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Bio::Variation::Allele.3pm

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:

   http://bugzilla.open-bio.org/
 
 

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