Bio::Community - A biological community
use Bio::Community; my $community = Bio::Community->new( -name => 'soil_1' ); $community->add_member( $member1 ); # add 1 such Bio::Community::Member $community->add_member( $member2, 3 ); # add 3 such members print "There are ".$community->get_members_count." members in the community\n"; print "The total diversity is ".$community->get_richness." species\n"; while (my $member = $community->next_member) { my $member_id = $member->id; my $member_count = $community->get_count($member); my $member_rel_ab = $community->get_rel_ab($member); print "The relative abundance of member $member_id is $member_rel_ab % ($member_count counts)\n"; }
The Bio::Community module represents communities of biological organisms. It is composed of Bio::Community::Member objects at a specified abundance. Each member can represent a species (e.g. an elephant, a bacterium), taxon, OTU, or any proxy for a species.
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 2011-2014 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.
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Function: Create a new Bio::Community object Usage : my $community = Bio::Community->new( ... ); Args : -name and -use_weights, see below... Returns : a new Bio::Community object
Function: Get or set the name of the community Usage : $community->name('ocean sample 3'); my $name = $community->name(); Args : string for the name Returns : string for the name
Function: Set whether or not relative abundance should be normalized by taking into accout the weights of the different members (e.g. genome length, gene copy number). Refer to the C<Bio::Community::Member->weights()> method for more details. The default is to use the weights that have given to community members. Usage : $community->use_weights(1); Args : boolean Returns : boolean
Function: If any weights have been set using Bio::Community::IO, return their averages. Usage : my $averages = $community->get_average_weights; Args : none Returns : Arrayref of averages (one average for each file of weights)
Function: Get the total count of members sampled from the community. Usage : my $total_count = $community->get_members_count(); Args : none Returns : integer
Function: Get or set the total abundance of members in the community. Setting this option implies that you know the total abundance of the members in the community, even though you have not have sampled them all. If this value has not been set explicitly, this method returns C<get_members_count> by default. Usage : $community->set_members_abundance( 1.63e6 ); # or my $total_abundance = $community->get_members_abundance(); Args : number Returns : number
Function: Add members to a community Usage : $community->add_member($member, 3); Args : * a Bio::Community::Member to add * how many of this member to add (positive number, default: 1) Returns : 1 on success
Function: Remove members from a community Usage : $community->remove_member($member, 3); Args : * A Bio::Community::Member to remove * Optional: how many of this member to remove. If no value is provided, all such members are removed. Returns : Number of this member removed
Function: Access the next member in a community (in no specific order). Be warned that each time you change the community, this iterator has to start again from the beginning! By default, a single iterator is created. However, if you need several independent iterators, simply provide an arbitrary iterator name. Usage : # Get members through the default iterator my $member = $community->next_member(); # Get members through an independent, named iterator my $member = $community->next_member('other_ite'); Args : an optional name to give to the iterator (must not start with '_') Returns : a Bio::Community::Member object
Function: Generate a list of all members in the community. Usage : my $members = $community->get_all_members(); Args : An arrayref of Bio::Community objects Returns : An arrayref of Bio::Community::Member objects
Function: Fetch a member based on its ID. Usage : my $member = $community->get_member_by_id(3); Args : integer for the member ID Returns : a Bio::Community::Member object or undef if member was not found
Function: Fetch a member based on its abundance rank. A smaller rank corresponds to a larger relative abundance. Usage : my $member = $community->get_member_by_rank(1); Args : strictly positive integer for the member rank Returns : a Bio::Community::Member object or undef if member was not found
Function: Report the community richness or number of different types of members. This is a form of alpha diversity. Usage : my $alpha_richness = $community->get_richness(); Args : none Returns : integer for the richness
Function: Fetch the abundance or count of a member Usage : my $count = $community->get_count($member); Args : a Bio::Community::Member object Returns : An integer for the count of this member, including zero if the member was not present in the community.
Function: Determine the relative abundance (in percent) of a member in the community. Usage : my $rel_ab = $community->get_rel_ab($member); Args : a Bio::Community::Member object Returns : an integer between 0 and 100 for the relative abundance of this member
Function: Determine the absolute abundance of a member in the community, i.e., its C<get_rel_ab()> multiplied by its C<get_members_abundance()>. Usage : my $abs_ab = $community->get_abs_ab($member); Args : a Bio::Community::Member object Returns : a number for the absolute abundance of this member
Function: Determine the abundance rank of a member in the community. The organism with the highest relative abundance has rank 1, the second- most abundant has rank 2, etc. Usage : my $rank = $community->get_rank($member); Args : a Bio::Community::Member object Returns : integer for the abundance rank of this member or undef if the member was not found
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.