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Bio::Cluster::SequenceFamily.3pm

NAME

Bio::Cluster::SequenceFamily - Sequence Family object

SYNOPSIS

   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");
 
 

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
 
 

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:

   http://bugzilla.open-bio.org/
 
 

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