#
# BioPerl module for Bio::Cluster::SequenceFamily
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Shawn Hoon <shawnh@fugu-sg.org>
#
# Copyright Shawn Hoon
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Cluster::SequenceFamily - Sequence Family object
=head1 SYNOPSIS
use Bio::SeqIO;
use Bio::Cluster::SequenceFamily;
use File::Spec;
my $file = File::Spec->catfile('t','data','swiss.dat');
my $seqio= Bio::SeqIO->new(-format => 'swiss',
-file => $file);
my @mem;
while(my $seq = $seqio->next_seq){
push @mem, $seq;
}
#create the family
my $family = Bio::Cluster::SequenceFamily->new(
-family_id=>"Family_1",
-description=>"Family Description Here",
-annotation_score=>"100",
-members=>\@mem);
#access the family
foreach my $mem ($family->get_members){
print $mem->display_id."\t".$mem->desc."\n";
}
#select members if members have a Bio::Species Object
my @mem = $family->get_members(-binomial=>"Homo sapiens");
@mem = $family->get_members(-ncbi_taxid => 9606);
@mem = $family->get_members(-common_name=>"Human");
@mem = $family->get_members(-species=>"sapiens");
@mem = $family->get_members(-genus=>"Homo");
=head1 DESCRIPTION
This is a simple Family object that may hold any group of object. For more
specific families, one should derive from FamilyI.
=head1 FEEDBACK
Email bioperl-l@bioperl.org for support and feedback.
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 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:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Shawn Hoon
Email shawnh@fugu-sg.org
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a "_".
=cut
# Let the code begin...
package Bio::Cluster::SequenceFamily;
use strict;
use warnings;
use base qw(Bio::Root::Root Bio::Cluster::FamilyI);
=head2 new
Title : new
Usage : my $family = Bio::Cluster::SequenceFamily->new(
-family_id=>"Family_1",
-description=>"Family Description Here",
-annotation_score=>"100",
-members=>\@mem);
Function: Constructor for SequenceFamily object
Returns : Bio::Cluster::SequenceFamily object
See L<Bio::Cluster::SequenceFamily>.
=cut
sub new {
my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($id,$description,$version,$annot_score,
$family_score,$members) = $self->_rearrange([qw(FAMILY_ID DESCRIPTION VERSION
ANNOTATION_SCORE
FAMILY_SCORE MEMBERS)],@args);
$self->{'_members'} = [];
$id && $self->family_id($id);
$description && $self->description($description);
$version && $self->version($version);
$annot_score && $self->annotation_score($annot_score);
$family_score && $self->family_score($family_score);
$members && $self->add_members($members);
return $self;
}
=head2 version
Title : version
Usage : $family->version("1.0");
Function: get/set for version
Returns : a string version of the family generated.
=cut
sub version{
my ($self,$value) = @_;
if($value){
$self->{'_version'} =$value;
}
return $self->{'_version'};
}
=head2 annotation_score
Title : annotation_score
Usage : $family->annotation_score(100);
Function: get/set for annotation_score which
represent the confidence in which the
consensus description has been assigned
to the family.
Returns : Bio::SimpleAlign
See L<Bio::SimpleAlign>
=cut
sub annotation_score{
my ($self,$score) = @_;
if($score){
$self->{'_annotation_score'} = $score;
}
return $self->{'_annotation_score'};
}
=head2 alignment
Title : alignment
Usage : $family->alignment($align);
Function: get/set for an alignment object representing
the multiple alignment of the members of the family.
Returns : Bio::SimpleAlign
See L<Bio::SimpleAlign>
=cut
sub alignment {
my ($self,$align) = @_;
if($align){
$self->{'_alignment'} = $align;
}
return $self->{'_alignment'};
}
=head2 tree
Title : tree
Usage : $family->tree($tree);
Function: get/set for an tree object representing
the phylogenetic tree of the family.
Returns : Bio::Tree
See L<Bio::Tree>
=cut
sub tree {
my ($self,$tree) = @_;
if($tree) {
$self->{'_tree'} = $tree;
}
return $self->{'_tree'};
}
=head1 L<Bio::Cluster::FamilyI> methods
=cut
=head2 family_score
Title : family_score
Usage : Bio::Cluster::FamilyI->family_score(95);
Function: get/set for the score of algorithm used to generate
the family if present
This is aliased to cluster_score().
Returns : the score
Args : the score
=cut
sub family_score {
return shift->cluster_score(@_);
}
=head2 family_id
Title : family_id
Usage : $family->family_id("Family_1");
Function: get/set for family id
This is aliased to display_id().
Returns : a string specifying identifier of the family
=cut
sub family_id{
return shift->display_id(@_);
}
=head1 L<Bio::ClusterI> methods
=cut
=head2 display_id
Title : display_id
Usage :
Function: Get/set the display name or identifier for the cluster
Returns : a string
Args : optional, on set the display ID ( a string)
=cut
sub display_id{
my ($self,$id) = @_;
if($id){
$self->{'_cluster_id'} = $id;
}
return $self->{'_cluster_id'};
}
=head2 description
Title : description
Usage : $fam->description("POLYUBIQUITIN")
Function: get/set for the consensus description of the cluster
Returns : the description string
Args : Optional the description string
=cut
sub description{
my ($self,$desc) = @_;
if($desc){
$self->{'_description'} = $desc;
}
return $self->{'_description'};
}
=head2 get_members
Title : get_members
Usage : Valid criteria:
-common_name
-binomial
-ncbi_taxid
-organelle
-genus
$family->get_members(-common_name =>"human");
$family->get_members(-species =>"homo sapiens");
$family->get_members(-ncbi_taxid => 9606);
For now, multiple critieria are ORed.
Will return all members if no criteria are provided.
Function: get members using methods from L<Bio::Species>
the phylogenetic tree of the family.
Returns : an array of objects that are member of this family.
=cut
sub get_members {
my $self = shift;
return @{$self->{'_members'}} unless @_;
## since the logic behind the checks is OR, we keep the ids in an hash for
## performance (skip the test if it's already there) and to avoid repats
my %match;
my %filter = @_;
foreach my $key (keys %filter) {
(my $method = $key) =~ s/^-//;
%match = (%match, map { $_ => $_ } grep {
! $match{$_} && $_->species &&
($_->species->can($method) ||
$self->throw("$method is an invalid criteria")) &&
$_->species->$method() eq $filter{$key}
} @{$self->{'_members'}});
}
return map {$match{$_}} keys (%match);
}
=head2 size
Title : size
Usage : $fam->size();
Function: get/set for the size of the family,
calculated from the number of members
Returns : the size of the family
Args :
=cut
sub size {
my ($self) = @_;
return scalar(@{$self->{'_members'}});
}
=head2 cluster_score
Title : cluster_score
Usage : $fam->cluster_score(100);
Function: get/set for cluster_score which
represent the score in which the clustering
algorithm assigns to this cluster.
Returns : a number
=cut
sub cluster_score{
my ($self,$score) = @_;
if($score){
$self->{'_cluster_score'} = $score;
}
return $self->{'_cluster_score'};
}
=head1 Implementation specific methods
These are mostly for adding/removing/changing.
=cut
=head2 add_members
Title : add_members
Usage : $fam->add_member([$seq1,$seq1]);
Function: add members to a family
Returns :
Args : the member(s) to add, as an array or arrayref
=cut
sub add_members{
my ($self,@mems) = @_;
if (@mems) {
my $mem = shift(@mems);
if(ref($mem) eq "ARRAY"){
push @{$self->{'_members'}},@{$mem};
} else {
push @{$self->{'_members'}},$mem;
}
push @{$self->{'_members'}}, @mems;
}
return 1;
}
=head2 remove_members
Title : remove_members
Usage : $fam->remove_members();
Function: remove all members from a family
Returns : the previous array of members
Args : none
=cut
sub remove_members{
my ($self) = @_;
my $mems = $self->{'_members'};
$self->{'_members'} = [];
return @$mems;
}
#####################################################################
# aliases for naming consistency or other reasons #
#####################################################################
*flush_members = \&remove_members;
*add_member = \&add_members;
=head2 members
Title : members
Usage : $members = $fam->members([$seq1,$seq1]);
Function: Deprecated. Use add_members() or get_members() instead
=cut
sub members{
my $self = shift;
if(@_) {
# this is in set mode
$self->warn("setting members() in ".ref($self)." is deprecated.\n".
"Use add_members() instead.");
return $self->add_members(@_);
} else {
# get mode
$self->warn("members() in ".ref($self)." is deprecated.\n".
"Use get_members() instead.");
return $self->get_members();
}
}
1;