Raw content of Bio::SeqFeature::SimilarityPair
<![CDATA[# $Id: SimilarityPair.pm,v 1.21 2002/12/24 15:15:32 jason Exp $
#
# BioPerl module for Bio::SeqFeature::SimilarityPair
#
# Cared for by Hilmar Lapp <hlapp@gmx.net>
#
# Copyright Hilmar Lapp
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::SeqFeature::SimilarityPair - Sequence feature based on the similarity
of two sequences.
=head1 SYNOPSIS
$sim_pair = Bio::SeqFeature::SimilarityPair->from_searchResult($blastHit);
$sim = $sim_pair->query(); # a Bio::SeqFeature::Similarity object - the query
$sim = $sim_pair->hit(); # dto - the hit.
# some properties for the similarity pair
$expect = $sim_pair->significance();
$score = $sim_pair->score();
$bitscore = $sim_pair->bits();
# this will not write the description for the sequence (only its name)
print $sim_pair->query()->gff_string(), "\n";
=head1 DESCRIPTION
Lightweight similarity search result as a pair of Similarity
features. This class inherits off Bio::SeqFeature::FeaturePair and
therefore implements Bio::SeqFeatureI, whereas the two features of the
pair are descendants of Bio::SeqFeature::Generic, with better support
for representing similarity search results in a cleaner way.
=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 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
=head2 Reporting Bugs
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/
=head1 AUTHOR - Hilmar Lapp
Email hlapp@gmx.net or hilmar.lapp@pharma.novartis.com
Describe contact details here
=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::SeqFeature::SimilarityPair;
use vars qw(@ISA);
use strict;
use Bio::SeqFeature::FeaturePair;
use Bio::SeqFeature::Similarity;
use Bio::SearchIO;
@ISA = qw(Bio::SeqFeature::FeaturePair);
=head2 new
Title : new
Usage : my $similarityPair = new Bio::SeqFeature::SimilarityPair
(-hit => $hit,
-query => $query,
-source => 'blastp');
Function: Initializes a new SimilarityPair object
Returns : Bio::SeqFeature::SimilarityPair
Args : -query => The query in a Feature pair
-hit => (formerly '-subject') the subject/hit in a Feature pair
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
# Hack to deal with the fact that SimilarityPair calls strand()
# which will lead to an error in Bio::Search::HSP::BlastHSP
# because parsing hasn't yet occurred.
# TODO: Remove this when BlastHSP doesn't do lazy parsing.
$self->{'_initializing'} = 1;
my ($primary, $hit, $query, $fea1, $source,$sbjct) =
$self->_rearrange([qw(PRIMARY
HIT
QUERY
FEATURE1
SOURCE
SUBJECT
)],@args);
if( $sbjct ) {
# undeprecated by Jason before 1.1 release
# $self->deprecated("use of -subject deprecated: SimilarityPair now uses 'hit'");
if(! $hit) { $hit = $sbjct }
else {
$self->warn("-hit and -subject were specified, using -hit and ignoring -subject");
}
}
# make sure at least the query feature exists -- this refers to feature1
if($query && ! $fea1) { $self->query( $query); }
else { $self->query('null'); } # call with no args sets a default value for query
$hit && $self->hit($hit);
# the following refer to feature1, which has been ensured to exist
if( defined $primary || ! defined $self->primary_tag) {
$primary = 'similarity' unless defined $primary;
$self->primary_tag($primary);
}
$source && $self->source_tag($source);
$self->strand(0) unless( defined $self->strand() );
$self->{'_initializing'} = 0; # See "Hack" note above
return $self;
}
#
# Everything else is just inherited from SeqFeature::FeaturePair.
#
=head2 query
Title : query
Usage : $query_feature = $obj->query();
$obj->query($query_feature);
Function: The query object for this similarity pair
Returns : Bio::SeqFeature::Similarity
Args : [optional] Bio::SeqFeature::Similarity
See L<Bio::SeqFeature::Similarity>, L<Bio::SeqFeature::FeaturePair>
=cut
sub query {
my ($self, @args) = @_;
my $f = $self->feature1();
if( ! @args || ( !ref($args[0]) && $args[0] eq 'null') ) {
if( ! defined( $f) ) {
@args = Bio::SeqFeature::Similarity->new();
} elsif( ! $f->isa('Bio::SeqFeature::Similarity') &&
$f->isa('Bio::SeqFeatureI') ) {
# a Bio::SeqFeature::Generic was placeholder for feature1
my $newf = new
Bio::SeqFeature::Similarity( -start => $f->start(),
-end => $f->end(),
-strand => $f->strand(),
-primary => $f->primary_tag(),
-source => $f->source_tag(),
-seq_id => $f->seq_id(),
-score => $f->score(),
-frame => $f->frame(),
);
foreach my $tag ( $newf->all_tags ) {
$tag->add_tag($tag, $newf->each_tag($tag));
}
@args = $newf;
} else {
@args = ();
}
}
return $self->feature1(@args);
}
=head2 subject
Title : subject
Usage : $sbjct_feature = $obj->subject();
$obj->subject($sbjct_feature);
Function: Get/Set Subject for a SimilarityPair
Returns : Bio::SeqFeature::Similarity
Args : [optional] Bio::SeqFeature::Similarity
Notes : Deprecated. Use the method 'hit' instead
=cut
sub subject {
my $self = shift;
# $self->deprecated("Method subject deprecated: use hit() instead");
$self->hit(@_);
}
*sbjct = \&subject;
=head2 hit
Title : hit
Usage : $sbjct_feature = $obj->hit();
$obj->hit($sbjct_feature);
Function: Get/Set Hit for a SimilarityPair
Returns : Bio::SeqFeature::Similarity
Args : [optional] Bio::SeqFeature::Similarity
=cut
sub hit {
my ($self, @args) = @_;
my $f = $self->feature2();
if(! @args || (!ref($args[0]) && $args[0] eq 'null') ) {
if( ! defined( $f) ) {
@args = Bio::SeqFeature::Similarity->new();
} elsif( ! $f->isa('Bio::SeqFeature::Similarity') &&
$f->isa('Bio::SeqFeatureI')) {
# a Bio::SeqFeature::Generic was placeholder for feature2
my $newf = new
Bio::SeqFeature::Similarity( -start => $f->start(),
-end => $f->end(),
-strand => $f->strand(),
-primary => $f->primary_tag(),
-source => $f->source_tag(),
-seq_id => $f->seq_id(),
-score => $f->score(),
-frame => $f->frame(),
);
foreach my $tag ( $newf->all_tags ) {
$tag->add_tag($tag, $newf->each_tag($tag));
}
@args = $newf;
}
}
return $self->feature2(@args);
}
=head2 source_tag
Title : source_tag
Usage : $source = $obj->source_tag(); # i.e., program
$obj->source_tag($evalue);
Function: Gets the source tag (program name typically) for a feature
Returns : string
Args : [optional] string
=cut
sub source_tag {
my ($self, @args) = @_;
if(@args) {
$self->hit()->source_tag(@args);
}
return $self->query()->source_tag(@args);
}
=head2 significance
Title : significance
Usage : $evalue = $obj->significance();
$obj->significance($evalue);
Function:
Returns :
Args :
=cut
sub significance {
my ($self, @args) = @_;
if(@args) {
$self->hit()->significance(@args);
}
return $self->query()->significance(@args);
}
=head2 score
Title : score
Usage : $score = $obj->score();
$obj->score($value);
Function:
Returns :
Args :
=cut
sub score {
my ($self, @args) = @_;
if(@args) {
$self->hit()->score(@args);
}
return $self->query()->score(@args);
}
=head2 bits
Title : bits
Usage : $bits = $obj->bits();
$obj->bits($value);
Function:
Returns :
Args :
=cut
sub bits {
my ($self, @args) = @_;
if(@args) {
$self->hit()->bits(@args);
}
return $self->query()->bits(@args);
}
1;
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