Início / coding / Perguntas / 79568360
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Matteo
Asked: 2025-04-11 16:22:05 +0800 CST

determinar a posição de uma string inserida dentro de outra

  • 772

Após esta postagem, consegui montar uma pequena função para colocar dentro de um corpo de texto maior (FASTA) strings mais curtas determinadas de outro arquivo com base em algumas condições ( por exemplo, 100 eventos de um subconjunto de apenas 400 a 500 caracteres de comprimento e selecionados aleatoriamente).

Agora, estou satisfeito com o resultado; no entanto, desejo imprimir exatamente onde esses 100 eventos foram adicionados no corpo de texto maior — idealmente, posição inicial-final, se não for muito difícil.

Acho que isso poderia ser integrado get_retro_text()ou, se for mais fácil, criado como uma função externa, mas não consigo descobrir por onde começar... qualquer ajuda é muito apreciada, obrigado antecipadamente!

###library import
from Bio import SeqIO
import random

###string import and wrangling
input_file = open("homo_sapiens_strings.fasta.txt")
my_dict = SeqIO.to_dict(SeqIO.parse(input_file, "fasta"))

s = []
for j in my_dict.values():
   s.append(j)

###import FASTA --> some already made function I found to import and print whole FASTA genomes but testing on a part of it
def fasta_reader(filename):
  from Bio.SeqIO.FastaIO import FastaIterator
  with open(filename) as handle:
    for record in FastaIterator(handle):
      yield record

head = ""
body = ""
for entry in fasta_reader("hg37_chr1.fna"):
  head = str(entry.id)
  body = str(entry.seq)

###randomly selects 100 sequences and adds them to the FASTA
def insert (source_str, insert_str, pos):
    return source_str[:pos] + insert_str + source_str[pos:]

def get_retro_text(genome, all_strings):
    string_of_choice = [string for string in all_strings if 400 < len(string) < 500]
    hundred_strings = random.sample(string_of_choice, k=100)

    text_of_strings = []
    for k in range(len(hundred_strings)):
        text_of_strings.append(str(hundred_strings[k].seq))

    single_string = ",".join(text_of_strings)
    new_genome = insert(genome, single_string, random.randint(0, len(genome)))
    
    return new_genome

big_genome = get_retro_text(body, s)

EDIT exemplo de estrutura de bodyes

body


NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNtaaccctaaccctaacccta
accctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaacccta
accctaaccctaaccctaaccctaacccaaccctaaccctaaccctaaccctaaccctaa
ccctaacccctaaccctaaccctaaccctaaccctaacctaaccctaaccctaaccctaa
ccctaaccctaaccctaaccctaaccctaacccctaaccctaaccctaaaccctaaaccc
taaccctaaccctaaccctaaccctaaccccaaccccaaccccaaccccaaccccaaccc
caaccctaacccctaaccctaaccctaaccctaccctaaccctaaccctaaccctaaccc
taaccctaacccctaacccctaaccctaaccctaaccctaaccctaaccctaaccctaac
ccctaaccctaaccctaaccctaaccctcgCGGTACCCTCAGCCGGCCCGCCCGCCCGGG
TCTGACCTGAGGAGAACTGTGCTCCGCCTTCAGAGTACCACCGAAATCTGTGCAGAGGAc
aacgcagctccgccctcgcggtGCTCtccgggtctgtgctgaggagaacgCAACTCCGCC
GTTGCAAAGGCGcgccgcgccggcgcaggcgcagagaggcgcgccgcgccggcgcaggcg
cagagaggcgcgccgcgccggcgcaggcgcagagaggcgcgccgcgccggcgcaggcgca
gagaggcgcgccgcgccggcgcaggcgcagagaggcgcgccgcgccggcgcaggcgcaga
caCATGCTAGCGCGTCGGGGTGGAGGCgtggcgcaggcgcagagaggcgcgccgcgccgg
cgcaggcgcagagacaCATGCTACCGCGTCCAGGGGTGGAGGCgtggcgcaggcgcagag
aggcgcaccgcgccggcgcaggcgcagagacaCATGCTAGCGCGTCCAGGGGTGGAGGCG
TggcgcaggcgcagagacgcAAGCCTAcgggcgggggttgggggggcgTGTGTTGCAGGA
GCAAAGTCGCACGGCGCCGGGCTGGGGCGGGGGGAGGGTGGCGCCGTGCACGCGCAGAAA
CTCACGTCACGGTGGCGCGGCGCAGAGACGGGTAGAACCTCAGTAATCCGAAAAGCCGGG
ATCGACCGCCCCTTGCTTGCAGCCGGGCACTACAGGACCCGCTTGCTCACGGTGCTGTGC
CAGGGCGCCCCCTGCTGGCGACTAGGGCAACTGCAGGGCTCTCTTGCTTAGAGTGGTGGC
CAGCGCCCCCTGCTGGCGCCGGGGCACTGCAGGGCCCTCTTGCTTACTGTATAGTGGTGG
CACGCCGCCTGCTGGCAGCTAGGGACATTGCAGGGTCCTCTTGCTCAAGGTGTAGTGGCA
GCACGCCCACCTGCTGGCAGCTGGGGACACTGCCGGGCCCTCTTGCTCCAACAGTACTGG
CGGATTATAGGGAAACACCCGGAGCATATGCTGTTTGGTCTCAGTAGACTCCTAAATATG
GGATTCCTgggtttaaaagtaaaaaataaatatgtttaatttgtGAACTGATTACCATCA
GAATTGTACTGTTCTGTATCCCACCAGCAATGTCTAGGAATGCCTGTTTCTCCACAAAGT
GTTtacttttggatttttgccagTCTAACAGGTGAAGCCCTGGAGATTCTTATTAGTGAT
TTGGGCTGGGGCCTGgccatgtgtatttttttaaatttccactgaTGATTTTGCTGCATG
GCCGGTGTTGAGAATGACTGCGCAAATTTGCCGGATTTCCTTTGCTGTTCCTGCATGTAG
TTTAAACGAGATTGCCAGCACCGGGTATCATTCACCATTTTTCTTTTCGTTAACTTGCCG
TCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGA
CTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTT
CATCTGCAGGTGTCTGACTTCCAGCAACTGCTGGCCTGTGCCAGGGTGCAAGCTGAGCAC
TGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAGTGGGATGGGCCATTGTTCAT

s

[[SeqRecord(seq=Seq('ATGGCGGGACACCCGAAAGAGAGGGTGGTCACAGATGAGGTCCATCAGAACCAG...TAG'), id='retro_hsap_1', name='retro_hsap_1', description='retro_hsap_1', dbxrefs=[]), SeqRecord(seq=Seq('ATGGTCAACGTACCTAAAACCCGAAGAACCTTCTGTAAGAAGTGTGGCAAGCAT...TAA'), id='retro_hsap_2', name='retro_hsap_2', description='retro_hsap_2', dbxrefs=[]), SeqRecord(seq=Seq('ATGTCCACAATGGGAAACGAGGCCAGTTACCCGGCGGAGATGTGCTCCCACTTT...TGA'), id='retro_hsap_3', name='retro_hsap_3', description='retro_hsap_3', dbxrefs=[])]]
python

1 respostas

  1. Best Answer

    Seu código atual tem alguns problemas:

    • Ele insere as 100 sequências selecionadas aleatoriamente, todas adjacentes umas às outras no genoma

    • As 100 strings são concatenadas com vírgulas, que terminam na string final do gnome

    Então isso precisaria ser corrigido primeiro antes de chegarmos à questão das posições onde as inserções acontecem.

    Eu abordaria essas questões da seguinte maneira. Coloquei comentários onde alterei o código

    import random

# removed the insert function: will not be used

def get_retro_text(genome, all_strings):
    string_of_choice = [string for string in all_strings if 400 < len(string) < 500]
    hundred_strings = random.sample(string_of_choice, k=100)
    # get a sorted list of randomly selected insertion points in the genome    
    indices = sorted(random.randrange(len(genome)) for _ in hundred_strings)
    # get a list sub strings that result from slicing up the genome at the random insertion points   
    slices = [genome[i:j] for i, j in zip([0] + indices, indices + [len(genome)])]
    
    # determine what the offsets will be once the selected strings are inserted into the genome   
    start = 0
    offsets = [(start := start + len(infix), start := start + len(string)) for infix, string in zip(slices, hundred_strings)]
    # finally build the new genome by alternating the slices (substrings) with the strings to insert
    new_genome = "".join("".join(pairs) for pairs in zip(slices, hundred_strings)) + slices[-1]
    # return both the new genome and the information of where insertions were made
    return new_genome, offsets


# if you have items with a seq attribute, then extract that first:
s = [str(item.seq) for item in s]
# get both the genome and the information about the insertion points
big_genome, offsets = get_retro_text(body, s)

print(big_genome)
print(offsets)
    • 1

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