Bio::Cluster
SequenceFamily
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Summary
Bio::Cluster::SequenceFamily - Sequence Family object
Package variables
No package variables defined.
Inherit
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
Methods description
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. |
Title : version
Usage : $family->version("1.0");
Function: get/set for version
Returns : a string version of the family generated. |
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 |
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 |
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 |
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 |
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 |
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) |
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 |
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. |
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 : |
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 |
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 |
Title : remove_members
Usage : $fam->remove_members();
Function: remove all members from a family
Returns : the previous array of members
Args : none |
Title : members
Usage : $members = $fam->members([$seq1,$seq1]);
Function: Deprecated. Use add_members() or get_members() instead |
Methods code
sub new
{ my ($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 $self;} | sub version
{ my ($self,$value) = @_;
if($value){
$self->{'_version'} =$value;
}
return $self->{'_version'};} | sub annotation_score
{ my ($self,$score) = @_;
if($score){
$self->{'_annotation_score'} = $score;
}
return $self->{'_annotation_score'};} | sub alignment
{ my ($self,$align) = @_;
if($align){
$self->{'_alignment'} = $align;
}
return $self->{'_alignment'};} | sub tree
{ my ($self,$tree) = @_;
if($tree) {
$self->{'_tree'} = $tree;
}
return $self->{'_tree'};} | sub family_score
{ return shift->cluster_score(@_); } | sub family_id
{ return shift->display_id(@_); } | sub display_id
{ my ($self,$id) = @_;
if($id){
$self->{'_cluster_id'} = $id;
}
return $self->{'_cluster_id'};} | sub description
{ my ($self,$desc) = @_;
if($desc){
$self->{'_description'} = $desc;
}
return $self->{'_description'};} | 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'}};} | sub size
{ my ($self) = @_;
return scalar(@{$self->{'_members'}});} | sub cluster_score
{ my ($self,$score) = @_;
if($score){
$self->{'_cluster_score'} = $score;
}
return $self->{'_cluster_score'};} | sub add_members
{ my ($self,@mems) = @_;
if (@mems) {
my $mem = shift(@mems);
if(ref($mem) eq "ARRAY"){
push @{$self->{'_members'}},@{$mem};
} else {
push @{$self->{'_members'}},$mem;
}
push @{$self->{'_members'}}, @mems;
}
return 1;} | sub remove_members
{ my ($self) = @_;
my $mems = $self->{'_members'};
$self->{'_members'} = [];
return @$mems;
}
*flush_members =\& remove_members;
*add_member =\& add_members;} | sub members
{ my $self = shift;
if(@_) {
$self->warn("setting members() in ".ref($self)." is deprecated.\n".
"Use add_members() instead.");
return $self->add_members(@_);
} else {
$self->warn("members() in ".ref($self)." is deprecated.\n".
"Use get_members() instead.");
return $self->get_members();
}
}
1;} | General documentation
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The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a "_".
| Implementation specific methods | Top |
These are mostly for adding/removing/changing.