如何在Python中找到一个开放的阅读框架

Question

我正在使用Python和正则表达式来查找ORF(开放阅读框架).

查找一个子字符串,该字符串仅由字母组成ATGC(不包含空格或新行):

开头ATG,结尾TAG或TAA或TGA并应考虑从第一个字符的序列,那么第二和第三然后:

Seq= "CCTCAGCGAGGACAGCAAGGGACTAGCCAGGAGGGAGAACAGAAACTCCAGAACATCTTGGAAATAGCTCCCAGAAAAGC
AAGCAGCCAACCAGGCAGGTTCTGTCCCTTTCACTCACTGGCCCAAGGCGCCACATCTCCCTCCAGAAAAGACACCATGA
GCACAGAAAGCATGATCCGCGACGTGGAACTGGCAGAAGAGGCACTCCCCCAAAAGATGGGGGGCTTCCAGAACTCCAGG
CGGTGCCTATGTCTCAGCCTCTTCTCATTCCTGCTTGTGGCAGGGGCCACCACGCTCTTCTGTCTACTGAACTTCGGGGT
GATCGGTCCCCAAAGGGATGAGAAGTTCCCAAATGGCCTCCCTCTCATCAGTTCTATGGCCCAGACCCTCACACTCAGAT
CATCTTCTCAAAATTCGAGTGACAAGCCTGTAGCCCACGTCGTAGCAAACCACCAAGTGGAGGAGCAGCTGGAGTGGCTG
AGCCAGCGCGCCAACGCCCTCCTGGCCAACGGCATGGATCTCAAAGACAACCAACTAGTGGTGCCAGCCGATGGGTTGTA
CCTTGTCTACTCCCAGGTTCTCTTCAAGGGACAAGGCTGCCCCGACTACGTGCTCCTCACCCACACCGTCAGCCGATTTG
CTATCTCATACCAGGAGAAAGTCAACCTCCTCTCTGCCGTCAAGAGCCCCTGCCCCAAGGACACCCCTGAGGGGGCTGAG
CTCAAACCCTGGTATGAGCCCATATACCTGGGAGGAGTCTTCCAGCTGGAGAAGGGGGACCAACTCAGCGCTGAGGTCAA
TCTGCCCAAGTACTTAGACTTTGCGGAGTCCGGGCAGGTCTACTTTGGAGTCATTGCTCTGTGAAGGGAATGGGTGTTCA
TCCATTCTCTACCCAGCCCCCACTCTGACCCCTTTACTCTGACCCCTTTATTGTCTACTCCTCAGAGCCCCCAGTCTGTA
TCCTTCTAACTTAGAAAGGGGATTATGGCTCAGGGTCCAACTCTGTGCTCAGAGCTTTCAACAACTACTCAGAAACACAA
GATGCTGGGACAGTGACCTGGACTGTGGGCCTCTCATGCACCACCATCAAGGACTCAAATGGGCTTTCCGAATTCACTGG
AGCCTCGAATGTCCATTCCTGAGTTCTGCAAAGGGAGAGTGGTCAGGTTGCCTCTGTCTCAGAATGAGGCTGGATAAGAT
CTCAGGCCTTCCTACCTTCAGACCTTTCCAGATTCTTCCCTGAGGTGCAATGCACAGCCTTCCTCACAGAGCCAGCCCCC
CTCTATTTATATTTGCACTTATTATTTATTATTTATTTATTATTTATTTATTTGCTTATGAATGTATTTATTTGGAAGGC
CGGGGTGTCCTGGAGGACCCAGTGTGGGAAGCTGTCTTCAGACAGACATGTTTTCTGTGAAAACGGAGCTGAGCTGTCCC
CACCTGGCCTCTCTACCTTGTTGCCTCCTCTTTTGCTTATGTTTAAAACAAAATATTTATCTAACCCAATTGTCTTAATA
ACGCTGATTTGGTGACCAGGCTGTCGCTACATCACTGAACCTCTGCTCCCCACGGGAGCCGTGACTGTAATCGCCCTACG
GGTCATTGAGAGAAATAA"

我尝试过的:

# finding the  stop codon here 

def stop_codon(seq_0):

        for i in range(0,len(seq_0),3):
            if (seq_0[i:i+3]== "TAA" and i%3==0) or (seq_0[i:i+3]== "TAG" and i%3==0) or (seq_0[i:i+3]== "TGA" and i%3==0) :
                a =i+3

                break

            else:
                a = None

# finding the start codon here 

startcodon_find =[m.start() for m in re.finditer('ATG', seq_0)]

我怎样才能找到检查起始密码子然后找到第一个终止密码子的方法.随后找到下一个起始密码子和下一个终止​​密码子.

我希望将它运行三帧.如前所述,三个帧将把序列的第一,第二和第三个字符视为开始.

此序列需要分为3个小部分.因为它应该是这样的事情:

ATG TTT AAA ACA AAA TAT TTA TCT AAC CCA ATT GTC TTA ATA ACG CTG ATT TGA

任何帮助将不胜感激.

我的最终答案是:

def orf_find(st0):

    seq_0=""
    for i in range(0,len(st0),3):
        if len(st0[i:i+3])==3:
            seq_0 = seq_0 + st0[i:i+3]+ " "

    ms_1 =[m.start() for m in re.finditer('ATG', seq_0)]
    ms_2 =[m.start() for m in re.finditer('(TAA)|(TAG)|(TGA)', seq_0)]

    def get_next(arr,value):
        for a in arr:
            if a > value:
                return a
        return -1




    codons = []
    start_codon=ms_1[0]
    while (True):
        stop_codon = get_next(ms_2,start_codon)
        if stop_codon == -1:
            break
        codons.append((start_codon,stop_codon))
        start_codon = get_next(ms_1,stop_codon)
        if start_codon==-1:
            break

    max_val = 0
    selected_tupple = ()
    for i in codons:
        k=i[1]-i[0]
        if k > max_val:
            max_val = k
            selected_tupple = i

    print "selected tupple is ", selected_tupple

    final_seq=seq_0[selected_tupple[0]:selected_tupple[1]+3]

    print final_seq
    print "The longest orf length is " + str(max_val)



output_file = open('Longorf.txt','w')
output_file.write(str(orf_find(st0)))

output_file.close()

上面的写入功能无助于我将内容写入文本文件.我进去的只有NONE ..为什么这个错误..有人可以帮忙吗？

Answer 1

如果你想手工编码:

import re
from string import maketrans

pattern = re.compile(r'(?=(ATG(?:...)*?)(?=TAG|TGA|TAA))')

def revcomp(dna_seq):
    return dna_seq[::-1].translate(maketrans("ATGC","TACG"))

def orfs(dna):
    return set(pattern.findall(dna) + pattern.findall(revcomp(dna)))

print orfs(Seq)

Answer 2

正如你已经标记了它Biopython我想你知道Biopython.你有没有检查过这些文件？http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc231可能有所帮助.

我调整了上面链接中的代码以处理您的序列:

from Bio.Seq import Seq

seq = Seq("CCTCAGCGAGGACAGCAAGGGACTAGCCAGGAGGGAGAACAGAAACTCCAGAACATCTTGGAAATAGCTCCCAGAAAAGCAAGCAGCCAACCAGGCAGGTTCTGTCCCTTTCACTCACTGGCCCAAGGCGCCACATCTCCCTCCAGAAAAGACACCATGAGCACAGAAAGCATGATCCGCGACGTGGAACTGGCAGAAGAGGCACTCCCCCAAAAGATGGGGGGCTTCCAGAACTCCAGGCGGTGCCTATGTCTCAGCCTCTTCTCATTCCTGCTTGTGGCAGGGGCCACCACGCTCTTCTGTCTACTGAACTTCGGGGTGATCGGTCCCCAAAGGGATGAGAAGTTCCCAAATGGCCTCCCTCTCATCAGTTCTATGGCCCAGACCCTCACACTCAGATCATCTTCTCAAAATTCGAGTGACAAGCCTGTAGCCCACGTCGTAGCAAACCACCAAGTGGAGGAGCAGCTGGAGTGGCTGAGCCAGCGCGCCAACGCCCTCCTGGCCAACGGCATGGATCTCAAAGACAACCAACTAGTGGTGCCAGCCGATGGGTTGTACCTTGTCTACTCCCAGGTTCTCTTCAAGGGACAAGGCTGCCCCGACTACGTGCTCCTCACCCACACCGTCAGCCGATTTGCTATCTCATACCAGGAGAAAGTCAACCTCCTCTCTGCCGTCAAGAGCCCCTGCCCCAAGGACACCCCTGAGGGGGCTGAGCTCAAACCCTGGTATGAGCCCATATACCTGGGAGGAGTCTTCCAGCTGGAGAAGGGGGACCAACTCAGCGCTGAGGTCAATCTGCCCAAGTACTTAGACTTTGCGGAGTCCGGGCAGGTCTACTTTGGAGTCATTGCTCTGTGAAGGGAATGGGTGTTCATCCATTCTCTACCCAGCCCCCACTCTGACCCCTTTACTCTGACCCCTTTATTGTCTACTCCTCAGAGCCCCCAGTCTGTATCCTTCTAACTTAGAAAGGGGATTATGGCTCAGGGTCCAACTCTGTGCTCAGAGCTTTCAACAACTACTCAGAAACACAAGATGCTGGGACAGTGACCTGGACTGTGGGCCTCTCATGCACCACCATCAAGGACTCAAATGGGCTTTCCGAATTCACTGGAGCCTCGAATGTCCATTCCTGAGTTCTGCAAAGGGAGAGTGGTCAGGTTGCCTCTGTCTCAGAATGAGGCTGGATAAGATCTCAGGCCTTCCTACCTTCAGACCTTTCCAGATTCTTCCCTGAGGTGCAATGCACAGCCTTCCTCACAGAGCCAGCCCCCCTCTATTTATATTTGCACTTATTATTTATTATTTATTTATTATTTATTTATTTGCTTATGAATGTATTTATTTGGAAGGCCGGGGTGTCCTGGAGGACCCAGTGTGGGAAGCTGTCTTCAGACAGACATGTTTTCTGTGAAAACGGAGCTGAGCTGTCCCCACCTGGCCTCTCTACCTTGTTGCCTCCTCTTTTGCTTATGTTTAAAACAAAATATTTATCTAACCCAATTGTCTTAATAACGCTGATTTGGTGACCAGGCTGTCGCTACATCACTGAACCTCTGCTCCCCACGGGAGCCGTGACTGTAATCGCCCTACGGGTCATTGAGAGAAATAA")


table = 1
min_pro_len = 100

for strand, nuc in [(+1, seq), (-1, seq.reverse_complement())]:
    for frame in range(3):
        for pro in nuc[frame:].translate(table).split("*"):
            if len(pro) >= min_pro_len:
                print "%s...%s - length %i, strand %i, frame %i" % (pro[:30], pro[-3:], len(pro), strand, frame)

ORF也被翻译.您可以选择其他转换表.查看http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec:translation

编辑:代码说明:

在顶部我从你的字符串中创建一个序列对象.请注意seq = Seq("ACGT").两个for循环创建了6个不同的帧.内部for循环根据所选择的转换表翻译每个框架并返回氨基酸链,其中每个终止密码子被编码为*.该split函数拆分此字符串,删除这些占位符,从而得到可能的蛋白质序列列表.通过设置min_pro_len,您可以定义要检测的蛋白质的最小氨基酸链长度.1是标准表.退房http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi#SG1这里可以看到,在起始密码子AUG(等于ATG)和结束密码子(*核苷酸序列)是TAA,TAG,和TGA,就像你想要的那样.您还可以使用其他转换表.

当你添加

print nuc[frame:].translate(table)

在第二个for-loop里面你得到类似的东西:

PQRGQQGTSQEGEQKLQNILEIAPRKASSQPGRFCPFHSLAQGATSPSRKDTMSTESMIRDVELAEEALPQKMGGFQNSRRCLCLSLFSFLLVAGATTLFCLLNFGVIGPQRDEKFPNGLPLISSMAQTLTLRSSSQNSSDKPVAHVVANHQVEEQLEWLSQRANALLANGMDLKDNQLVVPADGLYLVYSQVLFKGQGCPDYVLLTHTVSRFAISYQEKVNLLSAVKSPCPKDTPEGAELKPWYEPIYLGGVFQLEKGDQLSAEVNLPKYLDFAESGQVYFGVIAL*REWVFIHSLPSPHSDPFTLTPLLSTPQSPQSVSF*LRKGIMAQGPTLCSELSTTTQKHKMLGQ*PGLWASHAPPSRTQMGFPNSLEPRMSIPEFCKGRVVRLPLSQNEAG*DLRPSYLQTFPDSSLRCNAQPSSQSQPPSIYICTYYLLFIYYLFICL*MYLFGRPGCPGGPSVGSCLQTDMFSVKTELSCPHLASLPCCLLFCLCLKQNIYLTQLS**R*FGDQAVATSLNLCSPREP*L*SPYGSLREI

(注意星号位于终止密码子位置)

编辑:回答你的第二个问题:

您必须将要写入的字符串返回到文件中.创建一个输出字符串并在函数末尾返回它:

output = "selected tupple is " + str(selected_tupple) + "\n"
output += final_seq + "\n"
output += "The longest orf length is " + str(max_val) + "\n"
return output