NAME

Bio::Cluster::SequenceFamily - Sequence Family object

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.

FEEDBACK

Email bioperl-l@bioperl.org for support and feedback.

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

Support

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 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

AUTHOR - Shawn Hoon

Email shawnh@fugu-sg.org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a "_".

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 Bio::Cluster::SequenceFamily.

version

Title   : version
Usage   : $family->version("1.0");
Function: get/set for version
Returns : a string version of the family generated.

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 Bio::SimpleAlign

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 Bio::SimpleAlign

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 Bio::Tree

Bio::Cluster::FamilyI methods

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

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

Bio::ClusterI methods

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)

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

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.

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    :

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

Implementation specific methods

These are mostly for adding/removing/changing.

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

remove_members

Title   : remove_members
Usage   : $fam->remove_members();
Function: remove all members from a family
Returns : the previous array of members
Args    : none

members

Title   : members
Usage   : $members = $fam->members([$seq1,$seq1]);
Function: Deprecated. Use add_members() or get_members() instead

cpanm Bio::Cluster

perl -MCPAN -e shell
install Bio::Cluster