Bio::Tools::Spidey Exon
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Summary
Bio::Tools::Spidey::Exon - A single exon determined by an alignment
Package variables
No package variables defined.
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
new
No description
Code
percentage_idDescriptionCode
est_hitDescriptionCode
mismatchesDescriptionCode
gapsDescriptionCode
donorDescriptionCode
acceptorDescriptionCode
Methods description
percentage_idcode    nextTop
 Title   : percentage_id
Usage : $obj->percentage_id
Function: This is the percent id as reported by Spidey
Returns : value of percentage_id
Args :
est_hitcodeprevnextTop
 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 :
mismatchescodeprevnextTop
 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 :
gapscodeprevnextTop
 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 :
donorcodeprevnextTop
 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 :
acceptorcodeprevnextTop
 Title   : acceptor
Usage : $obj->acceptor;
Function: Returns 0 if a splice acceptor site does not exist, or
1 if a splice acceptor site exists
Returns : value of existence of acceptor splice site (0 or 1)
Args :
Methods code
newdescriptionprevnextTop
sub new {
    my ($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 $self;
}
percentage_iddescriptionprevnextTop
sub percentage_id {
	my ($self, @args) = @_;
	my $val;
    
	if(@args) {
	    $val = shift(@args);
	    $self->{'percentage_id'} = $val;
	} else {
	    $val = $self->{'percentage_id'};
	}
	return $val;
}
est_hitdescriptionprevnextTop
sub est_hit {
    my $self = shift;
    return $self->feature2(@_);
}
mismatchesdescriptionprevnextTop
sub mismatches {
	my ($self, @args) = @_;
	my $val;
    
	if(@args) {
	    $val = shift(@args);
	    $self->{'mismatches'} = $val;
	} else {
	    $val = $self->{'mismatches'};
	}
	return $val;
}
gapsdescriptionprevnextTop
sub gaps {
	my ($self, @args) = @_;
	my $val;
    
	if(@args) {
	    $val = shift(@args);
	    $self->{'gaps'} = $val;
	} else {
	    $val = $self->{'gaps'};
	}
	return $val;
}
donordescriptionprevnextTop
sub donor {
	my ($self, @args) = @_;
	my $val;

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

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


1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Support Top
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.
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 the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Ryan GolharTop
Email golharam@umdnj.edu
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _