[Biopython] [Biopython-dev] Upcoming NCBI BLAST XML2 format
Fields, Christopher J
cjfields at illinois.edu
Thu May 7 00:14:13 UTC 2015
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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