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

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

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 )