diff commons/core/coord/test/Test_MapUtils.py @ 6:769e306b7933

Change the repository level.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/coord/test/Test_MapUtils.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,384 @@
+# Copyright INRA (Institut National de la Recherche Agronomique)
+# http://www.inra.fr
+# http://urgi.versailles.inra.fr
+#
+# This software is governed by the CeCILL license under French law and
+# abiding by the rules of distribution of free software.  You can  use, 
+# modify and/ or redistribute the software under the terms of the CeCILL
+# license as circulated by CEA, CNRS and INRIA at the following URL
+# "http://www.cecill.info". 
+#
+# As a counterpart to the access to the source code and  rights to copy,
+# modify and redistribute granted by the license, users are provided only
+# with a limited warranty  and the software's author,  the holder of the
+# economic rights,  and the successive licensors  have only  limited
+# liability. 
+#
+# In this respect, the user's attention is drawn to the risks associated
+# with loading,  using,  modifying and/or developing or reproducing the
+# software by the user in light of its specific status of free software,
+# that may mean  that it is complicated to manipulate,  and  that  also
+# therefore means  that it is reserved for developers  and  experienced
+# professionals having in-depth computer knowledge. Users are therefore
+# encouraged to load and test the software's suitability as regards their
+# requirements in conditions enabling the security of their systems and/or 
+# data to be ensured and,  more generally, to use and operate it in the 
+# same conditions as regards security. 
+#
+# The fact that you are presently reading this means that you have had
+# knowledge of the CeCILL license and that you accept its terms.
+
+
+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 )