如何在 python 3 中将字符串划分为子字符串

Question

I need help finding a more effective way of separating a string into all possible substrings. This program needs to take a desired string sequence (ex. GTCCAGCTTAAG), with a maximum length of 12, and a minimum of 6. This string needs to be separated by decreasing length (so ideally it would stop at 6). Also all the reversed counterparts need to be included in this (ex. for the 10 character length it would show GTCCAGCTTA and CAGGTCGAAT), I would imagine by a loop. Finally it would be put together in a list.

This is what I have come up with so far after trying many different, yet unsuccessful combinations. This one returns me somewhat the closest, but still a mess:

tar = "GTCCAGCTTAAG"

def subs(tar):
    substring = []
    for i in range(len(tar)):
        string_portion = tar[:i + 1]  
        string_portion1 = tar[i:]     
        substring.append(string_portion)
        print(substring)
    return 

subs(tar)

I want to separate a string into all substrings of lengths 6-12. I would also like to the original string and replace G/CA/T and find all substrings of that as well.

input: ACTGACTG -->TGACTGAC

output: [ACTGAC, ACTGACT, ACTGACTG, CTGACT..., TGACTG, TGACTGA, TGACTGAC, GACTGA...]

Then that output list would be sorted in decreasing length.

Answer 1

You could make a recursive generator using islice form itertools to zip through your string in parallel from offset starting positions and going down in size to a minimum of 6:

from itertools import islice

pairing = str.maketrans("GCAT","CGTA")

def getSubs(A,subLen=11,minLen=6,inverse=None):
    subLen = min(subLen,len(A)-1)
    if subLen<minLen: return
    for s in map("".join,zip(*(islice(A,i,None) for i in range(subLen)))):
        if inverse is not True:  yield s       # substring of length minLen
        if inverse is not False: yield s.translate(pairing)  # it's inverse
    yield from getSubs(A,subLen-1,minLen) # shorter substring lengths

Here islice(A,i,None) is an iterator over the whole string starting at position i . The *(... for i in range(subLen)) part creates subLen such iterators and feeds them to the zip() function. With each iterator starting one position farther than the previous one, zip() will produce tuples corresponding to all substrings of length subLen . This is mapped into "".join to turn the tuples back into strings.

The substrings s are output using yield (this is a generator function) and the translate method is used to output the inverse of each substring as well.

Once all substrings of length subLen are out, we recurse to the next shorter length until a length of 6 reached.

The advantage of using a generator function is that, if you apply this to very large strings and are merely searching for the first occurrence of a given pattern, then you can scan through the substrings without creating a huge list of them in memory. And, if needed, you can easily place the result in a list ( L = list(getSubs(tar)) ).

output:

tar = "GTCCAGCTTAAG"
for s in getSubs(tar):print(s)

# you can call getSubs(tar,inverse=True) to get only the inverted substrings
# or call getSubs(tar,inverse=False) to get only the non-inverted substrings
# when the inverse parameter is not provided, you get both

GTCCAGCTTAA
CAGGTCGAATT
TCCAGCTTAAG
AGGTCGAATTC
GTCCAGCTTA
CAGGTCGAAT
TCCAGCTTAA
AGGTCGAATT
CCAGCTTAAG
GGTCGAATTC
GTCCAGCTT
CAGGTCGAA
TCCAGCTTA
AGGTCGAAT
CCAGCTTAA
GGTCGAATT
CAGCTTAAG
GTCGAATTC
GTCCAGCT
CAGGTCGA
TCCAGCTT
AGGTCGAA
CCAGCTTA
GGTCGAAT
CAGCTTAA
GTCGAATT
AGCTTAAG
TCGAATTC
GTCCAGC
CAGGTCG
TCCAGCT
AGGTCGA
CCAGCTT
GGTCGAA
CAGCTTA
GTCGAAT
AGCTTAA
TCGAATT
GCTTAAG
CGAATTC
GTCCAG
CAGGTC
TCCAGC
AGGTCG
CCAGCT
GGTCGA
CAGCTT
GTCGAA
AGCTTA
TCGAAT
GCTTAA
CGAATT
CTTAAG
GAATTC

Answer 2

Using a pythonic way

>>> tar = "GTCCAGCTTAAG"

>>> k = 6
>>> K = 12

>>> res = [tar[i: j] for i in range(len(tar)) for j in range(i + 1, len(tar) + 1) if len(tar[i:j]) >= k and len(tar[i:j]) <= K]


>>> res
['GTCCAG', 'GTCCAGC', 'GTCCAGCT', 'GTCCAGCTT', 'GTCCAGCTTA', 'GTCCAGCTTAA', 'GTCCAGCTTAAG', 'TCCAGC', 'TCCAGCT', 'TCCAGCTT', 'TCCAGCTTA', 'TCCAGCTTAA', 'TCCAGCTTAAG', 'CCAGCT', 'CCAGCTT', 'CCAGCTTA', 'CCAGCTTAA', 'CCAGCTTAAG', 'CAGCTT', 'CAGCTTA', 'CAGCTTAA', 'CAGCTTAAG', 'AGCTTA', 'AGCTTAA', 'AGCTTAAG', 'GCTTAA', 'GCTTAAG', 'CTTAAG']

Answer 3

I am not sure i fully understand your problem, but I think I figured out a solution:

tar = "GTCCAGCTTAAG"

def subs(tar, substring = [], sorted_list = []):
  for i in range(len(tar)):
    for n in range(len(tar)):

   #Tries all possible solution and passes if len in lower than 6
   #also passes if substring is None

      if i >= n: 
        pass
      else:
        a = tar[i:n]
        if len(a) >= 6:
          substring.append(a)

  #Sorting the list
  for i in range(11):
    i +=6
    for sub in substring:
      if len(sub) == i:
        sorted_list.append(sub)
        
  return sorted_list
  

a = subs(tar)