Summary

Bio::Search::Result::BlastResult - A top-level BLAST Report object

Package variables

Included modules

Inherit

Bio::Root::Root Bio::Search::Result::ResultI

Synopsis

The construction of BlastResult objects is performed by
by the Bio::SearchIO::psiblast parser.
Therefore, you do not need to
use Bio::Search::Result::BlastResult) directly. If you need to construct
BlastHits directly, see the new() function for details.
For Bio::SearchIO BLAST parsing usage examples, see the
examples/search-blast directory of the Bioperl distribution.

Description

This module supports BLAST versions 1.x and 2.x, gapped and ungapped,
and PSI-BLAST.

Methods

Methods description

 Usage     : $blastdb = $result->analyis_subject();
 Purpose   : Get a Bio::Search::DatabaseI object containing
             information about the database used in the BLAST analysis.
 Returns   : Bio::Search::DatabaseI object.
 Argument  : n/a

 Title   : next_feature
 Usage   : while( my $feat = $blast_result->next_feature ) { # do something }
 Function: Returns the next feature available in the analysis result, or
           undef if there are no more features.
 Example :
 Returns : A Bio::SeqFeatureI compliant object, in this case, 
           each Bio::Search::HSP::BlastHSP object within each BlastHit.
 Args    : None

 Title   : available_parameters
 Usage   : my @params = $report->available_paramters
 Function: Returns the names of the available parameters
 Returns : Return list of available parameters used for this report
 Args    : none

 Title   : get_parameter
 Usage   : my $gap_ext = $report->get_parameter('gapext')
 Function: Returns the value for a specific parameter used
           when running this report
 Returns : string
 Args    : name of parameter (string)

 Title   : get_statistic
 Usage   : my $gap_ext = $report->get_statistic('kappa')
 Function: Returns the value for a specific statistic available 
           from this report
 Returns : string
 Args    : name of statistic (string)

 Title   : available_statistics
 Usage   : my @statnames = $report->available_statistics
 Function: Returns the names of the available statistics
 Returns : Return list of available statistics used for this report
 Args    : none

 Title   : to_string
 Usage   : print $blast->to_string;
 Function: Returns a string representation for the Blast result. 
           Primarily intended for debugging purposes.
 Example : see usage
 Returns : A string of the form:
           [BlastResult]  query=  db=

 Title   : database_entries
 Usage   : $num_entries = $result->database_entries()
 Function: Used to obtain the number of entries contained in the database.
 Returns : a scalar integer representing the number of entities in the database
           or undef if the information was not available.
 Args    : [optional] new integer for the number of sequence entries in the db

 Title   : database_letters
 Usage   : $size = $result->database_letters()
 Function: Used to obtain the size of database that was searched against.
 Returns : a scalar integer (units specific to algorithm, but probably the
           total number of residues in the database, if available) or undef if
           the information was not available to the Processor object.
 Args    : [optional] new scalar integer for number of letters in db

 Usage     : $blast->add_hit( $hit );
 Purpose   : Adds a hit object to the collection of hits in this BLAST result.
 Returns   : n/a
 Argument  : A Bio::Search::Hit::HitI object
 Comments  : For PSI-BLAST, hits from all iterations are lumped together.
             For any given hit, you can determine the iteration in which it was
             found by checking $hit->iteration().

 Usage     : $blast->is_signif();
 Purpose   : Determine if the BLAST report contains significant hits.
 Returns   : Boolean
 Argument  : n/a
 Comments  : BLAST reports without significant hits but with defined
           : significance criteria will throw exceptions during construction.
           : This obviates the need to check significant() for
           : such objects.

 Usage     : $blast_object->matrix();
 Purpose   : Get the name of the scoring matrix used.
           : This is extracted from the report.
 Argument  : n/a
 Returns   : string or undef if not defined
 Comments  : TODO: Deprecate this and implement get_parameter('matrix').

 Usage     : @stats = $blast_result->raw_statistics();
 Purpose   : Get the raw, unparsed statistical parameter section of the Blast report.
             This is the section at the end after the last HSP alignment.
 Argument  : n/a
 Returns   : Array of strings

 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.

 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)

 Usage     : $num_iterations = $blast->iterations;  (get)
             $blast->iterations($num_iterations);   (set)
 Purpose   : Set/get the number of iterations in the Blast Report (PSI-BLAST).
 Returns   : Total number of iterations in the report
 Argument  : integer  (when setting)

 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)

Methods code

sub new {

#----------------
    my ($class, @args) = @_; 
    my $self = $class->SUPER::new(@args);
    return $self;

}

sub next_hit {

#----------------
    my ($self) = @_;
    
    unless(defined $self->{'_hit_queue'}) {	
        $self->{'_hit_queue'} = [$self->hits()];	
    }
    
    shift @{$self->{'_hit_queue'}};

}

sub query_name {

#----------------
    my $self = shift;
    if (@_) { 
        my $name = shift;
        $name =~ s/^\s+|(\s+|,)$//g;
        $self->{'_query_name'} = $name;
    }
    return $self->{'_query_name'};

}

sub query_length {

#----------------
    my $self = shift;
    if(@_) { $self->{'_query_length'} = shift; }
    return $self->{'_query_length'};

}

sub query_description {

#----------------
    my $self = shift;
    if(@_) { 
        my $desc = shift;
        defined $desc && $desc =~ s/(^\s+|\s+$)//g;
        # Remove duplicated ID at beginning of description string
        defined $desc && $desc =~ s/^$self->{'_query_name'}//o;
        $self->{'_query_query_desc'} = $desc || '';
    }
    return $self->{'_query_query_desc'};

}

sub analysis_method {

 #----------------
    my ($self, $method) = @_;  
    if($method ) {
      if( $method =~ /blast/i) {
	$self->{'_analysis_prog'} = $method;
      } else {
	$self->throw("method $method not supported in " . ref($self));
      }
    }
    return $self->{'_analysis_prog'};

}

sub analysis_method_version {

#----------------
    my ($self, $version) = @_; 
    if($version) {
	$self->{'_analysis_progVersion'} = $version;
    }
    return $self->{'_analysis_progVersion'};

}

sub analysis_query {

#----------------

    my ($self) = @_;
    if(not defined $self->{'_analysis_query'}) {
        require Bio::PrimarySeq;
        my $moltype = $self->analysis_method =~ /blastp|tblastn/i ? 'protein' : 'dna';
	$self->{'_analysis_query'} =  Bio::PrimarySeq->new( -display_id => $self->query_name,
                                                            -desc => $self->query_description,
                                                            -moltype => $moltype
                                                          );
        $self->{'_analysis_query'}->length( $self->query_length );
    }
    return $self->{'_analysis_query'};

}

sub analysis_subject {

 #---------------
    my ($self, $blastdb) = @_; 
    if($blastdb) {
        if( ref $blastdb and $blastdb->isa('Bio::Search::DatabaseI')) {
            $self->{'_analysis_sbjct'} = $blastdb;
        }
        else {
            $self->throw(-class =>'Bio::Root::BadParameter',
                         -text => "Can't set BlastDB: not a Bio::Search::DatabaseI $blastdb"
                         );
        }
    }
    return $self->{'_analysis_sbjct'};

}

sub next_feature {

#---------------
   my ($self) = @_;
   my ($hit, $hsp);
   $hit = $self->{'_current_hit'};
   unless( defined $hit ) {
       $hit = $self->{'_current_hit'} = $self->next_hit;
       return undef unless defined $hit;
   }
   $hsp = $hit->next_hsp;
   unless( defined $hsp ) {
       $self->{'_current_hit'} = undef;
       return $self->next_feature;
   }
   return $hsp || undef;

}

sub algorithm {

 shift->analysis_method( @_ );

}

sub algorithm_version {

 shift->analysis_method_version( @_ );

}

sub available_parameters {

    return ();

}

sub get_parameter {

    return '';

}

sub get_statistic {

    return '';

}

sub available_statistics {

    return ();

}

sub to_string {

#---------------
    my $self = shift;
    my $str = "[BlastResult] " . $self->analysis_method . " query=" . $self->query_name . " " . $self->query_description .", db=" . $self->database_name;
    return $str;

}

sub database_name {

#---------------
    my $self = shift;
    my $dbname = '';
    if( ref $self->analysis_subject) {
      $dbname = $self->analysis_subject->name;
    } 
    return $dbname;

}

sub database_entries {

#---------------
    my $self = shift;
    my $dbentries = '';
    if( ref $self->analysis_subject) {
      $dbentries = $self->analysis_subject->entries;
    } 
    return $dbentries;

}

sub database_letters {

#---------------
    my $self = shift;
    my $dbletters = '';
    if( ref $self->analysis_subject) {
      $dbletters = $self->analysis_subject->letters;
    } 
    return $dbletters;

}

sub hits {

#---------------
    my $self = shift;
    my @hits = ();
    if( ref $self->{'_hits'}) {
        @hits = @{$self->{'_hits'}};
    }
    return @hits;

}

sub add_hit {

#---------------
    my ($self, $hit) = @_;
    my $add_it = 1;
    unless( ref $hit and $hit->isa('Bio::Search::Hit::HitI')) {
        $add_it = 0;
        $self->throw(-class =>'Bio::Root::BadParameter',
                     -text => "Can't add hit: not a Bio::Search::Hit::HitI: $hit"
                    );
    }

    # Avoid adding duplicate hits if we're doing multiple iterations (PSI-BLAST)
#    if( $self->iterations > 1 ) {
#        my $hit_name = $hit->name;
#        if( grep $hit_name eq $_, @{$self->{'_hit_names'}}) {
#            $add_it = 0;
#        }
#    }

    if( $add_it ) {
        push @{$self->{'_hits'}}, $hit;
        push @{$self->{'_hit_names'}}, $hit->name;
    }

}

sub is_signif {

 my $self = shift; return $self->{'_is_significant'};

}

sub matrix {

 #------------
    my $self = shift; 
    if(@_) {
         $self->{'_matrix'} = shift;
    }
    $self->{'_matrix'};

}

sub raw_statistics {

 #------------
    my $self = shift; 
    if(@_) {
	my $params = shift;
	if( ref $params eq 'ARRAY') {
	    $self->{'_raw_statistics'} = $params;
	}
	else {
            $self->throw(-class =>'Bio::Root::BadParameter',
                         -text => "Can't set statistical params: not an ARRAY ref: $params"
                         );
        }
    }
    if(not defined $self->{'_raw_statistics'}) {
	$self->{'_raw_statistics'} = [];
    }

    @{$self->{'_raw_statistics'}};

}

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 iterations {

#----------------
    my ($self, $num ) = @_;
    if( defined $num ) {
        $self->{'_iterations'} = $num;
    }
    return $self->{'_iterations'};

}

sub psiblast {

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

}

General documentation

Bio::Search::Result::BlastResult.pm is a concrete class that inherits from Bio::Root::Root and Bio::Search::Result::ResultI. It relies on two other modules:
    Encapsulates a single a single BLAST hit.
    Provides an interface to a blast database metadata.

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

    bioperl-l@bioperl.org              - General discussion
    http://bio.perl.org/MailList.html  - About the mailing lists

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

    bioperl-bugs@bio.perl.org                   
    http://bugzilla.bioperl.org/

Steve Chervitz <sac@bioperl.org>
See the FEEDBACK section for where to send bug reports and comments.

This software was originally developed in the Department of Genetics
at Stanford University. I would also like to acknowledge my
colleagues at Affymetrix for useful feedback.

Copyright (c) 2001 Steve Chervitz. All Rights Reserved.

This software is provided "as is" without warranty of any kind.

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