Python SequenceCollection.iteritems方法代码示例

本文整理汇总了Python中skbio.SequenceCollection.iteritems方法的典型用法代码示例。如果您正苦于以下问题：Python SequenceCollection.iteritems方法的具体用法？Python SequenceCollection.iteritems怎么用？Python SequenceCollection.iteritems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.iteritems方法的3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 iteritems [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)

开发者ID:AndreaEdwards，项目名称:scikit-bio，代码行数:104，代码来源:test_alignment.py

示例2: SequenceCollectionTests

# 需要导入模块: from skbio import SequenceCollection [as 别名]
# 或者: from skbio.SequenceCollection import iteritems [as 别名]

#.........这里部分代码省略.........
    def test_update_ids_ids_parameter(self):
        # 3 seqs
        exp_sc = SequenceCollection([
            RNA('GAUUACA', metadata={'id': "abc"}),
            RNA('UUG', metadata={'id': "def"}),
            RNA('U-----UGCC--', metadata={'id': "ghi"})
        ])
        exp_id_map = {'abc': 'r1', 'def': 'r2', 'ghi': 'r3'}
        obs_sc, obs_id_map = self.s2.update_ids(ids=('abc', 'def', 'ghi'))
        self.assertEqual(obs_sc, exp_sc)
        self.assertEqual(obs_id_map, exp_id_map)

        # empty
        obs_sc, obs_id_map = self.empty.update_ids(ids=[])
        self.assertEqual(obs_sc, self.empty)
        self.assertEqual(obs_id_map, {})

    def test_update_ids_sequence_attributes_propagated(self):
        # 1 seq
        exp_sc = Alignment([
            DNA('ACGT', metadata={'id': "abc", 'description': 'desc'},
                positional_metadata={'quality': range(4)})
        ])
        exp_id_map = {'abc': 'seq1'}

        obj = Alignment([
            DNA('ACGT', metadata={'id': "seq1", 'description': 'desc'},
                positional_metadata={'quality': range(4)})
        ])

        obs_sc, obs_id_map = obj.update_ids(ids=('abc',))
        self.assertEqual(obs_sc, exp_sc)
        self.assertEqual(obs_id_map, exp_id_map)

        # 2 seqs
        exp_sc = Alignment([
            DNA('ACGT', metadata={'id': "abc", 'description': 'desc1'},
                positional_metadata={'quality': range(4)}),
            DNA('TGCA', metadata={'id': "def", 'description': 'desc2'},
                positional_metadata={'quality': range(4)[::-1]})
        ])
        exp_id_map = {'abc': 'seq1', 'def': 'seq2'}

        obj = Alignment([
            DNA('ACGT', metadata={'id': "seq1", 'description': 'desc1'},
                positional_metadata={'quality': (0, 1, 2, 3)}),
            DNA('TGCA', metadata={'id': "seq2", 'description': 'desc2'},
                positional_metadata={'quality': (3, 2, 1, 0)})
        ])

        obs_sc, obs_id_map = obj.update_ids(ids=('abc', 'def'))
        self.assertEqual(obs_sc, exp_sc)
        self.assertEqual(obs_id_map, exp_id_map)

    def test_update_ids_invalid_parameter_combos(self):
        with six.assertRaisesRegex(self, SequenceCollectionError,
                                   'ids and func'):
            self.s1.update_ids(func=lambda e: e, ids=['foo', 'bar'])

        with six.assertRaisesRegex(self, SequenceCollectionError, 'prefix'):
            self.s1.update_ids(ids=['foo', 'bar'], prefix='abc')

        with six.assertRaisesRegex(self, SequenceCollectionError, 'prefix'):
            self.s1.update_ids(func=lambda e: e, prefix='abc')

    def test_update_ids_invalid_ids(self):
        # incorrect number of new ids
        with six.assertRaisesRegex(self, SequenceCollectionError, '3 != 2'):
            self.s1.update_ids(ids=['foo', 'bar', 'baz'])
        with six.assertRaisesRegex(self, SequenceCollectionError, '4 != 2'):
            self.s1.update_ids(func=lambda e: ['foo', 'bar', 'baz', 'abc'])

        # duplicates
        with six.assertRaisesRegex(self, SequenceCollectionError, 'foo'):
            self.s2.update_ids(ids=['foo', 'bar', 'foo'])
        with six.assertRaisesRegex(self, SequenceCollectionError, 'bar'):
            self.s2.update_ids(func=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_iteritems(self):
        self.assertEqual(list(self.s1.iteritems()),
                         [(s.metadata['id'], s) for s in self.s1])

    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(), [])

开发者ID:jhcepas，项目名称:scikit-bio，代码行数:104，代码来源:test_alignment.py

示例3: SequenceCollectionTests

# 需要导入模块: from skbio import SequenceCollection [as 别名]
# 或者: from skbio.SequenceCollection import iteritems [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)

开发者ID:nbresnick，项目名称:scikit-bio，代码行数:104，代码来源:test_alignment.py

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