[Biopython-dev] [Biopython] Upcoming NCBI BLAST XML2 format

[Alex Leach]

I recommend asking on their cpp mailing list. It gets very little activity,
but the development team always respond quite quickly...

http://www.ncbi.nlm.nih.gov/toolkit/doc/book/ch_faq/#ch_faq.mailing_lists

Cheers,
Alex
On 7 May 2015 01:18, "Fields, Christopher J" <cjfields at illinois.edu> wrote:

> I agree, it’s worth asking NCBI about this.  Now, whether we get an answer
> or not is another issue…
>
> chris
>
> > On May 6, 2015, at 3:44 PM, Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
> >
> > Hi Travis,
> >
> > I've no idea what the rational is for this bit of the change
> > (other than the existing blast XML abuses the <iteration>
> > tag for multiple queries), but haven't yet tried looking at
> > the example output so I'm not panicking yet.
> >
> > However, we may want to lobby the NCBI about this...
> >
> > Peter
> >
> > On Wed, May 6, 2015 at 5:50 PM, Travis Wrightsman <twrig002 at ucr.edu>
> wrote:
> >> Peter,
> >>
> >> It seems that if support for the original single XML output for multiple
> >> queries is dropped then BioPython will need to either stitch together
> all
> >> the XML files using the base Xinclude file or iterate through all the
> files
> >> and concatenate them in an object.
> >>
> >> Does anyone know why NCBI is changing to a multi-file output instead of
> a
> >> single-file output that is easier to work with programmatically? There
> must
> >> be someone or some software suite benefiting from this change and it's
> not
> >> BioPython.
> >>
> >> Travis
> >>
> >> On Wed, May 6, 2015 at 7:49 AM, Peter Cock <p.j.a.cock at googlemail.com>
> >> wrote:
> >>>
> >>> On Wed, May 6, 2015 at 3:22 PM, Martin Mokrejs
> >>> <mmokrejs at fold.natur.cuni.cz> wrote:
> >>>> Hi,
> >>>>  are you aware of new changes in BLAST's XML format? Time for feedback
> >>>> before it emerges. ;-)
> >>>>
> >>>> ftp://ftp.ncbi.nlm.nih.gov/blast/documents/NEWXML/xml2.pdf
> >>>>
> >>>> Martin
> >>>
> >>> Yes, but thanks for double checking:
> >>>
> >>> http://lists.open-bio.org/pipermail/biopython-dev/2015-May/020923.html
> >>>
> >>> I'm a little nervous about the idea that BLAST+ will not provide single
> >>> (large) XML files for multiple-query searches, and instead appears to
> >>> be going to produce one file per query and a manifest xinclude file.
> >>>
> >>> This sounds problematic for things like parsing via stdout.
> >>>
> >>> What have you noticed?
> >>>
> >>> Peter
> >>> _______________________________________________
> >>> Biopython-dev mailing list
> >>> Biopython-dev at mailman.open-bio.org
> >>> http://mailman.open-bio.org/mailman/listinfo/biopython-dev
> >>
> >>
> > _______________________________________________
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> > http://mailman.open-bio.org/mailman/listinfo/biopython
>
>
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