RNA 拼接 Python答案

【问题标题】：RNA Splicing PythonRNA 拼接 Python
【发布时间】：2018-11-01 17:48:05
【问题描述】：

我有一个基因序列——

"acguccgcaagagaagccuuaauauauucaaaaagcuacgccucagauuucgcgcucgagcccaaaacaacugguguacggguugaucacaucaaaugaagucgcuaaagucggugaucucacuauccuugucuucggcuuuugcucucucggcuaucaucuaagcaggcgaguuccauggugaccggaacgacggcuacuggaguccaugaucgcaagcgucgggcugggguaaaagaggcucagcucauaauaguccgccccaccaguacgggacucgauaggccccgucguugccguagaaacgcaauuuuccucagacccacuauacgcaccucgauuuagcaugguuccgggguugcgcuuugagaaucauacguaaggaucggaaccuaggaaugcaccacagaacuuugaaauacuagaacaaguugauugacaacggaguaucggcgccccacauuuaacgaauaauugcaggcgccagacgaugcuaggugcguccguaucaagauucgaggucgcuacuggcuucgcuugccgaucgagcucagaguuugugagaguuguuacuaauugcguggucgccuaauauccuugauacuacguggguguacuagacaucccggacagaaaaucucuuaaacgcuagaguucucuuggaagcgccugcacuucuugugaacauacgaugauagccacucuaagcccaacgcacuucgcuuggcccacauugcccccagagcuuauucaucgacaggcguuccacucuuggauucaucaguaaacuuuauuauacgugguaagcgugcuuauagcugucggaaucucacuuaggcggauugaagugagacagccugaaaguaaccguguacaggcgccgucaauguguuuugagugugcaccuacaaaaaguguuauuuaggcaggggagcuuuguaguuucuuuagaagagccgcgaaugaaccaacgguagacugcgagcgcguucaaccuaau"

我想拼接 RNA 并想提取两个列表（外显子和内含子）。关键是RNA的内含子部分以gu开头，以ag结尾。但是，如果ag 出现在gu 之前，则它是外显子的一部分，而不是内含子。

def splice(sequence):
    introns = list()
    exons = list()

    while(sequence.count("gu")):

        if "gu" not in sequence:
            break
        else:    

            exons.append(sequence[:sequence.find("gu")])
            sequence = sequence[sequence.find("gu"):]

        if "ag" not in sequence:
            break
        else:

            introns.append(sequence[:sequence.find("ag")+2])
            sequence = sequence[sequence.find("ag")+2:]

    return introns, exons

这是我目前所拥有的。它进展顺利，但问题从最后开始，当gu 出现时，剩余字符串中没有ag。

输出：

Exons:
['ac',
 'agaagccuuaauauauucaaaaagcuacgccucagauuucgcgcucgagcccaaaacaacug',
 'ucgcuaaa',
 'caggcga',
 'uccaugaucgcaagc',
 'aggcucagcucauaaua',
 'uacgggacucgauaggcccc',
 'aaacgcaauuuuccucagacccacuauacgcaccucgauuuagcaug',
 'aaucauac',
 'gaucggaaccuaggaaugcaccacagaacuuugaaauacuagaacaa',
 'uaucggcgccccacauuuaacgaauaauugcaggcgccagacgaugcuag',
 'auucgag',
 'cucaga',
 'a',
 'acaucccggacagaaaaucucuuaaacgcuaga',
 'cgccugcacuucuu',
 'ccacucuaagcccaacgcacuucgcuuggcccacauugcccccagagcuuauucaucgacaggc',
 'uaaacuuuauuauac',
 'c',
 'cu',
 'gcggauugaa',
 'acagccugaaa',
 'gcgcc',
 'u',
 'u',
 'gcaggggagcuuu',
 'uuucuuuagaagagccgcgaaugaaccaacg',
 'acugcgagcgc']

Introns:
['guccgcaag',
 'guguacggguugaucacaucaaaugaag',
 'gucggugaucucacuauccuugucuucggcuuuugcucucucggcuaucaucuaag',
 'guuccauggugaccggaacgacggcuacuggag',
 'gucgggcugggguaaaag',
 'guccgccccaccag',
 'gucguugccguag',
 'guuccgggguugcgcuuugag',
 'guaag',
 'guugauugacaacggag',
 'gugcguccguaucaag',
 'gucgcuacuggcuucgcuugccgaucgag',
 'guuugugag',
 'guuguuacuaauugcguggucgccuaauauccuugauacuacguggguguacuag',
 'guucucuuggaag',
 'gugaacauacgaugauag',
 'guuccacucuuggauucaucag',
 'gugguaag',
 'gugcuuauag',
 'gucggaaucucacuuag',
 'gugag',
 'guaaccguguacag',
 'gucaauguguuuugag',
 'gugcaccuacaaaaag',
 'guuauuuag',
 'guag',
 'guag']

【问题讨论】：

我使用正则表达式修复了查询。 def splice(gene_Sequence): # 正则表达式查找 'gu' 和 'ag' 之间的序列 regex = r"gu(?:\w{0,}?)ag" introns = re.findall(regex, gene_Sequence) for内含子中的内含子： exon = gene_Sequence.replace(intron, "") return introns, exon
所以这解决了问题？
@IbtihajTahir 最好将您的修复/答案作为答案而不是作为评论发布
@ColinAnthony 好的，我现在就去做。
@IbtihajTahir 太棒了！现在你可以接受它作为答案了！ :D

标签： bioinformatics dna-sequence

【解决方案1】：

我使用正则表达式修复了查询。

def splice(gene_Sequence): 

    regex = r"gu(?:\w{0,}?)ag" 
    introns = re.findall(regex, gene_Sequence) 

    for intron in introns: 
        exon = gene_Sequence.replace(intron, "") 

    return introns, exon

【讨论】：