Biopython Entrez efetch

Question

我的代码给出了这个错误：

File "Entrez.py", line 16, in <module>
    record = Entrez.read (handle2)
  File "/usr/local/lib/python2.7/dist-packages/Bio/Entrez/__init__.py", line 454, in read
    record = handler.read(handle)
  File "/usr/local/lib/python2.7/dist-packages/Bio/Entrez/Parser.py", line 248, in read
    raise NotXMLError(e)
Bio.Entrez.Parser.NotXMLError: Failed to parse the XML data (syntax error: line 1, column 0). Please make sure that the input data are in XML format

代码：

import numpy as np 
from Bio import Entrez
Entrez.email = "shayezkarimcide@gmail.com"

handle = Entrez.esearch(db="pmc", term = "Antimicrobial resistance",rettype = "medline",retmode = "xml",retmax= "10",sort = "pub date")

result = Entrez.read(handle)

Id = result ['IdList']

handle.close()

for val in Id :

    handle2 = Entrez.efetch(db="pmc", id=val, rettype="abstract", retmode="text")
    record = Entrez.read (handle2)

    print (record)
    handle2.close()

Answer 1

这在错误消息中是正确的:解析器不认为您的输入是有效的XML。无论Entrez.efetch(...)返回什么都不是XML，或者它有其他一些问题，比如数据类型与它的DTD不匹配。首先，我会打印或转储efetch的返回值，并查看其中的实际内容。