NCBI未运行

Question

我试着在网络上运行ncbi在python上的爆炸。

from Bio.Blast import NCBIWWW 
from Bio.Blast import NCBIXML 
from Bio import SeqIO

record = SeqIO.read(r"C:\Users\loops\Downloads\biopy_resources\Section1\Chap8\buccal_swab.unmapped1.fasta",format="fasta")
handle = NCBIWWW.qblast("blastn","nt",record.seq)

blast_records = NCBIXML.parse(handle)
E_VALUE_THRESH = 0.0001
for blast_record in blast_records: 
    for alignment in blast_record.alignments: 
        for hsp in alignment.hsps: 
            if hsp.expect < E_VALUE_THRESH: 
                print(alignment.title) 
                print(alignment.length) 
                print(hsp.expect) 
                print(hsp.query[0:75]) 
                print(hsp.match[0:75]) 
                print(hsp.sbjct[0:75]) 

读取fasta文件成功，但没有显示结果。我想它卡在这里了: handle = NCBIWWW.qblast("blastn"，"nt"，record.seq)

from Bio.Blast import NCBIWWW 
handle = NCBIWWW.qblast("blastn","nt","8332116")

这也不管用。

Answer 1

如果没有错误，可能没有结果，因为e值是否超过阈值？您可以禁用if条件或可能与最终在python中缓慢运行的问题有关：NCBIWWW.qblast parsing xml files