<div dir="ltr">Peter and others,<div><br></div><div>Here is the gist: <a href="https://gist.github.com/twrightsman/a94c66016692fd4295be">https://gist.github.com/twrightsman/a94c66016692fd4295be</a></div><div><br></div><div>The xml output shows the tool version and I included my shell commands used to get the results; it is still using the "current" BLAST XML format with iteration blocks.</div><div><br></div><div>-Travis</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Jul 29, 2015 at 1:44 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">Right, the new "blastxml2" output in BLAST+ 2.2.31 is a whole new format,<br>
but the existing "blastxml" which Biopython already has a parser for is<br>
still available as usual via -outfmt 5.<br>
<br>
And that parser ought to work fine with multiple queries.<br>
<br>
Travis, can you post more details? e.g. BLAST+ command line used<br>
and ideally sample output (on <a href="http://gist.github.com" rel="noreferrer" target="_blank">gist.github.com</a> or similar)<br>
<br>
Thanks,<br>
<br>
Peter<br>
<span class=""><br>
On Wed, Jul 29, 2015 at 6:29 AM, Fields, Christopher J<br>
<<a href="mailto:cjfields@illinois.edu">cjfields@illinois.edu</a>> wrote:<br>
> Keep in mind there are significant changes for BLAST+ XML output in the<br>
> latest release, not all of them good IMHO. Peter has a pretty good writeup<br>
> on this:<br>
><br>
> <a href="http://blastedbio.blogspot.com/2015/07/blast-xml-2-include-trouble.html" rel="noreferrer" target="_blank">http://blastedbio.blogspot.com/2015/07/blast-xml-2-include-trouble.html</a><br>
><br>
</span>> chris<br>
><br>
> On Jul 29, 2015, at 12:21 AM, Wibowo Arindrarto <<a href="mailto:w.arindrarto@gmail.com">w.arindrarto@gmail.com</a>><br>
<span class="">> wrote:<br>
><br>
> Hi Travis,<br>
><br>
> There hasn't been any new test cases added for BLAST 2.2.30, as I<br>
> recall. Did you get the same behavior when using Bio.SearchIO to parse<br>
> it?<br>
><br>
> Best regards,<br>
> Bow<br>
><br>
</span><span class="">> On Wed, Jul 29, 2015 at 7:12 AM, Travis Wrightsman <<a href="mailto:twrig002@ucr.edu">twrig002@ucr.edu</a>> wrote:<br>
><br>
> Biopython Devs,<br>
><br>
> I was trying to parse through a tblastn XML output with multiple queries in<br>
> the query file and it was generating a BLAST record object for each contig<br>
> in the subject file instead of each run. Is this the intended behavior or<br>
> has this not been updated for ncbi tools 2.2.30?<br>
><br>
> If it needs to be updated or finished, I'm more than happy to rewrite or<br>
> update some of the code in NCBIXML for the latest version.<br>
><br>
> -Travis<br>
><br>
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