Bio::Community::Member - The basic constituent of a biological community
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;
A Bio::Community::Member represents an organism, individual, species, amplicon sequence, shotgun sequence or anything you like.
my $member = Bio::Community::Member->new();
The new() class method constructs a new Bio::Community::Member object and accepts the following parameters:
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.
Florent Angly florent.angly@gmail.com
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 2011,2012,2013 by the BioPerl Team bioperl-l@bioperl.org
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.
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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
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
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
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
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
1 POD Error
The following errors were encountered while parsing the POD:
'=item' outside of any '=over'
To install Bio::Community, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Community
CPAN shell
perl -MCPAN -e shell install Bio::Community
For more information on module installation, please visit the detailed CPAN module installation guide.