本文整理汇总了Python中skbio.SequenceCollection.lower方法的典型用法代码示例。如果您正苦于以下问题：Python SequenceCollection.lower方法的具体用法？Python SequenceCollection.lower怎么用？Python SequenceCollection.lower使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类skbio.SequenceCollection的用法示例。
在下文中一共展示了SequenceCollection.lower方法的2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: SequenceCollectionTests
# 需要导入模块: from skbio import SequenceCollection [as 别名]
# 或者: from skbio.SequenceCollection import lower [as 别名]
class SequenceCollectionTests(TestCase):
def setUp(self):
self.d1 = DNASequence('GATTACA', id="d1")
self.d2 = DNASequence('TTG', id="d2")
self.d3 = DNASequence('GTATACA', id="d3")
self.d1_lower = DNASequence('gattaca', id="d1")
self.d2_lower = DNASequence('ttg', id="d2")
self.d3_lower = DNASequence('gtataca', id="d3")
self.r1 = RNASequence('GAUUACA', id="r1")
self.r2 = RNASequence('UUG', id="r2")
self.r3 = RNASequence('U-----UGCC--', id="r3")
self.i1 = DNASequence('GATXACA', id="i1")
self.seqs1 = [self.d1, self.d2]
self.seqs1_lower = [self.d1_lower, self.d2_lower]
self.seqs2 = [self.r1, self.r2, self.r3]
self.seqs3 = self.seqs1 + self.seqs2
self.seqs4 = [self.d1, self.d3]
self.seqs1_t = [('d1', 'GATTACA'), ('d2', 'TTG')]
self.seqs2_t = [('r1', 'GAUUACA'), ('r2', 'UUG'),
('r3', 'U-----UGCC--')]
self.seqs3_t = self.seqs1_t + self.seqs2_t
self.s1 = SequenceCollection(self.seqs1)
self.s1_lower = SequenceCollection(self.seqs1_lower)
self.s2 = SequenceCollection(self.seqs2)
self.s3 = SequenceCollection(self.seqs3)
self.s4 = SequenceCollection(self.seqs4)
self.empty = SequenceCollection([])
self.invalid_s1 = SequenceCollection([self.i1])
def test_init(self):
SequenceCollection(self.seqs1)
SequenceCollection(self.seqs2)
SequenceCollection(self.seqs3)
SequenceCollection([])
def test_init_fail(self):
# sequences with overlapping ids
s1 = [self.d1, self.d1]
self.assertRaises(SequenceCollectionError, SequenceCollection, s1)
def test_init_validate(self):
SequenceCollection(self.seqs1, validate=True)
SequenceCollection(self.seqs1, validate=True)
# can't validate self.seqs2 as a DNASequence
self.assertRaises(SequenceCollectionError, SequenceCollection,
self.invalid_s1, validate=True)
def test_contains(self):
self.assertTrue('d1' in self.s1)
self.assertTrue('r2' in self.s2)
self.assertFalse('r2' in self.s1)
def test_eq(self):
self.assertTrue(self.s1 == self.s1)
self.assertFalse(self.s1 == self.s2)
# different objects can be equal
self.assertTrue(self.s1 == SequenceCollection([self.d1, self.d2]))
self.assertTrue(SequenceCollection([self.d1, self.d2]) == self.s1)
# SequenceCollections with different number of sequences are not equal
self.assertFalse(self.s1 == SequenceCollection([self.d1]))
class FakeSequenceCollection(SequenceCollection):
pass
# SequenceCollections of different types are not equal
self.assertFalse(self.s4 == FakeSequenceCollection([self.d1, self.d3]))
self.assertFalse(self.s4 == Alignment([self.d1, self.d3]))
# SequenceCollections with different sequences are not equal
self.assertFalse(self.s1 == SequenceCollection([self.d1, self.r1]))
def test_getitem(self):
self.assertEqual(self.s1[0], self.d1)
self.assertEqual(self.s1[1], self.d2)
self.assertEqual(self.s2[0], self.r1)
self.assertEqual(self.s2[1], self.r2)
self.assertRaises(IndexError, self.empty.__getitem__, 0)
self.assertRaises(KeyError, self.empty.__getitem__, '0')
def test_iter(self):
s1_iter = iter(self.s1)
count = 0
for actual, expected in zip(s1_iter, self.seqs1):
count += 1
self.assertEqual(actual, expected)
self.assertEqual(count, len(self.seqs1))
self.assertRaises(StopIteration, lambda: next(s1_iter))
def test_len(self):
self.assertEqual(len(self.s1), 2)
self.assertEqual(len(self.s2), 3)
self.assertEqual(len(self.s3), 5)
self.assertEqual(len(self.empty), 0)
#.........这里部分代码省略.........
示例2: SequenceCollectionTests
# 需要导入模块: from skbio import SequenceCollection [as 别名]
# 或者: from skbio.SequenceCollection import lower [as 别名]
class SequenceCollectionTests(TestCase):
"""Tests of the SequenceCollection class """
def setUp(self):
"""Initialize values to be used in tests
"""
self.d1 = DNASequence('GATTACA', id="d1")
self.d2 = DNASequence('TTG', id="d2")
self.d1_lower = DNASequence('gattaca', id="d1")
self.d2_lower = DNASequence('ttg', id="d2")
self.r1 = RNASequence('GAUUACA', id="r1")
self.r2 = RNASequence('UUG', id="r2")
self.r3 = RNASequence('U-----UGCC--', id="r3")
self.i1 = DNASequence('GATXACA', id="i1")
self.seqs1 = [self.d1, self.d2]
self.seqs1_lower = [self.d1_lower, self.d2_lower]
self.seqs2 = [self.r1, self.r2, self.r3]
self.seqs3 = self.seqs1 + self.seqs2
self.seqs1_t = [('d1', 'GATTACA'), ('d2', 'TTG')]
self.seqs2_t = [('r1', 'GAUUACA'), ('r2', 'UUG'),
('r3', 'U-----UGCC--')]
self.seqs3_t = self.seqs1_t + self.seqs2_t
self.s1 = SequenceCollection(self.seqs1)
self.s1_lower = SequenceCollection(self.seqs1_lower)
self.s2 = SequenceCollection(self.seqs2)
self.s3 = SequenceCollection(self.seqs3)
self.empty = SequenceCollection([])
self.invalid_s1 = SequenceCollection([self.i1])
def test_init(self):
"""Initialization functions as expected with varied input types
"""
SequenceCollection(self.seqs1)
SequenceCollection(self.seqs2)
SequenceCollection(self.seqs3)
SequenceCollection([])
def test_init_fail(self):
"""initialization with sequences with overlapping ids fails
"""
s1 = [self.d1, self.d1]
self.assertRaises(SequenceCollectionError, SequenceCollection, s1)
def test_init_validate(self):
"""initialization with validation functions as expected
"""
SequenceCollection(self.seqs1, validate=True)
SequenceCollection(self.seqs1, validate=True)
# can't validate self.seqs2 as a DNASequence
self.assertRaises(SequenceCollectionError, SequenceCollection,
self.invalid_s1, validate=True)
def test_from_fasta_records(self):
"""Initialization from list of tuples functions as expected
"""
SequenceCollection.from_fasta_records(self.seqs1_t, DNASequence)
SequenceCollection.from_fasta_records(self.seqs2_t, RNASequence)
SequenceCollection.from_fasta_records(self.seqs3_t, NucleotideSequence)
def test_contains(self):
"""in operator functions as expected
"""
self.assertTrue('d1' in self.s1)
self.assertTrue('r2' in self.s2)
self.assertFalse('r2' in self.s1)
def test_eq(self):
"""equality operator functions as expected
"""
self.assertTrue(self.s1 == self.s1)
self.assertFalse(self.s1 == self.s2)
# different objects can be equal
self.assertTrue(self.s1 == SequenceCollection([self.d1, self.d2]))
self.assertTrue(SequenceCollection([self.d1, self.d2]) == self.s1)
# SequenceCollections with different number of sequences are not equal
self.assertFalse(self.s1 == SequenceCollection([self.d1]))
class FakeSequenceCollection(SequenceCollection):
pass
# SequenceCollections of different types are not equal
self.assertFalse(self.s1 == FakeSequenceCollection([self.d1, self.d2]))
self.assertFalse(self.s1 == Alignment([self.d1, self.d2]))
# SequenceCollections with different sequences are not equal
self.assertFalse(self.s1 == SequenceCollection([self.d1, self.r1]))
def test_getitem(self):
"""getitem functions as expected
"""
self.assertEqual(self.s1[0], self.d1)
self.assertEqual(self.s1[1], self.d2)
self.assertEqual(self.s2[0], self.r1)
#.........这里部分代码省略.........