Python ProfileHMMSegment Examples

Example #1

File: __init__.py Project: UCL-RITS/CSB-structural-bio-tools

    def setUp(self):

        super(TestProfileHMMSegment, self).setUp()

        self.hmm = build_hmm()
        self.segment = ProfileHMMSegment(self.hmm, 1, 2)
        self.string = self.config.getContent('test2.hhm')

Example #2

File: __init__.py Project: UCL-RITS/CSB-structural-bio-tools

class TestProfileHMMSegment(test.Case):
    def setUp(self):

        super(TestProfileHMMSegment, self).setUp()

        self.hmm = build_hmm()
        self.segment = ProfileHMMSegment(self.hmm, 1, 2)
        self.string = self.config.getContent('test2.hhm')

    def testConstructor(self):

        self.segment.convert_scores(ScoreUnits.Probability)

        self.assertEqual(self.hmm.segment(1, 1).layers.length, 1)
        self.assertEqual(self.segment.layers.length, 2)
        self.assertEqual(
            self.segment.start.transitions[States.Match].probability, 1)
        self.assertEqual(
            self.segment.layers[1][States.Match].emission[ProteinAlphabet.CYS],
            0.5)
        self.assertRaises(IndexError, self.hmm.segment, 1, 3)

        self.hmm.convert_scores(ScoreUnits.LogScales)
        segment = ProfileHMMSegment(self.hmm, 1, 2)
        self.assertEqual(segment.source_start, 1)

    def testToHMM(self):

        self.segment.convert_scores(ScoreUnits.LogScales)
        self.assertEqual(self.string, self.segment.to_hmm().strip())

Example #3

File: __init__.py Project: jakebarnwell/PythonGenerator

class TestProfileHMMSegment(test.Case):

    def setUp(self):
        
        super(TestProfileHMMSegment, self).setUp()
        
        self.hmm = build_hmm()
        self.segment = ProfileHMMSegment(self.hmm, 1, 2)
        self.string = self.config.getContent('test2.hhm')
    
    def testConstructor(self):
        
        self.segment.convert_scores(ScoreUnits.Probability)
        
        self.assertEqual(self.hmm.segment(1, 1).layers.length, 1)
        self.assertEqual(self.segment.layers.length, 2)
        self.assertEqual(self.segment.start.transitions[States.Match].probability, 1)
        self.assertEqual(self.segment.layers[1][States.Match].emission[ProteinAlphabet.CYS], 0.5)
        self.assertRaises(IndexError, self.hmm.segment, 1, 3)
        
        self.hmm.convert_scores(ScoreUnits.LogScales)
        segment = ProfileHMMSegment(self.hmm, 1, 2)
        self.assertEqual(segment.source_start, 1)
                    
    def testToHMM(self):
        
        self.segment.convert_scores(ScoreUnits.LogScales) 
        self.assertEqual(self.string, self.segment.to_hmm().strip())

Example #4

File: __init__.py Project: jakebarnwell/PythonGenerator

 def setUp(self):
     
     super(TestProfileHMMSegment, self).setUp()
     
     self.hmm = build_hmm()
     self.segment = ProfileHMMSegment(self.hmm, 1, 2)
     self.string = self.config.getContent('test2.hhm')

Example #5

File: __init__.py Project: UCL-RITS/CSB-structural-bio-tools

    def testConstructor(self):

        self.segment.convert_scores(ScoreUnits.Probability)

        self.assertEqual(self.hmm.segment(1, 1).layers.length, 1)
        self.assertEqual(self.segment.layers.length, 2)
        self.assertEqual(
            self.segment.start.transitions[States.Match].probability, 1)
        self.assertEqual(
            self.segment.layers[1][States.Match].emission[ProteinAlphabet.CYS],
            0.5)
        self.assertRaises(IndexError, self.hmm.segment, 1, 3)

        self.hmm.convert_scores(ScoreUnits.LogScales)
        segment = ProfileHMMSegment(self.hmm, 1, 2)
        self.assertEqual(segment.source_start, 1)