Bio::Variation::Allele

NAME

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

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).

FEEDBACK

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 AT bioperl DOT org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists

Support
Please direct usage questions or support issues to the mailing list:

bioperl-l AT bioperl DOT 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 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

AUTHOR - Heikki Lehvaslaiho

Email: heikki-at-bioperl-dot-org

APPENDIX

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

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

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

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

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

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

count
Title : count
Usage : $obj->count();
Function:
Sets and returns the number of times this allele was observed.
Example :
Returns : string
Args : string

frequency
Title : frequency
Usage : $obj->frequency();
Function:
Sets and returns the frequency of the allele in the observed
population.
Example :
Returns : string
Args : string