Question

我在使用Bio.Entrez搜索蛋白质时遇到了问题。我这样做：

>>> handle=Entrez.esearch(db="protein", term="insulin AND homo")
>>> record=Entrez.read(handle)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib/pymodules/python2.7/Bio/Entrez/__init__.py", line 351, in read
    record = handler.read(handle)
  File "/usr/lib/pymodules/python2.7/Bio/Entrez/Parser.py", line 169, in read
    self.parser.ParseFile(handle)
  File "/usr/lib/pymodules/python2.7/Bio/Entrez/Parser.py", line 307, in endElementHandler
    raise RuntimeError(value)
RuntimeError: Search Backend failed: Database is not supported: protein

我也遇到了einfo（）的问题，请查看：

>>> handler=Entrez.einfo(db="protein")
>>> record=Entrez.read(handler)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib/pymodules/python2.7/Bio/Entrez/__init__.py", line 351, in read
    record = handler.read(handle)
  File "/usr/lib/pymodules/python2.7/Bio/Entrez/Parser.py", line 169, in read
    self.parser.ParseFile(handle)
  File "/usr/lib/pymodules/python2.7/Bio/Entrez/Parser.py", line 285, in startElementHandler
    raise ValidationError(name)
Bio.Entrez.Parser.ValidationError: Failed to find tag 'Build' in the DTD. To skip all tags that are not represented in the DTD, please call Bio.Entrez.read or Bio.Entrez.parse with validate=False.

为什么不支持蛋白质数据库？有人可以帮我解决这个问题吗？

Answer 1

也在Biopython邮件列表上提出，现在显然有效： http://lists.open-bio.org/pipermail/biopython/2013-January/008306.html

我们认为这是NCBI的暂时性问题。

在Biopython 1.60中使用Bio.Entrez和蛋白质的问题

1 个答案: