")
        fileHandle.close()
         
        self.assertTrue( FileUtils.are2FilesIdentical( expFileName, obsFileName ) )
        
        os.remove(obsFileName)
        os.remove(expFileName)
        
    def test_writeListInFile_list_one_set(self):
        lMaps = [ Map( "map1", "map1seq", 1, 10 ) ]
        line =  "map1\tmap1seq\t1\t10\n"
       
        expFileName = "expFileName"
 
        fileHandle = open(expFileName, "w")
        fileHandle.write(line)
        fileHandle.close()
 
        obsFileName = "obsFileName"
        fileHandle = open(obsFileName, "w")
        MapUtils.writeListInFile(lMaps, obsFileName, "w")
        fileHandle.close()
         
        self.assertTrue( FileUtils.are2FilesIdentical( expFileName, obsFileName ) )
        
        os.remove(obsFileName)
        os.remove(expFileName)

    def test_getMinLengthOfMapFile(self):
        mapFileName = "%s/Gnome_tools/Vein_v4_scaffold_00001.fa.Nstretch.map" % os.environ["REPET_DATA"]
        expMinLengthofMapFile = 20
        iMap = MapUtils()
        obsMinLengthofMapFile = iMap.getMinLengthOfMapFile(mapFileName)
        self.assertEquals(expMinLengthofMapFile, obsMinLengthofMapFile)
       
    def test_getMaxLengthOfMapFile(self):
        mapFileName = "%s/Gnome_tools/Vein_v4_scaffold_00001.fa.Nstretch.map" % os.environ["REPET_DATA"]
        expMinLengthofMapFile = 6344
        iMap = MapUtils()
        obsMinLengthofMapFile = iMap.getMaxLengthOfMapFile(mapFileName)
        self.assertEquals(expMinLengthofMapFile, obsMinLengthofMapFile)
       

        
test_suite = unittest.TestSuite()
test_suite.addTest( unittest.makeSuite( Test_MapUtils ) )
if __name__ == "__main__":
    unittest.TextTestRunner(verbosity=2).run( test_suite )