统计细菌基因组ORF

 1 # -*- coding: utf-8 -*-
 2 """
 3 Created on Thu Dec 14 13:19:00 2017
 4 
 5 @author: zxzhu
 6 """
 7 
 8 import re
 9 def N2M(sequence):                    #正负链转换
10     hash = {‘A‘: ‘T‘, ‘T‘: ‘A‘, ‘C‘: ‘G‘, ‘G‘: ‘C‘,‘N‘:‘N‘}
11     sequence = ‘‘.join([hash[i] for i in sequence])     
12     return sequence[::-1]
13 
14 def translate(seq):                    #将序列转换为起始，终止，其他密码子
15     pa1 = re.compile(r‘TAA|TAG|TGA‘)
16     after_trans = ‘‘
17     for i in range(0,len(seq),3):
18         if seq[i:i+3]==‘ATG‘:
19             after_trans+=‘I‘
20         elif pa1.match(seq[i:i+3]):
21             after_trans+=‘T‘
22         else:
23             after_trans+=‘O‘
24     return after_trans
25 
26 def get_orf(seq,length=90):
27     pa2 = re.compile(r‘I[IO]+?T‘)   #匹配模式：起始1非终止1~N终止1
28     trans_seq = translate(seq)
29     m = pa2.finditer(trans_seq)     #所有匹配结果的迭代
30     index = []
31     orf = []
32     for i in m:
33         index.append(i.span())     #序列起始，终止位置
34     for i in index:
35         orf_start = i[0]*3
36         orf_end = i[1]*3
37         #print(orf_start,orf_end)
38         if orf_end - orf_start >= length:   #不小于90bp
39             orf.append(seq[orf_start:orf_end])
40     return orf
41 
42 def Seq2AA(sequence,hash):    #翻译为AA序列
43     AA=‘‘                                 
44     for i in range(0, len(sequence) - 3, 3):
45         AA += hash[sequence[i:i + 3]]
46     return AA
47 
48 def main(fna,length=90):
49     fn = open(fna)
50     pa = re.compile(r‘\s+‘)
51     hash_seq = {}  # CDS hash,CDS2sequence
52     result1 = open(‘orf_seq.txt‘,‘w‘)
53     result2 = open(‘orf_AA.txt‘,‘w‘)
54     start = [0,1,2]       #相位
55     strain = ‘+-‘         #正负链
56     hash_AA = {}  # AA hash,sequence2AA
57     with open(‘AA.txt‘, ‘r‘) as f:                         #AA.txt 为密码子表
58         for line in f:
59             line = line.strip()
60             if line:
61                 line = pa.split(line)
62                 hash_AA[line[0]] = line[1]      #AA hash
63     
64     for line in fn:                             #获取序列
65         line = line.strip()
66         if line.startswith(‘>‘):
67             A = pa.split(line)[0].replace(‘>‘, ‘‘)
68             hash_seq[A] = ‘‘
69         else:
70             hash_seq[A] += line
71     
72     for key in hash_seq.keys():             #分+-链，3个相位统计ORF
73         seq = hash_seq[key]
74         for r in strain:
75             if r == ‘-‘:
76                 seq = N2M(seq)
77             for s in start:
78                 seq = seq[s:]
79                 #trans_seq = translate(seq)
80                 orf = get_orf(seq)
81                 for i in orf:
82                     if ‘N‘ not in i:      #去除N
83                         AA =Seq2AA(i,hash_AA) 
84                         result1.write(‘>‘+key+‘\t‘+r+‘\t‘+str(s)+‘\n‘+i+‘\n‘)
85                         result2.write(‘>‘+key+‘\t‘+r+‘\t‘+str(s)+‘\n‘+AA+‘\n‘)
86     fn.close()
87     result1.close()
88     result2.close()
89 
90     
91 fna = ‘GCA_000160075.2_ASM16007v2_genomic.fna‘
92 main(fna)