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Bio::Search::Result::BlastResult.3pm

NAME

Bio::Search::Result::BlastResult - Blast-specific subclass of Bio::Search::Result::GenericResult

SYNOPSIS

     # Working with iterations (PSI-BLAST results)
 
     $result->next_iteration();
     $result->num_iterations();
     $result->iteration();
     $result->iterations();
 
 

# See Bio::Search::Result::GenericResult for information about working with Results.

# See Bio::Search::Iteration::IterationI # for details about working with iterations.

# TODO: # * Show how to configure a SearchIO stream so that it generates # BlastResult objects.

DESCRIPTION

This object is a subclass of Bio::Search::Result::GenericResult and provides some operations that facilitate working with BLAST and PSI-BLAST results.

For general information about working with Results, see Bio::Search::Result::GenericResult.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

   http://bugzilla.open-bio.org/
 
 

AUTHOR - Steve Chervitz

Email sac@bioperl.org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

  Title   : new
  Usage   : my $obj = Bio::Search::Result::BlastResult->new();
  Function: Builds a new Bio::Search::Result::BlastResult object
  Returns : Bio::Search::Result::BlastResult
  Args    : See Bio::Search::Result::GenericResult();
            The following parameters are specific to BlastResult:
              -iterations  => array ref of Bio::Search::Iteration::IterationI objects
              -inclusion_threshold => e-value threshold for inclusion in the
                                      PSI-BLAST score matrix model (blastpgp)
 
 

hits

  Title   : hits
  Usage   : my @hits = $result->hits
  Function: Returns the available hits for this Result
  Returns : Array of L<Bio::Search::Hit::HitI> objects
  Args    : none
  Note    : This method overrides L<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: L<Bio::Search::Result::GenericResult::hits>
 
 

next_hit

  Title   : next_hit
  Usage   : while( $hit = $result->next_hit()) { ... }
  Function: Returns the next available Hit object, representing potential
            matches between the query and various entities from the database.
  Returns : a Bio::Search::Hit::HitI object or undef if there are no more.
  Args    : none
  Note    : This method overrides L<Bio::Search::Result::GenericResult::next_hit>
            to take into account the possibility of multiple iterations, as
            occurs in PSI-BLAST reports.
 
            If there are multiple iterations, calling next_hit() traverses the
            all of the hits, old and new, for each iteration, calling next_hit()
            on each iteration.
 
            See Also: L<Bio::Search::Iteration::GenericIteration::next_hit>
 
 

num_hits

  Title   : num_hits
  Usage   : my $hitcount= $result->num_hits
  Function: returns the number of hits for this query result
  Returns : integer
  Args    : none
  Note    : This method overrides L<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: L<Bio::Search::Result::GenericResult::num_hits>
 
 

add_hit

  Title   : add_hit
  Usage   : $report->add_hit($hit)
  Function: Adds a HitI to the stored list of hits
  Returns : Number of HitI currently stored
  Args    : Bio::Search::Hit::HitI
 
 

add_iteration

  Title   : add_iteration
  Usage   : $report->add_iteration($iteration)
  Function: Adds a IterationI to the stored list of iterations
  Returns : Number of IterationI currently stored
  Args    : Bio::Search::Iteration::IterationI
 
 

next_iteration

  Title   : next_iteration
  Usage   : while( $it = $result->next_iteration()) { ... }
  Function: Returns the next Iteration object, representing all hits
            found within a given PSI-Blast iteration.
  Returns : a Bio::Search::Iteration::IterationI object or undef if there are no more.
  Args    : none
 
 

iteration

  Usage     : $iteration = $blast->iteration( $number );
  Purpose   : Get an IterationI object for the specified iteration
              in the search result (PSI-BLAST).
  Returns   : Bio::Search::Iteration::IterationI object
  Throws    : Bio::Root::NoSuchThing exception if $number is not within 
              range of the number of iterations in this report.
  Argument  : integer (optional, if not specified get the last iteration)
              First iteration = 1
 
 

num_iterations

  Usage     : $num_iterations = $blast->num_iterations; 
  Purpose   : Get the number of iterations in the search result (PSI-BLAST).
  Returns   : Total number of iterations in the report
  Argument  : none (read-only)
 
 

number_of_iterations

  Usage     : $num_iterations = $blast->number_of_iterations; 
  Purpose   : Get the number of iterations in the search result (PSI-BLAST).
  Returns   : Total number of iterations in the report
  Argument  : none (read-only)
  Note      : Alias of L<num_iterations>.
 
 

round

  Usage     : $round = $blast->round( $number );
  Purpose   : Get an IterationI object for the specified iteration
              in the search result (PSI-BLAST).
  Returns   : Bio::Search::Iteration::IterationI object
  Throws    : Bio::Root::NoSuchThing exception if $number is not within 
              range of the number of iterations in this report.
  Argument  : integer (optional, if not specified get the last iteration)
              First iteration = 1
  Note      : Alias of L<iteration>.
 
 

iterations

  Title   : iterations
  Usage   : my @iterations = $result->iterations
  Function: Returns the IterationI objects contained within this Result
  Returns : Array of L<Bio::Search::Iteration::IterationI> objects
  Args    : none
 
 

psiblast

  Usage     : if( $blast->psiblast ) { ... }
  Purpose   : Set/get a boolean indicator whether or not the report 
              is a PSI-BLAST report.
  Returns   : 1 if PSI-BLAST, undef if not.
  Argument  : 1 (when setting)
 
 

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.
 
 

set_no_hits_found

  Usage     : $blast->set_no_hits_found( $iteration_number ); 
  Purpose   : Set boolean indicator indicating whether or not any hits
              were present in the report.
  Returns   : n/a
  Argument  : (optional) integer indicating the iteration number (PSI-BLAST)
 
 

_next_iteration_index

  Title   : _next_iteration_index
  Usage   : private
 
 

rewind

  Title   : rewind
  Usage   : $result->rewind;
  Function: Allow one to reset the Iteration iterator to the beginning
            Since this is an in-memory implementation
  Returns : none
  Args    : none
 
 

inclusion_threshold

  Title   : inclusion_threshold
  Usage   : my $incl_thresh = $result->inclusion_threshold; (read-only)
  Function: Gets the e-value threshold for inclusion in the PSI-BLAST 
            score matrix model (blastpgp) that was used for generating the report
            being parsed.
  Returns : number (real) or undef if not a PSI-BLAST report.
  Args    : none