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

Peter Cock p.j.a.cock at googlemail.com
Wed May 6 20:44:34 UTC 2015

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...


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
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