Bio::Variation::AlleleUser Contributed Perl DocumentaBio::Variation::Allele(3)NAMEBio::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
perl v5.14.1 2011-07-22 Bio::Variation::Allele(3)
