在 cs50x 中加速我的 pset6 DNA 代码

Question

我目前正在做 CS50 DNA pset 并且我编写了所有代码，但是对于大文件来说速度较慢，这导致 check50 认为它是错误的。我附上了我的代码，错误检查50如下所示。

import sys
import csv


def main():
        argc = len(sys.argv)
        if (argc != 3):
            print("Usage: python dna.py [database] [sequence]")
            exit()
    
        # Sets variable name for each argv argument
        arg_database = sys.argv[1]
        arg_sequence = sys.argv[2]
    
        # Converts sequence csv file to string, and returns as thus
        sequence = get_sequence(arg_sequence)
        seq_len = len(sequence)
    
        # Returns STR patterns as list
        STR_array = return_STRs(arg_database)
        STR_array_len = len(STR_array)
    
        # Counts highest instance of consecutively reoccurring STRs
        STR_values = STR_count(sequence, seq_len, STR_array, STR_array_len)
    
        DNA_match(STR_values, arg_database, STR_array_len)
    
    
    # Reads argv2 (sequence), and returns text within as a string
    def get_sequence(arg_sequence):
        with open(arg_sequence, 'r') as csv_sequence:
            sequence = csv_sequence.read()
    
        return sequence
    
    
    # Reads STR headers from arg1 (database) and returns as list
    def return_STRs(arg_database):
        with open(arg_database, 'r') as csv_database:
            database = csv.reader(csv_database)
    
            STR_array = []
    
            for row in database:
                for column in row:
                    STR_array.append(column)
                break
    
            # Removes first column header (name)
            del STR_array[0]
        return STR_array
    
    
    def STR_count(sequence, seq_len, STR_array, STR_array_len):
        # Creates a list to store max recurrence values for each STR
        STR_count_values = [0] * STR_array_len
        # Temp value to store current count of STR recurrence
        temp_value = 0
    
        # Iterates over each STR in STR_array
        for i in range(STR_array_len):
            STR_len = len(STR_array[i])
    
            # Iterates over each sequence element
            for j in range(seq_len):
                # Ensures it's still physically possible for STR to be present in sequence
                while (seq_len - j >= STR_len):
                    # Gets sequence substring of length STR_len, starting from jth element
                    sub = sequence[j:(j + (STR_len))]
    
                    # Compares current substring to current STR
                    if (sub == STR_array[i]):
                        temp_value += 1
                        j += STR_len
                    else:
                        # Ensures current STR_count_value is highest
                        if (temp_value > STR_count_values[i]):
                            STR_count_values[i] = temp_value
                        # Resets temp_value to break count, and pushes j forward by 1
                        temp_value = 0
                        j += 1
            i += 1
    
        return STR_count_values
    
    
    # Searches database file for DNA matches
    def DNA_match(STR_values, arg_database, STR_array_len):
        with open(arg_database, 'r') as csv_database:
            database = csv.reader(csv_database)
    
            name_array = [] * (STR_array_len + 1)
            next(database)
    
            # Iterates over one row of database at a time
            for row in database:
                name_array.clear()
                # Copies entire row into name_array list
                for column in row:
                    name_array.append(column)
    
                # Converts name_array number strings to actual ints
                for i in range(STR_array_len):
                    name_array[i + 1] = int(name_array[i + 1])
    
                # Checks if a row's STR values match the sequence's values, prints the row name if match is found
                match = 0
                for i in range(0, STR_array_len, + 1):
                    if (name_array[i + 1] == STR_values[i]):
                        match += 1
    
                    if (match == STR_array_len):
                        print(name_array[0])
                        exit()
    
            print("No match")
            exit()
    
    
    main()

Check50 错误链接： https://submit.cs50.io/check50/fd890301a0dc9414cd29c2b4dcb27bd47e6d0a48

如果你等待很长时间，那么你会得到答案，但由于我的程序运行缓慢，所以 check50 认为它是错误的

Answer 1

好吧，我只是通过添加一个 break 语句来解决它。