Toolbar

Summary

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

Package variables

Inherit

Bio::SeqFeature::SimilarityPair

Synopsis

  # See Bio::Tools::Spidey::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 Spidey 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   : percentage_id
 Usage   : $obj->percentage_id
 Function: This is the percent id as reported by Spidey
 Returns : value of percentage_id
 Args    :

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

 Title   : mismatches
 Usage   : $obj->mismatches;
 Function: Returns the mismatches of the cDNA to (i.e., aligned to by Spidey) this
           exon (i.e., genomic region). 
 Returns : value of mismatches.
 Args    :

 Title   : gaps
 Usage   : $obj->gaps;
 Function: Returns the gaps of the cDNA to (i.e., aligned to by Spidey) this
           exon (i.e., genomic region). 
 Returns : value of gaps.
 Args    :

 Title   : donor
 Usage   : $obj->donor;
 Function: Returns 0 if a splice donor site does not exist, or 
           1 if a splice donor site exists
 Returns : value of existence of donor splice site (0 or 1)
 Args    :

 Title   : acceptor
 Usage   : $obj->acceptor;
 Function: Returns 0 if a splice acceptor site does not exist, or 
           1 if a splice acceptor site exists
 Returns : value of existence of acceptor splice site (0 or 1)
 Args    :

Methods code

sub new {

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

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

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

}

sub percentage_id {

	my ($self, @args) = @_;
	my $val;
    
	if(@args) {
	    $val = shift(@args);
	    $self->{'percentage_id'} = $val;
	} else {
	    $val = $self->{'percentage_id'};
	}
	return $val;

}

sub est_hit {

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

}

sub mismatches {

	my ($self, @args) = @_;
	my $val;
    
	if(@args) {
	    $val = shift(@args);
	    $self->{'mismatches'} = $val;
	} else {
	    $val = $self->{'mismatches'};
	}
	return $val;

}

sub gaps {

	my ($self, @args) = @_;
	my $val;
    
	if(@args) {
	    $val = shift(@args);
	    $self->{'gaps'} = $val;
	} else {
	    $val = $self->{'gaps'};
	}
	return $val;

}

sub donor {

	my ($self, @args) = @_;
	my $val;

	if (@args) {
		$val = shift @args;
		$self->{'donor'} = $val;
	} else {
		$val = $self->{'donor'};
	}
	return $val;

}

sub acceptor {

	my ($self, @args) = @_;
	my $val;

	if (@args) {
		$val = shift @args;
		$self->{'acceptor'} = $val;
	} else {
		$val = $self->{'acceptor'};
	}
	return $val;
}


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 one of the Bioperl mailing lists.
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
the bugs and their resolution. Bug reports can be submitted via the
web:

  https://redmine.open-bio.org/projects/bioperl/

Email golharam@umdnj.edu

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