Florent Angly > Bio-Community > Bio::Community::Member

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NAME ^

Bio::Community::Member - The basic constituent of a biological community

SYNOPSIS ^

  use Bio::Community::Member;

  my $member1 = Bio::Community::Member->new( -id => 2, -desc => 'Homo sapiens' );
  print "Got member ".$member1->desc." (ID ".$member1->id.")\n";

  my $member2 = Bio::Community::Member->new( );
  my $member2_id = $member2->id;

DESCRIPTION ^

A Bio::Community::Member represents an organism, individual, species, amplicon sequence, shotgun sequence or anything you like.

CONSTRUCTOR ^

Bio::Community::Member->new()

   my $member = Bio::Community::Member->new();

The new() class method constructs a new Bio::Community::Member object and accepts the following parameters:

OBJECT METHODS ^

id

The identifier for this community member. An ID is necessary and sufficient to identify a community member, but additional information can be attached to a member.

  my $obj1 = Bio::Community::Member->new( -id => 153 );
  my $obj2 = $obj1;
  my $obj3 = Bio::Community::Member->new( -id => 153 );
  my $obj4 = Bio::Community::Member->new( -id => 6123 );
  my $obj5 = Bio::Community::Member->new( ); # automatically assigned ID

In the above example, $obj1, $obj2 and $obj3 represent the same member, while $obj4 represents a different member, and $obj5 yet another member.

AUTHOR ^

Florent Angly florent.angly@gmail.com

SUPPORT AND BUGS ^

User feedback is an integral part of the evolution of this and other Bioperl modules. 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.

If you have found a bug, please report it on the BioPerl bug tracking system to help us keep track the bugs and their resolution: https://redmine.open-bio.org/projects/bioperl/

COPYRIGHT ^

Copyright 2011-2014 by Florent Angly <florent.angly@gmail.com>

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.10.1 or, at your option, any later version of Perl 5 you may have available.

APPENDIX ^

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

new

 Function: Create a new Bio::Community::Member object
 Usage   : my $member = Bio::Community::Member->new( );
 Args    : -id, -desc, -taxon, -seqs, -weights
 Returns : a new Bio::Community::Member object

id

 Function: my $description = $member->id();
 Usage   : Get or set the ID for the member. If an ID is not provided, a unique
           ID prefixed with 'bc' is generated, e.g. 'bc1', 'bc2', etc. This
           makes it easy to distinguish IDs assigned by Bio::Community::Member
           from IDs obtained from other sources, e.g. Greengenes taxa ID or
           QIIME aritrary OTU ID. Use of the 'bc' prefix is restricted to the
           L<Bio::Community::Member> module; please refrain from using it yourself.
 Args    : A string
 Returns : A string

desc

 Usage   : my $description = $member->desc();
 Function: Get or set a description for this object.
           See L<Bio::Community::Role::Described>.
 Args    : A string
 Returns : A string

taxon

 Usage   : my $taxon = $member->taxon();
 Function: Get or set a taxon (or species) for this object.
           See L<Bio::Community::Role::Classified>.
 Args    : A Bio::Taxon object
 Returns : A Bio::Taxon object

seqs

 Usage   : my $seqs = $member->seqs();
 Function: Get or set some sequences for this object.
           See L<Bio::Community::Role::Sequenced>.
 Args    : An arrayref of Bio::SeqI objects
 Returns : An arrayref of Bio::SeqI objects

weights

 Usage   : my $weights = $member->weights();
 Function: Get or set some weights for this object. Weights represent how biased
           the sampling of this organism is. For example, when random shotgun
           sequencing microorganisms in the environment, the relative abundance
           of reads in the sequence library is not proportional to the relative
           abundance of the genomes because larger genomes contribute
           disproportionalely more reads than small genomes. In such a case, you
           could set the weight to the length of the genome. See
           L<Bio::Community::Role::Weighted>. Also see get_count() and get_rel_ab()
           in L<Bio::Community>.
 Args    : An arrayref of positive integers
 Returns : An arrayref of positive integers
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