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Python MutableSeq.remove方法代码示例

本文整理汇总了Python中Bio.Seq.MutableSeq.remove方法的典型用法代码示例。如果您正苦于以下问题:Python MutableSeq.remove方法的具体用法?Python MutableSeq.remove怎么用?Python MutableSeq.remove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.remove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: TestMutableSeq

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

#.........这里部分代码省略.........

        self.mutable_s[1:3] = array.array(array_indicator, "GAT")
        self.assertEqual(MutableSeq("TGATTAAAGGATGCATCATG", IUPAC.ambiguous_dna),
                         self.mutable_s, "Set slice with array")

    def test_setting_item(self):
        self.mutable_s[3] = "G"
        self.assertEqual(MutableSeq("TCAGAAGGATGCATCATG", IUPAC.ambiguous_dna),
                         self.mutable_s)

    def test_deleting_slice(self):
        del self.mutable_s[4:5]
        self.assertEqual(MutableSeq("TCAAAGGATGCATCATG", IUPAC.ambiguous_dna),
                         self.mutable_s)

    def test_deleting_item(self):
        del self.mutable_s[3]
        self.assertEqual(MutableSeq("TCAAAGGATGCATCATG", IUPAC.ambiguous_dna),
                         self.mutable_s)

    def test_appending(self):
        self.mutable_s.append("C")
        self.assertEqual(MutableSeq("TCAAAAGGATGCATCATGC", IUPAC.ambiguous_dna),
                         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()
开发者ID:BrianLinSu,项目名称:rop,代码行数:70,代码来源:test_seq.py

示例2: print

# 需要导入模块: from Bio.Seq import MutableSeq [as 别名]
# 或者: from Bio.Seq.MutableSeq import remove [as 别名]
    "AATCGTGGCTATTACTGGGATGGAGGTCACTGGCGCGACCACGGCTGGTGGAAACAACAT" +
    "TATGAATGGCGAGGCAATCGCTGGCACCTACACGGACCGCCGCCACCGCCGCGCCACCAT" +
    "AAGAAAGCTCCTCATGATCATCACGGCGGTCATGGTCCAGGCAAACATCACCGCTAA",
    generic_dna)

print(gene.translate(table="Bacterial"))
print(gene.translate(table="Bacterial", cds=True))

##查看密码子表
from Bio.Data import CodonTable
standard_table = CodonTable.unambiguous_dna_by_name["Standard"]
mito_table = CodonTable.unambiguous_dna_by_id[2]

print(standard_table)
print(mito_table.start_codons)
print(mito_table.stop_codons)
print(mito_table.forward_table["ACG"])

##可变对象
from Bio.Seq import MutableSeq
mutable_seq = MutableSeq("GCCATTGTAATGGGCCGCTGAAAGGGTGCCCGA", IUPAC.unambiguous_dna)
print(mutable_seq)
mutable_seq[5] = "C"
print(mutable_seq)
mutable_seq.remove("T")
print(mutable_seq)
mutable_seq.reverse()
print(mutable_seq)
new_seq = mutable_seq.toseq()
print(new_seq)
开发者ID:guochangjiang,项目名称:Python.learn,代码行数:32,代码来源:03.code.py

示例3: Seq

# 需要导入模块: from Bio.Seq import MutableSeq [as 别名]
# 或者: from Bio.Seq.MutableSeq import remove [as 别名]
seq2 = Seq('ACGT',IUPAC.unambiguous_dna)
seq3 = Seq('ACGT',IUPAC.protein)
print id(seq1) == id(seq2)    # seq1 == seq2 look for the same object
print str(seq1) == str(seq2)    # convert to string
print str(seq1) == str(seq3)    # dna similar enought to protein

#MutableSeq
from Bio.Seq import MutableSeq
mutseq = seq1.tomutable()    # convert to MutableSeq
print mutseq, type(mutseq)
mutSeq = MutableSeq('CGTTTAAGCTGC',IUPAC.unambiguous_dna)
print mutSeq, type(mutSeq)
mutseq[1]='T'    # imposible on simple Seq
print mutseq
seq1 = mutseq.toseq()    # convert to Seq
mutSeq.remove('A')    # remove first A
mutSeq[2:-5]='TTTT'
mutSeq.reverse()    # reverse() and reverse_complement() change object itself
print mutSeq
#MutableSeq can't be a dictionary key, Seq and string can

#UnknownSeq
# Subclass of Seq when you know length but not the characters to save memory
from Bio.Seq import UnknownSeq
unk = UnknownSeq(25)
print unk, len(unk), type(unk)
unkDNA = UnknownSeq(20, alphabet=IUPAC.ambiguous_dna)
print unkDNA    # N = any base
unkProt = UnknownSeq(10, alphabet=IUPAC.protein)
print unkProt    # X = any aminoacid
开发者ID:ajonjoli,项目名称:Mytest,代码行数:32,代码来源:biopython2.py


注:本文中的Bio.Seq.MutableSeq.remove方法示例由纯净天空整理自Github/MSDocs等开源代码及文档管理平台,相关代码片段筛选自各路编程大神贡献的开源项目,源码版权归原作者所有,传播和使用请参考对应项目的License;未经允许,请勿转载。