[Biopython-dev] Blast XML Parse Improvements

[Travis Wrightsman]

Peter and others,

Here is the gist: https://gist.github.com/twrightsman/a94c66016692fd4295be

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.

-Travis

On Wed, Jul 29, 2015 at 1:44 AM, Peter Cock <p.j.a.cock at googlemail.com>
wrote:

> 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
> >
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