Mercurial > repos > yufei-luo > s_mart
view commons/core/coord/test/Test_MapUtils.py @ 17:b0e8584489e6
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author | m-zytnicki |
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date | Mon, 22 Apr 2013 11:11:10 -0400 |
parents | 769e306b7933 |
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# 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 )