本文整理汇总了Python中skbio.core.sequence.NucleotideSequence类的典型用法代码示例。如果您正苦于以下问题：Python NucleotideSequence类的具体用法？Python NucleotideSequence怎么用？Python NucleotideSequence使用的例子？那么, 这里精选的类代码示例或许可以为您提供帮助。
在下文中一共展示了NucleotideSequence类的15个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: test_lower
def test_lower(self):
""" lower functions as expected
"""
b = NucleotideSequence('GAt.ACa-', identifier='x', description='42')
expected = NucleotideSequence('gat.aca-', identifier='x',
description='42')
self.assertEqual(b.lower(), expected)示例2: test_iupac_degeneracies
def test_iupac_degeneracies(self):
exp = {
# upper
'B': set(['C', 'U', 'T', 'G']), 'D': set(['A', 'U', 'T', 'G']),
'H': set(['A', 'C', 'U', 'T']), 'K': set(['U', 'T', 'G']),
'M': set(['A', 'C']), 'N': set(['A', 'C', 'U', 'T', 'G']),
'S': set(['C', 'G']), 'R': set(['A', 'G']),
'W': set(['A', 'U', 'T']), 'V': set(['A', 'C', 'G']),
'Y': set(['C', 'U', 'T']),
# lower
'b': set(['c', 'u', 't', 'g']), 'd': set(['a', 'u', 't', 'g']),
'h': set(['a', 'c', 'u', 't']), 'k': set(['u', 't', 'g']),
'm': set(['a', 'c']), 'n': set(['a', 'c', 'u', 't', 'g']),
's': set(['c', 'g']), 'r': set(['a', 'g']),
'w': set(['a', 'u', 't']), 'v': set(['a', 'c', 'g']),
'y': set(['c', 'u', 't'])
}
self.assertEqual(self.b1.iupac_degeneracies(), exp)
self.assertEqual(NucleotideSequence.iupac_degeneracies(), exp)
# Test that we can modify a copy of the mapping without altering the
# canonical representation.
degen = NucleotideSequence.iupac_degeneracies()
degen.update({'V': set("BRO"), 'Z': set("ZORRO")})
self.assertNotEqual(degen, exp)
self.assertEqual(NucleotideSequence.iupac_degeneracies(), exp)示例3: test_upper
def test_upper(self):
""" upper functions as expected
"""
b = NucleotideSequence('GAt.ACa-', identifier='x', description='42')
expected = NucleotideSequence('GAT.ACA-', identifier='x',
description='42')
self.assertEqual(b.upper(), expected)示例4: setUp
def setUp(self):
""" Initialize values to be used in tests
"""
self.empty = NucleotideSequence('')
self.b1 = NucleotideSequence('GATTACA')
self.b2 = NucleotideSequence(
'ACCGGUACC', identifier="test-seq-2",
description="A test sequence")示例5: test_iupac_characters
def test_iupac_characters(self):
exp = {
'A', 'C', 'B', 'D', 'G', 'H', 'K', 'M', 'N', 'S', 'R', 'U', 'T',
'W', 'V', 'Y', 'a', 'c', 'b', 'd', 'g', 'h', 'k', 'm', 'n', 's',
'r', 'u', 't', 'w', 'v', 'y'
}
self.assertEqual(self.b1.iupac_characters(), exp)
self.assertEqual(NucleotideSequence.iupac_characters(), exp)示例6: test_alphabet
def test_alphabet(self):
exp = {
'A', 'C', 'B', 'D', 'G', 'H', 'K', 'M', 'N', 'S', 'R', 'U', 'T',
'W', 'V', 'Y', 'a', 'c', 'b', 'd', 'g', 'h', 'k', 'm', 'n', 's',
'r', 'u', 't', 'w', 'v', 'y'
}
# Test calling from an instance and purely static context.
self.assertEqual(self.b1.alphabet(), exp)
self.assertEqual(NucleotideSequence.alphabet(), exp)示例7: test_iupac_degenerate_characters
def test_iupac_degenerate_characters(self):
exp = set(['B', 'D', 'H', 'K', 'M', 'N', 'S', 'R', 'W', 'V', 'Y',
'b', 'd', 'h', 'k', 'm', 'n', 's', 'r', 'w', 'v', 'y'])
self.assertEqual(self.b1.iupac_degenerate_characters(), exp)
self.assertEqual(NucleotideSequence.iupac_degenerate_characters(), exp)示例8: test_iupac_standard_characters
def test_iupac_standard_characters(self):
exp = set("ACGTUacgtu")
self.assertEqual(self.b1.iupac_standard_characters(), exp)
self.assertEqual(NucleotideSequence.iupac_standard_characters(), exp)示例9: test_complement_map
def test_complement_map(self):
exp = {}
self.assertEqual(self.b1.complement_map(), exp)
self.assertEqual(NucleotideSequence.complement_map(), exp)示例10: setUp
def setUp(self):
self.empty = NucleotideSequence('')
self.b1 = NucleotideSequence('GATTACA')
self.b2 = NucleotideSequence(
'ACCGGUACC', id="test-seq-2",
description="A test sequence")示例11: NucelotideSequenceTests
class NucelotideSequenceTests(TestCase):
def setUp(self):
self.empty = NucleotideSequence('')
self.b1 = NucleotideSequence('GATTACA')
self.b2 = NucleotideSequence(
'ACCGGUACC', id="test-seq-2",
description="A test sequence")
def test_alphabet(self):
exp = {
'A', 'C', 'B', 'D', 'G', 'H', 'K', 'M', 'N', 'S', 'R', 'U', 'T',
'W', 'V', 'Y', 'a', 'c', 'b', 'd', 'g', 'h', 'k', 'm', 'n', 's',
'r', 'u', 't', 'w', 'v', 'y'
}
# Test calling from an instance and purely static context.
self.assertEqual(self.b1.alphabet(), exp)
self.assertEqual(NucleotideSequence.alphabet(), exp)
def test_gap_alphabet(self):
self.assertEqual(self.b1.gap_alphabet(), set('-.'))
def test_complement_map(self):
exp = {}
self.assertEqual(self.b1.complement_map(), exp)
self.assertEqual(NucleotideSequence.complement_map(), exp)
def test_iupac_standard_characters(self):
exp = set("ACGTUacgtu")
self.assertEqual(self.b1.iupac_standard_characters(), exp)
self.assertEqual(NucleotideSequence.iupac_standard_characters(), exp)
def test_iupac_degeneracies(self):
exp = {
# upper
'B': set(['C', 'U', 'T', 'G']), 'D': set(['A', 'U', 'T', 'G']),
'H': set(['A', 'C', 'U', 'T']), 'K': set(['U', 'T', 'G']),
'M': set(['A', 'C']), 'N': set(['A', 'C', 'U', 'T', 'G']),
'S': set(['C', 'G']), 'R': set(['A', 'G']),
'W': set(['A', 'U', 'T']), 'V': set(['A', 'C', 'G']),
'Y': set(['C', 'U', 'T']),
# lower
'b': set(['c', 'u', 't', 'g']), 'd': set(['a', 'u', 't', 'g']),
'h': set(['a', 'c', 'u', 't']), 'k': set(['u', 't', 'g']),
'm': set(['a', 'c']), 'n': set(['a', 'c', 'u', 't', 'g']),
's': set(['c', 'g']), 'r': set(['a', 'g']),
'w': set(['a', 'u', 't']), 'v': set(['a', 'c', 'g']),
'y': set(['c', 'u', 't'])
}
self.assertEqual(self.b1.iupac_degeneracies(), exp)
self.assertEqual(NucleotideSequence.iupac_degeneracies(), exp)
# Test that we can modify a copy of the mapping without altering the
# canonical representation.
degen = NucleotideSequence.iupac_degeneracies()
degen.update({'V': set("BRO"), 'Z': set("ZORRO")})
self.assertNotEqual(degen, exp)
self.assertEqual(NucleotideSequence.iupac_degeneracies(), exp)
def test_iupac_degenerate_characters(self):
exp = set(['B', 'D', 'H', 'K', 'M', 'N', 'S', 'R', 'W', 'V', 'Y',
'b', 'd', 'h', 'k', 'm', 'n', 's', 'r', 'w', 'v', 'y'])
self.assertEqual(self.b1.iupac_degenerate_characters(), exp)
self.assertEqual(NucleotideSequence.iupac_degenerate_characters(), exp)
def test_iupac_characters(self):
exp = {
'A', 'C', 'B', 'D', 'G', 'H', 'K', 'M', 'N', 'S', 'R', 'U', 'T',
'W', 'V', 'Y', 'a', 'c', 'b', 'd', 'g', 'h', 'k', 'm', 'n', 's',
'r', 'u', 't', 'w', 'v', 'y'
}
self.assertEqual(self.b1.iupac_characters(), exp)
self.assertEqual(NucleotideSequence.iupac_characters(), exp)
def test_complement(self):
self.assertRaises(BiologicalSequenceError,
self.b1.complement)
def test_reverse_complement(self):
self.assertRaises(BiologicalSequenceError,
self.b1.reverse_complement)
def test_is_reverse_complement(self):
self.assertRaises(BiologicalSequenceError,
self.b1.is_reverse_complement, self.b1)
def test_nondegenerates_invalid(self):
with self.assertRaises(BiologicalSequenceError):
list(NucleotideSequence('AZA').nondegenerates())
def test_nondegenerates_empty(self):
self.assertEqual(list(self.empty.nondegenerates()), [self.empty])
def test_nondegenerates_no_degens(self):
self.assertEqual(list(self.b1.nondegenerates()), [self.b1])
def test_nondegenerates_all_degens(self):
# Same chars.
#.........这里部分代码省略.........
示例12: test_lower
def test_lower(self):
b = NucleotideSequence('GAt.ACa-', id='x', description='42')
expected = NucleotideSequence('gat.aca-', id='x',
description='42')
self.assertEqual(b.lower(), expected)示例13: test_upper
def test_upper(self):
b = NucleotideSequence('GAt.ACa-', id='x', description='42')
expected = NucleotideSequence('GAT.ACA-', id='x',
description='42')
self.assertEqual(b.upper(), expected)示例14: test_iupac_standard_characters
def test_iupac_standard_characters(self):
"""iupac_standard_characters property functions as expected"""
exp = set("ACGTUacgtu")
self.assertEqual(self.b1.iupac_standard_characters(), exp)
self.assertEqual(NucleotideSequence.iupac_standard_characters(), exp)示例15: test_complement_map
def test_complement_map(self):
"""complement_map property functions as expected"""
exp = {}
self.assertEqual(self.b1.complement_map(), exp)
self.assertEqual(NucleotideSequence.complement_map(), exp)