本文整理汇总了Python中skbio.SequenceCollection.is_valid方法的典型用法代码示例。如果您正苦于以下问题：Python SequenceCollection.is_valid方法的具体用法？Python SequenceCollection.is_valid怎么用？Python SequenceCollection.is_valid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.is_valid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 is_valid [as 别名]
#.........这里部分代码省略.........
exp_id_map = {'abc': 'r1', 'def': 'r2', 'ghi': 'r3'}
obs_sc, obs_id_map = self.s2.update_ids(ids=('abc', 'def', 'ghi'))
self._assert_sequence_collections_equal(obs_sc, exp_sc)
self.assertEqual(obs_id_map, exp_id_map)
# empty
obs_sc, obs_id_map = self.empty.update_ids(ids=[])
self._assert_sequence_collections_equal(obs_sc, self.empty)
self.assertEqual(obs_id_map, {})
def test_update_ids_sequence_attributes_propagated(self):
# 1 seq
exp_sc = Alignment([
DNA('ACGT', id="abc", description='desc', quality=range(4))
])
exp_id_map = {'abc': 'seq1'}
obj = Alignment([
DNA('ACGT', id="seq1", description='desc', quality=range(4))
])
obs_sc, obs_id_map = obj.update_ids(ids=('abc',))
self._assert_sequence_collections_equal(obs_sc, exp_sc)
self.assertEqual(obs_id_map, exp_id_map)
# 2 seqs
exp_sc = Alignment([
DNA('ACGT', id="abc", description='desc1', quality=range(4)),
DNA('TGCA', id="def", description='desc2', quality=range(4)[::-1])
])
exp_id_map = {'abc': 'seq1', 'def': 'seq2'}
obj = Alignment([
DNA('ACGT', id="seq1", description='desc1', quality=(0, 1, 2, 3)),
DNA('TGCA', id="seq2", description='desc2', quality=(3, 2, 1, 0))
])
obs_sc, obs_id_map = obj.update_ids(ids=('abc', 'def'))
self._assert_sequence_collections_equal(obs_sc, exp_sc)
self.assertEqual(obs_id_map, exp_id_map)
def test_update_ids_invalid_parameter_combos(self):
with self.assertRaisesRegexp(SequenceCollectionError, 'ids and fn'):
self.s1.update_ids(fn=lambda e: e, ids=['foo', 'bar'])
with self.assertRaisesRegexp(SequenceCollectionError, 'prefix'):
self.s1.update_ids(ids=['foo', 'bar'], prefix='abc')
with self.assertRaisesRegexp(SequenceCollectionError, 'prefix'):
self.s1.update_ids(fn=lambda e: e, prefix='abc')
def test_update_ids_invalid_ids(self):
# incorrect number of new ids
with self.assertRaisesRegexp(SequenceCollectionError, '3 != 2'):
self.s1.update_ids(ids=['foo', 'bar', 'baz'])
with self.assertRaisesRegexp(SequenceCollectionError, '4 != 2'):
self.s1.update_ids(fn=lambda e: ['foo', 'bar', 'baz', 'abc'])
# duplicates
with self.assertRaisesRegexp(SequenceCollectionError, 'foo'):
self.s2.update_ids(ids=['foo', 'bar', 'foo'])
with self.assertRaisesRegexp(SequenceCollectionError, 'bar'):
self.s2.update_ids(fn=lambda e: ['foo', 'bar', 'bar'])
def test_is_empty(self):
self.assertFalse(self.s1.is_empty())
self.assertFalse(self.s2.is_empty())
self.assertFalse(self.s3.is_empty())
self.assertTrue(self.empty.is_empty())
def test_is_valid(self):
self.assertTrue(self.s1.is_valid())
self.assertTrue(self.s2.is_valid())
self.assertTrue(self.s3.is_valid())
self.assertTrue(self.empty.is_valid())
self.assertFalse(self.invalid_s1.is_valid())
def test_iteritems(self):
self.assertEqual(list(self.s1.iteritems()),
[(s.id, s) for s in self.s1])
def test_lower(self):
self.assertEqual(self.s1.lower(), self.s1_lower)
def test_sequence_count(self):
self.assertEqual(self.s1.sequence_count(), 2)
self.assertEqual(self.s2.sequence_count(), 3)
self.assertEqual(self.s3.sequence_count(), 5)
self.assertEqual(self.empty.sequence_count(), 0)
def test_sequence_lengths(self):
self.assertEqual(self.s1.sequence_lengths(), [7, 3])
self.assertEqual(self.s2.sequence_lengths(), [7, 3, 12])
self.assertEqual(self.s3.sequence_lengths(), [7, 3, 7, 3, 12])
self.assertEqual(self.empty.sequence_lengths(), [])
def test_upper(self):
self.assertEqual(self.s1_lower.upper(), self.s1)示例2: SequenceCollectionTests
# 需要导入模块: from skbio import SequenceCollection [as 别名]
# 或者: from skbio.SequenceCollection import is_valid [as 别名]
#.........这里部分代码省略.........
def test_degap(self):
"""degap functions as expected
"""
expected = [(id_, seq.replace('.', '').replace('-', ''))
for id_, seq in self.seqs2_t]
expected = SequenceCollection.from_fasta_records(expected, RNASequence)
actual = self.s2.degap()
self.assertEqual(actual, expected)
def test_get_seq(self):
"""getseq functions asexpected
"""
self.assertEqual(self.s1.get_seq('d1'), self.d1)
self.assertEqual(self.s1.get_seq('d2'), self.d2)
def test_ids(self):
"""ids functions as expected
"""
self.assertEqual(self.s1.ids(), ['d1', 'd2'])
self.assertEqual(self.s2.ids(), ['r1', 'r2', 'r3'])
self.assertEqual(self.s3.ids(),
['d1', 'd2', 'r1', 'r2', 'r3'])
self.assertEqual(self.empty.ids(), [])
def test_int_map(self):
"""int_map functions as expected
"""
expected1 = {"1": self.d1, "2": self.d2}
expected2 = {"1": "d1", "2": "d2"}
self.assertEqual(self.s1.int_map(), (expected1, expected2))
expected1 = {"h-1": self.d1, "h-2": self.d2}
expected2 = {"h-1": "d1", "h-2": "d2"}
self.assertEqual(self.s1.int_map(prefix='h-'), (expected1, expected2))
def test_is_empty(self):
"""is_empty functions as expected
"""
self.assertFalse(self.s1.is_empty())
self.assertFalse(self.s2.is_empty())
self.assertFalse(self.s3.is_empty())
self.assertTrue(self.empty.is_empty())
def test_is_valid(self):
"""is_valid functions as expected
"""
self.assertTrue(self.s1.is_valid())
self.assertTrue(self.s2.is_valid())
self.assertTrue(self.s3.is_valid())
self.assertTrue(self.empty.is_valid())
self.assertFalse(self.invalid_s1.is_valid())
def test_iteritems(self):
"""iteritems functions as expected
"""
self.assertEqual(list(self.s1.iteritems()),
[(s.id, s) for s in self.s1])
def test_lower(self):
"""lower functions as expected
"""
self.assertEqual(self.s1.lower(), self.s1_lower)
def test_sequence_count(self):
"""num_seqs functions as expected
"""
self.assertEqual(self.s1.sequence_count(), 2)
self.assertEqual(self.s2.sequence_count(), 3)
self.assertEqual(self.s3.sequence_count(), 5)
self.assertEqual(self.empty.sequence_count(), 0)
def test_sequence_lengths(self):
"""sequence_lengths functions as expected
"""
self.assertEqual(self.s1.sequence_lengths(), [7, 3])
self.assertEqual(self.s2.sequence_lengths(), [7, 3, 12])
self.assertEqual(self.s3.sequence_lengths(), [7, 3, 7, 3, 12])
self.assertEqual(self.empty.sequence_lengths(), [])
def test_to_fasta(self):
"""to_fasta functions as expected
"""
exp1 = ">d1\nGATTACA\n>d2\nTTG\n"
self.assertEqual(self.s1.to_fasta(), exp1)
exp2 = ">r1\nGAUUACA\n>r2\nUUG\n>r3\nU-----UGCC--\n"
self.assertEqual(self.s2.to_fasta(), exp2)
def test_toFasta(self):
with warnings.catch_warnings():
warnings.simplefilter("ignore")
exp = ">d1\nGATTACA\n>d2\nTTG\n"
self.assertEqual(self.s1.toFasta(), exp)
def test_upper(self):
"""upper functions as expected
"""
self.assertEqual(self.s1_lower.upper(), self.s1)