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python - 使用“findall”查找蛋白质序列的序列基序

问题描述

我有一个程序需要用户输入来查找包含蛋白质序列的 FASTA 文件（如果找不到文件，则会给出错误），然后扫描序列并找到以下四个字母序列规则：以“N”开头，然后是除“P”之外的任何内容，然后是“S”或“T”，然后是除“P”之外的任何内容。如果找不到文件，我有一部分会给出错误。但是，在扫描序列时，我只收到一个字母的序列。

这是我的代码：

import re
userinput = input("Please provide a FASTA file.")
while userinput:
    try:
        if userinput == "0":
            break
        with open(userinput, mode = 'r') as protein:
            readprotein = protein.read()
        matches = re.findall('N[^P](S|T)[^P]', readprotein)
        for match in matches:
            print(match)
        break
    except FileNotFoundError:
        print("File not found. Please ensure that you are typing the file name exactly as it is found with the file extension.")
        userinput = input("Please provide a FASTA file. 0 to quit.")

我正在使用的 FASTA 文件是 HIV Type-2 蛋白质组，这里有一个小片段：

>sp|P18096|POL_HV2BE Gag-Pol polyprotein OS=Human immunodeficiency virus type 2 subtype A (isolate BEN) OX=11714 GN=gag-pol PE=3 SV=4
MGARNSVLRGKKADELEKVRLRPGGKKKYRLKHIVWAANELDKFGLAESLLESKEGCQKI
LRVLDPLVPTGSENLKSLFNTVCVIWCLHAEEKVKDTEEAKKLAQRHLVAETGTAEKMPN
TSRPTAPPSGKRGNYPVQQAGGNYVHVPLSPRTLNAWVKLVEEKKFGAEVVPGFQALSEG
CTPYDINQMLNCVGDHQAAMQIIREIINEEAADWDSQHPIPGPLPAGQLRDPRGSDIAGT
TSTVDEQIQWMYRPQNPVPVGNIYRRWIQIGLQKCVRKYNPTNILDIKQGPKEPFQSYVD
RFYKSLRAEQTDPAVKNWMTQTLLIQNANPDCKLVLKGLGMNPTLEEMLTACQGVGGPGQ
KARLMAEALKEAMGPSPIPFAAAQQRKAIRYWNCGKEGHSARQCRAPRRQGCWKCGKPGH
IMANCPERQAGFFRVGPTGKEASQLPRDPSPSGADTNSTSGRSSSGTVGEIYAAREKAEG
AEGETIQRGDGGLAAPRAERDTSQRGDRGLAAPQFSLWKRPVVTAYIEDQPVEVLLDTGA
DDSIVAGIELGDNYTPKIVGGIGGFINTKEYKNVEIKVLNKRVRATIMTGDTPINIFGRN
ILTALGMSLNLPVAKIEPIKVTLKPGKDGPRLKQWPLTKEKIEALKEICEKMEKEGQLEE
APPTNPYNTPTFAIKKKDKNKWRMLIDFRELNKVTQDFTEIQLGIPHPAGLAKKKRISIL
DVGDAYFSIPLHEDFRQYTAFTLPAVNNMEPGKRYIYKVLPQGWKGSPAIFQYTMRQVLE
PFRKANPDVILIQYMDDILIASDRTGLEHDKVVLQLKELLNGLGFSTPDEKFQKDPPFQW
MGCELWPTKWKLQKLQLPQKDIWTVNDIQKLVGVLNWAAQIYSGIKTKHLCRLIRGKMTL
TEEVQWTELAEAELEENKIILSQEQEGYYYQEEKELEATIQKSQGHQWTYKIHQEEKILK
VGKYAKIKNTHTNGVRLLAQVVQKIGKEALVIWGRIPKFHLPVERETWEQWWDNYWQVTW
IPEWDFVSTPPLVRLTFNLVGDPIPGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKVLE
QTTNQQAELEVFRMALADSGPKVNIIVDSQYVMGIVAGQPTESENRIVNQIIEEMIKKEA
VYVAWVPAHKGIGGNQEVDHLVSQGIRQVLFLEKIEPAQEEHEKYHSIIKELTHKFGIPL
LVARQIVNSCAQCQQKGEAIHGQVNAEIGVWQMDYTHLEGKIIIVAVHVASGFIEAEVIP
QESGRQTALFLLKLASRWPITHLHTDNGPNFTSQEVKMVAWWVGIEQSFGVPYNPQSQGV
VEAMNHHLKNQISRIREQANTIETIVLMAVHCMNFKRRGGIGDMTPAERLINMITTEQEI
QFLQRKNSNFKNFQVYYREGRDQLWKGPGELLWKGEGAVIVKVGTDIKVVPRRKAKIIRD
YGGRQELDSSPHLEGAREDGEMACPCQVPEIQNKRPRGGALCSPPQGGMGMVDLQQGNIP
TTRKKSSRNTGILEPNTRKRMALLSCSKINLVYRKVLDRCYPRLCRHPNT
>sp|P18095|GAG_HV2BE Gag polyprotein OS=Human immunodeficiency virus type 2 subtype A (isolate BEN) OX=11714 GN=gag PE=3 SV=3
MGARNSVLRGKKADELEKVRLRPGGKKKYRLKHIVWAANELDKFGLAESLLESKEGCQKI
LRVLDPLVPTGSENLKSLFNTVCVIWCLHAEEKVKDTEEAKKLAQRHLVAETGTAEKMPN
TSRPTAPPSGKRGNYPVQQAGGNYVHVPLSPRTLNAWVKLVEEKKFGAEVVPGFQALSEG
CTPYDINQMLNCVGDHQAAMQIIREIINEEAADWDSQHPIPGPLPAGQLRDPRGSDIAGT
TSTVDEQIQWMYRPQNPVPVGNIYRRWIQIGLQKCVRKYNPTNILDIKQGPKEPFQSYVD
RFYKSLRAEQTDPAVKNWMTQTLLIQNANPDCKLVLKGLGMNPTLEEMLTACQGVGGPGQ
KARLMAEALKEAMGPSPIPFAAAQQRKAIRYWNCGKEGHSARQCRAPRRQGCWKCGKPGH
IMANCPERQAGFLGLGPRGKKPRNFPVTQAPQGLIPTAPPADPAAELLERYMQQGRKQRE
QRERPYKEVTEDLLHLEQRETPHREETEDLLHLNSLFGKDQ

显然，我的代码中的错误在于教授指示我使用的“findall”函数，我认为这可能只是因为我无法完全理解正则表达式的使用。我所拥有的是 re.findall('N^P[^P]', readprotein)。我不明白为什么我得到的单个字母序列甚至不以“N”开头，它只是一堆“T”或“S”。任何帮助表示赞赏！

标签： pythonfastaprotein-database

解决方案

问题是这(S|T)是一个捕获组，因此re.findall只返回它捕获的匹配部分。(?:S|T)您可以通过写入使其成为非捕获组来修复它，以便re.findall返回整个匹配项。

例子：

>>> import re
>>> re.findall('N[^P](S|T)[^P]', 'NSTN')
['T']
>>> re.findall('N[^P](?:S|T)[^P]', 'NSTN')
['NSTN']

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