[Bioperl-l] blastxml interation

David Messina dmessina at wustl.edu
Wed Jun 6 18:18:26 EDT 2007


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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