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

[Fields, Christopher J]

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
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>> 
>> 
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