<p dir="ltr">I recommend asking on their cpp mailing list. It gets very little activity, but the development team always respond quite quickly...</p>
<p dir="ltr"><a href="http://www.ncbi.nlm.nih.gov/toolkit/doc/book/ch_faq/#ch_faq.mailing_lists">http://www.ncbi.nlm.nih.gov/toolkit/doc/book/ch_faq/#ch_faq.mailing_lists</a></p>
<p dir="ltr">Cheers,<br>
Alex</p>
<div class="gmail_quote">On 7 May 2015 01:18, "Fields, Christopher J" <<a href="mailto:cjfields@illinois.edu">cjfields@illinois.edu</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">I agree, it’s worth asking NCBI about this. Now, whether we get an answer or not is another issue…<br>
<br>
chris<br>
<br>
> On May 6, 2015, at 3:44 PM, Peter Cock <<a href="mailto:p.j.a.cock@googlemail.com">p.j.a.cock@googlemail.com</a>> wrote:<br>
><br>
> Hi Travis,<br>
><br>
> I've no idea what the rational is for this bit of the change<br>
> (other than the existing blast XML abuses the <iteration><br>
> tag for multiple queries), but haven't yet tried looking at<br>
> the example output so I'm not panicking yet.<br>
><br>
> However, we may want to lobby the NCBI about this...<br>
><br>
> Peter<br>
><br>
> On Wed, May 6, 2015 at 5:50 PM, Travis Wrightsman <<a href="mailto:twrig002@ucr.edu">twrig002@ucr.edu</a>> wrote:<br>
>> Peter,<br>
>><br>
>> It seems that if support for the original single XML output for multiple<br>
>> queries is dropped then BioPython will need to either stitch together all<br>
>> the XML files using the base Xinclude file or iterate through all the files<br>
>> and concatenate them in an object.<br>
>><br>
>> Does anyone know why NCBI is changing to a multi-file output instead of a<br>
>> single-file output that is easier to work with programmatically? There must<br>
>> be someone or some software suite benefiting from this change and it's not<br>
>> BioPython.<br>
>><br>
>> Travis<br>
>><br>
>> On Wed, May 6, 2015 at 7:49 AM, Peter Cock <<a href="mailto:p.j.a.cock@googlemail.com">p.j.a.cock@googlemail.com</a>><br>
>> wrote:<br>
>>><br>
>>> On Wed, May 6, 2015 at 3:22 PM, Martin Mokrejs<br>
>>> <<a href="mailto:mmokrejs@fold.natur.cuni.cz">mmokrejs@fold.natur.cuni.cz</a>> wrote:<br>
>>>> Hi,<br>
>>>> are you aware of new changes in BLAST's XML format? Time for feedback<br>
>>>> before it emerges. ;-)<br>
>>>><br>
>>>> <a href="ftp://ftp.ncbi.nlm.nih.gov/blast/documents/NEWXML/xml2.pdf" target="_blank">ftp://ftp.ncbi.nlm.nih.gov/blast/documents/NEWXML/xml2.pdf</a><br>
>>>><br>
>>>> Martin<br>
>>><br>
>>> Yes, but thanks for double checking:<br>
>>><br>
>>> <a href="http://lists.open-bio.org/pipermail/biopython-dev/2015-May/020923.html" target="_blank">http://lists.open-bio.org/pipermail/biopython-dev/2015-May/020923.html</a><br>
>>><br>
>>> I'm a little nervous about the idea that BLAST+ will not provide single<br>
>>> (large) XML files for multiple-query searches, and instead appears to<br>
>>> be going to produce one file per query and a manifest xinclude file.<br>
>>><br>
>>> This sounds problematic for things like parsing via stdout.<br>
>>><br>
>>> What have you noticed?<br>
>>><br>
>>> Peter<br>
>>> _______________________________________________<br>
>>> Biopython-dev mailing list<br>
>>> <a href="mailto:Biopython-dev@mailman.open-bio.org">Biopython-dev@mailman.open-bio.org</a><br>
>>> <a href="http://mailman.open-bio.org/mailman/listinfo/biopython-dev" target="_blank">http://mailman.open-bio.org/mailman/listinfo/biopython-dev</a><br>
>><br>
>><br>
> _______________________________________________<br>
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<br>
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