Bio::Cluster SequenceFamily
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Summary
Bio::Cluster::SequenceFamily - Sequence Family object
Package variables
No package variables defined.
Inherit
Bio::Cluster::FamilyI Bio::Root::Root
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");
Description
This is a simple Family object that may hold any group of object. For more
specific families, one should derive from FamilyI.
Methods
newDescriptionCode
versionDescriptionCode
annotation_scoreDescriptionCode
alignmentDescriptionCode
treeDescriptionCode
family_scoreDescriptionCode
family_idDescriptionCode
display_idDescriptionCode
descriptionDescriptionCode
get_membersDescriptionCode
sizeDescriptionCode
cluster_scoreDescriptionCode
add_membersDescriptionCode
remove_membersDescriptionCode
membersDescriptionCode
Methods description
newcode    nextTop
 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 Bio::Cluster::SequenceFamily.
versioncodeprevnextTop
 Title   : version
Usage : $family->version("1.0");
Function: get/set for version
Returns : a string version of the family generated.
annotation_scorecodeprevnextTop
 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 Bio::SimpleAlign
alignmentcodeprevnextTop
 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 Bio::SimpleAlign
treecodeprevnextTop
 Title   : tree
Usage : $family->tree($tree);
Function: get/set for an tree object representing
the phylogenetic tree of the family.
Returns : Bio::Tree
See Bio::Tree
family_scorecodeprevnextTop
 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
family_idcodeprevnextTop
 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
display_idcodeprevnextTop
 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)
descriptioncodeprevnextTop
 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
get_memberscodeprevnextTop
 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 Bio::Species
the phylogenetic tree of the family.
Returns : an array of objects that are member of this family.
sizecodeprevnextTop
 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 :
cluster_scorecodeprevnextTop
 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
add_memberscodeprevnextTop
 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
remove_memberscodeprevnextTop
 Title   : remove_members
Usage : $fam->remove_members();
Function: remove all members from a family
Returns : the previous array of members
Args : none
memberscodeprevnextTop
 Title   : members
Usage : $members = $fam->members([$seq1,$seq1]);
Function: Deprecated. Use add_members() or get_members() instead
Methods code
newdescriptionprevnextTop
sub new {
	my ($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 $self;
}
versiondescriptionprevnextTop
sub version {
  my ($self,$value) = @_;
  if($value){
    $self->{'_version'} =$value;
  }
  return $self->{'_version'};
}
annotation_scoredescriptionprevnextTop
sub annotation_score {
  my ($self,$score) = @_;
  if($score){
    $self->{'_annotation_score'} = $score;
  }
  return $self->{'_annotation_score'};
}
alignmentdescriptionprevnextTop
sub alignment {
	my ($self,$align) = @_;
  if($align){
    $self->{'_alignment'} = $align;
  }
    return $self->{'_alignment'};
}
treedescriptionprevnextTop
sub tree {
  my ($self,$tree) = @_;
  if($tree) {
    $self->{'_tree'} = $tree;
  }
  return $self->{'_tree'};
}
family_scoredescriptionprevnextTop
sub family_score {
    return shift->cluster_score(@_);
}
family_iddescriptionprevnextTop
sub family_id {
	return shift->display_id(@_);
}
display_iddescriptionprevnextTop
sub display_id {
	my ($self,$id) = @_;
	if($id){
		$self->{'_cluster_id'} = $id;
	}
	return $self->{'_cluster_id'};
}
descriptiondescriptionprevnextTop
sub description {
	my ($self,$desc) = @_;
	if($desc){
		$self->{'_description'} = $desc;
	}
	return $self->{'_description'};
}
get_membersdescriptionprevnextTop
sub get_members {
	my $self = shift;
	my @ret;

	if(@_) {
		my %hash = @_;
		foreach my $mem ( @{$self->{'_members'}} ) {
			foreach my $key ( keys %hash){
				my $method = $key;
				$method=~s/-//g;
if($mem->can('species')){ my $species = $mem->species; $species->can($method) || $self->throw("$method is an invalid criteria"); if($species->$method() eq $hash{$key} ){ push @ret, $mem; } } } } return @ret; } return @{$self->{'_members'}};
}
sizedescriptionprevnextTop
sub size {
  my ($self) = @_;

  return scalar(@{$self->{'_members'}});
}
cluster_scoredescriptionprevnextTop
sub cluster_score {
  my ($self,$score) = @_;
  if($score){
    $self->{'_cluster_score'} = $score;
  }
  return $self->{'_cluster_score'};
}
add_membersdescriptionprevnextTop
sub add_members {
    my ($self,@mems) = @_;

    if (@mems) {
        my $mem = shift(@mems);
        if(ref($mem) eq "ARRAY"){
            push @{$self->{'_members'}},@{$mem};
        } else {
            push @{$self->{'_members'}},$mem;
        }
        push @{$self->{'_members'}}, @mems;
    }
    return 1;
}
remove_membersdescriptionprevnextTop
sub remove_members {
    my ($self) =  @_;
    my $mems = $self->{'_members'};
    $self->{'_members'} = [];
    return @$mems;
}

#####################################################################
# aliases for naming consistency or other reasons #
#####################################################################
*flush_members =\& remove_members; *add_member =\& add_members;
}
membersdescriptionprevnextTop
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;
}
General documentation
FEEDBACKTop
Email bioperl-l@bioperl.org for support and feedback.
Mailing ListsTop
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
Support Top
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 BugsTop
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Shawn HoonTop
Email shawnh@fugu-sg.org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a "_".
Bio::Cluster::FamilyI methodsTop
Bio::ClusterI methodsTop
Implementation specific methodsTop
  These are mostly for adding/removing/changing.