统计细菌基因组ORF

提取细菌基因组ORF思路：

1.通过FNA文件得到细菌基因组序列

2.分正负链和三个相位共6种情况统计ORF

3.写入文件

转载请保留出处！

统计细菌基因组ORF

贴上Python代码（版本：3.6）

 # -*- coding: utf-8 -*-
 """
 Created on Thu Dec 14 13:19:00 2017

 @author: zxzhu
 """

 import re
 def N2M(sequence):                    #正负链转换
     hash = {'A': 'T', 'T': 'A', 'C': 'G', 'G': 'C','N':'N'}
     sequence = ''.join([hash[i] for i in sequence])
     return sequence[::-1]

 def translate(seq):                    #将序列转换为起始，终止，其他密码子
     pa1 = re.compile(r'TAA|TAG|TGA')
     after_trans = ''
     for i in range(0,len(seq),3):
         if seq[i:i+3]=='ATG':
             after_trans+='I'
         elif pa1.match(seq[i:i+3]):
             after_trans+='T'
         else:
             after_trans+='O'
     return after_trans

 def get_orf(seq,length=90):
     pa2 = re.compile(r'I[IO]+?T')   #匹配模式：起始1非终止1~N终止1
     trans_seq = translate(seq)
     m = pa2.finditer(trans_seq)     #所有匹配结果的迭代
     index = []
     orf = []
     for i in m:
         index.append(i.span())     #序列起始，终止位置
     for i in index:
         orf_start = i[0]*3
         orf_end = i[1]*3
         #print(orf_start,orf_end)
         if orf_end - orf_start >= length:   #不小于90bp
             orf.append(seq[orf_start:orf_end])
     return orf

 def Seq2AA(sequence,hash):    #翻译为AA序列
     AA=''
     for i in range(0, len(sequence) - 3, 3):
         AA += hash[sequence[i:i + 3]]
     return AA

 def main(fna,length=90):
     fn = open(fna)
     pa = re.compile(r'\s+')
     hash_seq = {}  # CDS hash,CDS2sequence
     result1 = open('orf_seq.txt','w')
     result2 = open('orf_AA.txt','w')
     start = [0,1,2]       #相位
     strain = '+-'         #正负链
     hash_AA = {}  # AA hash,sequence2AA
     with open('AA.txt', 'r') as f:                         #AA.txt 为密码子表
         for line in f:
             line = line.strip()
             if line:
                 line = pa.split(line)
                 hash_AA[line[0]] = line[1]      #AA hash

     for line in fn:                             #获取序列
         line = line.strip()
         if line.startswith('>'):
             A = pa.split(line)[0].replace('>', '')
             hash_seq[A] = ''
         else:
             hash_seq[A] += line

     for key in hash_seq.keys():             #分+-链，3个相位统计ORF
         seq = hash_seq[key]
         for r in strain:
             if r == '-':
                 seq = N2M(seq)
             for s in start:
                 seq = seq[s:]
                 #trans_seq = translate(seq)
                 orf = get_orf(seq)
                 for i in orf:
                     if 'N' not in i:      #去除N
                         AA =Seq2AA(i,hash_AA)
                         result1.write('>'+key+'\t'+r+'\t'+str(s)+'\n'+i+'\n')
                         result2.write('>'+key+'\t'+r+'\t'+str(s)+'\n'+AA+'\n')
     fn.close()
     result1.close()
     result2.close()

 fna = 'GCA_000160075.2_ASM16007v2_genomic.fna'
 main(fna)

NCBI可以找ORF，很方便。码一下：ORFfinder