Summary

Bio::Variation::Allele - Sequence object with allele-specific attributes

Package variables

Included modules

Inherit

Bio::DBLinkContainerI Bio::PrimarySeq

Synopsis

  $allele1 = Bio::Variation::Allele->new ( -seq => 'A',
                                           -id  => 'AC00001.1',
                                           -alphabet => 'dna',
                                           -is_reference => 1
                                         );

Description

List of alleles describe known sequence alternatives in a variable region.
Alleles are contained in Bio::Variation::VariantI complying objects.
See Bio::Variation::VariantI for details.
Bio::Varation::Alleles are PrimarySeqI complying objects which can
contain database cross references as specified in
Bio::DBLinkContainerI interface, too.
A lot of the complexity with dealing with Allele objects are caused by
null alleles; Allele objects that have zero length sequence string.
In addition describing the allele by its sequence , it possible to
give describe repeat structure within the sequence. This done using
methods repeat_unit (e.g. 'ca') and repeat_count (e.g. 7).

Methods

Methods description

 Title   : is_reference
 Usage   : $obj->is_reference()
 Function: sets and returns boolean values. 
           Unset values return false.
 Example : $obj->is_reference()
 Returns : boolean
 Args    : optional true of false value

 Title   : add_DBLink
 Usage   : $self->add_DBLink($ref)
 Function: adds a link object
 Example :
 Returns : 
 Args    :

 Title   : each_DBLink
 Usage   : foreach $ref ( $self->each_DBlink() )
 Function: gets an array of DBlink of objects
 Example :
 Returns : 
 Args    :

 Title   : repeat_unit
 Usage   : $obj->repeat_unit('ca');
 Function: 

            Sets and returns the sequence of the repeat_unit the
            allele is composed of.

 Example : 
 Returns : string
 Args    : string

 Title   : repeat_count
 Usage   : $obj->repeat_count();
 Function: 

            Sets and returns the number of repeat units in the allele.

 Example : 
 Returns : string
 Args    : string

Methods code

sub _initialize {

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

    my($seq,$id,$acc,$pid,$desc,$alphabet,$given_id, 
       $is_reference, $repeat_unit, $repeat_count) =
	   $self->_rearrange([qw(SEQ
				 DISPLAY_ID
				 ACCESSION_NUMBER
				 PRIMARY_ID
				 DESC
				 ALPHABET
				 ID
				 IS_REFERENCE
				 REPEAT_UNIT
				 REPEAT_COUNT
				 )],
			     @args);

    my $make = $self->SUPER::_initialize(@args);

    if( defined $given_id ) { $id = $given_id; }

    $seq     && $self->SUPER::seq($seq);
    $id      && $self->SUPER::display_id($id);
    $acc     && $self->SUPER::accession_number($acc);
    $pid     && $self->SUPER::primary_id($pid);
    $desc    && $self->SUPER::desc($desc);
    $alphabet && $self->SUPER::alphabet($alphabet);

    $is_reference && $self->is_reference($is_reference);
    $repeat_unit && $self->repeat_unit($repeat_unit);
    $repeat_count && $self->repeat_count($repeat_count);

    return $make; # success - we hope!

}

sub is_reference {

    my ($self,$value) = @_;
    if( defined $value) {
	$value ? ($value = 1) : ($value = 0);
	$self->{'is_reference'} = $value;
    }
    if( ! exists $self->{'is_reference'} ) {
	return 0;
    } 
    else {
	return $self->{'is_reference'};
    }

}

sub add_DBLink {

   my ($self,$com) = @_;
   if( ! $com->isa('Bio::Annotation::DBLink') ) {
       $self->throw("Is not a link object but a  [$com]");
   }
   push(@{$self->{'link'}},$com);

}

sub each_DBLink {

   my ($self) = @_;   
   return @{$self->{'link'}};

}

sub repeat_unit {

    my ($self,$value) = @_;
    if( defined $value) {
	$self->{'repeat_unit'} = $value;
    }
    if ($self->{'seq'} && $self->{'repeat_unit'} && $self->{'repeat_count'} ) {
	$self->warn("Repeats do not add up!") 
	    if ( $self->{'repeat_unit'} x $self->{'repeat_count'})  ne $self->{'seq'};
    }
    return $self->{'repeat_unit'};

}

sub repeat_count {

    my ($self,$value) = @_;
    if( defined $value) {
	if (  not $value =~ /^\d+$/ ) {
	    $self->throw("[$value] for repeat_count has to be a positive integer\n");
	} else {
	    $self->{'repeat_count'} = $value;
	}
    }
    if ($self->{'seq'} && $self->{'repeat_unit'} && $self->{'repeat_count'} ) {
	$self->warn("Repeats do not add up!") 
	    if ( $self->{'repeat_unit'} x $self->{'repeat_count'})  ne $self->{'seq'};
    }
    return $self->{'repeat_count'};

}

General documentation

User feedback is an integral part of the evolution of this and other
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  bioperl-bugs@bio.perl.org
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Email: heikki@ebi.ac.uk
Address:

     EMBL Outstation, European Bioinformatics Institute
     Wellcome Trust Genome Campus, Hinxton
     Cambs. CB10 1SD, United Kingdom

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