diff commons/tools/tests/Test_OrientSequences.py @ 18:94ab73e8a190

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/tools/tests/Test_OrientSequences.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,101 @@
+import unittest
+import time
+import os
+from commons.core.utils.FileUtils import FileUtils
+from commons.tools.OrientSequences import OrientSequences
+
+
+class Test_OrientSequences( unittest.TestCase ):
+    
+    def setUp( self ):
+        self._i = OrientSequences ()
+        self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S"), os.getpid() )
+        
+        
+    def tearDown( self ):
+        self._i = None
+        self._uniqId = None
+        
+        
+    def test_parseMummerOutput( self ):
+        inFileName = "dummyInFile_%s" % ( self._uniqId )
+        inF = open( inFileName, "w" )
+        inF.write( "> seq1\n" )
+        inF.write( "  seq2      20        1        20\n" )
+        inF.write( "> seq1 Reverse\n" )
+        inF.write( "  seq2      100        1        100\n" )
+        inF.write( "  seq2      450      400        50\n" )
+        inF.close()
+        dExp = { "direct": 1, "reverse": 2 }
+        self._i._verbose = 0
+        dObs = self._i.parseMummerOutput( inFileName, "seq1", "seq2" )
+        self.assertEqual( dObs, dExp )
+        os.remove( inFileName )
+        
+        
+    def test_getSequencesToReverseFromMatrix_2seq( self ):
+        lNewHeaders = [ "seq1", "seq2" ]
+        dMatrix = { "1_vs_2": { "direct": 1, "reverse": 2 } }
+        lExp = [ "seq2" ]
+        self._i._verbose = 0
+        lObs = self._i.getSequencesToReverseFromMatrix( dMatrix, lNewHeaders )
+        lExp.sort()
+        lObs.sort()
+        self.assertEqual( lObs, lExp )
+        
+        
+    def test_getSequencesToReverseFromMatrix_3seq( self ):
+        lNewHeaders = [ "seq1", "seq2", "seq3" ]
+        dMatrix = { "1_vs_2": { "direct": 1, "reverse": 10 },
+                   "1_vs_3": { "direct": 10, "reverse": 1 },
+                   "2_vs_3": { "direct": 1, "reverse": 10 } }
+        lExp = [ "seq2" ]
+        self._i._verbose = 0
+        lObs = self._i.getSequencesToReverseFromMatrix( dMatrix, lNewHeaders )
+        lExp.sort()
+        lObs.sort()
+        self.assertEqual( lExp, lObs )
+        
+        
+    def test_getSequencesToReverseFromMatrix_4seq( self ):
+        lNewHeaders = [ "seq1", "seq2", "seq3", "seq4" ]
+        dMatrix = { "1_vs_2": { "direct": 10, "reverse": 1 },
+                   "1_vs_3": { "direct": 1, "reverse": 10 },
+                   "1_vs_4": { "direct": 1, "reverse": 10 },
+                   "2_vs_3": { "direct": 1, "reverse": 10 },
+                   "2_vs_4": { "direct": 1, "reverse": 10 },
+                   "3_vs_4": { "direct": 1, "reverse": 2 } }
+        lExp = [ "seq3", "seq4" ]
+        self._i._verbose = 0
+        lObs = self._i.getSequencesToReverseFromMatrix( dMatrix, lNewHeaders )
+        lExp.sort()
+        lObs.sort()
+        self.assertEqual( lExp, lObs )
+        
+        
+    def test_orientInputSequences( self ):
+        lSeqToOrient = [ "seq1" ]
+        tmpFileName = "dummyInFile_%s" % ( self._uniqId )
+        tmpF = open( tmpFileName, "w" )
+        tmpF.write( ">seq1\n" )
+        tmpF.write( "ATGCGGTGCATG\n" )
+        tmpF.write( ">seq2\n" )
+        tmpF.write( "GGCGAAGTGAAA\n" )
+        tmpF.close()
+        expFileName = "dummyExpFile_%s" % ( self._uniqId )
+        expF = open( expFileName, "w" )
+        expF.write( ">seq1 re-oriented\n" )
+        expF.write( "CATGCACCGCAT\n" )
+        expF.write( ">seq2\n" )
+        expF.write( "GGCGAAGTGAAA\n" )
+        expF.close()
+        obsFileName = "dummyObsFile_%s" % ( self._uniqId )
+        self._i._verbose = 0
+        self._i._outFileName = obsFileName
+        self._i.orientInputSequences( lSeqToOrient, tmpFileName )
+        self.assertTrue( FileUtils.are2FilesIdentical( obsFileName, expFileName ) )
+        for f in [ tmpFileName, expFileName, obsFileName ]:
+            os.remove( f )
+            
+if __name__ == "__main__":
+        unittest.main()
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