NCBI的新RefSeq版本与Bio.Entrez.Parser兼容吗? [英] The new RefSeq release from NCBI is compatible with Bio.Entrez.Parser?

问题描述

我是python的新手，尤其是Biopython.我正在尝试使用Entrez.efetch从XML文件中获取一些信息，然后再读取它.上周，该脚本运行良好:

I'm new with python and especially with Biopython. I'm trying to take some information from an XML file with Entrez.efetch and then read it. Last week this script worked well:

handle = Entrez.efetch(db="Protein", id="YP_008872780.1", retmode="xml")
records = Entrez.read(handle)

但是现在我遇到一个错误:

But now I'm getting an Error:

> Bio.Entrez.Parser.ValidationError: Failed to find tag 'GBSeq_xrefs' 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.

所以我运行这个:

records = Entrez.read(handle, validate=False)

但是我仍然遇到错误:

TypeError: 'str' object does not support item assignment

经过研究，我意识到NCBI制作了有关RefSeq的新更改，该RefSeq在(GenPept的)xml文件中创建新标签

After some research I realized that NCBI made new changes concerning the RefSeq which creates new tags in the xml file (of GenPept)

我是否需要在DTD中进行某些更改以支持这些新标签?

Do I need to change something in the DTD to support these new tags?

推荐答案

我的DTD文件似乎已过期.
可以在此处或

It appears that my DTD file was out of date.
A new version can be found here or here.

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