如何在 Python 中查找所有出現的非連續子字符串？

Question

前提：

我目前正在解決以下問題：

http://rosalind.info/problems/sseq/

我必須找到字符串中所有出現的子字符串的索引組合，其中子字符串不一定是連續的。

我的測試參數：

Main_String = ACGGTTAACGTGACGGTTAAGSSGSSTSSTSSASSA
Substring = GGTTAA

不連續意味着Main_String出現的Substring可能如下所示： GGSTTSAASSS其中子字符串是GGTTAA和 MAIN_STRING - GGSTTSAASSS 。

子字符串雖然被隨機字符（在我們的例子中是 S）切割，但仍然可以在主字符串中找到。 因此，可能的答案是(format:Letter((index + 1) in Main_String)) G(1)G(2)T(4)T(5)A(7)A(8) = 1, 2, 4, 5, 7, 8.這很容易獲得第一場比賽。 我需要得到所有可能的變化，所以如果我們使用上面的測試參數，正確的答案是：

3, 4, 5, 6, 7, 8 and 3, 12, 17, 18, 19, 20 and 3, 15, 17, 18, 19, 20 and so on up to 21, 24, 27, 30, 33, 36 .

題：

我需要一種算法，它可以為我提供給定字符串中非連續子字符串的所有可能變體。

問題：

這是我到目前為止的代碼，它在一定程度上起作用，但不返回所有可能的變化，只返回其中的一些。

    dna = ''
counter = -1
dna_subseq = ''
dna_subseq_indexes = []


with open('Rosalind_dna.txt', 'r') as file:
    data = file.read().split('\n')
    for line in data:
        if line == '':
            continue
        if 'Rosalind' in line and counter < 1:
            counter += 1
            continue
        elif 'Rosalind' not in line and counter < 1:
            dna += line
        elif 'Rosalind' not in line and counter >= 1:
            dna_subseq += line

result = 0
dna_subseq_minus_start = dna_subseq[1:]


def find_next(start_parameter, base):
    result_func = dna.find(base, start_parameter)
    if result_func + 1 in dna_subseq_indexes_subcombo:
        if result_func + 1 == 0:
            return
        find_next(start_parameter + 1, base)
    else:
        dna_subseq_indexes_subcombo.append(result_func + 1)
        return


for index, value in enumerate(dna):
    global_start = index
    result = 0
    while result != -1:
        dna_subseq_indexes_subcombo = []
        if value == dna_subseq[0]:
            dna_subseq_indexes_subcombo.append(index + 1)
            Flag = True
            for base in dna_subseq_minus_start:
                if Flag:
                    start = global_start
                    Flag = False
                result = dna.find(base, start)
                if result + 1 in dna_subseq_indexes_subcombo:
                    find_next(start + 1, base)
                else:
                    dna_subseq_indexes_subcombo.append(result + 1)
                    start += 1
            dna_subseq_indexes.append(dna_subseq_indexes_subcombo)
            global_start += 1
        else:
            break


final_result = []
for x in dna_subseq_indexes:
    test = x.copy()
    test.sort()
    if test == x:
        final_result.append(x)
    else:
        continue
print(final_result)

Answer 1

我不確定您的算法是否可以找到所有解決方案，即使它會被修復。 我嘗試了這種邏輯：找到最接近 dna 左側的初始序列，並遞歸搜索從右到左的所有偏角。 這樣，解決方案會自動排序。

dna        = 'ACGGTTAACGTGACGGTTAAGSSGSSTSSTSSASSA'
dna_len    = len(dna)
dna_subseq = 'GGTTAA'
subseq_len = len(dna_subseq)
count      = 0
print_mode = True # Prints the solutions, set to False to collect them instead

# Finds a single solution starting from the previous one or from a null solution
def find_one_solution(prev_solution, subseq_start, dna_start):
    global dna, dna_subseq, subseq_len, count, mode
    searched   = dna_subseq[subseq_start]
    coll       = prev_solution[:subseq_start]
    subseq_idx = subseq_start

    for i in range(dna_start, len(dna), 1):
        letter = dna[i]
        if letter == searched:
            coll.append(i)
            subseq_idx += 1
        if (subseq_idx == subseq_len): break
        else: searched = dna_subseq[subseq_idx]
    if len(coll) < subseq_len: return None
    count += 1
    if (print_mode): print(coll)
    return coll

# Recursive function
def find_all_solutions(solutions, solution, subseq_start, limit):
    global dna, dna_subseq, subseq_len, print_mode

    for start in range(subseq_len-1, limit-1, -1):
        # last element
        if start == subseq_len-1:
            while True:
                temp = find_one_solution(solution, start, solution[-1]+1)
                if temp == None: break
                else: solution = temp
                if (not print_mode): solutions.append(solution)
        # other elements
        else:
            # finds the next solution
            temp = find_one_solution(solution, start, solution[start]+1)
            if temp == None:
                continue
            else:
                solution = temp
                if (not print_mode): solutions.append(solution)
                # and restarts from end with subseq_start as the left limit
                find_all_solutions(solutions, solution, subseq_len-1, start)


def main():
    all_solutions       = []
    # Finds the initial solution
    initial_solution    = [0] * subseq_len
    initial_solution    = find_one_solution(initial_solution, 0, initial_solution[0])
    if initial_solution == None:
        print("No solution found")
    else:
        if (not print_mode): all_solutions.append(initial_solution)
        # Finds all other solutions
        find_all_solutions(all_solutions, initial_solution, subseq_len-1, 0)
        if (not print_mode): print(all_solutions)
        print("Total count:", count)


if __name__=="__main__":
    main()


#289 solutions found : [[2, 3, 4, 5, 6, 7], [2, 3, 4, 5, 6, 12], [2, 3, 4, 5, 6, 18], [2, 3, 4, 5, 6, 19], [2, 3, 4, 5, 6, 32], [2, 3, 4, 5, 6, 35], [2, 3, 4, 5, 7, 12], [2, 3, 4, 5, 7, 18], [2, 3, 4, 5, 7, 19], [2, 3, 4, 5, 7, 32], [2, 3, 4, 5, 7, 35], [2, 3, 4, 5, 12, 18], [2, 3, 4, 5, 12, 19], [2, 3, 4, 5, 12, 32], [2, 3, 4, 5, 12, 35], [2, 3, 4, 5, 18, 19], [2, 3, 4, 5, 18, 32], [2, 3, 4, 5, 18, 35], [2, 3, 4, 5, 19, 32], [2, 3, 4, 5, 19, 35], [2, 3, 4, 5, 32, 35], [2, 3, 4, 10, 12, 18], [2, 3, 4, 10, 12, 19], [2, 3, 4, 10, 12, 32], [2, 3, 4, 10, 12, 35], [2, 3, 4, 10, 18, 19], [2, 3, 4, 10, 18, 32], [2, 3, 4, 10, 18, 35], [2, 3, 4, 10, 19, 32], [2, 3, 4, 10, 19, 35], [2, 3, 4, 10, 32, 35], [2, 3, 4, 16, 18, 19], [2, 3, 4, 16, 18, 32], [2, 3, 4, 16, 18, 35], [2, 3, 4, 16, 19, 32], [2, 3, 4, 16, 19, 35], [2, 3, 4, 16, 32, 35], [2, 3, 4, 17, 18, 19], [2, 3, 4, 17, 18, 32], [2, 3, 4, 17, 18, 35], [2, 3, 4, 17, 19, 32], [2, 3, 4, 17, 19, 35], [2, 3, 4, 17, 32, 35], [2, 3, 4, 26, 32, 35], [2, 3, 4, 29, 32, 35], [2, 3, 5, 10, 12, 18], [2, 3, 5, 10, 12, 19], [2, 3, 5, 10, 12, 32], [2, 3, 5, 10, 12, 35], [2, 3, 5, 10, 18, 19], [2, 3, 5, 10, 18, 32], [2, 3, 5, 10, 18, 35], [2, 3, 5, 10, 19, 32], [2, 3, 5, 10, 19, 35], [2, 3, 5, 10, 32, 35], [2, 3, 5, 16, 18, 19], [2, 3, 5, 16, 18, 32], [2, 3, 5, 16, 18, 35], [2, 3, 5, 16, 19, 32], [2, 3, 5, 16, 19, 35], [2, 3, 5, 16, 32, 35], [2, 3, 5, 17, 18, 19], [2, 3, 5, 17, 18, 32], [2, 3, 5, 17, 18, 35], [2, 3, 5, 17, 19, 32], [2, 3, 5, 17, 19, 35], [2, 3, 5, 17, 32, 35], [2, 3, 5, 26, 32, 35], [2, 3, 5, 29, 32, 35], [2, 3, 10, 16, 18, 19], [2, 3, 10, 16, 18, 32], [2, 3, 10, 16, 18, 35], [2, 3, 10, 16, 19, 32], [2, 3, 10, 16, 19, 35], [2, 3, 10, 16, 32, 35], [2, 3, 10, 17, 18, 19], [2, 3, 10, 17, 18, 32], [2, 3, 10, 17, 18, 35], [2, 3, 10, 17, 19, 32], [2, 3, 10, 17, 19, 35], [2, 3, 10, 17, 32, 35], [2, 3, 10, 26, 32, 35], [2, 3, 10, 29, 32, 35], [2, 3, 16, 17, 18, 19], [2, 3, 16, 17, 18, 32], [2, 3, 16, 17, 18, 35], [2, 3, 16, 17, 19, 32], [2, 3, 16, 17, 19, 35], [2, 3, 16, 17, 32, 35], [2, 3, 16, 26, 32, 35], [2, 3, 16, 29, 32, 35], [2, 3, 17, 26, 32, 35], [2, 3, 17, 29, 32, 35], [2, 3, 26, 29, 32, 35], [2, 9, 10, 16, 18, 19], [2, 9, 10, 16, 18, 32], [2, 9, 10, 16, 18, 35], [2, 9, 10, 16, 19, 32], [2, 9, 10, 16, 19, 35], [2, 9, 10, 16, 32, 35], [2, 9, 10, 17, 18, 19], [2, 9, 10, 17, 18, 32], [2, 9, 10, 17, 18, 35], [2, 9, 10, 17, 19, 32], [2, 9, 10, 17, 19, 35], [2, 9, 10, 17, 32, 35], [2, 9, 10, 26, 32, 35], [2, 9, 10, 29, 32, 35], [2, 9, 16, 17, 18, 19], [2, 9, 16, 17, 18, 32], [2, 9, 16, 17, 18, 35], [2, 9, 16, 17, 19, 32], [2, 9, 16, 17, 19, 35], [2, 9, 16, 17, 32, 35], [2, 9, 16, 26, 32, 35], [2, 9, 16, 29, 32, 35], [2, 9, 17, 26, 32, 35], [2, 9, 17, 29, 32, 35], [2, 9, 26, 29, 32, 35], [2, 11, 16, 17, 18, 19], [2, 11, 16, 17, 18, 32], [2, 11, 16, 17, 18, 35], [2, 11, 16, 17, 19, 32], [2, 11, 16, 17, 19, 35], [2, 11, 16, 17, 32, 35], [2, 11, 16, 26, 32, 35], [2, 11, 16, 29, 32, 35], [2, 11, 17, 26, 32, 35], [2, 11, 17, 29, 32, 35], [2, 11, 26, 29, 32, 35], [2, 14, 16, 17, 18, 19], [2, 14, 16, 17, 18, 32], [2, 14, 16, 17, 18, 35], [2, 14, 16, 17, 19, 32], [2, 14, 16, 17, 19, 35], [2, 14, 16, 17, 32, 35], [2, 14, 16, 26, 32, 35], [2, 14, 16, 29, 32, 35], [2, 14, 17, 26, 32, 35], [2, 14, 17, 29, 32, 35], [2, 14, 26, 29, 32, 35], [2, 15, 16, 17, 18, 19], [2, 15, 16, 17, 18, 32], [2, 15, 16, 17, 18, 35], [2, 15, 16, 17, 19, 32], [2, 15, 16, 17, 19, 35], [2, 15, 16, 17, 32, 35], [2, 15, 16, 26, 32, 35], [2, 15, 16, 29, 32, 35], [2, 15, 17, 26, 32, 35], [2, 15, 17, 29, 32, 35], [2, 15, 26, 29, 32, 35], [2, 20, 26, 29, 32, 35], [2, 23, 26, 29, 32, 35], [3, 9, 10, 16, 18, 19], [3, 9, 10, 16, 18, 32], [3, 9, 10, 16, 18, 35], [3, 9, 10, 16, 19, 32], [3, 9, 10, 16, 19, 35], [3, 9, 10, 16, 32, 35], [3, 9, 10, 17, 18, 19], [3, 9, 10, 17, 18, 32], [3, 9, 10, 17, 18, 35], [3, 9, 10, 17, 19, 32], [3, 9, 10, 17, 19, 35], [3, 9, 10, 17, 32, 35], [3, 9, 10, 26, 32, 35], [3, 9, 10, 29, 32, 35], [3, 9, 16, 17, 18, 19], [3, 9, 16, 17, 18, 32], [3, 9, 16, 17, 18, 35], [3, 9, 16, 17, 19, 32], [3, 9, 16, 17, 19, 35], [3, 9, 16, 17, 32, 35], [3, 9, 16, 26, 32, 35], [3, 9, 16, 29, 32, 35], [3, 9, 17, 26, 32, 35], [3, 9, 17, 29, 32, 35], [3, 9, 26, 29, 32, 35], [3, 11, 16, 17, 18, 19], [3, 11, 16, 17, 18, 32], [3, 11, 16, 17, 18, 35], [3, 11, 16, 17, 19, 32], [3, 11, 16, 17, 19, 35], [3, 11, 16, 17, 32, 35], [3, 11, 16, 26, 32, 35], [3, 11, 16, 29, 32, 35], [3, 11, 17, 26, 32, 35], [3, 11, 17, 29, 32, 35], [3, 11, 26, 29, 32, 35], [3, 14, 16, 17, 18, 19], [3, 14, 16, 17, 18, 32], [3, 14, 16, 17, 18, 35], [3, 14, 16, 17, 19, 32], [3, 14, 16, 17, 19, 35], [3, 14, 16, 17, 32, 35], [3, 14, 16, 26, 32, 35], [3, 14, 16, 29, 32, 35], [3, 14, 17, 26, 32, 35], [3, 14, 17, 29, 32, 35], [3, 14, 26, 29, 32, 35], [3, 15, 16, 17, 18, 19], [3, 15, 16, 17, 18, 32], [3, 15, 16, 17, 18, 35], [3, 15, 16, 17, 19, 32], [3, 15, 16, 17, 19, 35], [3, 15, 16, 17, 32, 35], [3, 15, 16, 26, 32, 35], [3, 15, 16, 29, 32, 35], [3, 15, 17, 26, 32, 35], [3, 15, 17, 29, 32, 35], [3, 15, 26, 29, 32, 35], [3, 20, 26, 29, 32, 35], [3, 23, 26, 29, 32, 35], [9, 11, 16, 17, 18, 19], [9, 11, 16, 17, 18, 32], [9, 11, 16, 17, 18, 35], [9, 11, 16, 17, 19, 32], [9, 11, 16, 17, 19, 35], [9, 11, 16, 17, 32, 35], [9, 11, 16, 26, 32, 35], [9, 11, 16, 29, 32, 35], [9, 11, 17, 26, 32, 35], [9, 11, 17, 29, 32, 35], [9, 11, 26, 29, 32, 35], [9, 14, 16, 17, 18, 19], [9, 14, 16, 17, 18, 32], [9, 14, 16, 17, 18, 35], [9, 14, 16, 17, 19, 32], [9, 14, 16, 17, 19, 35], [9, 14, 16, 17, 32, 35], [9, 14, 16, 26, 32, 35], [9, 14, 16, 29, 32, 35], [9, 14, 17, 26, 32, 35], [9, 14, 17, 29, 32, 35], [9, 14, 26, 29, 32, 35], [9, 15, 16, 17, 18, 19], [9, 15, 16, 17, 18, 32], [9, 15, 16, 17, 18, 35], [9, 15, 16, 17, 19, 32], [9, 15, 16, 17, 19, 35], [9, 15, 16, 17, 32, 35], [9, 15, 16, 26, 32, 35], [9, 15, 16, 29, 32, 35], [9, 15, 17, 26, 32, 35], [9, 15, 17, 29, 32, 35], [9, 15, 26, 29, 32, 35], [9, 20, 26, 29, 32, 35], [9, 23, 26, 29, 32, 35], [11, 14, 16, 17, 18, 19], [11, 14, 16, 17, 18, 32], [11, 14, 16, 17, 18, 35], [11, 14, 16, 17, 19, 32], [11, 14, 16, 17, 19, 35], [11, 14, 16, 17, 32, 35], [11, 14, 16, 26, 32, 35], [11, 14, 16, 29, 32, 35], [11, 14, 17, 26, 32, 35], [11, 14, 17, 29, 32, 35], [11, 14, 26, 29, 32, 35], [11, 15, 16, 17, 18, 19], [11, 15, 16, 17, 18, 32], [11, 15, 16, 17, 18, 35], [11, 15, 16, 17, 19, 32], [11, 15, 16, 17, 19, 35], [11, 15, 16, 17, 32, 35], [11, 15, 16, 26, 32, 35], [11, 15, 16, 29, 32, 35], [11, 15, 17, 26, 32, 35], [11, 15, 17, 29, 32, 35], [11, 15, 26, 29, 32, 35], [11, 20, 26, 29, 32, 35], [11, 23, 26, 29, 32, 35], [14, 15, 16, 17, 18, 19], [14, 15, 16, 17, 18, 32], [14, 15, 16, 17, 18, 35], [14, 15, 16, 17, 19, 32], [14, 15, 16, 17, 19, 35], [14, 15, 16, 17, 32, 35], [14, 15, 16, 26, 32, 35], [14, 15, 16, 29, 32, 35], [14, 15, 17, 26, 32, 35], [14, 15, 17, 29, 32, 35], [14, 15, 26, 29, 32, 35], [14, 20, 26, 29, 32, 35], [14, 23, 26, 29, 32, 35], [15, 20, 26, 29, 32, 35], [15, 23, 26, 29, 32, 35], [20, 23, 26, 29, 32, 35]]

為了測試算法的有效性，我使用了一個更簡單的序列，從中可以很容易地手動找到所有解決方案：

dna = 'AAAAAAAA'
dna_subseq = 'AAAA'

請注意，我使用基於零的索引，因為它更簡單，但如果需要，您可以輕松地將 1 添加到所有結果中。