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

BioPerl documentation Contained in the BioPerl distribution.

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NAME

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

SYNOPSIS

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    # 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

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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

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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:

  https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Steve Chervitz

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Email sac@bioperl.org

APPENDIX

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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
BioPerl documentation Contained in the BioPerl distribution. 
#
# BioPerl module for Bio::Search::Result::BlastResult
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Steve Chervitz <sac@bioperl.org>
#
# Copyright Steve Chervitz
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code



# Let the code begin...


package Bio::Search::Result::BlastResult;
use strict;

use Bio::Search::BlastStatistics;

use base qw(Bio::Search::Result::GenericResult);


sub new {
  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);

  $self->{'_iterations'} = [];
  $self->{'_iteration_index'} = 0;
  $self->{'_iteration_count'} = 0;

  my( $iters, $ithresh ) = $self->_rearrange([qw(ITERATIONS
                                                 INCLUSION_THRESHOLD)],@args);

  $self->{'_inclusion_threshold'} = $ithresh;  # This is a read-only variable

  if( defined $iters  ) {
      $self->throw("Must define arrayref of Iterations when initializing a $class\n") unless ref($iters) =~ /array/i;

      foreach my $i ( @{$iters} ) {
          $self->add_iteration($i);
      }
  } 
  else {
      # This shouldn't get called with the new SearchIO::blast.
      print STDERR "BlastResult::new(): Not adding iterations.\n";
      $self->{'_no_iterations'} = 1;
  }

  return $self;
}



sub hits {
   my ($self) = shift;
   if ($self->{'_no_iterations'}) {
       return $self->SUPER::hits;
   }
   my @hits = ();
   foreach my $it ($self->iterations) {
       push @hits, $it->hits;
   }
   return @hits;
}


sub next_hit {
    my ($self,@args) = @_;
    if ($self->{'_no_iterations'}) {
        return $self->SUPER::next_hit(@args);
    }

    my $iter_index;
    if (not defined $self->{'_last_hit'}) {
        $iter_index = $self->{'_iter_index'} = $self->_next_iteration_index;
    } else {
        $iter_index = $self->{'_iter_index'};
    }

    return if $iter_index >= scalar @{$self->{'_iterations'}};

    my $it = $self->{'_iterations'}->[$iter_index];
    my $hit = $self->{'_last_hit'} = $it->next_hit;

    return defined($hit) ? $hit : $self->next_hit;
}



sub num_hits{
   my ($self) = shift;
   if ($self->{'_no_iterations'}) {
       return $self->SUPER::num_hits;
   }
   if (not defined $self->{'_iterations'}) {
       $self->throw("Can't get Hits: data not collected.");
    }
    return scalar( $self->hits );
}


sub add_hit {
    my ($self,$hit) = @_;
    my $iter = $self->iteration;
    if( $hit->isa('Bio::Search::Hit::HitI') ) { 
	return $iter->add_hit(-hit => $hit);
    } else { 
        $self->throw("Passed in a " .ref($hit). 
                     " as a Iteration which is not a Bio::Search::Hit::HitI.");
    }
    return $iter->num_hits;
}


sub add_iteration {
    my ($self,$i) = @_;
    if( $i->isa('Bio::Search::Iteration::IterationI') ) { 
        push @{$self->{'_iterations'}}, $i;
        $self->{'_iteration_count'}++;
    } else { 
        $self->throw("Passed in a " .ref($i). 
                     " as a Iteration which is not a Bio::Search::Iteration::IterationI.");
    }
    return scalar @{$self->{'_iterations'}};
}



sub next_iteration {
    my ($self) = @_;

   unless($self->{'_iter_queue_started'}) {
       $self->{'_iter_queue'} = [$self->iterations()];
       $self->{'_iter_queue_started'} = 1;
   }
   return shift @{$self->{'_iter_queue'}};
}


sub iteration {
    my ($self,$num) = @_;
    $num = scalar @{$self->{'_iterations'}} unless defined $num;
    unless ($num >= 1 and $num <= scalar $self->{'_iteration_count'}) {
        $self->throw(-class=>'Bio::Root::NoSuchThing',
                     -text=>"No such iteration number: $num. Valid range=1-$self->{'_iteration_count'}",
                     -value=>$num);
    }
    return $self->{'_iterations'}->[$num-1];
}


sub num_iterations { shift->{'_iteration_count'} }

# Methods provided for consistency with BPpsilite.pm (now deprecated);
# these are now merely synonyms


sub number_of_iterations { shift->num_iterations }


sub round { shift->iteration(@_) }



sub iterations { 
    my $self = shift;
    my @its = ();
    if( ref($self->{'_iterations'}) =~ /ARRAY/i ) {
       @its = @{$self->{'_iterations'}};
    }
    return @its;
}


#----------------
sub psiblast {
#----------------
    my ($self, $val ) = @_;
    if( $val ) {
        $self->{'_psiblast'} = 1;
    }
    return $self->{'_psiblast'};
}



sub no_hits_found {
    my ($self, $round) = @_;

    my $result = 0;   # final return value of this method.
    # Watch the double negative! 
    # result = 0 means "yes hits were found"
    # result = 1 means "no hits were found" (for the indicated iteration or all iterations)

    # If a iteration was not specified and there were multiple iterations,
    # this method should return true only if all iterations had no hits found.
    if( not defined $round ) {
        if( $self->{'_iterations'} > 1) {
            $result = 1;
            foreach my $i( 1..$self->{'_iterations'} ) {
                if( not defined $self->{"_iteration_$i"}->{'_no_hits_found'} ) {
                    $result = 0;
                    last;
                }
            }
        }
        else {
            $result = $self->{"_iteration_1"}->{'_no_hits_found'};
        }
    }
    else {
        $result = $self->{"_iteration_$round"}->{'_no_hits_found'};
    }

    return $result;
}



sub set_no_hits_found {
    my ($self, $round) = @_;
    $round ||= 1;
    $self->{"_iteration_$round"}->{'_no_hits_found'} = 1;
}


sub _next_iteration_index{
   my ($self,@args) = @_;
   return $self->{'_iteration_index'}++;
}



sub rewind {
   my $self = shift;
   $self->SUPER::rewind(@_);
   $self->{'_iteration_index'} = 0;
   foreach ($self->iterations) {
       $_->rewind;
   }
}



sub inclusion_threshold {
    my $self = shift;
    return $self->{'_inclusion_threshold'};
}

1;