python - Biopython 1.60 中的 Bio.Entrez 和蛋白质问题

Question

我在使用 Bio.Entrez 搜索蛋白质时遇到问题。我正在这样做:

>>> 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() 问题，请检查以下内容:

>>> 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，并且显然现在正在工作: http://lists.open-bio.org/pipermail/biopython/2013-January/008306.html

我们认为这是 NCBI 的一个暂时性问题。