[BioRuby] Interesting BLAST 2.2.25+ XML behaviour

[Pjotr Prins]

Something also rather odd. Can you imagine that a basic BLAST
lesson would make it into PLoS Biology?

PLoS Biology states: the journal features works of exceptional
significance, originality, and relevance in all areas of biological
science, from molecules to ecosystems, including works at the
interface of other disciplines, such as chemistry, medicine, and
mathematics. 

Well, so much for that. Check out a copy of the BLAST help page, as
published in PLoS Biology:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3032543/

I checked the date. It is not April 1st. It ticks, however, the
relevance box. But I am not sure about its significance. It is
certainly not original. Where are we heading? Can we start submitting
man pages now?

Pj.

On Tue, May 03, 2011 at 08:31:55AM -0500, Chris Fields wrote:
> Haven't tried this using the latest BLAST+ myself, but it doesn't surprise me too much.  Also agree re: some kind of bug tracking with NCBI; I believe they have an internal one, but it would be nice to have a public interface to it.
> 
> chris
> 
> On May 3, 2011, at 4:24 AM, Peter Cock wrote:
> 
> > Hello all,
> > 
> > I've CC'd the BioPerl, BioRuby, BioJava and Biopython development mailing
> > lists to make sure you're aware of this, but can we continue any discussion
> > on the cross-project open-bio-l mailing list please?
> > 
> > I noticed that recent versions of BLAST are not using a single <iteration>
> > block for each query, which was the historical behaviour and assumed
> > by the Biopython BLAST XML parser. This may be a bug in BLAST.
> > See link below for an example.
> > 
> > Has anyone else noticed this, and has it been reported to the NCBI yet?
> > 
> > Thanks,
> > 
> > Peter
> > 
> > (Not for the first time, I wish there was a public bug tracker for BLAST,
> > or at least a private bug tracker so we could talk about issues with an
> > NCBI assigned reference number.)
> > 
> > ---------- Forwarded message ----------
> > From: Peter Cock <p.j.a.cock at googlemail.com>
> > Date: Wed, Apr 20, 2011 at 6:08 PM
> > Subject: Interesting BLAST 2.2.25+ XML behaviour
> > To: Biopython-Dev Mailing List <biopython-dev at biopython.org>
> > 
> > 
> > Hi all,
> > 
> > Have a look at this XML file from a FASTA vs FASTA search
> > using blastp from  BLAST 2.2.25+ (current release), which
> > is a test file I created for the BLAST+ wrappers in Galaxy:
> > 
> > https://bitbucket.org/galaxy/galaxy-central/src/8eaf07a46623/test-data/blastp_four_human_vs_rhodopsin.xml
> > 
> > I just put it though the Biopython BLAST XML parser, and
> > was surprised not to get four records back (since as you
> > might guess from the filename, there were four queries).
> > 
> > It appears this version of BLAST+ is incrementing the
> > iteration counter for each match... or something like that.
> > 
> > Has anyone else noticed this? I wonder if it is accidental...
> > 
> > Peter
> > 
> > _______________________________________________
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> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
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> 
> 
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