CS50问题集6“蟒蛇”，我无法计算间歇性DNA序列，我的代码在小数据库中成功，在大数据库中失败

Question

我是编程的初学者，所以我决定参加CS50课程。在问题集6（Python）中，我编写了代码，它适用于小型数据库，但对于大型数据库却失败了，所以我只寻求有关该想法的帮助。这是课程页面，您可以在此处下载（从Google云端硬盘）我的代码import csvfrom sys import argvclass DnaTest(object):    """CLASS HELP: the DNA test, simply give DNA sequence to the program, and it searches in the database to       determine the person who owns the sample.    type the following in cmd to run the program:    python dna.py databases/small.csv sequences/1.txt """    def __init__(self):        # get filename from the command line without directory names "database" and "sequence"        self.sequence_argv = str(argv[2][10:])        self.database_argv = str(argv[1][10:])        # Automatically open and close the database file        with open(f"databases/{self.database_argv}", 'r') as database_file:            self.database_file = database_file.readlines()        # Automatically open and close the sequence file        with open(f"sequences/{self.sequence_argv}", 'r') as sequence_file:            self.sequence_file = sequence_file.readline()        # Read CSV file as a dictionary, function: compare_database_with_sequence()        self.csv_database_dictionary = csv.DictReader(self.database_file)        # Read CSV file to take the first row, function: get_str_list()        self.reader = csv.reader(self.database_file)        # computed dictionary from the sequence file        self.dict_from_sequence = {}    # returns the first row of the CSV file (database file)    def get_str_list(self):        # get first row from CSV file        self.keys = next(self.reader)        # remove 'name' from list, get STR only.        self.keys.remove("name")        return self.keys问题是在函数i使用计数，它是工作，但对于顺序序列，在序列文件中（示例5.txt），所需的序列是非序列的，我无法比较每个连续序列的数量。我搜索了一下，但我没有找到任何简单的东西。有些人使用正则表达式模块，有些人使用re模块，我还没有找到解决方案。get_str_count_from_sequence(self):

Answer 1

谢谢你“皮尤什·辛格”我接受了你的建议，并用它来解决问题。首先，我使用并设置了一个匹配组（最长的顺序序列），这是一个字典，然后我为每个STR取了最大值，然后我清除了字典数据以存储下一个STR，在这里我对比较函数字典进行了更新（从数据库中读取并从序列文件中计算）rere

import csv

from sys import argv

import re

class DnaTest(object):

    """CLASS HELP: the DNA test, simply give DNA sequence to the program, and it searches in the database to

       determine the person who owns the sample.

    type the following in cmd to run the program:

    python dna.py databases/small.csv sequences/1.txt """

    def __init__(self):

        # get filename from the command line without directory names "database" and "sequence"

        self.sequence_argv = str(argv[2][10:])

        self.database_argv = str(argv[1][10:])

        # Automatically open and close the database file

        with open(f"databases/{self.database_argv}", 'r') as database_file:

            self.database_file = database_file.readlines()

        # Automatically open and close the sequence file

        with open(f"sequences/{self.sequence_argv}", 'r') as sequence_file:

            self.sequence_file = sequence_file.readline()

        # Read CSV file as a dictionary, function: compare_database_with_sequence()

        self.csv_database_dictionary = csv.DictReader(self.database_file)

        # Read CSV file to take the first row, function: get_str_list()

        self.reader = csv.reader(self.database_file)

        # computed dictionary from the sequence file

        self.dict_from_sequence = {}

        self.select_max = {}

    # returns the first row of the CSV file (database file)

    def get_str_list(self):

        # get first row from CSV file

        keys = next(self.reader)

        # remove 'name' from list, get STR only.

        keys.remove("name")

        return keys

    # returns dictionary of computed STRs from the sequence file (key(STR): value(count))

    def get_str_count_from_sequence(self):  # PROBLEM HERE AND RETURN DICTIONARY FROM IT !

        for str_key in self.get_str_list():

            regex = rf"({str_key})+"

            matches = re.finditer(regex, self.sequence_file, re.MULTILINE)

            # my code

            for match in matches:

                match_len = len(match.group())

                key_len = len(str_key)

                self.select_max[match] = match_len

                #  select max value from results dictionary (select_max)

                max_values = max(self.select_max.values())

                if max_values >= key_len:

                    result = int(max_values / key_len)

                    self.select_max[str_key] = result

                    self.dict_from_sequence[str_key] = result

            # clear compare dictionary to select new key

            self.select_max.clear()

    # compare computed dictionary with the database dictionaries and get the person name

    def compare_database_with_sequence(self):

        # comparison function between database dictionary and sequence computed dictionary

        def dicts_equal(from_sequence, from_database):

            """ return True if all keys and values are the same """

            return all(k in from_database and int(from_sequence[k]) == int(from_database[k]) for k in from_sequence) \

                and all(k in from_sequence and int(from_sequence[k]) == int(from_database[k]) for k in from_database)

        def check_result():

            for dictionary in self.csv_database_dictionary:

                dict_from_database = dict(dictionary)

                dict_from_database.pop('name')

                if dicts_equal(self.dict_from_sequence, dict_from_database):

                    dict_from_database = dict(dictionary)

                    print(dict_from_database['name'])

                    return True

        if check_result():

            pass

        else:

            print("No match")

# run the class and its functions (Program control)

if __name__ == '__main__':

    RunTest = DnaTest()

    RunTest.get_str_count_from_sequence()

    RunTest.compare_database_with_sequence()

检查解决方案

Run your program as python dna.py databases/small.csv sequences/1.txt. Your program should output Bob.

Run your program as python dna.py databases/small.csv sequences/2.txt. Your program should output No match.

有关更多检查，请访问 CS50 DNA 问题集

Answer 2

为了获得每个STR的最大连续STR数量，我只写了几行代码。这个想法是：你搜索一个STR，如果你找到它，然后你搜索STRx2，如果再次找到，然后搜索STRX3，依此类推，直到你找不到STRXn，那么你的最大数量是n-1。由于STRxn始终是连续的，因此如果发现任何非连续的事物，则无需担心。除了系统和csv之外，您不需要蟒蛇库。我的整段代码不到30行。

enter code here

import csv

import sys

# check command-line arguments, expect 3 including dna.py

n = len(sys.argv)

if n != 3:

    print("Usage: python dna.py data.csv sequence.txt")

    exit(0)

with open(sys.argv[1], 'r') as database:  # read database

    data_lines = csv.reader(database)  # read line-by-line, store in data_lines

    data = [row for row in data_lines]  # convert to list of lists, store in data

with open(sys.argv[2], 'r') as sequences:

    dna = sequences.read()  # read sequence data, store in string dna

counts = []  # list to store counts of the longest run of consecutive repeats of each STR

for i in range(1, len(data[0])):  # loop through all STR

    count = 1

    string = data[0][i]  # assign each STR to a string

    while string * count in dna:  # if find 1 string, then try to find string*2, and so on

        count += 1

    counts.append(str(count - 1))  # should be decreased by 1 as initialized to 1. int to str

for j in range(1, len(data)):  # loop through all rows in database

    if data[j][1:len(data[0])] == counts:  # compare only numebrs in each row to counts

        print(data[j][0])  # print corresponding name

        exit(0)

print('No Match')