[Bioperl-l] blastxml interation

Chris Fields cjfields at uiuc.edu
Wed Jun 6 20:51:00 EDT 2007


Joshua,

Just to make sure there is no confusion, do you mean a  
Bio::Search::Iteration::IterationI-based object?  The iteration tags  
have multiple meanings apparently in BLAST XML output (multiple  
queries, multiple PSI-BLAST iterations).  The current  
SearchIO::blastxml parser returns multiple  
Bio::Search::Result::BlastResult objects based on the iterations, so  
PSI-BLAST output is treated as multiple BLAST reports regardless  
(i.e. no Iteration objects).  This is something I want to rectify but  
it may not be a easy fix.

chris

On Jun 6, 2007, at 5:18 PM, David Messina wrote:

> I think you want to look at the hits(), num_hits() and no_hits_found
> () methods. There is a private method _next_iteration_index() which
> should do what you asked for, but num_hits() looks like the better  
> way.
>
> By the way, hits() and num_hits() are listed on the Deobfuscator as
> having no documentation. This (as the below shows) is incorrect and
> is due to some nonstandard formatting issues which I will correct.
> _next_iteration_index() isn't listed on the Deobfuscator because it's
> a private method.
>
>
> Hope this helps!
> Dave
>
>
> hits()
>
> This method overrides Bio::Search::Result::GenericResult::hits to take
> into account the possibility of multiple iterations, as occurs in PSI-
> BLAST reports.
> If there are multiple iterations, all 'new' hits for all iterations
> are returned.
> These are the hits that did not occur in a previous iteration.
> See Also: Bio::Search::Result::GenericResult::hits
>
> num_hits()
>
> This method overrides Bio::Search::Result::GenericResult::num_hits to
> take
> into account the possibility of multiple iterations, as occurs in PSI-
> BLAST reports.
> If there are multiple iterations, calling num_hits() returns the
> number of
> 'new' hits for each iteration. These are the hits that did not occur
> in a previous iteration.
> See Also: Bio::Search::Result::GenericResult::num_hits
>
> no_hits_found()
>
>   Usage     : $nohits = $blast->no_hits_found( $iteration_number );
>   Purpose   : Get boolean indicator indicating whether or not any hits
>               were present in the report.
>               This is NOT the same as determining the number of  
> hits via
>               the hits() method, which will return zero hits if there
> were no
>               hits in the report or if all hits were filtered out
> during the parse.
>
>               Thus, this method can be used to distinguish these
> possibilities
>               for hitless reports generated when filtering.
>
>   Returns   : Boolean
>   Argument  : (optional) integer indicating the iteration number (PSI-
> BLAST)
>               If iteration number is not specified and this is a PSI-
> BLAST result,
>               then this method will return true only if all
> iterations had
>               no hits found.
>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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