[Biopython-dev] Blast XML Parse Improvements

[Fields, Christopher J]

Yep, true.  Though I don't see it outside the realm of possibility becoming the de facto XML output at some future point.

chris

> On Jul 29, 2015, at 3:44 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> 
> Right, the new "blastxml2" output in BLAST+ 2.2.31 is a whole new format,
> but the existing "blastxml" which Biopython already has a parser for is
> still available as usual via -outfmt 5.
> 
> And that parser ought to work fine with multiple queries.
> 
> Travis, can you post more details? e.g. BLAST+ command line used
> and ideally sample output (on gist.github.com or similar)
> 
> Thanks,
> 
> Peter
> 
> On Wed, Jul 29, 2015 at 6:29 AM, Fields, Christopher J
> <cjfields at illinois.edu> wrote:
>> Keep in mind there are significant changes for BLAST+ XML output in the
>> latest release, not all of them good IMHO.  Peter has a pretty good writeup
>> on this:
>> 
>> http://blastedbio.blogspot.com/2015/07/blast-xml-2-include-trouble.html
>> 
>> chris
>> 
>> On Jul 29, 2015, at 12:21 AM, Wibowo Arindrarto <w.arindrarto at gmail.com>
>> wrote:
>> 
>> Hi Travis,
>> 
>> There hasn't been any new test cases added for BLAST 2.2.30, as I
>> recall. Did you get the same behavior when using Bio.SearchIO to parse
>> it?
>> 
>> Best regards,
>> Bow
>> 
>> On Wed, Jul 29, 2015 at 7:12 AM, Travis Wrightsman <twrig002 at ucr.edu> wrote:
>> 
>> Biopython Devs,
>> 
>> I was trying to parse through a tblastn XML output with multiple queries in
>> the query file and it was generating a BLAST record object for each contig
>> in the subject file instead of each run. Is this the intended behavior or
>> has this not been updated for ncbi tools 2.2.30?
>> 
>> If it needs to be updated or finished, I'm more than happy to rewrite or
>> update some of the code in NCBIXML for the latest version.
>> 
>> -Travis
>> 
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