xenial (3) Bio::Variation::Allele.3pm.gz

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