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Bio::Variation::AlleleUser Contributed Perl DocumentaBio::Variation::Allele(3)

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@bioperl.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@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 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

perl v5.24.1			  2017-07-08	     Bio::Variation::Allele(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Heikki Lehvaslaiho | APPENDIX

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