如何打印 BLAST 搜索中的最佳匹配结果？ / BioPython

Question

我正在尝试使用核苷酸序列进行BLAST搜索并打印最佳匹配命中，但不确定应该使用哪个选项/命令。有

max_hpsp

和

best_hit_overhang

等选项。我不知道它们的差异，我只想打印 1 个命中。 （最匹配的一个）我应该使用

 max_hpsp 1

吗？

我写了这段代码，但它仍然没有用。如果您能告诉我，我错在哪里以及应该做什么，我将非常感激:) 谢谢！

from Bio.Blast import NCBIWWW
seq = Seq("GTTGA......CT")
def best_matching_hit(seq):
    try:
        result_handle = NCBIWWW.qblast("blastn", "nt", seq)
    except:
        print('BLAST run failed!')
        return None
    blast_record = NCBIXML.read(result_handle)
    for hit in blast_record.alignments:
        for hsp in hit.hsps:
            if hsp.expect == max_hsps 1:
                print(hit.title)
                print(hsp.sbjct)

    
best_matching_hit(seq)

Answer 1

这仅返回一次点击，我想是第一个点击，按照

限制 Biostars 上 Biopython NCBIWWW 搜索中的点击次数：

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Jun  7 15:28:11 2021

@author: Pietro


https://stackoverflow.com/questions/67872118/how-to-print-the-best-matching-hit-in-the-blast-search-biopython

"""


from Bio.Blast import NCBIWWW

from Bio.Seq import Seq

seq = Seq("ATGGCGTGGAATGAGCCTGGAAATAACAACGGCAACAATGGCCGCGATAATGACCCTTGGGGTAATAA\
          TAATCGTGGTGGCCAGCGTCCTGGTGGCCGAGATCAAGGTCCGCCAGATTTAGATGAAGTGTTCAACAA\
          ACTGAGTCAAAAGCTGGGTGGCAAGTTTGGTAAAAAAGGCGGCGGTGGTTCCTCTATCGGCGGTGGCGG\
          TGGTGCAATTGGCTTTGGTGTCATTGCGATCATTGCAATTGCGGTGTGGATTTTCGCTGGTTTTTACAC\
          CATCGGTGAAGCAGAGCGTGGTGTTGTACTGCGTTTAGGTAAATACGATCGTATCGTAGACCCAGGCCT\
          TAACTGGCGTCCTCGTTTTATTGATGAATACGAAGCGGTTAACGTACAAGCGATTCGCTCACTACGTGC\
          ATCTGGTCTAATGCTGACGAAAGATGAAAACGTAGTAACGGTTGCAATGGACGTTCAATACCGAGTTGC\
          TGACCCATACAAATACCTATACCGCGTGACCAATGCAGATGATAGCTTGCGTCAAGCAACAGACTCTGC\
          GCTACGTGCGGTAATTGGTGATTCACTAATGGATAGCATTCTAACCAGTGGTCGTCAGCAAATTCGTCA\
          AAGCACTCAAGAAACACTAAACCAAATCATCGATAGCTATGATATGGGTCTGGTGATTGTTGACGTGAA\
          CTTCCAGTCTGCACGTCCGCCAGAGCAAGTAAAAGATGCGTTTGATGACGCGATTGCTGCGCGTGAGGA\
          TGAAGAGCGTTTCATCCGTGAAGCAGAAGCTTACAAGAACGAAATCTTGCCGAAGGCAACGGGTCGTGC\
          TGAACGTTTGAAGAAGGAAGCTCAAGGTTACAACGAGCGTGTAACTAACGAAGCATTAGGTCAAGTAGC\
          ACAGTTTGAAAAACTACTACCTGAATACCAAGCGGCTCCTGGCGTAACACGTGACCGTCTGTACATTGA\
          CGCGATGGAAGAGGTTTACACCAACACATCTAAAGTGTTGATTGACTCTGAATCAAGCGGCAACCTTTT\
          GTACCTACCAATCGATAAATTGGCAGGTCAAGAAGGCCAAACAGACACTAAACGTAAATCGAAATCTTC\
          TTCAACCTACGATCACATTCAACTAGAGTCTGAGCGTACACAAGAAGAAACATCGAACACGCAGTCTCG\
          TTCAACAGGTACACGTCAAGGGAGATACTAA")

def best_matching_hit(seq):
    try:
        result_handle = NCBIWWW.qblast("blastn", "nt", seq,  hitlist_size=1)
    except:
        print('BLAST run failed!')
        return None
    blast_record = result_handle.read()
   
    print(blast_record)


best_matching_hit(seq)

Answer 2

您正在尝试将 E 值 (hsp.expect) 与未定义的变量 max_hsps 进行比较，这对于检索最佳命中不是必需的。另外，要限制命中数，您应该使用 NCBIWWW.qblast 中的 hitlist_size 参数而不是 max_hsps。我提供了您的函数的更正版本，该版本可以正确检索并打印最佳命中的信息，或指示是否未找到命中。

from Bio.Blast import NCBIWWW
from Bio.Blast import NCBIXML
from Bio.Seq import Seq

def best_matching_hit(seq):
    try:
        result_handle = NCBIWWW.qblast("blastn", "nt", seq, hitlist_size=1)
    except Exception as e:
        print('BLAST run failed:', e)
        return None
    
    blast_record = NCBIXML.read(result_handle)
    if blast_record.alignments:
        best_hit = blast_record.alignments[0] # Access the first (best) alignment
        best_hsp = best_hit.hsps[0] ## Access the first high-scoring segment pair
        print("Best Hit Title:", best_hit.title) 
        print("Best Hit Subject Sequence:", best_hsp.sbjct)
        #if u want alignment aswell u can do below one otherwise skip these four steps and continue with else
        print("Alignment:")
        print(best_hsp.query)
        print(best_hsp.match)
        print(best_hsp.sbjct)
    else:
        print("No hits found.")

seq = Seq("ATGGCGTGGAATGAGCCTGGAAATAACAACGGCAACAATGGCCGCGATAATGACCCTTGGGGTAATAA\
          TAATCGTGGTGGCCAGCGTCCTGGTGGCCGAGATCAAGGTCCGCCAGATTTAGATGAAGTGTTCAACAA\
          ACTGAGTCAAAAGCTGGGTGGCAAGTTTGGTAAAAAAGGCGGCGGTGGTTCCTCTATCGGCGGTGGCGG\
          TGGTGCAATTGGCTTTGGTGTCATTGCGATCATTGCAATTGCGGTGTGGATTTTCGCTGGTTTTTACAC\
          CATCGGTGAAGCAGAGCGTGGTGTTGTACTGCGTTTAGGTAAATACGATCGTATCGTAGACCCAGGCCT\
          TAACTGGCGTCCTCGTTTTATTGATGAATACGAAGCGGTTAACGTACAAGCGATTCGCTCACTACGTGC\
          ATCTGGTCTAATGCTGACGAAAGATGAAAACGTAGTAACGGTTGCAATGGACGTTCAATACCGAGTTGC\
          TGACCCATACAAATACCTATACCGCGTGACCAATGCAGATGATAGCTTGCGTCAAGCAACAGACTCTGC\
          GCTACGTGCGGTAATTGGTGATTCACTAATGGATAGCATTCTAACCAGTGGTCGTCAGCAAATTCGTCA\
          AAGCACTCAAGAAACACTAAACCAAATCATCGATAGCTATGATATGGGTCTGGTGATTGTTGACGTGAA\
          CTTCCAGTCTGCACGTCCGCCAGAGCAAGTAAAAGATGCGTTTGATGACGCGATTGCTGCGCGTGAGGA\
          TGAAGAGCGTTTCATCCGTGAAGCAGAAGCTTACAAGAACGAAATCTTGCCGAAGGCAACGGGTCGTGC\
          TGAACGTTTGAAGAAGGAAGCTCAAGGTTACAACGAGCGTGTAACTAACGAAGCATTAGGTCAAGTAGC\
          ACAGTTTGAAAAACTACTACCTGAATACCAAGCGGCTCCTGGCGTAACACGTGACCGTCTGTACATTGA\
          CGCGATGGAAGAGGTTTACACCAACACATCTAAAGTGTTGATTGACTCTGAATCAAGCGGCAACCTTTT\
          GTACCTACCAATCGATAAATTGGCAGGTCAAGAAGGCCAAACAGACACTAAACGTAAATCGAAATCTTC\
          TTCAACCTACGATCACATTCAACTAGAGTCTGAGCGTACACAAGAAGAAACATCGAACACGCAGTCTCG\
          TTCAACAGGTACACGTCAAGGGAGATACTAA")
best_matching_hit(seq)