Mercurial > repos > yufei-luo > s_mart
diff commons/pyRepetUnit/convCoord/test/TestConvCoordWithOverlapps.py @ 18:94ab73e8a190
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| author | m-zytnicki |
|---|---|
| date | Mon, 29 Apr 2013 03:20:15 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/commons/pyRepetUnit/convCoord/test/TestConvCoordWithOverlapps.py Mon Apr 29 03:20:15 2013 -0400 @@ -0,0 +1,169 @@ +import unittest +import os +import time +from commons.core.utils.FileUtils import FileUtils +from commons.core.sql.DbMySql import DbMySql + + +class Test_ConvCoordWithOverlaps( unittest.TestCase ): + pass + +# def setUp(self): +# self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S") , os.getpid() ) +# self._mapFile = "map_file.map" +# _MockMapFile( self._mapFile ) +# self._resultFile = "dummyObsFile_%s" % ( self._uniqId ) +# self._refFileToCompare = "dummyExpFile_%s" % ( self._uniqId ) +# self._configFileName = "dummyConfigFile_%s" % ( self._uniqId ) +# configF = open(self._configFileName, "w" ) +# configF.write( "[repet_env]\n" ) +# configF.write( "repet_host: %s\n" % ( os.environ["REPET_HOST"] ) ) +# configF.write( "repet_user: %s\n" % ( os.environ["REPET_USER"] ) ) +# configF.write( "repet_pw: %s\n" % ( os.environ["REPET_PW"] ) ) +# configF.write( "repet_db: %s\n" % ( os.environ["REPET_DB"] ) ) +# configF.write( "repet_port: %s\n" % ( os.environ["REPET_PORT"] ) ) +# configF.close() +# self._db = DbMySql( cfgFileName = self._configFileName ) +# +# def tearDown(self): +# os.remove( self._mapFile ) +# os.remove( self._resultFile ) +# os.remove( self._refFileToCompare ) +# self._db.close() +# self._uniqId = None +# +# +# def test_run_TwoHitsOverlapOnFirstAndSecondChunks( self ): +# file2Process = "two_hits_overlap_on_first_and_second_chunk.align" +# linesToProcess = [ "chunk1" + "\t" + "95535" + "\t" + "95570" + "\t" + "sbj2" + "\t" + "125423" + "\t" + "125467" + "\t" + "7e-15" + "\t" + "82" + "\t" + "97.78" + "\n", +# "chunk2" + "\t" + "5544" + "\t" + "5575" + "\t" + "sbj2" + "\t" + "125457" + "\t" + "133465" + "\t" + "2e-38" + "\t" + "83" + "\t" + "65" + "\n" ] +# _MockAlignFile( file2Process, linesToProcess ) +# +# convCoord = ConvCoord( file2Process, "q", self._mapFile, self._resultFile, "", 0, self._db ) +# convCoord.run() +# +# refLine = ["dmel_chr4" + "\t" + "95535" + "\t" + "95575" + "\t" + "sbj2" + "\t" + "125423" + "\t" + "133465" + "\t" + "2e-38" + "\t" + "83" + "\t" + "97.78" + "\n"] +# _MockAlignFile( self._refFileToCompare, refLine ) +# +# self.assertTrue( FileUtils.are2FilesIdentical( self._refFileToCompare, self._resultFile ) ) +# os.remove( file2Process ) +# +# +# def test_run_ThreeHitsOverlapOnFirstAndSecondChunks( self ): +# file2Process = "three_hits_overlap_on_first_and_second_chunk.align" +# linesToProcess = [ "chunk1" + "\t" + "95535" + "\t" + "95570" + "\t" + "sbj2" + "\t" + "125423" + "\t" + "125467" + "\t" + "7e-15" + "\t" + "82" + "\t" + "97.78" + "\n", +# "chunk2" + "\t" + "5544" + "\t" + "5575" + "\t" + "sbj2" + "\t" + "125457" + "\t" + "133465" + "\t" + "2e-38" + "\t" + "83" + "\t" + "65" + "\n" +# "chunk2" + "\t" + "5540" + "\t" + "5573" + "\t" + "sbj2" + "\t" + "125454" + "\t" +"125750" + "\t" + "8e-58" + "\t" + "224" + "\t" + "86.43" + "\n" ] +# _MockAlignFile( file2Process, linesToProcess ) +# +# convCoord = ConvCoord( file2Process, "q", self._mapFile, self._resultFile, "", 0, self._db ) +# convCoord.run() +# +# refLine = ["dmel_chr4" + "\t" + "95535" + "\t" + "95575" + "\t" + "sbj2" + "\t" + "125423" + "\t" + "133465" + "\t" + "8e-58" + "\t" + "224" + "\t" + "97.78" + "\n"] +# _MockAlignFile( self._refFileToCompare, refLine ) +# +# self.assertTrue( FileUtils.are2FilesIdentical( self._refFileToCompare, self._resultFile ) ) +# os.remove( file2Process ) +# +# +# def test_run_HitsOnDifferentStrandsAndDifferentSubjects( self ): +# file2Process = "hits_on_different_strands_and_different_subjects.align" +# linesToProcess = [ "chunk1" + "\t" + "95535" + "\t" + "95570" + "\t" + "sbj2" + "\t" + "125423" + "\t" + "125467" + "\t" + "7e-15" + "\t" + "82" + "\t" + "97.78" + "\n", +# "chunk2" + "\t" + "5575" + "\t" + "5544" + "\t" + "sbj2" + "\t" + "125457" + "\t" + "133465" + "\t" + "2e-38" + "\t" + "83" + "\t" + "65" + "\n", +# "chunk2" + "\t" + "5540" + "\t" + "5573" + "\t" + "sbj3" + "\t" + "125454" + "\t" +"125750" + "\t" + "8e-58" + "\t" + "224" + "\t" + "86.43" + "\n" ] +# _MockAlignFile( file2Process, linesToProcess ) +# +# convCoord = ConvCoord( file2Process, "q", self._mapFile, self._resultFile, "", 0, self._db ) +# convCoord.run() +# +# refLine = ["dmel_chr4" + "\t" + "95535" + "\t" + "95570" + "\t" + "sbj2" + "\t" + "125423" + "\t" + "125467" + "\t" + "7e-15" + "\t" + "82" + "\t" + "97.78" + "\n", +# "dmel_chr4" + "\t" + "95544" + "\t" + "95575" + "\t" + "sbj2" + "\t" + "133465" + "\t" + "125457" + "\t" + "2e-38" + "\t" + "83" + "\t" + "65" + "\n", +# "dmel_chr4" + "\t" + "95540" + "\t" + "95573" + "\t" + "sbj3" + "\t" + "125454" + "\t" +"125750" + "\t" + "8e-58" + "\t" + "224" + "\t" + "86.43" + "\n" ] +# _MockAlignFile( self._refFileToCompare, refLine ) +# +# self.assertTrue( FileUtils.are2FilesIdentical( self._refFileToCompare, self._resultFile ) ) +# os.remove( file2Process ) +# +# +# def test_run_TwoHitsOnChunksOnlyAndOnOverlap( self ): +# file2Process = "two_hits_on_chunks_only_and_on_overlap.align" +# linesToProcess = [ "chunk2" + "\t" + "85000" + "\t" + "95000" + "\t" + "sbj2" + "\t" + "125457" + "\t" + "133465" + "\t" + "2e-38" + "\t" + "83" + "\t" + "65" + "\n", +# "chunk3" + "\t" + "1000" + "\t" +" 5000" + "\t" + "sbj2" + "\t" + "125454" + "\t" + "125750" + "\t" + "8e-58" + "\t" + "224" + "\t" + "86.43" + "\n" ] +# _MockAlignFile( file2Process, linesToProcess ) +# +# convCoord = ConvCoord( file2Process, "q", self._mapFile, self._resultFile, "", 0, self._db ) +# convCoord.run() +# +# refLine = ["dmel_chr4" + "\t" + "175000"+ "\t" + "185000"+ "\t" + "sbj2"+ "\t" + "125454"+ "\t" + "133465"+ "\t" + "8e-58"+ "\t" + "224"+ "\t" + "86.43"+"\n"] +# _MockAlignFile( self._refFileToCompare, refLine ) +# +# self.assertTrue( FileUtils.are2FilesIdentical( self._refFileToCompare, self._resultFile ) ) +# os.remove( file2Process ) +# +# +# def test_run_TwoHitsOnChunks_And_OnOverlap_OnReverseStrand_ForSubject( self ): +# file2Process = "two_hits_on_chunks_and_on_overlap_on_reverse_strand_for_subject.align" +# linesToProcess = [ "chunk2" + "\t" + "85000" + "\t" + "95000" + "\t" + "sbj2" + "\t" + "133465" + "\t" + "125457" + "\t" + "2e-38" + "\t" + "83" + "\t" + "65" + "\n", +# "chunk3" + "\t" + "1000" + "\t" + "5000" + "\t" + "sbj2" + "\t" + "125750" + "\t" + "125454" + "\t" + "8e-58" + "\t" + "224" + "\t" + "86.43" + "\n" ] +# _MockAlignFile( file2Process, linesToProcess ) +# +# convCoord = ConvCoord( file2Process, "q", self._mapFile, self._resultFile, "", 0, self._db ) +# convCoord.run() +# +# refLine = ["dmel_chr4" + "\t" + "175000"+ "\t" + "185000" + "\t" + "sbj2"+ "\t" + "133465" + "\t" + "125454" + "\t" + "8e-58"+ "\t" + "224"+ "\t" + "86.43"+"\n"] +# _MockAlignFile( self._refFileToCompare, refLine ) +# +# self.assertTrue( FileUtils.are2FilesIdentical( self._refFileToCompare, self._resultFile ) ) +# os.remove( file2Process ) +# +# +# def test_run_ThreeHitsAllByAllWithTwoHitsWithinAChunkOverlap( self ): +# file2Process = "dummyAlignFile_%s" % ( self._uniqId ) +# linesToProcess = [ "chunk1"+"\t"+"192"+"\t"+"197"+"\t"+"chunk2"+"\t"+"2"+"\t"+"7"+"\t"+"8e-58"+"\t"+"11"+"\t"+"97.8"+"\n", +# "chunk1"+"\t"+"192"+"\t"+"197"+"\t"+"chunk2"+"\t"+"51"+"\t"+"56"+"\t"+"8e-58"+"\t"+"11"+"\t"+"97.8"+"\n", +# "chunk2"+"\t"+"2"+"\t"+"7"+"\t"+"chunk2"+"\t"+"51"+"\t"+"56"+"\t"+"8e-58"+"\t"+"11"+"\t"+"97.8"+"\n" ] +# _MockAlignFile( file2Process, linesToProcess ) +# +# mapFileName = "dummyMapFile_%s" % ( self._uniqId ) +# mapF = open( mapFileName, "w" ) +# mapF.write( "chunk1\tdmel_chr4\t1\t200\n" ) +# mapF.write( "chunk2\tdmel_chr4\t191\t390\n" ) +# mapF.close() +# +# convCoord = ConvCoord( file2Process, "qs", mapFileName, self._resultFile, "", 0, self._db ) +# convCoord.run() +# +# refLine = [ "dmel_chr4"+"\t"+"192"+"\t"+"197"+"\t"+"dmel_chr4"+"\t"+"241"+"\t"+"246"+"\t"+"8e-58"+"\t"+"11"+"\t"+"97.8"+"\n" ] +# _MockAlignFile( self._refFileToCompare, refLine ) +# +# self.assertTrue( FileUtils.are2FilesIdentical( self._refFileToCompare, self._resultFile ) ) +# os.remove( file2Process ) +# os.remove( mapFileName ) +# +# +#class _MockAlignFile: +# +# def __init__(self, fileName, lines): +# alignF = open(fileName, "w"); +# for line in lines: +# alignF.write(line) +# alignF.close +# +# +#class _MockMapFile: +# +# def __init__ (self, fileName): +# mapF = open(fileName, "w") +# line1 = "chunk1" + '\t' + "dmel_chr4" + '\t' + "1" + '\t'+ "100000" + "\n" +# line2 = "chunk2" + '\t' + "dmel_chr4" + '\t' + "90001" + '\t'+ "190000" + "\n" +# line3 = "chunk3" + '\t' + "dmel_chr4" + '\t' + "180001" + '\t' + "280000" + "\n" +# mapF.write(line1) +# mapF.write(line2) +# mapF.write(line3) +# mapF.close + + +test_suite = unittest.TestSuite() +test_suite.addTest( unittest.makeSuite( Test_ConvCoordWithOverlaps ) ) +if __name__ == "__main__": + unittest.TextTestRunner(verbosity=2).run( test_suite )