为函数创建循环

Question

我基本上创建了一个函数，它输入一个字符串，然后添加出现在每个唯一字母之前的整数。（例如21M4D35M，将提供56M和4D）。

import re
import itertools

# example input: X is "21M4D35M1I84M9S15=92X"

def CIGAR(X):
    m = list(map(int, (re.findall(r"(\d+)M", X)))) #need to create a loop for these.
    d = list(map(int, (re.findall(r"(\d+)D", X))))
    n = list(map(int, (re.findall(r"(\d+)N", X))))
    i = list(map(int, (re.findall(r"(\d+)I", X))))
    s = list(map(int, (re.findall(r"(\d+)S", X))))
    h = list(map(int, (re.findall(r"(\d+)H", X))))
    x = list(map(int, (re.findall(r"(\d+)X", X))))
    equals = list(map(int, (re.findall(r"(\d+)=", X))))
    
    query = itertools.chain(m,n,d,i,s,h,x,equals)
    reference = itertools.chain(m,n,d,i,s,h,x,equals)
    
    query = m + i + s + equals + x #according to samtools, these operations cause the alignment to step along the query sequence 
    reference = m + d + n + equals + x
    
    print(sum(m), "Exact Matches\n", 
          sum(d), "Deletions\n", 
          sum(n), "Skipped region from the reference\n",
          sum(i), "Insertions\n",
          sum(s), "Soft Clippings\n", 
          sum(h), "Hard Clippings\n",
          sum(x), "sequence match\n",
          sum(equals), "sequence mismatch\n",
          sum(query), "bases in query sequence\n",
          sum(reference), "bases in the reference sequence")

但是，我正在尝试实现一种更有效的方法来执行函数的第一部分（第 7-14 行）。我正在尝试做类似的事情，但不知道如何实现这个

acronyms = [m,d,i,s,h,x,"="]
for i in acronyms:
i = list(map(int, (re.findall(r"(\d+)capitalize[i]", X))))

一如既往，非常感谢任何帮助，如果有什么不清楚的地方，请告诉我！

Answer 1

一个有效的解决方案是使用 collections.Counter:

def CIGAR(cigar_string):
    from collections import Counter

    c = Counter()
    for n, k in re.findall('(\d+)(\D)', cigar_string):
        c[k] += int(n)


    keys = {'M': 'Exact Matches', 
            'D': 'Deletions', 
            'N': 'Skipped region from the reference',
            'I': 'Insertions',
            'S': 'Soft Clippings', 
            'H': 'Hard Clippings',
            'X': 'sequence match',
            '=': 'sequence mismatch',
            }

    for k in keys:
        print(f'{c[k]:>5}: {keys[k]}')

    query = sum(c[x] for x in 'MIS=X')
    ref   = sum(c[x] for x in 'MDN=X')
    print(f'{query:>5}: bases in query sequence')
    print(f'{ref:>5}: bases in reference sequence')

    return c

示例：

>>> CIGAR('21M4D35M')
   56: Exact Matches
    4: Deletions
    0: Skipped region from the reference
    0: Insertions
    0: Soft Clippings
    0: Hard Clippings
    0: sequence match
    0: sequence mismatch
   56: bases in query sequence
   60: bases in reference sequence

Counter({'M': 56, 'D': 4})

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