python中实现RNA序列的翻译

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RNA序列
AUGGCCAUGGCGCCCAGAACUGAGAUCAAUAGUACCCGUAUUAACGGGUGA
[root@PC1 test01]# cat test.py         ## 翻译程序
#!/usr/bin/env python
# -*- coding: utf-8 -*-

in_file = open("a.fa", "r")
file = in_file.read().strip()
in_file.close()

table = {
                'UUU':'F','CUU':'L','AUU':'I','GUU':'V',
                'UUC':'F','CUC':'L','AUC':'I','GUC':'V',
                'UUA':'L','CUA':'L','AUA':'I','GUA':'V',
                'UUG':'L','CUG':'L','AUG':'M','GUG':'V',
                'UCU':'S','CCU':'P','ACU':'T','GCU':'A',
                'UCC':'S','CCC':'P','ACC':'T','GCC':'A',
                'UCA':'S','CCA':'P','ACA':'T','GCA':'A',
                'UCG':'S','CCG':'P','ACG':'T','GCG':'A',
                'UAU':'Y','CAU':'H','AAU':'N','GAU':'D',
                'UAC':'Y','CAC':'H','AAC':'N','GAC':'D',
                'UAA':'Stop','CAA':'Q','AAA':'K','GAA':'E',
                'UAG':'Stop','CAG':'Q','AAG':'K','GAG':'E',
                'UGU':'C','CGU':'R','AGU':'S','GGU':'G',
                'UGC':'C','CGC':'R','AGC':'S','GGC':'G',
                'UGA':'Stop','CGA':'R','AGA':'R','GGA':'G',
                'UGG':'W','CGG':'R','AGG':'R','GGG':'G'
                }

str1 = ""
if len(file) % 3 != 0:
        print("no integrate sequence!")
        exit
else:
        for i in range(0, len(file), 3):
                idx = file[i:i+3]
                if table[idx] == "Stop":
                        exit
                else:
                        str1 += table[idx]

print(str1)
[root@PC1 test01]# python test.py        ## 翻译结果
MAMAPRTEINSTRING

002、解法2 循环结构

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

in_file = open("a.fa", "r")
file = in_file.read().strip()

table = {
                'UUU':'F','CUU':'L','AUU':'I','GUU':'V',
                'UUC':'F','CUC':'L','AUC':'I','GUC':'V',
                'UUA':'L','CUA':'L','AUA':'I','GUA':'V',
                'UUG':'L','CUG':'L','AUG':'M','GUG':'V',
                'UCU':'S','CCU':'P','ACU':'T','GCU':'A',
                'UCC':'S','CCC':'P','ACC':'T','GCC':'A',
                'UCA':'S','CCA':'P','ACA':'T','GCA':'A',
                'UCG':'S','CCG':'P','ACG':'T','GCG':'A',
                'UAU':'Y','CAU':'H','AAU':'N','GAU':'D',
                'UAC':'Y','CAC':'H','AAC':'N','GAC':'D',
                'UAA':'Stop','CAA':'Q','AAA':'K','GAA':'E',
                'UAG':'Stop','CAG':'Q','AAG':'K','GAG':'E',
                'UGU':'C','CGU':'R','AGU':'S','GGU':'G',
                'UGC':'C','CGC':'R','AGC':'S','GGC':'G',
                'UGA':'Stop','CGA':'R','AGA':'R','GGA':'G',
                'UGG':'W','CGG':'R','AGG':'R','GGG':'G'
                }

str1 = ""
while(len(file) >= 3):
        idx = file[0:3]
        if table[idx] != "Stop":
                str1 += table[idx]
        else:
                break
        file = file[3:]
print(str1)
[root@PC1 test01]# python3 test.py           ## 翻译结果
MAMAPRTEINSTRING

003、利用函数结构实现

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

in_file = open("a.fa", "r")
file = in_file.read().strip()

table = {
                'UUU':'F','CUU':'L','AUU':'I','GUU':'V',
                'UUC':'F','CUC':'L','AUC':'I','GUC':'V',
                'UUA':'L','CUA':'L','AUA':'I','GUA':'V',
                'UUG':'L','CUG':'L','AUG':'M','GUG':'V',
                'UCU':'S','CCU':'P','ACU':'T','GCU':'A',
                'UCC':'S','CCC':'P','ACC':'T','GCC':'A',
                'UCA':'S','CCA':'P','ACA':'T','GCA':'A',
                'UCG':'S','CCG':'P','ACG':'T','GCG':'A',
                'UAU':'Y','CAU':'H','AAU':'N','GAU':'D',
                'UAC':'Y','CAC':'H','AAC':'N','GAC':'D',
                'UAA':'Stop','CAA':'Q','AAA':'K','GAA':'E',
                'UAG':'Stop','CAG':'Q','AAG':'K','GAG':'E',
                'UGU':'C','CGU':'R','AGU':'S','GGU':'G',
                'UGC':'C','CGC':'R','AGC':'S','GGC':'G',
                'UGA':'Stop','CGA':'R','AGA':'R','GGA':'G',
                'UGG':'W','CGG':'R','AGG':'R','GGG':'G'
                }

#amino_acid = ""
def translation(rna, table):                  ## 翻译函数，参数为RNA序列和密码子字典
        amino_acid = ""
        for i in range(0, len(rna), 3):
                codon = rna[i:i+3]
                if codon not in table or table[codon] == "Stop":
                        exit
                else:
                        amino_acid += table[codon]
        return amino_acid

print(translation(file, table))
[root@PC1 test01]# python test.py             ## 翻译结果
MAMAPRTEINSTRING