本文整理匯總了Python中skbio.core.sequence.NucleotideSequence.nondegenerates方法的典型用法代碼示例。如果您正苦於以下問題：Python NucleotideSequence.nondegenerates方法的具體用法？Python NucleotideSequence.nondegenerates怎麽用？Python NucleotideSequence.nondegenerates使用的例子？那麽, 這裏精選的方法代碼示例或許可以為您提供幫助。您也可以進一步了解該方法所在類skbio.core.sequence.NucleotideSequence的用法示例。
在下文中一共展示了NucleotideSequence.nondegenerates方法的1個代碼示例，這些例子默認根據受歡迎程度排序。您可以為喜歡或者感覺有用的代碼點讚，您的評價將有助於係統推薦出更棒的Python代碼示例。
示例1: NucelotideSequenceTests
# 需要導入模塊: from skbio.core.sequence import NucleotideSequence [as 別名]
# 或者: from skbio.core.sequence.NucleotideSequence import nondegenerates [as 別名]
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.
#.........這裏部分代碼省略.........