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Summary

Bio::Tools::Sim4::Exon - A single exon determined by an alignment

Package variables

Included modules

Inherit

Bio::SeqFeature::SimilarityPair

Synopsis

  # See Bio::Tools::Sim4::Results for a description of the context.

  # an instance of this class is-a Bio::SeqFeature::SimilarityPair

  # coordinates of the exon (recommended way):
  print "exon from ", $exon->start(),
  	" to ", $exon->end(), "\n";

  # the same (feature1() inherited from Bio::SeqFeature::FeaturePair)
  print "exon from ", $exon->feature1()->start(),
  	" to ", $exon->feature1()->end(), "\n";
  # also the same (query() inherited from Bio::SeqFeature::SimilarityPair):
  print "exon from ", $exon->query()->start(),
  	" to ", $exon->query()->end(), "\n";

  # coordinates on the matching EST (recommended way):
  print "matches on EST from ", $exon->est_hit()->start(),
  	" to ", $exon->est_hit()->end(), "\n";

  # the same (feature2() inherited from Bio::SeqFeature::FeaturePair)
  print "matches on EST from ", $exon->feature2()->start(),
  	" to ", $exon->feature2()->end(), "\n";
  # also the same (subject() inherited from Bio::SeqFeature::SimilarityPair):
  print "exon from ", $exon->subject()->start(),
  	" to ", $exon->subject()->end(), "\n";

Description

This class inherits from Bio::SeqFeature::SimilarityPair and represents an
exon on a genomic sequence determined by similarity, that is, by aligning an
EST sequence (using Sim4 in this case). Consequently, the notion of query and
subject is always from the perspective of the genomic sequence: query refers
to the genomic seq, subject to the aligned EST hit. Because of this,
$exon->start(), $exon->end() etc will always return what you expect.
To get the coordinates on the matching EST, refer to the properties of the
feature returned by est_hit().

Methods

Methods description

 Title   : est_hit
 Usage   : $est_feature = $obj->est_hit();
 Function: Returns the EST hit pointing to (i.e., aligned to by Sim4) this
           exon (i.e., genomic region). At present, merely a synonym for
           $obj->feature2().
 Returns : An Bio::SeqFeatureI implementing object.
 Args    :

 Title   : percentage_id
 Usage   : $obj->percentage_id($newval)
 Function: This is a synonym for 100 * $obj->est_hit()->frac_identical().
 Returns : value of percentage_id
 Args    : newvalue (optional)

Methods code

sub est_hit {

    my $self = shift;
    return $self->feature2(@_);
}

1;

}

sub new {

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

    my ($prim, $source) = $self->_rearrange([qw(PRIMARY SOURCE)], @args);

    $self->primary_tag('exon') unless $prim;
    $self->source_tag('Sim4') unless $source;
    $self->strand(0) unless defined($self->strand());
    $self->query();
    return $self;

}

sub percentage_id {

    my ($self, @args) = @_;
    my $frac;
    my $val;
    my $delegated = 0;
    
    if(@args) {
	$frac = $args[0];
	$frac /= 100.0 if defined($frac);
    }
    if($self->query()->can('frac_identical')) {
	if(defined($frac)) {
	    $self->query()->frac_identical($frac);
	}
	$val = 100.0 * $self->query()->frac_identical();
	$delegated = 1;
    }
    if($self->est_hit()->can('frac_identical')) {
	if(defined($frac)) {
	    $self->est_hit()->frac_identical($frac);
	}
	# this intentiously overwrites previous $val
	$val = 100.0 * $self->est_hit()->frac_identical();
	$delegated = 1;
    }
    if(! $delegated) {
	if(@args) {
	    $val = shift(@args);
	    $self->{'percentage_id'} = $val;
	} else {
	    $val = $self->{'percentage_id'};
	}
    }
    return $val;

}

General documentation

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.

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Email birney@sanger.ac.uk
Hilmar Lapp <hlapp@gmx.net> or <hilmar.lapp@pharma.novartis.com>.
Describe contact details here

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