#
# BioPerl module for Bio::Variation::Allele
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Heikki Lehvaslaiho <heikki-at-bioperl-dot-org>
#
# Copyright Heikki Lehvaslaiho
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Variation::Allele - Sequence object with allele-specific attributes
=head1 SYNOPSIS
$allele1 = Bio::Variation::Allele->new ( -seq => 'A',
-id => 'AC00001.1',
-alphabet => 'dna',
-is_reference => 1
);
=head1 DESCRIPTION
List of alleles describe known sequence alternatives in a variable region.
Alleles are contained in Bio::Variation::VariantI complying objects.
See L<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).
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 Reporting Bugs
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://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Heikki Lehvaslaiho
Email: heikki-at-bioperl-dot-org
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Variation::Allele;
use strict;
# Object preamble - inheritance
use base qw(Bio::PrimarySeq Bio::DBLinkContainerI);
sub new {
my($class, @args) = @_;
my $self = $class->SUPER::new(@args);
my($is_reference, $repeat_unit, $repeat_count) =
$self->_rearrange([qw(IS_REFERENCE
REPEAT_UNIT
REPEAT_COUNT
)],
@args);
$is_reference && $self->is_reference($is_reference);
$repeat_unit && $self->repeat_unit($repeat_unit);
$repeat_count && $self->repeat_count($repeat_count);
return $self; # success - we hope!
}
=head2 is_reference
Title : is_reference
Usage : $obj->is_reference()
Function: sets and returns boolean values.
Unset values return false.
Example : $obj->is_reference()
Returns : boolean
Args : optional true of false value
=cut
sub is_reference {
my ($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'};
}
}
=head2 add_DBLink
Title : add_DBLink
Usage : $self->add_DBLink($ref)
Function: adds a link object
Example :
Returns :
Args :
=cut
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);
}
=head2 each_DBLink
Title : each_DBLink
Usage : foreach $ref ( $self->each_DBlink() )
Function: gets an array of DBlink of objects
Example :
Returns :
Args :
=cut
sub each_DBLink{
my ($self) = @_;
return @{$self->{'link'}};
}
=head2 repeat_unit
Title : repeat_unit
Usage : $obj->repeat_unit('ca');
Function:
Sets and returns the sequence of the repeat_unit the
allele is composed of.
Example :
Returns : string
Args : string
=cut
sub repeat_unit {
my ($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'};
}
=head2 repeat_count
Title : repeat_count
Usage : $obj->repeat_count();
Function:
Sets and returns the number of repeat units in the allele.
Example :
Returns : string
Args : string
=cut
sub repeat_count {
my ($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'};
}
=head2 count
Title : count
Usage : $obj->count();
Function:
Sets and returns the number of times this allele was observed.
Example :
Returns : string
Args : string
=cut
sub count {
my ($self,$value) = @_;
if( defined $value) {
if ( not $value =~ /^\d+$/ ) {
$self->throw("[$value] for count has to be a positive integer\n");
} else {
$self->{'count'} = $value;
}
}
return $self->{'count'};
}
=head2 frequency
Title : frequency
Usage : $obj->frequency();
Function:
Sets and returns the frequency of the allele in the observed
population.
Example :
Returns : string
Args : string
=cut
sub frequency {
my ($self,$value) = @_;
if( defined $value) {
if ( not $value =~ /^\d+$/ ) {
$self->throw("[$value] for frequency has to be a positive integer\n");
} else {
$self->{'frequency'} = $value;
}
}
return $self->{'frequency'};
}
1;