[Biopython-dev] Blast XML Parse Improvements

[Peter Cock]

Right, the new "blastxml2" output in BLAST+ 2.2.31 is a whole new format,
but the existing "blastxml" which Biopython already has a parser for is
still available as usual via -outfmt 5.

And that parser ought to work fine with multiple queries.

Travis, can you post more details? e.g. BLAST+ command line used
and ideally sample output (on gist.github.com or similar)

Thanks,

Peter

On Wed, Jul 29, 2015 at 6:29 AM, Fields, Christopher J
<cjfields at illinois.edu> wrote:
> Keep in mind there are significant changes for BLAST+ XML output in the
> latest release, not all of them good IMHO.  Peter has a pretty good writeup
> on this:
>
> http://blastedbio.blogspot.com/2015/07/blast-xml-2-include-trouble.html
>
> chris
>
> On Jul 29, 2015, at 12:21 AM, Wibowo Arindrarto <w.arindrarto at gmail.com>
> wrote:
>
> Hi Travis,
>
> There hasn't been any new test cases added for BLAST 2.2.30, as I
> recall. Did you get the same behavior when using Bio.SearchIO to parse
> it?
>
> Best regards,
> Bow
>
> On Wed, Jul 29, 2015 at 7:12 AM, Travis Wrightsman <twrig002 at ucr.edu> wrote:
>
> Biopython Devs,
>
> I was trying to parse through a tblastn XML output with multiple queries in
> the query file and it was generating a BLAST record object for each contig
> in the subject file instead of each run. Is this the intended behavior or
> has this not been updated for ncbi tools 2.2.30?
>
> If it needs to be updated or finished, I'm more than happy to rewrite or
> update some of the code in NCBIXML for the latest version.
>
> -Travis
>
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython-dev
>
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython-dev
>
>
>
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython-dev