Python生物信息学①将RNA序列翻译成蛋白质序列。

环境

  

   

    

     

    
    

     

      OS version : Win10 x64
     
    
   

    

     

    
    

     

      python_version  : Python 3.6.5 
     
    
  
 

实例代码

  

   

    

     

    
    

     

      codon_table = {
     
    
   

    

     

    
    

     
 'GCU':'A', 'GCC':'A', 'GCA':'A', 'GCG':'A', 'CGU':'R', 'CGC':'R',   
     
    
   

    

     

    
    

     
 'CGA':'R', 'CGG':'R', 'AGA':'R', 'AGG':'R', 'UCU':'S', 'UCC':'S',
     
    
   

    

     

    
    

     
 'UCA':'S', 'UCG':'S', 'AGU':'S', 'AGC':'S', 'AUU':'I', 'AUC':'I',
     
    
   

    

     

    
    

     
 'AUA':'I', 'UUA':'L', 'UUG':'L', 'CUU':'L', 'CUC':'L', 'CUA':'L',
     
    
   

    

     

    
    

     
 'CUG':'L', 'GGU':'G', 'GGC':'G', 'GGA':'G', 'GGG':'G', 'GUU':'V',
     
    
   

    

     

    
    

     
 'GUC':'V', 'GUA':'V', 'GUG':'V', 'ACU':'T', 'ACC':'T', 'ACA':'T',
     
    
   

    

     

    
    

     
 'ACG':'T', 'CCU':'P', 'CCC':'P', 'CCA':'P', 'CCG':'P', 'AAU':'N',
     
    
   

    

     

    
    

     
 'AAC':'N', 'GAU':'D', 'GAC':'D', 'UGU':'C', 'UGC':'C', 'CAA':'Q',
     
    
   

    

     

    
    

     
 'CAG':'Q', 'GAA':'E', 'GAG':'E', 'CAU':'H', 'CAC':'H', 'AAA':'K',
     
    
   

    

     

    
    

     
 'AAG':'K', 'UUU':'F', 'UUC':'F', 'UAU':'Y', 'UAC':'Y', 'AUG':'M',
     
    
   

    

     

    
    

     
 'UGG':'W',
     
    
   

    

     

    
    

     
 'UAG':'STOP', 'UGA':'STOP', 'UAA':'STOP'
     
    
   

    

     

    
    

     

       }
     
    
  
 

  

   

    

     

    
    

     

      # 读取RNA序列字符串
     
    
   

    

     

    
    

     

      rna = ''
     
    
   

    

     

    
    

     

      for line in open('A06662-RNA.fasta'):
     
    
   

    

     

    
    

     
 if not line.startswith('>'): 
     
    
   

    

     

    
    

     

       rna = rna + line.strip()
     
    
  
 

  

   

    

     

    
    

     

      # translate one frame at a time
     
    
   

    

     

    
    

     

      for frame in range(3):
     
    
   

    

     

    
    

     

       prot = '' 
     
    
   

    

     

    
    

     
 print ('Reading frame ' + str(frame + 1))
     
    
   

    

     

    
    

     
 for i in range(frame, len(rna), 3):
     
    
   

    

     

    
    

     

       codon = rna[i:i + 3]
     
    
   

    

     

    
    

     
 if codon in codon_table:
     
    
   

    

     

    
    

     
 if codon_table[codon] == 'STOP':
     
    
   

    

     

    
    

     

       prot = prot + '*'
     
    
   

    

     

    
    

     
 else: 
     
    
   

    

     

    
    

     

       prot = prot + codon_table[codon]
     
    
   

    

     

    
    

     
 else:
     
    
   

    

     

    
    

     
 # handle too short codons
     
    
   

    

     

    
    

     

       prot = prot + '-' 	
     
    
   

    

     

    
    

     
 
     
    
   

    

     

    
    

     
 # format to blocks of 48 columns
     
    
   

    

     

    
    

     

       i = 0
     
    
   

    

     

    
    

     
 while i < len(prot):
     
    
   

    

     

    
    

     
 print (prot[i:i + 48])
     
    
   

    

     

    
    

     

       i = i + 48
     
    
  
 

文章来源: drugai.blog.csdn.net，作者：DrugAI，版权归原作者所有，如需转载，请联系作者。

原文链接：drugai.blog.csdn.net/article/details/88782828