Bio::Cluster::SequenceFamily - Sequence Family object use Bio::Cluster::SequenceFamily; use Bio::SeqIO; use Bio::Cluster::SequenceFamily; my $file = Bio::Root::IO->catfile('t','data','swiss.dat'); my $seqio= new Bio::SeqIO('-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"); This is a simple Family object that may hold any group of object. For more specific families, one should derive from FamilyI.

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://bio.perl.org/MailList.html - About the mailing lists

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 email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ Email shawnh@fugu-sg.org 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 : L<Bio::Cluster::SequenceFamily> object

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 : L<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 : L<Bio::SimpleAlign>

tree
Title : tree Usage : $family->tree($tree); Function: get/set for an tree object representing the phylogenetic tree of the family. Returns : L<Bio::Tree>

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

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 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