Bio::SeqFeature SimilarityPair
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Summary
Bio::SeqFeature::SimilarityPair - Sequence feature based on the similarity
of two sequences.
Package variables
No package variables defined.
Included modules
Bio::SearchIO
Bio::SeqFeature::FeaturePair
Bio::SeqFeature::Similarity
Inherit
Bio::SeqFeature::FeaturePair
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";
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.
Methods
bitsDescriptionCode
hitDescriptionCode
newDescriptionCode
queryDescriptionCode
scoreDescriptionCode
significanceDescriptionCode
source_tagDescriptionCode
subjectDescriptionCode
Methods description
bitscode    nextTop
 Title   : bits
Usage : $bits = $obj->bits();
$obj->bits($value);
Function:
Returns :
Args :
hitcodeprevnextTop
 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
newcodeprevnextTop
 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
querycodeprevnextTop
 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 Bio::SeqFeature::Similarity, Bio::SeqFeature::FeaturePair
scorecodeprevnextTop
 Title   : score
Usage : $score = $obj->score();
$obj->score($value);
Function:
Returns :
Args :
significancecodeprevnextTop
 Title   : significance
Usage : $evalue = $obj->significance();
$obj->significance($evalue);
Function:
Returns :
Args :
source_tagcodeprevnextTop
 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
subjectcodeprevnextTop
 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
Methods code
bitsdescriptionprevnextTop
sub bits {
    my ($self, @args) = @_;

    if(@args) {
	$self->hit()->bits(@args);
    }
    return $self->query()->bits(@args);
}

1;
}
hitdescriptionprevnextTop
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 $self->feature2(@args);
}
newdescriptionprevnextTop
sub new {
    my($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 $self; } #
# Everything else is just inherited from SeqFeature::FeaturePair.
#
}
querydescriptionprevnextTop
sub query {
    my ($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 $self->feature1(@args);
}
scoredescriptionprevnextTop
sub score {
    my ($self, @args) = @_;

    if(@args) {
	$self->hit()->score(@args);
    }
    return $self->query()->score(@args);
}
significancedescriptionprevnextTop
sub significance {
    my ($self, @args) = @_;

    if(@args) {
	$self->hit()->significance(@args);
    }
    return $self->query()->significance(@args);
}
source_tagdescriptionprevnextTop
sub source_tag {
    my ($self, @args) = @_;

    if(@args) {
	$self->hit()->source_tag(@args);
    }
    return $self->query()->source_tag(@args);
}
subjectdescriptionprevnextTop
sub subject {
     my $self = shift;
#    $self->deprecated("Method subject deprecated: use hit() instead");
$self->hit(@_); } *sbjct =\& subject;
}
General documentation
FEEDBACKTop
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Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via
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  bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
AUTHOR - Hilmar LappTop
Email hlapp@gmx.net or hilmar.lapp@pharma.novartis.com
Describe contact details here
APPENDIXTop
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _