Пример #1
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 def test_positionalBases(self):
     """BaseUsage positionalBases should have copy of self at each position"""
     b = BaseUsage('A')
     p = b.positionalBases()
     for i in p:
         assert i is not b
         self.assertEqual(i, {'A':1,'U':0,'C':0,'G':0})
Пример #2
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 def test_setitem(self):
     """BaseUsage should map keys on setitem"""
     b = BaseUsage()
     b['t'] = 3
     b['G'] = 3
     b.normalize()
     i = b.items()
     i.sort()
     self.assertEqual(i, [('A',0.0),('C',0.0),('G',0.5),('U',0.5)])
Пример #3
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 def test_fromCartesian(self):
     """BaseUsage fromCartesian should init instance from x,y,z"""
     b = BaseUsage.fromCartesian(0.5,.5,.5)
     self.assertFloatEqual(b['A'], 0.25)
     self.assertFloatEqual(b['C'], 0.25)
     self.assertFloatEqual(b['G'], 0.25)
     self.assertFloatEqual(b['U'], 0.25)
     b = BaseUsage.fromCartesian(1/3.0, 1/3.0, 1/3.0)
     self.assertEqual(b['U'], 0)
     self.assertEqual(b['A'], 1/3.0)
Пример #4
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 def test_getitem(self):
     """BaseUsage should map key on getitem"""
     b = BaseUsage({'a':3, 'T':2, 'X':1})
     self.assertEqual(b['X'], 1)
     self.assertEqual(b['A'], 3)
     self.assertEqual(b['U'], 2)
     self.assertEqual(b['a'], 3)
     self.assertEqual(b['t'], 2)
     b.normalize()
     assert 'X' not in b
     self.assertFloatEqual(b['A'], 0.6)
     self.assertFloatEqual(b['u'], 0.4)
Пример #5
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    def test_init_empty(self):
        """BaseUsage should init with empty freqs"""
        b = BaseUsage()
        self.assertEqual(len(b), 4)
        for nt in 'UTACGutacg':
            assert nt in b
            self.assertEqual(b[nt], 0)
        for nt in 'UCAG':
            assert nt in b.keys()

        items = list(iter(b))
        items.sort()
        self.assertEqual(items, ['A', 'C', 'G', 'U'])
Пример #6
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 def test_distance(self):
     """BaseUsage distance() should return dist between two BUs"""
     #absolute numbers, will normalize to calculate distance
     self.assertFloatEqual(BaseUsage('GC').distance(BaseUsage('AU')),1)
     self.assertFloatEqual(BaseUsage('AU').distance(BaseUsage('GC')),1)
     self.assertFloatEqual(BaseUsage('GCAU').distance(BaseUsage('AUAU')),.5)
     #should work even against dict with 'T's
     self.assertFloatEqual(BaseUsage('GCAU').distance(\
         BaseUsage({'A':2,'T':2,'C':0,'G':0,})),.5)
     #rounding error
     self.assertEqual(BaseUsage('ACG').distance(BaseUsage('CCGGAA')),0)
     #normalized - as in unit simplex
     ag = BaseUsage('AG')
     ag.normalize()
     uc = BaseUsage('UC')
     uc.normalize()
     self.assertFloatEqual(ag.distance(uc),1)
     self.assertFloatEqual(BaseUsage({'A':0.4,'G':0.1,'C':0.4,'U':0.1})\
     .distance(BaseUsage({'A':0.1,'G':0.4,'U':0.4,'C':0.1})),0.6)
     self.assertFloatEqual(BaseUsage({'A':0.25,'G':0.25,'C':0.25,'U':0.25})\
         .distance(BaseUsage({'A':0.25,'G':0.25,'U':0.25,'C':0.25})),0.0)
     self.assertFloatEqual(BaseUsage({'A':0.245,'G':0.255,'C':0.245,\
         'U':0.255}).distance(BaseUsage({'A':0.255,'G':0.245,'U':0.245,\
         'C':0.255})),0.02)
     self.assertFloatEqual(BaseUsage({'A':0.245,'G':0.255,'C':0.245,\
         'U':0.255}).distance(BaseUsage({'A':0.25,'G':0.25,'U':0.25,\
         'C':0.25})),0.01)
     self.assertFloatEqual(BaseUsage({'A':0.248,'G':0.252,'C':0.248,\
         'U':0.252}).distance(BaseUsage({'A':0.25,'G':0.25,'U':0.25,\
         'C':0.25})),0.004)
Пример #7
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 def test_aminoAcids(self):
     """BaseUsage aminoAcids should give the same results as the codons"""
     known_data = {
         'AAA' : .6 * .6 * .6,
         'AAU' : .6 * .6 * .4,
         'AUA' : .6 * .4 * .6,
         'AUU' : .6 * .4 * .4,
         'UAA' : .4 * .6 * .6,
         'UAU' : .4 * .6 * .4,
         'UUA' : .4 * .4 * .6,
         'UUU' : .4 * .4 * .4,
     }
     known = CodonUsage(known_data)
     b = BaseUsage({'a':3, 'T':2, 'X':1})
     self.assertEqual(b.aminoAcids(), known.aminoAcids())
     #check that the genetic code is passed through correctly
     all_g = GeneticCode('G'*64)
     self.assertEqual(b.aminoAcids(all_g), AminoAcidUsage({'G':1}))
Пример #8
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 def test_codons(self):
     """BaseUsage codons should return most likely codon freqs"""
     b = BaseUsage({'a':3, 'T':2, 'X':1})
     c = b.codons()
     known = {
         'AAA' : .6 * .6 * .6,
         'AAU' : .6 * .6 * .4,
         'AUA' : .6 * .4 * .6,
         'AUU' : .6 * .4 * .4,
         'UAA' : .4 * .6 * .6,
         'UAU' : .4 * .6 * .4,
         'UUA' : .4 * .4 * .6,
         'UUU' : .4 * .4 * .4,
     }
     for codon in c:
         if codon in known:
             self.assertFloatEqual(c[codon], known[codon])
         else:
             self.assertEqual(c[codon], 0)
Пример #9
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 def test_toCartesian(self):
     """BaseUsage toCartesian should return x, y, z from instance"""
     b = BaseUsage('ACGU')
     self.assertEqual(b.toCartesian(), (0.5,0.5,0.5))
     b = BaseUsage('A')
     self.assertEqual(b.toCartesian(), (0,0,1))
     b = BaseUsage('CGA')
     self.assertEqual(b.toCartesian(), (1/3.0,1/3.0,1/3.0))
Пример #10
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 def test_normalize(self):
     """BaseUsage normalize should work when empty"""
     b = BaseUsage()
     b.normalize()
     self.assertEqual(b, {'U':0,'C':0,'A':0,'G':0})
     b = BaseUsage('AACG')
     b.normalize()
     self.assertEqual(b, {'U':0, 'C':0.25, 'A':0.5, 'G':0.25})
Пример #11
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 def test_content(self):
     """BaseUsage content should return sum of specified bases."""
     b = BaseUsage('UUUUUCCCAG')
     #should work for combinations
     self.assertEqual(b.content('UCAG'), 10)
     self.assertEqual(b.content('GC'), 4)
     self.assertEqual(b.content('AU'), 6)
     #should map T to U
     self.assertEqual(b.content('AT'), 6)
     #should work for single bases
     self.assertEqual(b.content('U'), 5)
     #shouldn't complain about invalid bases
     self.assertEqual(b.content('X'), 0)
Пример #12
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 def test_bases(self):
     """BaseUsage bases() should return same object"""
     b = BaseUsage({'a':3, 'T':2, 'C':5, 'X':1})
     c = b.bases()
     assert b is c
Пример #13
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 def test_copy(self):
     """BaseUsage copy should work correctly"""
     b = BaseUsage({'a':3, 'T':2, 'C':5, 'X':1})
     c = b.copy()
     self.assertEqual(c['AT'], 0.5)
Пример #14
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 def test_init_data(self):
     """BaseUsage should init with arbitrary data"""
     b = BaseUsage('UUUUUGGGCA')
     self.assertEqual(b, {'U':5, 'G':3, 'C':1, 'A':1})
     b.normalize()
     self.assertEqual(b, {'U':0.5, 'G':0.3, 'C':0.1, 'A':0.1})