Bio::Search::Result
BlastResult
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Summary
Bio::Search::Result::BlastResult - Blast-specific subclass of Bio::Search::Result::GenericResult
Package variables
No package variables defined.
Included modules
Inherit
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.
Methods
Methods description
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) |
Title : hits
Usage : my @hits = $result->hits
Function: Returns the available hits for this Result
Returns : Array of Bio::Search::Hit::HitI objects
Args : none
Note : 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 |
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 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: Bio::Search::Iteration::GenericIteration::next_hit |
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 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 |
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 |
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 |
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 |
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 |
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) |
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 num_iterations. |
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 iteration. |
Title : iterations
Usage : my @iterations = $result->iterations
Function: Returns the IterationI objects contained within this Result
Returns : Array of Bio::Search::Iteration::IterationI objects
Args : none |
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) |
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) |
Title : _next_iteration_index
Usage : private |
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 |
Title : inclusion_threshold
Usage : my $incl_thresh = $result->inclusion_threshold; (read-only)
Function: Gets the e-value threshold for inclusion in the PSI-BLAST
score matrix model (blastpgp) that was used for generating the report
being parsed.
Returns : number (real) or undef if not a PSI-BLAST report.
Args : none |
Methods code
sub new
{ my($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;
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 {
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'}} | 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;
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;} | General documentation
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
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.
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 | Top |
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _