Biopython 1.60中Bio.Entrez和蛋白质的问题

Question

我在使用Bio.Entrez来搜索一个蛋白质时遇到了问题。我是这样做的：

>>> 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

我在使用einfo()时也遇到了问题，看看这个：

>>> 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.

为什么蛋白质数据库不被支持呢？有没有人能帮我解决这个问题？

Answer 1

这个问题也在Biopython的邮件列表上提到过，现在看来已经解决了：http://lists.open-bio.org/pipermail/biopython/2013-January/008306.html

我们认为这只是NCBI那边的一个临时问题。