[Biopython-dev] Fwd: Blast XML Parse Improvements

[Travis Wrightsman]

Forgot to reply all, see below. Issue Resolved!

Travis Wrightsman

Begin forwarded message:

> From: Travis Wrightsman <twrig002 at ucr.edu>
> Date: July 29, 2015 at 12:32:08 PM PDT
> To: Peter Cock <p.j.a.cock at googlemail.com>
> Subject: Re: [Biopython-dev] Blast XML Parse Improvements
> 
> That is an unfortunately labeled feature, hopefully NCBI will implement a subject-like feature that works the way we expect it to.
> 
> Thank you for the clarification!
> 
> Travis Wrightsman
> 
>> On Jul 29, 2015, at 11:26 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>> 
>> Hi Travis,
>> 
>> This is an NCBI "feature", not a Biopython bug.
>> 
>> Using -subject means BLAST does lots of pairwise comparisons,
>> so you get lots of iteration blocks in the XML. To get the results
>> you probably want (and meaningful e-values), first make a BLAST
>> database. See:
>> 
>> http://blastedbio.blogspot.co.uk/2012/05/blast-ingoring-search-space-size-for-e.html
>> 
>> Regards,
>> 
>> Peter
>> 
>>> On Wed, Jul 29, 2015 at 5:19 PM, Travis Wrightsman <twrig002 at ucr.edu> wrote:
>>> Peter and others,
>>> 
>>> Here is the gist: https://gist.github.com/twrightsman/a94c66016692fd4295be
>>> 
>>> The xml output shows the tool version and I included my shell commands used
>>> to get the results; it is still using the "current" BLAST XML format with
>>> iteration blocks.
>>> 
>>> -Travis
>>> 
>>> On Wed, Jul 29, 2015 at 1:44 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
>>>>> 
>>>>> _______________________________________________
>>>>> Biopython-dev mailing list
>>>>> Biopython-dev at mailman.open-bio.org
>>>>> http://mailman.open-bio.org/mailman/listinfo/biopython-dev
>>>>> 
>>>>> _______________________________________________
>>>>> Biopython-dev mailing list
>>>>> Biopython-dev at mailman.open-bio.org
>>>>> http://mailman.open-bio.org/mailman/listinfo/biopython-dev
>>>>> 
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> Biopython-dev mailing list
>>>>> Biopython-dev at mailman.open-bio.org
>>>>> http://mailman.open-bio.org/mailman/listinfo/biopython-dev
>>>> _______________________________________________
>>>> Biopython-dev mailing list
>>>> Biopython-dev at mailman.open-bio.org
>>>> http://mailman.open-bio.org/mailman/listinfo/biopython-dev
>>> 
>>> 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biopython-dev/attachments/20150730/dee55a6c/attachment.html>