Python 计数最大k-mer重复频率

如果n为3，则序列atag包含4x ATA、3x TAT和1x标记。因此，该比例为4/8=0.5。这个数字越高，序列的重复性就越高

编写函数Simple，n其中S是序列，n是K-Mo的长度考虑。该函数应返回上述比例

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有人能帮我吗？

这看起来像是家庭作业，但至少是脑筋急转弯

提示：itertools、生成器和集合对于解决此类问题非常方便

import itertools
import collections

ACIDS = ('A', 'C', 'T', 'G')


def walk_seq(s, chunk_size):
    assert len(s) >= chunk_size
    for i in range(0, len(s) - chunk_size + 1):
        yield s[i:i+chunk_size]


def simple(s, n):
    snip_counts = collections.defaultdict(int)
    for chunk in walk_seq(s, n):
        for snip_tuple in itertools.product(ACIDS, repeat=n):
            snip = ''.join(snip_tuple)
            if chunk == snip:
                snip_counts[snip] += 1
    total_matches = sum(snip_counts.values())
    maxi = max(snip_counts.values())
    return float(maxi) / total_matches

print simple('ATATATATAG', 3)

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这是一个非常好的算法问题，你自己也可以尝试一下，但这里的解决方案没有什么挑战

s = "ATATATATAG"
n = 3

def simple(s,n):
    dictionary = {}
    total = 0
    for i in range (len(s)-(n-1)): # (n-1) to get last element
        k = i+n
        if s[i:k] in dictionary:
            dictionary[s[i:k]] += 1
        else:
            dictionary.update({s[i:k]:1})
        total += 1 # doing it here to avoid sum(dictionary.values())

    for key, value in dictionary.items():
        dictionary[key] = value/total
    # As a challenge, edit the line above to lambda function
    print(dictionary)

simple(s,n)

# sample output
#{'TAT': 0.375, 'ATA': 0.5, 'TAG': 0.125}

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您可能希望使用for循环从输入字符串的开始到结束。为输入序列中遇到的每一个长度为n=3的序列保留一个python字典。你能公布你已经做了什么，甚至你自己对如何解决问题的想法吗？这不是家庭作业服务。漂亮的高尔夫：为什么要导入第三方库？seq[i:i+n]范围内的i seq-n+1将在ngrams上产生相同的发电机。

s = "ATATATATAG"
n = 3

def simple(s,n):
    dictionary = {}
    total = 0
    for i in range (len(s)-(n-1)): # (n-1) to get last element
        k = i+n
        if s[i:k] in dictionary:
            dictionary[s[i:k]] += 1
        else:
            dictionary.update({s[i:k]:1})
        total += 1 # doing it here to avoid sum(dictionary.values())

    for key, value in dictionary.items():
        dictionary[key] = value/total
    # As a challenge, edit the line above to lambda function
    print(dictionary)

simple(s,n)

# sample output
#{'TAT': 0.375, 'ATA': 0.5, 'TAG': 0.125}