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Python MutableSeq.extend方法代码示例

本文整理汇总了Python中Bio.Seq.MutableSeq.extend方法的典型用法代码示例。如果您正苦于以下问题:Python MutableSeq.extend方法的具体用法?Python MutableSeq.extend怎么用?Python MutableSeq.extend使用的例子?那么, 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Bio.Seq.MutableSeq的用法示例。


在下文中一共展示了MutableSeq.extend方法的1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: TestMutableSeq

# 需要导入模块: from Bio.Seq import MutableSeq [as 别名]
# 或者: from Bio.Seq.MutableSeq import extend [as 别名]

#.........这里部分代码省略.........
                         self.mutable_s)

    def test_inserting(self):
        self.mutable_s.insert(4, "G")
        self.assertEqual(MutableSeq("TCAAGAAGGATGCATCATG", IUPAC.ambiguous_dna),
                         self.mutable_s)

    def test_popping_last_item(self):
        self.assertEqual("G", self.mutable_s.pop())

    def test_remove_items(self):
        self.mutable_s.remove("G")
        self.assertEqual(MutableSeq("TCAAAAGATGCATCATG", IUPAC.ambiguous_dna),
                         self.mutable_s, "Remove first G")

        self.assertRaises(ValueError, self.mutable_s.remove, 'Z')

    def test_count(self):
        self.assertEqual(7, self.mutable_s.count("A"))
        self.assertEqual(2, self.mutable_s.count("AA"))

    def test_index(self):
        self.assertEqual(2, self.mutable_s.index("A"))
        self.assertRaises(ValueError, self.mutable_s.index, "8888")

    def test_reverse(self):
        """Test using reverse method"""
        self.mutable_s.reverse()
        self.assertEqual(MutableSeq("GTACTACGTAGGAAAACT", IUPAC.ambiguous_dna),
                         self.mutable_s)

    def test_reverse_with_stride(self):
        """Test reverse using -1 stride"""
        self.assertEqual(MutableSeq("GTACTACGTAGGAAAACT", IUPAC.ambiguous_dna),
                         self.mutable_s[::-1])

    def test_complement(self):
        self.mutable_s.complement()
        self.assertEqual(str("AGTTTTCCTACGTAGTAC"), str(self.mutable_s))

    def test_complement_rna(self):
        seq = Seq.MutableSeq("AUGaaaCUG", IUPAC.unambiguous_rna)
        seq.complement()
        self.assertEqual(str("UACuuuGAC"), str(seq))

    def test_complement_mixed_aphabets(self):
        seq = Seq.MutableSeq("AUGaaaCTG")
        with self.assertRaises(ValueError):
            seq.complement()

    def test_complement_rna_string(self):
        seq = Seq.MutableSeq("AUGaaaCUG")
        seq.complement()
        self.assertEqual('UACuuuGAC', str(seq))

    def test_complement_dna_string(self):
        seq = Seq.MutableSeq("ATGaaaCTG")
        seq.complement()
        self.assertEqual('TACtttGAC', str(seq))

    def test_reverse_complement(self):
        self.mutable_s.reverse_complement()
        self.assertEqual("CATGATGCATCCTTTTGA", str(self.mutable_s))

    def test_reverse_complement_of_protein(self):
        seq = Seq.MutableSeq("ACTGTCGTCT", Alphabet.generic_protein)
        with self.assertRaises(ValueError):
            seq.reverse_complement()

    def test_to_string_method(self):
        """This method is currently deprecated, probably will need to remove this test soon"""
        with warnings.catch_warnings(record=True):
            self.mutable_s.tostring()

    def test_extend_method(self):
        self.mutable_s.extend("GAT")
        self.assertEqual(MutableSeq("TCAAAAGGATGCATCATGGAT", IUPAC.ambiguous_dna),
                         self.mutable_s)

    def test_extend_with_mutable_seq(self):
        self.mutable_s.extend(MutableSeq("TTT", IUPAC.ambiguous_dna))
        self.assertEqual(MutableSeq("TCAAAAGGATGCATCATGTTT", IUPAC.ambiguous_dna),
                         self.mutable_s)

    def test_delete_stride_slice(self):
        del self.mutable_s[4:6 - 1]
        self.assertEqual(MutableSeq("TCAAAGGATGCATCATG", IUPAC.ambiguous_dna),
                         self.mutable_s)

    def test_extract_third_nucleotide(self):
        """Test extracting every third nucleotide (slicing with stride 3)"""
        self.assertEqual(MutableSeq("TAGTAA", IUPAC.ambiguous_dna), self.mutable_s[0::3])
        self.assertEqual(MutableSeq("CAGGTT", IUPAC.ambiguous_dna), self.mutable_s[1::3])
        self.assertEqual(MutableSeq("AAACCG", IUPAC.ambiguous_dna), self.mutable_s[2::3])

    def test_set_wobble_codon_to_n(self):
        """Test setting wobble codon to N (set slice with stride 3)"""
        self.mutable_s[2::3] = "N" * len(self.mutable_s[2::3])
        self.assertEqual(MutableSeq("TCNAANGGNTGNATNATN", IUPAC.ambiguous_dna),
                         self.mutable_s)
开发者ID:BrianLinSu,项目名称:rop,代码行数:104,代码来源:test_seq.py


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