<div dir="ltr"><div><div><div>Hi Peter,<br><br></div>This is me trying to get protein sequences from the protein database. I have a gi code in the variable 'gi' that I pass into the Entrez.efetch function. Specifically, I use:<br><br> handle = Entrez.efetch(db='protein', id=gi, retmode='xml')<br> record = Entrez.read(handle)<br><br></div>Best,<br></div>Lev<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Sep 4, 2015 at 11:12 AM, Peter Cock <span dir="ltr"><<a href="mailto:p.j.a.cock@googlemail.com" target="_blank">p.j.a.cock@googlemail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Lev,<br>
<br>
Which database was this with? Each has somewhat different XML behaviour./<br>
<br>
The NCBI have been quite good about versioning the DTD files -<br>
normally they add new files rather than edit an existing DTD file. So<br>
unless you've had a warning from Biopython there should be no reason<br>
to download a new DTD file.<br>
<br>
Peter<br>
<div><div class="h5"><br>
On Fri, Sep 4, 2015 at 3:44 PM, Lev Tsypin <<a href="mailto:ltsypin@uchicago.edu">ltsypin@uchicago.edu</a>> wrote:<br>
> Hi all,<br>
><br>
> I am encountering this error when using Bio.Entrez:<br>
><br>
> Bio.Entrez.Parser.ValidationError: Failed to find tag 'Error' in the DTD. To<br>
> skip all tags that are not represented in the DTD, please call<br>
> Bio.Entrez.read or Bio.Entrez.parse with validate=False.<br>
><br>
> I've found a discussion of the same issue from about a year ago, so I figure<br>
> the the NCBI updated their DTD file in a strange way. I found several<br>
> solutions: would you recommend that I download the new DTD file into my<br>
> local copy of Biopython or run Entrez.read with validate=False?<br>
><br>
> Best regards,<br>
> Lev Tsypin<br>
><br>
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