python中求DNA的反向互补序列

 

001、   利用循环结构实现

[root@PC1 test01]# ls
a.fa  test.py
[root@PC1 test01]# cat a.fa        ## 测试DNA序列
AAAACCCGGT
[root@PC1 test01]# cat test.py     ## 程序
#!/usr/bin/env python
# -*- coding: utf-8 -*-

in_file = open("a.fa", "r")
file = in_file.read().strip()[::-1]

str1 = str()
for i in file:
        if i == "A":
                str1 += "T"
        elif i == "C":
                str1 += "G"
        elif i == "G":
                str1 += "C"
        elif i == "T":
                str1 += "A"
        else:
                print("anomanous letter!")
                exit
print(str1)
[root@PC1 test01]# python test.py      ## 反向互补结果
ACCGGGTTTT

 

002、借助字典匹配碱基

[root@PC1 test01]# ls
a.fa  test.py
[root@PC1 test01]# cat a.fa            ## 测试DNA序列
AAAACCCGGT
[root@PC1 test01]# cat test.py         ## 求反向互补序列程序
#!/usr/bin/env python
# -*- coding: utf-8 -*-

in_file = open("a.fa", "r")
file = in_file.read().strip()[::-1]
in_file.close()

dict1 = {"A":"T", "C":"G", "G":"C", "T":"A"}
str1 = ""
for i in file:
        if i not in dict1:
                print("anomanous letters!")
                break
        else:
                str1 += dict1[i]
print(str1)
[root@PC1 test01]# python test.py         ## 转换结果
ACCGGGTTTT

 

003、借助函数结构实现

[root@PC1 test01]# ls
a.fa  test.py
[root@PC1 test01]# cat a.fa       ## 测试DNA序列
AAAACCCGGT
[root@PC1 test01]# cat test.py    ## 转换程序
#!/usr/bin/env python
# -*- coding: utf-8 -*-

in_file = open("a.fa", "r")
file = in_file.read().strip()[::-1]
in_file.close()

dict1 = {"A":"T", "C":"G", "G":"C", "T":"A"}
def rev_com(dna, table):
        str1 = str()
        for i in dna:
                if i not in table:
                        print("anomanous letter!")
                        break
                else:
                        str1 += table[i]
        return str1
print(rev_com(file, dict1))
[root@PC1 test01]# python test.py      ## 反向互补结果
ACCGGGTTTT

 

。