diff smart_toolShed/commons/core/coord/test/Test_SlidingWindow.py @ 0:e0f8dcca02ed

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/commons/core/coord/test/Test_SlidingWindow.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,109 @@
+import unittest
+from commons.core.coord.SlidingWindow import SlidingWindow
+from commons.core.coord.SlidingWindow import SlidingWindowToCountMatchingBases
+from commons.core.coord.Set import Set
+
+class Test_SlidingWindow( unittest.TestCase ):
+        
+    def test_slideWindowOnce( self ):
+        expStart = 91 
+        expEnd = 190
+        self.sw = SlidingWindow(100, 10)
+        self.sw.slideWindowOnce()
+        obsStart = self.sw._start
+        obsEnd = self.sw._end
+        
+        self.assertEqual(expStart, obsStart)
+        self.assertEqual(expEnd, obsEnd)
+        
+    def test_slideWindowOnceFourTime( self ):
+        expStart = 201 
+        expEnd = 300
+        self.sw = SlidingWindow(100, 50)
+        i = 0
+        for i in range(4):
+            self.sw.slideWindowOnce()
+            i += 1
+        obsStart = self.sw._start
+        obsEnd = self.sw._end
+        
+        self.assertEqual(expStart, obsStart)
+        self.assertEqual(expEnd, obsEnd)
+    
+        
+class Test_SlidingWindowToCountMatchingBases(unittest.TestCase):
+        
+    def test_getSetLengthOnWindow_featureIncluded( self ):
+        self.sw = SlidingWindowToCountMatchingBases(100, 1)
+        iSet = Set( 1, "TE3", "chr1", 21, 30 )
+        exp = 10
+        obs = self.sw.getSetLengthOnWindow( iSet)
+        self.assertEqual( exp, obs )
+        
+    def test_getSetLengthOnWindow_windowIncluded( self ):
+        self.sw = SlidingWindowToCountMatchingBases(100, 10)
+        self.sw.slideWindowOnce()
+        iSet = Set( 1, "TE3", "chr1", 21, 530 )
+        exp = 100
+        obs = self.sw.getSetLengthOnWindow( iSet)
+        self.assertEqual( exp, obs )
+        
+    def test_getSetLengthOnWindow_featureOverlapLeft( self ):
+        self.sw = SlidingWindowToCountMatchingBases(100, 10)
+        self.sw.slideWindowOnce()
+        iSet = Set( 1, "TE3", "chr1", 21, 130 )
+        exp = 40
+        obs = self.sw.getSetLengthOnWindow( iSet)
+        self.assertEqual( exp, obs )
+        
+    def test_getSetLengthOnWindow_featureOverlapRight( self ):
+        self.sw = SlidingWindowToCountMatchingBases(100, 10)
+        self.sw.slideWindowOnce()
+        iSet = Set( 1, "TE3", "chr1", 121, 230 )
+        exp = 70
+        obs = self.sw.getSetLengthOnWindow( iSet)
+        self.assertEqual( exp, obs )
+        
+    def test_getCoordSetOnWindow_featureIncluded( self ):
+        self.sw = SlidingWindowToCountMatchingBases(100, 1)
+        iSet = Set( 1, "TE3", "chr1", 21, 30 )
+        expStart = 21
+        expEnd = 30
+        obsStart,obsEnd = self.sw.getCoordSetOnWindow( iSet)
+        self.assertEqual( expStart, obsStart )
+        self.assertEqual( expEnd, obsEnd )
+        
+    def test_getCoordSetOnWindow_windowIncluded( self ):
+        self.sw = SlidingWindowToCountMatchingBases(100, 10)
+        self.sw.slideWindowOnce()
+        iSet = Set( 1, "TE3", "chr1", 21, 530 )
+        expStart = 91
+        expEnd = 190
+        obsStart,obsEnd = self.sw.getCoordSetOnWindow( iSet)
+        self.assertEqual( expStart, obsStart )
+        self.assertEqual( expEnd, obsEnd )
+        
+    def test_getCoordSetOnWindow_featureOverlapLeft( self ):
+        self.sw = SlidingWindowToCountMatchingBases(100, 10)
+        self.sw.slideWindowOnce()
+        iSet = Set( 1, "TE3", "chr1", 21, 130 )
+        expStart = 91
+        expEnd = 130
+        obsStart,obsEnd = self.sw.getCoordSetOnWindow( iSet)
+        self.assertEqual( expStart, obsStart )
+        self.assertEqual( expEnd, obsEnd )
+        
+    def test_getCoordSetOnWindow_featureOverlapRight( self ):
+        self.sw = SlidingWindowToCountMatchingBases(100, 10)
+        self.sw.slideWindowOnce()
+        iSet = Set( 1, "TE3", "chr1", 121, 230 )
+        expStart = 121
+        expEnd = 190
+        obsStart,obsEnd = self.sw.getCoordSetOnWindow( iSet)
+        self.assertEqual( expStart, obsStart )
+        self.assertEqual( expEnd, obsEnd )
+
+test_suite = unittest.TestSuite()
+test_suite.addTest( unittest.makeSuite( Test_SlidingWindow ) )
+if __name__ == "__main__":
+    unittest.TextTestRunner(verbosity=2).run( test_suite )
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