[Biopython] [eFetch] doesn't work with NLMcatalog

[Lenna Peterson]

The problem is that the DOCTYPE is missing from the XML file.

For example, a nucleotide XML file begins like this:

<?xml version="1.0"?>
 <!DOCTYPE GBSet PUBLIC "-//NCBI//NCBI GBSeq/EN" "
http://www.ncbi.nlm.nih.gov/dtd/NCBI_GBSeq.dtd">
 <GBSet>

As far as I can tell, this is the appropriate DTD:
http://www.nlm.nih.gov/databases/dtd/nlmcatalogrecordset_150101.dtd

However, because the DTD is not specified in the file, the parser does not
know where to find it.

Cheers,

Lenna

On Mon, Dec 7, 2015 at 2:03 PM, <c.buhtz at posteo.jp> wrote:

> See the attachment for the xml-file that gives h.read() back.
> --
> GnuPGP-Key ID 0751A8EC
>
> _______________________________________________
> Biopython mailing list  -  Biopython at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20151207/fd2bc2bc/attachment.html>