如何通过搜索列表1中的子字符串来查找列表2中的完整字符串？

Question

我有两个由氨基酸序列组成的列表（这不是生物学问题，但为上下文而陈述），其中List1包含完整字符串（完整序列）的子字符串（部分序列）List2包含完整字符串，其中一些包含来自List1的子字符串，而一些字符串不包含

这些列表很大，这就是为什么要创建它们，但现在我不知道如何跟踪子字符串到完整字符串

下面是使用我自己数据集中的真实数据修改后的两个列表的示例。对于List1中包含的两个子字符串，List2中应该有两个匹配项。我已经确认匹配项在List2

List1 = ['QSLNQNVVSRTCPAVVSHRARRAVRVMATGSPLTFSKYQGLGNDFILIDNRHTSEPVVTPEQAVKICDRNFGVGGDGVIFALPPVGETDLTMRIFNSDGSEPEMCGNGIRCLAKFVADIDKSSPRKYKIHTLAGLIQPELLADGQVRVDMGAPILDGSKVPTTLTPTEGNTVVQQDLVVDGKTYKVTCVSMGNPHAVIYTCNGKTIKIDDLESDLAALGPKFERNTVFPARTNTEFVEVISPSHVRMVVWERGAGRTLACGTGACALVVAGILEGRVDRSKTCRVDLPGGPLQIEWSTVDNHIYMTGPAELVFGGSLRV', 'DMRISYERGGLEEAAFRGRDPMQVFDEWFKAAVAGKVCEEPNAISLASSNPSGQPSVRVVLLKGYDERGFVFYTNYSSRKGTELESGSAAFSIYWEKLQRQIRVEGTVEHVSEEESTAYFHSRPRGSQIGAWVSAQSQPCRNRGEMEARNAELQQRFSDESVPVPKPPHWGGYLIRPTRIEFWQGRPSRLHDRIRFRRPSPNESWVMERLQP']
List2 = [Seq('SSLPSNSVWASGKSYLGHLY*CVHPAHTVTFTLPLVAA*YRALSYDVRRSKFLT...LHL', HasStopCodon(ExtendedIUPACProtein(), '*')), Seq('PLYHLILSGPLENPT*DTYTDAFILLTRSLSPSLS*PRNTALCHMTFAVQNFLL...CIF', HasStopCodon(ExtendedIUPACProtein(), '*')), Seq('LSTI*FCLGLWKILPRTPILMRSSCSHGHFHPPSRSRVIPRFVI*RSPFKISYS...TAS', HasStopCodon(ExtendedIUPACProtein(), '*')), Seq('EDAVIESKCGQSHMPGCCQPPGTQGCARNGYGIAPDVLQVSGPW*RFHLD*QSP...VER', HasStopCodon(ExtendedIUPACProtein(), '*')), Seq('KMQSLNQNVVSRTCPAVVSHRARRAVRVMATGSPLTFSKYQGLGNDFILIDNRH...*RG', HasStopCodon(ExtendedIUPACProtein(), '*')), Seq('RCSH*IKMWSVAHARLLSATGHAGLCA*WLRDRP*RSPSIRALVTISS*LTIAT...GRE', HasStopCodon(ExtendedIUPACProtein(), '*')) Seq('VLTHVVASDKELLARAVRWEALPSRKNLSGLHHPSAPKPLSNSQYYSKKKPIRL...DFV', HasStopCodon(ExtendedIUPACProtein(), '*')), Seq('FLHTWLLPTRSCSRVQSAGKHCQAEKTSQVCITHRRLSH*ATLNITVKKNQSVS...QTS', HasStopCodon(ExtendedIUPACProtein(), '*')), Seq('SYTRGCFRQGVARACSPLGSIAKQKKPLRSASPIGA*AIKQLSILQ*KKTNPSH...RLR', HasStopCodon(ExtendedIUPACProtein(), '*')), Seq('HEVCVSVT*QHYVLP*RTNLWGHPSSELLSRVRINC*LQLLSVLNQCSIAHHRA...CKN', HasStopCodon(ExtendedIUPACProtein(), '*')), Seq('TKSAFQ*HNNIMFFPNAQIYGDTPAPSCYHVCA*IANCNYYLCSINAV*HIIAP...CVR', HasStopCodon(ExtendedIUPACProtein(), '*')), Seq('RSLRFSNITTLCSSLTHKFMGTPQLRVAITCAHKLLTATIICAQSMQYSTSSRQ...V*E', HasStopCodon(ExtendedIUPACProtein(), '*'))]

以下是我的脚本的高度浓缩版本，以了解更多上下文：

import os
import xml.etree.ElementTree as ET
from Bio.Seq import Seq
from Bio.Alphabet import generic_dna

path_to_allxmlfiles = "path/to/xml/file/dir/"  # Path to a directory where a bunch of XML files are found.
xml_dir = os.listdir(path_to_allxmlfiles)

path_to_transcriptome = "path/to/transcriptome/file.fasta" #This is just a giant fasta file.
transcriptomefile = open(path_to_transcriptome, 'r')

List1=[]
for file in xml_dir:
    if file.endswith(".xml"):
        xml_file_path = os.path.join(path_to_allxmlfiles, file)
        xml_files = open(xml_file_path, 'r')
            for lines in xml_files:
                tree = ET.parse(xml_files)
                root = tree.getroot()

                for substring in root.findall("./BlastOutput_iterations/Iteration/Iteration_hits/Hit[1]/Hit_hsps/Hsp[1]/substring"):
                    SUBSTRING = substring.text
                    List1.append(SUBSTRING)
fullstrlist1 = []
fullstrlist2 = []
fullstrlist3 = []
fullstrlist4 = []
fullstrlist5 = []
fullstrlist6 = []
for line in transcriptomefile:
    if (stuff_was_done_here):

      A_lot_of_stuff_done_here_where_I_appended_full_strings_to_six_lists. # I am translating in 6 reading frames so this is necessary because each reading frame is unique.

        List2 = [fullstrlist1, fullstrlist2, fullstrlist3, fullstrlist4, fullstrlist5, fullstrlist6] #List2 is a combination of the six lists above.

for item in List2:
    if any(x in item for x in List1):
        print(item)

根据我所知，print(item)中返回的不是包含来自List1的子字符串的项

这是我关于StackOverflow的第一个问题。如果需要更多细节，请告诉我。我提前感谢你的帮助

Answer 1

我不太确定你问的是什么，但这里有两种搜索方法的示例

#Sub Strings
List1 = ["Apple", "Mulberry"]

# List of lists
List2 = [
    ["Apple", "Grapefruit", "Guava"],
    ["Banana", "Blueberry", "Grape"],
    ["Lemon", "Lime"],
    ["Loquat", "Lychee", "Mango"],
    ["Mulberry", "Nectarine", "Strawberry"],
    ["Pomegranate", "Raspberry"]
]

#a substring to search for.
List3 = ["berry", "ime"]

print("Search for whole matching strings", List1)
for item in List2:
    if any(x in item for x in List1):
        print(item)

print('\n Substring search for substrings', List3)
for group in List2:
    for item in group:
        if any(sbs in item for sbs in List3):
            print(group)
            break # no need to keep searching the group

以及输出

Search for whole matching strings ['Apple', 'Mulberry']
['Apple', 'Grapefruit', 'Guava']
['Mulberry', 'Nectarine', 'Strawberry']

 Substring search for substrings ['berry', 'ime']
['Banana', 'Blueberry', 'Grape']
['Lemon', 'Lime']
['Mulberry', 'Nectarine', 'Strawberry']
['Pomegranate', 'Raspberry']