#
# 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
=head1 NAME
Bio::Search::Result::BlastResult - Blast-specific subclass of Bio::Search::Result::GenericResult
=head1 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 L<Bio::Search::Iteration::IterationI|Bio::Search::Iteration::IterationI>
# for details about working with iterations.
# TODO:
# * Show how to configure a SearchIO stream so that it generates
# BlastResult objects.
=head1 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.
=head1 FEEDBACK
=head2 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 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/
=head1 AUTHOR - Steve Chervitz
Email sac@bioperl.org
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Search::Result::BlastResult;
use strict;
use Bio::Search::BlastStatistics;
use base qw(Bio::Search::Result::GenericResult);
=head2 new
Title : new
Usage : my $obj = Bio::Search::Result::BlastResult->new();
Function: Builds a new Bio::Search::Result::BlastResult object
Returns : Bio::Search::Result::BlastResult
Args : See Bio::Search::Result::GenericResult();
The following parameters are specific to BlastResult:
-iterations => array ref of Bio::Search::Iteration::IterationI objects
-inclusion_threshold => e-value threshold for inclusion in the
PSI-BLAST score matrix model (blastpgp)
=cut
sub new {
my($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;
}
=head2 hits
Title : hits
Usage : my @hits = $result->hits
Function: Returns the available hits for this Result
Returns : Array of L<Bio::Search::Hit::HitI> objects
Args : none
Note : This method overrides L<Bio::Search::Result::GenericResult::hits> to
take into account the possibility of multiple iterations, as occurs
in PSI-BLAST reports.
If there are multiple iterations, all 'new' hits for all iterations
are returned. These are the hits that did not occur in a previous
iteration.
See Also: L<Bio::Search::Result::GenericResult::hits>
=cut
sub hits {
my ($self) = shift;
if ($self->{'_no_iterations'}) {
return $self->SUPER::hits;
}
my @hits = ();
foreach my $it ($self->iterations) {
push @hits, $it->hits;
}
return @hits;
}
=head2 next_hit
Title : next_hit
Usage : while( $hit = $result->next_hit()) { ... }
Function: Returns the next available Hit object, representing potential
matches between the query and various entities from the database.
Returns : a Bio::Search::Hit::HitI object or undef if there are no more.
Args : none
Note : This method overrides L<Bio::Search::Result::GenericResult::next_hit>
to take into account the possibility of multiple iterations, as
occurs in PSI-BLAST reports.
If there are multiple iterations, calling next_hit() traverses the
all of the hits, old and new, for each iteration, calling next_hit()
on each iteration.
See Also: L<Bio::Search::Iteration::GenericIteration::next_hit>
=cut
sub next_hit {
my ($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;
}
=head2 num_hits
Title : num_hits
Usage : my $hitcount= $result->num_hits
Function: returns the number of hits for this query result
Returns : integer
Args : none
Note : This method overrides L<Bio::Search::Result::GenericResult::num_hits>
to take into account the possibility of multiple iterations, as
occurs in PSI-BLAST reports.
If there are multiple iterations, calling num_hits() returns the
number of 'new' hits for each iteration. These are the hits that did
not occur in a previous iteration.
See Also: L<Bio::Search::Result::GenericResult::num_hits>
=cut
sub num_hits{
my ($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 );
}
=head2 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
=cut
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;
}
=head2 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
=cut
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'}};
}
=head2 next_iteration
Title : next_iteration
Usage : while( $it = $result->next_iteration()) { ... }
Function: Returns the next Iteration object, representing all hits
found within a given PSI-Blast iteration.
Returns : a Bio::Search::Iteration::IterationI object or undef if there are no more.
Args : none
=cut
sub next_iteration {
my ($self) = @_;
unless($self->{'_iter_queue_started'}) {
$self->{'_iter_queue'} = [$self->iterations()];
$self->{'_iter_queue_started'} = 1;
}
return shift @{$self->{'_iter_queue'}};
}
=head2 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 $number is not within
range of the number of iterations in this report.
Argument : integer (optional, if not specified get the last iteration)
First iteration = 1
=cut
sub iteration {
my ($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];
}
=head2 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)
=cut
sub num_iterations { shift->{'_iteration_count'} }
# Methods provided for consistency with BPpsilite.pm (now deprecated);
# these are now merely synonyms
=head2 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>.
=cut
sub number_of_iterations { shift->num_iterations }
=head2 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>.
=cut
sub round { shift->iteration(@_) }
=head2 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
=cut
sub iterations {
my $self = shift;
my @its = ();
if( ref($self->{'_iterations'}) =~ /ARRAY/i ) {
@its = @{$self->{'_iterations'}};
}
return @its;
}
=head2 psiblast
Usage : if( $blast->psiblast ) { ... }
Purpose : Set/get a boolean indicator whether or not the report
is a PSI-BLAST report.
Returns : 1 if PSI-BLAST, undef if not.
Argument : 1 (when setting)
=cut
#----------------
sub psiblast {
#----------------
my ($self, $val ) = @_;
if( $val ) {
$self->{'_psiblast'} = 1;
}
return $self->{'_psiblast'};
}
=head2 no_hits_found
Usage : $nohits = $blast->no_hits_found( $iteration_number );
Purpose : Get boolean indicator indicating whether or not any hits
were present in the report.
This is NOT the same as determining the number of hits via
the hits() method, which will return zero hits if there were no
hits in the report or if all hits were filtered out during the parse.
Thus, this method can be used to distinguish these possibilities
for hitless reports generated when filtering.
Returns : Boolean
Argument : (optional) integer indicating the iteration number (PSI-BLAST)
If iteration number is not specified and this is a PSI-BLAST result,
then this method will return true only if all iterations had
no hits found.
=cut
sub no_hits_found {
my ($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;
}
=head2 set_no_hits_found
Usage : $blast->set_no_hits_found( $iteration_number );
Purpose : Set boolean indicator indicating whether or not any hits
were present in the report.
Returns : n/a
Argument : (optional) integer indicating the iteration number (PSI-BLAST)
=cut
sub set_no_hits_found {
my ($self, $round) = @_;
$round ||= 1;
$self->{"_iteration_$round"}->{'_no_hits_found'} = 1;
}
=head2 _next_iteration_index
Title : _next_iteration_index
Usage : private
=cut
sub _next_iteration_index{
my ($self,@args) = @_;
return $self->{'_iteration_index'}++;
}
=head2 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
=cut
sub rewind {
my $self = shift;
$self->SUPER::rewind(@_);
$self->{'_iteration_index'} = 0;
foreach ($self->iterations) {
$_->rewind;
}
}
=head2 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
=cut
sub inclusion_threshold {
my $self = shift;
return $self->{'_inclusion_threshold'};
}
1;